1
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Ghasemi DR, Okonechnikov K, Rademacher A, Tirier S, Maass KK, Schumacher H, Joshi P, Gold MP, Sundheimer J, Statz B, Rifaioglu AS, Bauer K, Schumacher S, Bortolomeazzi M, Giangaspero F, Ernst KJ, Clifford SC, Saez-Rodriguez J, Jones DTW, Kawauchi D, Fraenkel E, Mallm JP, Rippe K, Korshunov A, Pfister SM, Pajtler KW. Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage. Nat Commun 2024; 15:269. [PMID: 38191550 PMCID: PMC10774372 DOI: 10.1038/s41467-023-44117-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024] Open
Abstract
Medulloblastomas with extensive nodularity are cerebellar tumors characterized by two distinct compartments and variable disease progression. The mechanisms governing the balance between proliferation and differentiation in MBEN remain poorly understood. Here, we employ a multi-modal single cell transcriptome analysis to dissect this process. In the internodular compartment, we identify proliferating cerebellar granular neuronal precursor-like malignant cells, along with stromal, vascular, and immune cells. In contrast, the nodular compartment comprises postmitotic, neuronally differentiated malignant cells. Both compartments are connected through an intermediate cell stage resembling actively migrating CGNPs. Notably, we also discover astrocytic-like malignant cells, found in proximity to migrating and differentiated cells at the transition zone between the two compartments. Our study sheds light on the spatial tissue organization and its link to the developmental trajectory, resulting in a more benign tumor phenotype. This integrative approach holds promise to explore intercompartmental interactions in other cancers with varying histology.
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Affiliation(s)
- David R Ghasemi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anne Rademacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Stephan Tirier
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
- Resolve BioSciences GmbH, Monheim am Rhein, Germany
| | - Kendra K Maass
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hanna Schumacher
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Piyush Joshi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maxwell P Gold
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Julia Sundheimer
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Britta Statz
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ahmet S Rifaioglu
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Department of Electrical and Electronics Engineering, İskenderun Technical University, Hatay, Turkey
| | - Katharina Bauer
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | | | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
| | - Kati J Ernst
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - David T W Jones
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Andrey Korshunov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 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 Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany.
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2
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Sepp M, Leiss K, Murat F, Okonechnikov K, Joshi P, Leushkin E, Spänig L, Mbengue N, Schneider C, Schmidt J, Trost N, Schauer M, Khaitovich P, Lisgo S, Palkovits M, Giere P, Kutscher LM, Anders S, Cardoso-Moreira M, Sarropoulos I, Pfister SM, Kaessmann H. Cellular development and evolution of the mammalian cerebellum. Nature 2024; 625:788-796. [PMID: 38029793 PMCID: PMC10808058 DOI: 10.1038/s41586-023-06884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
The expansion of the neocortex, a hallmark of mammalian evolution1,2, was accompanied by an increase in cerebellar neuron numbers3. However, little is known about the evolution of the cellular programmes underlying the development of the cerebellum in mammals. In this study we generated single-nucleus RNA-sequencing data for around 400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse and the marsupial opossum. We established a consensus classification of the cellular diversity in the developing mammalian cerebellum and validated it by spatial mapping in the fetal human cerebellum. Our cross-species analyses revealed largely conserved developmental dynamics of cell-type generation, except for Purkinje cells, for which we observed an expansion of early-born subtypes in the human lineage. Global transcriptome profiles, conserved cell-state markers and gene-expression trajectories across neuronal differentiation show that cerebellar cell-type-defining programmes have been overall preserved for at least 160 million years. However, we also identified many orthologous genes that gained or lost expression in cerebellar neural cell types in one of the species or evolved new expression trajectories during neuronal differentiation, indicating widespread gene repurposing at the cell-type level. In sum, our study unveils shared and lineage-specific gene-expression programmes governing the development of cerebellar cells and expands our understanding of mammalian brain evolution.
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Affiliation(s)
- Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Piyush Joshi
- 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
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Lisa Spänig
- 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
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Noe Mbengue
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Céline Schneider
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Nils Trost
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Maria Schauer
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Philipp Khaitovich
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Miklós Palkovits
- Human Brain Tissue Bank, Semmelweis University, Budapest, Hungary
| | - Peter Giere
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Lena M Kutscher
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- BioQuant, Heidelberg University, Heidelberg, Germany
| | | | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
- Wellcome Sanger Institute, Cambridge, UK.
| | - 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.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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3
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Okonechnikov K, Joshi P, Sepp M, Leiss K, Sarropoulos I, Murat F, Sill M, Beck P, Chan KCH, Korshunov A, Sah F, Deng MY, Sturm D, DeSisto J, Donson AM, Foreman NK, Green AL, Robinson G, Orr BA, Gao Q, Darrow E, Hadley JL, Northcott PA, Gojo J, Kawauchi D, Hovestadt V, Filbin MG, von Deimling A, Zuckermann M, Pajtler KW, Kool M, Jones DTW, Jäger N, Kutscher LM, Kaessmann H, Pfister SM. Mapping pediatric brain tumors to their origins in the developing cerebellum. Neuro Oncol 2023; 25:1895-1909. [PMID: 37534924 PMCID: PMC10547518 DOI: 10.1093/neuonc/noad124] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas. METHODS We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques. RESULTS We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study. CONCLUSION Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar "lineage of origin."
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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
| | - Piyush Joshi
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mari Sepp
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | | | - Pengbo Beck
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kenneth Chun-Ho Chan
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sah
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Maximilian Y Deng
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - John DeSisto
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Adam L Green
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, University of Colorado School of Medicine, Aurora, CO, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Giles Robinson
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Qingsong Gao
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Emily Darrow
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jennifer L Hadley
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Johannes Gojo
- 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 Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Andreas von Deimling
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marc Zuckermann
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - 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
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - 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, 3584 CS Utrecht, the Netherlands
| | - David T W Jones
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), 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
| | - Lena M Kutscher
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - 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
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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4
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Korshunov A, Okonechnikov K, Schrimpf D, Tonn S, Mynarek M, Koster J, Sievers P, Milde T, Sahm F, Jones DTW, von Deimling A, Pfister SM, Kool M. Transcriptome analysis stratifies second-generation non-WNT/non-SHH medulloblastoma subgroups into clinically tractable subtypes. Acta Neuropathol 2023; 145:829-842. [PMID: 37093271 DOI: 10.1007/s00401-023-02575-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/06/2023] [Accepted: 04/16/2023] [Indexed: 04/25/2023]
Abstract
Medulloblastoma (MB), one of the most common malignant pediatric brain tumor, is a heterogenous disease comprised of four distinct molecular groups (WNT, SHH, Group 3, Group 4). Each of these groups can be further subdivided into second-generation MB (SGS MB) molecular subgroups, each with distinct genetic and clinical characteristics. For instance, non-WNT/non-SHH MB (Group 3/4) can be subdivided molecularly into eight distinct and clinically relevant tumor subgroups. A further molecular stratification/summarization of these SGS MB would allow for the assignment of patients to risk-associated treatment protocols. Here, we performed DNA- and RNA-based analysis of 574 non-WNT/non-SHH MB and analyzed the clinical significance of various molecular patterns within the entire cohort and the eight SGS MB, with the aim to develop an optimal risk stratification of these tumors. Multigene analysis disclosed several survival-associated genes highly specific for each molecular subgroup within this non-WNT/non-SHH MB cohort with minimal inter-subgroup overlap. These subgroup-specific and prognostically relevant genes were associated with pathways that could underlie SGS MB clinical-molecular diversity and tumor-driving mechanisms. By combining survival-associated genes within each SGS MB, distinct metagene sets being appropriate for their optimal risk stratification were identified. Defined subgroup-specific metagene sets were independent variables in the multivariate models generated for each SGS MB and their prognostic value was confirmed in a completely non-overlapping validation cohort of non-WNT/non-SHH MB (n = 377). In summary, the current results indicate that the integration of transcriptome data in risk stratification models may improve outcome prediction for each non-WNT/non-SHH SGS MB. Identified subgroup-specific gene expression signatures could be relevant for clinical implementation and survival-associated metagene sets could be adopted for further SGS MB risk stratification. Future studies should aim at validating the prognostic role of these transcriptome-based SGS MB subtypes in prospective clinical trials.
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Affiliation(s)
- Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Svenja Tonn
- Pediatric Hematology and Oncology and Mildred Scheel Cancer Career Center HaTriCS4, Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Mynarek
- Pediatric Hematology and Oncology and Mildred Scheel Cancer Career Center HaTriCS4, Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Koster
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam and Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Till Milde
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Okonechnikov K, Federico A, Schrimpf D, Sievers P, Sahm F, Koster J, Jones DTW, von Deimling A, Pfister SM, Kool M, Korshunov A. Comparison of transcriptome profiles between medulloblastoma primary and recurrent tumors uncovers novel variance effects in relapses. Acta Neuropathol Commun 2023; 11:7. [PMID: 36635768 PMCID: PMC9837941 DOI: 10.1186/s40478-023-01504-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Nowadays medulloblastoma (MB) tumors can be treated with risk-stratified approaches with up to 80% success rate. However, disease relapses occur in approximately 30% of patients and successful salvage treatment strategies at relapse remain scarce. Acquired copy number changes or TP53 mutations are known to occur frequently in relapses, while methylation profiles usually remain highly similar to those of the matching primary tumors, indicating that in general molecular subgrouping does not change during the course of the disease. In the current study, we have used RNA sequencing data to analyze the transcriptome profiles of 43 primary-relapse MB pairs in order to identify specific molecular features of relapses within various tumor groups. Gene variance analysis between primary and relapse samples demonstrated the impact of age in SHH-MB: the changes in gene expression relapse profiles were more pronounced in the younger patients (< 10 years old), which were also associated with increased DNA aberrations and somatic mutations at relapse probably driving this effect. For Group 3/4 MB transcriptome data analysis uncovered clear sets of genes either active or decreased at relapse that are significantly associated with survival, thus could be potential predictive markers. In addition, deconvolution analysis of bulk transcriptome data identified progression-associated differences in cell type enrichment. The proportion of undifferentiated progenitors increased in SHH-MB relapses with a concomitant decrease of differentiated neuron-like cells, while in Group 3/4 MB relapses cell cycle activity increases and differentiated neuron-like cells proportion decreases as well. Thus, our findings uncovered significant transcriptome changes in the molecular signatures of relapsed MB and could be potentially useful for further clinical purposes.
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Affiliation(s)
- Konstantin Okonechnikov
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aniello Federico
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Sievers
- grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jan Koster
- grid.7177.60000000084992262Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam and Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - David T. W. Jones
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M. Pfister
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.487647.ePrincess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Andrey Korshunov
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
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Camgöz A, Okonechnikov K, Chapman O, Maurmann M, Buchholz F, Pfister S, Chavez L, Kool M. Abstract 3886: 3D genome conformation analysis in ST-EPN-ZFTA ependymoma identifies RCOR2 as a potential target. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ependymoma (EPN) is a tumor of the central nervous system that occurs in children and adults. Childhood EPNs are one of the most aggressive pediatric brain tumors, arising both in infratentorial and supratentorial (ST) regions of the brain. Molecular profiling has identified distinct subgroups of ependymomas, including ST-EPN-ZFTA and PF-EPN-A as the most common and most aggressive ones in children. To this date, the only curative and indispensable treatment option is surgical resection followed by radiation. Unfortunately, there are no targeted therapies in clinical use. However, EPN cells have been extremely difficult to culture and expand in vitro, which explains why molecular studies on EPN cells have been hampered. This shortcoming has recently been overcome by establishing EPN models including human cell lines and organoids as well as patient derived xenografts (PDX). 3D genome conformation analysis has emerged as a powerful approach to understand tumor development and to identify novel drug targets for the treatment of different tumors. In this project we have used genome-wide chromosome conformation capture (Hi-C), complemented with H3K27ac (active enhancers) as well as gene expression in primary ependymoma tumors and cell lines to identify regulatory mechanisms underlying aberrant expression of genes that are essential for ependymoma tumorigenesis. Results of this study showed that the fusion between ZFTA and RELA leads to the formation of new regulatory environments that are recurrently associated with aberrant overexpression of RCOR2 only in ST-EPN-ZFTA ependymoma cells. Indeed, compared to all other ependymoma subgroups as well as to normal brain, RCOR2 is significantly upregulated only in ST-EPN-ZFTA patient samples. To test oncogenic relevance of RCOR2 for growth and maintenance, we depleted RCOR2 by RNAi and observed a strongly reduced cell survival in several ST-EPN-ZFTA cell lines but not or to a lesser extent in PF-EPN-A cells. Since RCOR2 is an adaptor protein lacking enzymatic activity, we looked at the expression of the proteins known as an interacting partner of RCOR2. Lysine-histone demethylase 1 (LSD1) is one of them and its expression in ST-EPN-ZFTA significantly correlates with RCOR2 expression. We therefore hypothesized that ST-EPN-ZFTA cells may be sensitive to LSD1 depletion, too. Indeed, depletion of LSD1 by RNAi resulted in a strong growth inhibition in ST-EPN-ZFTA cells, but not in PF-EPN-A cells. However, none of the tested LSD1 inhibitors exerted anti-proliferative activity at clinically reachable doses in the ST-EPN-ZFTA cells indicating a potential LSD1 non-enzymatic function in this particular tumor type. In summary, our study nominates RCOR2 as a oncogenic gene specific for ST-EPN-ZFTA ependymomas. Current studies focus on the identification of other interacting partners of the RCOR2-LSD1 complex and how to target these for therapeutic approaches.
Citation Format: Aylin Camgöz, Konstantin Okonechnikov, Owen Chapman, Monika Maurmann, Frank Buchholz, Stefan Pfister, Lukas Chavez, Marcel Kool. 3D genome conformation analysis in ST-EPN-ZFTA ependymoma identifies RCOR2 as a potential target [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3886.
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Affiliation(s)
| | | | - Owen Chapman
- 2University of California San Diego, San Diego, CA
| | | | | | | | - Lukas Chavez
- 2University of California San Diego, San Diego, CA
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Joshi P, Okonechnikov K, Sepp M, Sarropoulos I, Leiss K, Kutscher LM, Kaessmann H, Pfister SM. OTHR-04. Single-nucleus transcriptomic atlas of human hindbrain development identifies cellular origins of pediatric brainstem tumors. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The hindbrain is a key central nervous system structure involved in communication between the brain and the spinal cord, integrating sensory information and coordinating motor responses. Dysregulation in hindbrain development is frequently associated with behavioral disorders and maybe associated tumor formation, stressing the importance of understanding the intricacies of human hindbrain development. Here we performed RNA-sequencing of over 300,000 single nuclei to construct a developing human hindbrain atlas, focusing on pons and medulla, ranging from embryonic to adult stages, profiling the entirety of the hindbrain’s neural and glial populations from progenitors to mature cell types. We describe the transcriptional identity of neuronal cells constituting the pontine and medullary nerve centers including precerebellar, respiratory, auditory and vestibular nuclei; and their differentiation trajectory from the progenitor domains in the embryonic rhombencephalon. To identify the origins of pediatric brain tumors, we mapped ~2,900 bulk and ~50 single-cell transcriptome tumor datasets to the developmental hindbrain atlas, focusing on medulloblastomas, and pediatric low- and high-grade gliomas, and determined cell populations and differentiation states associated with specific tumor groups. We confirmed migrating lower rhombic lip derivatives as the lineage of origin for WNT medulloblastoma. Further, we ascertained early ventral neural progenitor-derived oligodendrocyte lineage as the source of diffuse midline glioma H3K27-altered and postnatal oligodendrocyte progenitors as the origin of pilocytic astrocytoma. In addition, the ependymal lineage originating from glial progenitors was identified as the best match for ependymomas. We show that tumor development has a component that transcriptomically follows its cellular lineage of origin, and identify genes with preserved expression between the respective normal and malignant cell populations. Tumor to normal comparisons also identified tumor-specific genes, providing promising therapeutic candidates. We plan to make our data and analysis pipeline publicly available via user-friendly graphical interface at brain-match.org for unrestricted use of the generated results.
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Affiliation(s)
- Piyush Joshi
- Hopp-Children's Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
| | | | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance , Heidelberg , Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance , Heidelberg , Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance , Heidelberg , Germany
| | - Lena M Kutscher
- Hopp-Children's Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance , Heidelberg , Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology , Heidelberg , Germany
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9
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von Soosten L, Haar J, Frehtman V, Holderbach S, Belzen JUZ, Jendrusch M, Okonechnikov K, Pfister SM, Grimm D, Leuchs B, Jones D, Kutscher LM, Zuckermann M. THER-01. Precision brain tumor therapy by AAV-mediated oncogene editing. Neuro Oncol 2022. [PMCID: PMC9165130 DOI: 10.1093/neuonc/noac079.695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Pediatric high-grade glioma is a heterogeneous group of highly malignant tumors of the central nervous system, with a median overall survival of less than two years after diagnosis, demanding novel treatment options. One innovative approach is gene therapy, which has so far been hampered for cancer treatment owing to the lack of a system targeting tumor cells specifically. To overcome this limitation, we established a novel strategy for gene therapy, combining tumor cell-specific adeno-associated virus (AAV) variants with oncogene-specific CRISPR-Cas nucleases. We screened 177 different Cas9/gRNA combinations targeting the genes encoding H3K27M or BRAFV600E, and identified highly specific nucleases that edited the oncogenic allele but left the respective WT loci intact, which we validated by PCR amplicon sequencing. Next, we intravenously injected an AAV library engineered to encode its own capsid DNA into mice harboring patient-derived xenograft tumors driven by H3K27M or BRAFV600E. After 21 days, we resected neoplasms and separated mCherry-labeled tumor cells from normal surrounding cells by fluorescence-activated cell sorting. Using the DNA from tumor cells as template, we generated a second AAV library, which was utilized in another round of in vivo selection. At the end of each screen, DNA from tumor cells, surrounding cells, and control tissues (liver and spleen) was analyzed by amplicon sequencing. Strikingly, we identified multiple AAV variants that were highly and recurrently enriched in the analyzed tumor tissues. We are currently validating these variants by intravenously injecting selected, GFP-encoding AAVs to tumor-bearing mice and by subsequently analyzing their distribution throughout the aforementioned tissues. We will combine oncogene-specific nucleases with these validated AAV variants and analyze their anti-tumoral efficacy in a preclinical setting. Furthermore, we plan to adapt this approach to allografted mice, evaluating its feasibility and efficacy in syngeneic models.
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Affiliation(s)
- Laura von Soosten
- Division of Pediatric Glioma Research, Hopp Children’s Cancer Center Heidelberg (KiTZ) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Faculty of Biosciences, Heidelberg University , Heidelberg , Germany
| | - Janina Haar
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg , BioQuant, Heidelberg , Germany
| | - Veronika Frehtman
- Tumor Virology, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stefan Holderbach
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg , BioQuant, Heidelberg , Germany
- Synthetic Biology Group, BioQuant Center, University of Heidelberg , Heidelberg , Germany
| | - Julius Upmeier zu Belzen
- Synthetic Biology Group, BioQuant Center, University of Heidelberg , Heidelberg , Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité University Medicine , Berlin , Germany
| | - Michael Jendrusch
- Synthetic Biology Group, BioQuant Center, University of Heidelberg , Heidelberg , Germany
- European Molecular Biology Laboratory (EMBL) , Heidelberg , Germany
| | - Konstantin Okonechnikov
- Division of Pediatric Neurooncology, Hopp Children’s Cancer Center Heidelberg (KiTZ) and German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, Hopp Children’s Cancer Center Heidelberg (KiTZ) and German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital , Heidelberg , Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg , BioQuant, Heidelberg , Germany
- German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK) , Heidelberg , Germany
| | - Barbara Leuchs
- Tumor Virology, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - David Jones
- Division of Pediatric Glioma Research, Hopp Children’s Cancer Center Heidelberg (KiTZ) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Lena M Kutscher
- JRG Developmental Origins of Pediatric Cancer, Hopp Children’s Cancer Center Heidelberg (KiTZ) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Marc Zuckermann
- Division of Pediatric Glioma Research, Hopp Children’s Cancer Center Heidelberg (KiTZ) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Division of Pediatric Neurooncology, Hopp Children’s Cancer Center Heidelberg (KiTZ) and German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
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10
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Okonechnikov K, Camgöz A, Park DE, Chapman O, Hübner JM, Jenseit A, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Hidalgo RA, Reid D, Juarez EF, Robinson JT, Pajtler KW, Milde T, Coufal N, Levy M, Malicki D, Nahas S, Snuderl M, Crawford J, Wechsler-Reya R, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Mesirov J, Pfister SP, Ay F, Dixon J, Kool M, Chavez L. EPEN-18. Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma. Neuro Oncol 2022. [PMCID: PMC9165136 DOI: 10.1093/neuonc/noac079.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Ependymoma (EPN) is an aggressive pediatric tumor that occurs throughout the central nervous system. The two most aggressive molecular subgroups of EPN are the supratentorial ZFTA-fusion associated group (ST-EPN-ZFTA) and the posterior fossa group A (PF-EPN-A). Although the molecular characteristics underlying the tumorigenesis of these subgroups have been extensively studied, these tumors remain difficult to treat. Hence, innovative therapeutic approaches are urgently needed. Here, we used genome-wide chromosome conformation capture (Hi-C), complemented with CTCF (insulators) and H3K27ac (active enhancers) ChIP-seq, as well as gene expression and whole-genome DNA methylation profiling in primary and relapsed EPN tumors and cell lines, to identify chromosomal rearrangements and regulatory mechanisms underlying aberrant expression of genes that are essential for EPN tumorigenesis. By integrating these heterogenous data types, we have observed the formation of new topologically associated domains (‘neo-TADs’) caused by intra- and inter-chromosomal structural variants in both tumors. In addition, we observed 3D chromatin complexes of regulatory elements, and the replacement of CTCF insulators by DNA hyper-methylation in PF-EPN-A tumors. These tumor-specific 3D genome conformations can be associated with the transcriptional upregulation of nearby genes. Through inhibition experiments we validated that these newly identified genes, including RCOR2, ITGA6, LAMC1, and ARL4C, are highly essential for the survival of patient-derived EPN cell lines in a disease subgroup-specific manner. Thus, our study identifies novel potential therapeutic vulnerabilities in EPN and extends our ability to reveal tumor-dependency genes and pathways by oncogenic 3D genome conformations even in tumors that lack known 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
| | - Donglim Esther Park
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego , La Jolla , USA
| | - Owen Chapman
- Division of Medical Genetics, 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
| | - Abhijit Chakraborty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology , La Jolla , USA
| | - Meghana Pagadala
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
| | - Rosalind Bump
- Salk Institute for Biological Studies , La Jolla , USA
| | | | - Katherina Kraft
- Center for Personal Dynamic Regulomes, Stanford University , Stanford , USA
| | | | | | - Edwin F Juarez
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
| | - James T Robinson
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center (KiTZ) , 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
| | - Nicole Coufal
- Department of Pediatrics, University of California San Diego , San Diego , USA
| | - Michael Levy
- Neurosurgery, University of California San Diego – Rady Children's Hospital , San Diego , USA
| | - Denise Malicki
- Pathology, University of California San Diego – Rady Children's Hospital , San Diego , USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine , San Diego , USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, NYU Grossman School of Medicine , New York , USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health , New York , USA
| | - John Crawford
- Department of Neurosciences, University of California San Diego – Rady Children's Hospital , San Diego , USA
| | - Robert Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Research Discovery Institute , La Jolla , USA
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics , Berlin , Germany
| | | | - Hannah Carter
- Division of Medical Genetics, 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 , Canada
| | - Sachin A Kumar
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto , Toronto , Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto , Toronto , Canada
| | - Jeremy Rich
- Division of Regenerative Medicine, Department of Medicine, University of California San Diego , La Jolla , USA
| | - Jill Mesirov
- Moores Cancer Center, University of California San Diego (UCSD) , La Jolla , USA
| | - Stefan P Pfister
- Hopp Children’s Cancer Center (KiTZ) , Heidelberg , Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital , Heidelberg , Germany
| | - Ferhat Ay
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology , La Jolla , USA
| | - Jesse Dixon
- Salk Institute for Biological Studies , La Jolla , USA
| | - Marcel Kool
- Hopp Children’s Cancer Center (KiTZ) , Heidelberg , Germany
- Princess Máxima Center for Pediatric Oncology , Utrecth , Netherlands
| | - Lukas Chavez
- Division of Medical Genetics, Department of Medicine, University of California San Diego (UCSD) , San Diego , USA
- Moores Cancer Center, University of California San Diego (UCSD) , La Jolla , USA
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11
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Okonechnikov K, Joshi P, Sepp M, Leiss K, Sarropoulos I, Jones DTW, Kool M, Jäger N, Kutscher LM, Kaessmann H, Pfister SM. TBIO-02. Mapping the origins of pediatric brain tumors to cell type lineages in the developing cerebellum. Neuro Oncol 2022. [PMCID: PMC9164824 DOI: 10.1093/neuonc/noac079.684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Understanding the cellular origins of cerebellar tumors at single cell resolution may help identify novel therapeutic vulnerabilities to overcome current impediments in pediatric neuro-oncology. One approach to answer this important question involves the mapping of tumor profiles onto normal embryonal central nervous system development. Previous attempts in this regard focused on integrating human tumor data with developing mouse cerebellum atlases, however, these approaches were inherently limited due to species-specific differences. In order to address this critical issue, we use a high resolution developing human cerebellum single cell atlas in order to compare to extended bulk and single cell transcriptomes profiles from pediatric solid tumors. In result, we provide novel and confirmatory findings for the cellular association of medulloblastoma SHH, Group3 and Group4 as well as pilocytic astrocytoma, using comprehensive approaches to decipher the cellular composition and map the origins of childhood brain tumors. We also shed light on the cellular origins of posterior fossa ependymoma and radiation-induced glioma (secondary tumor, occurring after medulloblastoma). As a common feature among the tumor similarity to normal cell types, we identify gradients of differentiation, starting from early progenitor cells to more differentiated cell states, observed in all cerebellar tumor entities investigated at single cell level; thus reflecting possible lineages of origin. Pertaining to clinical application, we identified specific developmental genes shared between cerebellar lineages and associated tumors, and tumor-specific genes absent in all cerebellar lineages. These two categories of genes comprise candidate lineage markers for faithful modeling and, if absent from other organ systems after birth, could become an important source of potential therapeutic targets. Importantly, all analysis results are publicly available via an interactive online user interface (brain-match.org) that serves as an open valuable resource for the scientific community.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children ́s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Piyush Joshi
- Hopp Children ́s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH) , Heidelberg , Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH) , Heidelberg , Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH) , Heidelberg , Germany
| | - David T W Jones
- Hopp Children ́s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Marcel Kool
- Hopp Children ́s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Natalie Jäger
- Hopp Children ́s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Lena M Kutscher
- Hopp Children ́s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH) , Heidelberg , Germany
| | - Stefan M Pfister
- Hopp Children ́s Cancer Center Heidelberg (KiTZ) , Heidelberg , Germany
- German Cancer Research Center (DKFZ) , Heidelberg , Germany
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12
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Ghasemi DR, Okonechnikov K, Tirier S, Rademacher A, Mallm JP, Ernst K, Rippe K, Korshunov A, Pfister SM, Pajtler KW. MEDB-60. Medulloblastoma with extensive nodularity mimics cerebellar development and differentiates along the granular precursor lineage. Neuro Oncol 2022. [PMCID: PMC9164840 DOI: 10.1093/neuonc/noac079.434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND: Medulloblastoma with extensive nodularity (MBEN) represents a rare type of cerebellar tumors of infancy comprising two histologically distinct components that differ in cell differentiation and mitotic activity. Whereas some children suffering from MBEN experience disease recurrence, MBEN can also spontaneously differentiate and discontinue to grow. The underlying mechanisms of this variable biological behavior may offer insight into how embryonal tumors develop. METHODS: Fresh frozen and FFPE tumor tissue from nine MBEN-patients was subjected to multi-omics characterization including bulk sequencing, microdissection followed by RNA sequencing, single nucleus RNA-sequencing using the 10X Genomics- and SMART Seq. V2-protocols and spatial transcriptomics via RNAscope. RESULTS: All cases were molecularly classified as Sonic Hedgehog (SHH)-MB, and harbored somatic mutations within the SHH-pathway. After quality control, a total of ~30.000 cells were subjected to downstream analysis. Several non-malignant cell types, such as glial cells, were identified. In accordance with previous studies, we found only sparse immune infiltration. Unsupervised clustering identified cell clusters that differed in differentiation state and represented a continuum from embryonal-like cells with SHH-upregulation over intermediate cell states, to neuronal-like, postmitotic cells. Mapping to a single nucleus sequencing atlas of cerebellar development indicated that tumor cells reflected various stages of normally developing cerebellar granular precursors. Interestingly, one cluster of malignant cells with tumor-specific copy number alterations showed both transcriptomic features of astrocytes and embryonal cells. Using spatial transcriptomics, we were able to correlate different clusters of MBEN cells with distinct histologic MBEN compartments, with astrocyte-like tumor cells being located in the internodular compartment and in close proximity to mitotically active cancer cells. CONCLUSION: MBEN is formed by a continuum of malignant cell differentiation along the granular precursor lineage, with a subset of cells developing into cells that may represent tumor astrocytes. This differentiation process is reflected in the bicompartmental structure of MBEN.
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Affiliation(s)
- David R Ghasemi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital , Heidelberg , Germany
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephan Tirier
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant , Heidelberg , Germany
| | - Anne Rademacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant , Heidelberg , Germany
| | - Jan-Philipp Mallm
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Single-cell Open Lab, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Kati Ernst
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant , Heidelberg , Germany
| | - Andrey Korshunov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital , Heidelberg , Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital , Heidelberg , Germany
| | - Kristian W Pajtler
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital , Heidelberg , Germany
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13
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Federico A, Okonechnikov K, Carmona EB, Lammers JAS, Kranendonk MEG, Gojo J, Englinger B, Jiang L, Nierkens S, Calkoen FGJ, van der Lugt J, Filbin MG, Jäger N, Pfister SM, Kool M. EPEN-08. Single-cell transcriptome analysis defines a tumor-supportive microenvironment and tumor-stroma crosstalk in pediatric ependymoma and medulloblastoma. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Brain tumors are the leading cause of disease-related death in childhood and strong efforts are required to develop innovative and efficient therapeutic strategies for patients with high-risk disease. Key critical factor of pediatric brain tumors is their molecular heterogeneity; one of the aspects that contributes to such heterogeneity is the intrinsic capacity of the tumor cells to organize, shape and exploit the surrounding brain tumor microenvironment (TME) to sustain tumor growth and malignant progression. TME was proved to play a crucial role in several malignancies, but in pediatric brain malignancies this has not been fully elucidated yet. Here, we aimed at characterizing the TME cell populations and their contributions in ependymoma and medulloblastoma, two of the most common pediatric brain tumor entities. Single-cell transcriptome analysis (n=65 ependymomas; n=39 medulloblastomas) of publicly available tumor datasets, as well as newly generated data of primary tumors and matching patient-derived tumor xenografts (PDX), showed an extensive heterogeneity of TME cell types with distinctive expression signatures. Amongst the identified TME populations, analysis revealed pro-inflammatory and proliferating myeloid cells, tumor-infiltrating lymphocytes, active regulatory T cells and vascular progenitor cells. Comparative analysis between primary and PDX tumors showed that tumor cells stimulated the host microenvironment, which in turn exhibited tumor-associated stromal signatures. Applying a deconvolution method, using our single cell data as reference, on a bulk tumor cohort including PFA ependymomas with different degree of immune infiltration, we observed an enrichment of polarized macrophages and microglia cells in tumor with high infiltration. Next, we identified TME markers involved in tumor-supportive functions, such as immune suppression (TIGIT, FOXP3, BCL2, CD19, ICAM2), pro-inflammatory stimuli (CCL3, CCL4, IL1B, GPNMB), extracellular matrix remodeling (COL4A1) and angiogenic processes (ANGPT2). TME markers with emerging role in ependymoma and medulloblastoma can be considered as possible targets for tailored and more effective anti-tumor therapeutic strategies.
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Affiliation(s)
- Aniello Federico
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | - Konstantin Okonechnikov
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | - Enrique Blanco Carmona
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | | | | | - Johannes Gojo
- Hopp Children’s Cancer Center , Heidelberg , Germany
- Medical University of Vienna , Vienna , Austria
| | - Bernhard Englinger
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston , USA
- Broad Institute of Harvard and MIT , Cambridge , USA
| | - Li Jiang
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston , USA
- Broad Institute of Harvard and MIT , Cambridge , USA
| | | | | | | | - Mariella G Filbin
- Dana-Farber Boston Children’s Cancer and Blood Disorders Center , Boston , USA
- Broad Institute of Harvard and MIT , Cambridge , USA
| | - Natalie Jäger
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center , Heidelberg , Germany
- German Cancer Research Center , Heidelberg , Germany
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14
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Morcavallo A, Barker K, Kwok C, Boult JKR, da Silva PBG, Okonechnikov K, Zuckermann M, Gorrini C, Jacques TS, Robinson SP, Clifford SC, Weiss WA, Pfister SM, Kawauchi D, Chesler L. MODL-02. A novel Cre-conditional cMYC-driven MB Group 3 transgenic mouse model shows traceable leptomeningeal dissemination. Neuro Oncol 2022. [PMCID: PMC9165051 DOI: 10.1093/neuonc/noac079.625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Medulloblastoma (MB), the most common embryonal tumour of the Central Nervous System, occurs in the cerebellum. Treatment regimens involve surgery, craniospinal radiotherapy, and chemotherapy. The greatest mortality is associated with disseminated disease, almost exclusively found in the leptomeningeal space. Unfortunately, knowledge about the aetiology of MB spread is limited and the need for kinder and efficacious therapy remains an unmet goal. Of the four molecular classified MB groups, Group3 (Gr3) MB presents with a high frequency of metastasis at diagnosis, with the worst overall survival. Gr3 MB tumours are dominated by primitive progenitor-like cells and cMYC deregulation; often, p53 deficiency is observed at relapse. To dissect the biology of primary and metastatic Gr3 MB, we have developed a new germline genetically engineered mouse model (GEMM), harbouring cMYC amplification in a Tamoxifen-inducible p53 functional background (Trp53ERTAM strain). A novel LSL-cMYC-CopGFP-Luciferase transgene was integrated into the Rosa-26 locus of the mouse genome. Transgenic mice were crossed with a strain expressing Cre recombinase under the Blbp promoter targeting embryonic neural progenitors, and subsequently bred to Trp53ERTAM mice. As result, the cMYC overexpression was sufficient to generate tumours. Tumour penetrance was observed in all the expected tumour bearing genotypes, with increased aggressiveness in a non-functional p53 background. Bioluminescence imaging demonstrated tumour onset in the brain and dissemination along the spinal cord. CopGFP positive tumour cells were isolated from primary and metastatic tumours. Pathological interrogation confirmed that tumours present large cell/anaplastic (LCA) histology. Analysis of preliminary transcriptional profiling data proved that tumours cluster with human Gr3 MB. Ongoing methylation profiling and multi-omics approaches will inform on the tumour cells of origin and clonal divergence of primary tumour versus metastasis. In conclusion, we have successfully developed a novel immunocompetent mouse model of metastatic Gr3 MB with which we can investigate therapeutic vulnerabilities of MB.
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Affiliation(s)
- Alaide Morcavallo
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton , Surrey , United Kingdom
| | - Karen Barker
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton , Surrey , United Kingdom
| | - Colin Kwok
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton , Surrey , United Kingdom
| | - Jessica K R Boult
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, Sutton , Surrey , United Kingdom
| | - Patricia Benites Goncalves da Silva
- Hopp Children′s Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), and Department of Pediatric Hematology and Oncology, Heidelberg University Hospital , Heidelberg , Germany
| | - Konstantin Okonechnikov
- Hopp Children′s Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), and Department of Pediatric Hematology and Oncology, Heidelberg University Hospital , Heidelberg , Germany
| | - Marc Zuckermann
- Hopp Children′s Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), and Department of Pediatric Hematology and Oncology, Heidelberg University Hospital , Heidelberg , Germany
| | - Chiara Gorrini
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton , Surrey , United Kingdom
| | - Thomas S Jacques
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health and Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust , London , United Kingdom
| | - Simon P Robinson
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, Sutton , Surrey , United Kingdom
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle Upon Tyne, United Kingdom
| | - William A Weiss
- Department of Neurology, University of California, San Francisco , CA , USA
| | - Stefan M Pfister
- Hopp Children′s Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), and Department of Pediatric Hematology and Oncology, Heidelberg University Hospital , Heidelberg , Germany
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), National Institute of Neuroscience , Tokyo , Japan
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton , Surrey , United Kingdom
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15
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Korshunov A, Okonechnikov K, Stichel D, Schrimpf D, Delaidelli A, Tonn S, Mynarek M, Sievers P, Sahm F, Jones DTW, von Deimling A, Pfister SM, Kool M. Gene expression profiling of Group 3 medulloblastomas defines a clinically tractable stratification based on KIRREL2 expression. Acta Neuropathol 2022; 144:339-352. [PMID: 35771282 PMCID: PMC9288368 DOI: 10.1007/s00401-022-02460-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022]
Abstract
Medulloblastomas (MB) molecularly designated as Group 3 (Grp 3) MB represent a more clinically aggressive tumor variant which, as a group, displays heterogeneous molecular characteristics and disease outcomes. Reliable risk stratification of Grp 3 MB would allow for appropriate assignment of patients to aggressive treatment protocols and, vice versa, for sparing adverse effects of high-dose radio-chemotherapy in patients with standard or low-risk tumors. Here we performed RNA-based analysis on an international cohort of 179 molecularly designated Grp 3 MB treated with HIT protocols. We analyzed the clinical significance of differentially expressed genes, thereby developing optimal prognostic subdivision of this MB molecular group. We compared the transcriptome profiles of two Grp 3 MB subsets with various outcomes (76 died within the first 60 months vs. 103 survived this period) and identified 224 differentially expressed genes (DEG) between these two clinical groups (Limma R algorithm, adjusted p-value < 0.05). We selected the top six DEG overexpressed in the unfavorable cohort for further survival analysis and found that expression of all six genes strongly correlated with poor outcomes. However, only high expression of KIRREL2 was identified as an independent molecular prognostic indicator of poor patients' survival. Based on clinical and molecular patterns, four risk categories were outlined for Grp 3 MB patients: i. low-risk: M0-1/MYC non-amplified/KIRREL2 low (n = 48; 5-year OS-95%); ii. standard-risk: M0-1/MYC non-amplified/KIRREL2 high or M2-3/MYC non-amplified/KIRREL2 low (n = 65; 5-year OS-70%); iii. high-risk: M2-3/MYC non-amplified/KIRREL2 high (n = 36; 5-year OS-30%); iv. very high risk-all MYC amplified tumors (n = 30; 5-year OS-0%). Cross-validated survival models incorporating KIRREL2 expression with clinical features allowed for the reclassification of up to 50% of Grp 3 MB patients into a more appropriate risk category. Finally, KIRREL2 immunopositivity was also identified as a predictive indicator of Grp 3 MB poor survival, thus suggesting its application as a possible prognostic marker in routine clinical settings. Our results indicate that integration of KIRREL2 expression in risk stratification models may improve Grp 3 MB outcome prediction. Therefore, simple gene and/or protein expression analyses for this molecular marker could be easily adopted for Grp 3 MB prognostication and may help in assigning patients to optimal therapeutic approaches in prospective clinical trials.
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Affiliation(s)
- Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany. .,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
| | - Konstantin Okonechnikov
- German Cancer Consortium (DKTK), Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC Canada ,Department of Pathology and Laboratory Medicine, British Columbia Cancer Research Centre, Vancouver, BC Canada
| | - Svenja Tonn
- Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Martin Mynarek
- Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T. W. Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Stefan M. Pfister
- German Cancer Consortium (DKTK), Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ), Heidelberg, Germany ,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- German Cancer Consortium (DKTK), Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ), Heidelberg, Germany ,Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
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16
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Coltin H, Sundaresan L, Smith KS, Skowron P, Massimi L, Eberhart CG, Schreck KC, Gupta N, Weiss WA, Tirapelli D, Carlotti C, Li KKW, Ryzhova M, Golanov A, Zheludkova O, Absalyamova O, Okonechnikov K, Stichel D, von Deimling A, Giannini C, Raskin S, Van Meir EG, Chan JA, Fults D, Chambless LB, Kim SK, Vasiljevic A, Faure-Conter C, Vibhakar R, Jung S, Leary S, Mora J, McLendon RE, Pollack IF, Hauser P, Grajkowska WA, Rubin JB, van Veelen MLC, French PJ, Kros JM, Liau LM, Pfister SM, Kool M, Kijima N, Taylor MD, Packer RJ, Northcott PA, Korshunov A, Ramaswamy V. Subgroup and subtype-specific outcomes in adult medulloblastoma. Acta Neuropathol 2021; 142:859-871. [PMID: 34409497 PMCID: PMC10723183 DOI: 10.1007/s00401-021-02358-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
Medulloblastoma, a common pediatric malignant central nervous system tumour, represent a small proportion of brain tumours in adults. Previously it has been shown that in adults, Sonic Hedgehog (SHH)-activated tumours predominate, with Wingless-type (WNT) and Group 4 being less common, but molecular risk stratification remains a challenge. We performed an integrated analysis consisting of genome-wide methylation profiling, copy number profiling, somatic nucleotide variants and correlation of clinical variables across a cohort of 191 adult medulloblastoma cases identified through the Medulloblastoma Advanced Genomics International Consortium. We identified 30 WNT, 112 SHH, 6 Group 3, and 41 Group 4 tumours. Patients with SHH tumours were significantly older at diagnosis compared to other subgroups (p < 0.0001). Five-year progression-free survival (PFS) for WNT, SHH, Group 3, and Group 4 tumours was 64.4 (48.0-86.5), 61.9% (51.6-74.2), 80.0% (95% CI 51.6-100.0), and 44.9% (95% CI 28.6-70.7), respectively (p = 0.06). None of the clinical variables (age, sex, metastatic status, extent of resection, chemotherapy, radiotherapy) were associated with subgroup-specific PFS. Survival among patients with SHH tumours was significantly worse for cases with chromosome 3p loss (HR 2.9, 95% CI 1.1-7.6; p = 0.02), chromosome 10q loss (HR 4.6, 95% CI 2.3-9.4; p < 0.0001), chromosome 17p loss (HR 2.3, 95% CI 1.1-4.8; p = 0.02), and PTCH1 mutations (HR 2.6, 95% CI 1.1-6.2; p = 0.04). The prognostic significance of 3p loss and 10q loss persisted in multivariable regression models. For Group 4 tumours, chromosome 8 loss was strongly associated with improved survival, which was validated in a non-overlapping cohort (combined cohort HR 0.2, 95% CI 0.1-0.7; p = 0.007). Unlike in pediatric medulloblastoma, whole chromosome 11 loss in Group 4 and chromosome 14q loss in SHH was not associated with improved survival, where MYCN, GLI2 and MYC amplification were rare. In sum, we report unique subgroup-specific cytogenetic features of adult medulloblastoma, which are distinct from those in younger patients, and correlate with survival disparities. Our findings suggest that clinical trials that incorporate new strategies tailored to high-risk adult medulloblastoma patients are urgently needed.
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Affiliation(s)
- Hallie Coltin
- Division of Haematology/Oncology, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
| | - Lakshmikirupa Sundaresan
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
| | - Kyle S Smith
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, MS 325, Room D2058, 262 Danny Thomas Place, Memphis, TN, 38105-3678, USA
| | - Patryk Skowron
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
| | - Luca Massimi
- Department of Neurosurgery, Fondazione Policlinico A. Gemelli IRCCS, Catholic University Medical School, Rome, Italy
| | - Charles G Eberhart
- Department of Neuropathology and Ophthalmic Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Karisa C Schreck
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Nalin Gupta
- Departments of Neurological Surgery and Pediatrics, University of California, San Francisco, CA, USA
| | - William A Weiss
- Departments of Neurology, Neurological Surgery, and Pediatrics, University of California, San Francisco, CA, USA
| | - Daniela Tirapelli
- Department of Surgery and Anatomy, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, São Paulo, Brazil
| | - Carlos Carlotti
- Department of Surgery and Anatomy, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, São Paulo, Brazil
| | - Kay K W Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Marina Ryzhova
- NN Burdenko Neurosurgical Research Centre, Moscow, Russia
| | - Andrey Golanov
- NN Burdenko Neurosurgical Research Centre, Moscow, Russia
| | | | | | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and Department of Neuropathology, University of Heidelberg, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and Department of Neuropathology, University of Heidelberg, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Scott Raskin
- Center for Cancer and Blood Disorders, Children's National Medical Center, Washington, DC, USA
| | - Erwin G Van Meir
- Department of Neurosurgery, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Jennifer A Chan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Daniel Fults
- Department of Neurosurgery, University of Utah, Salt Lake City, UT, USA
| | - Lola B Chambless
- Department of Neurological Surgery, Vanderbilt Medical Center, Nashville, TN, USA
| | - Seung-Ki Kim
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | - Alexandre Vasiljevic
- Centre de Pathologie et Neuropathologie Est, Centre de Biologie et Pathologie Est, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- ONCOFLAM, Neuro-Oncologie Et Neuro-Inflammation Centre de Recherche en Neurosciences de Lyon, Lyon, France
| | - Cecile Faure-Conter
- Department of Pediatrics, Institut d'Hemato-Oncologie Pediatrique, Lyon, France
| | - Rajeev Vibhakar
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Shin Jung
- Department of Neurosurgery, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Hwasun-gun, Chonnam, South Korea
| | - Sarah Leary
- Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA, USA
| | - Jaume Mora
- Developmental Tumor Biology Laboratory, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | | | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Peter Hauser
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | | | - Joshua B Rubin
- Departments of Pediatrics, Anatomy and Neurobiology, Washington University School of Medicine and St Louis Children's Hospital, St Louis, MO, USA
| | - Marie-Lise C van Veelen
- Department of Neurosurgery, Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Pim J French
- Department of Neurology, Brain Tumour Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at University of California at Los Angeles, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Noriyuki Kijima
- Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Michael D Taylor
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada
| | - Roger J Packer
- Center for Cancer and Blood Disorders, Children's National Medical Center, Washington, DC, USA
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, MS 325, Room D2058, 262 Danny Thomas Place, Memphis, TN, 38105-3678, USA.
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and Department of Neuropathology, University of Heidelberg, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada.
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Delaidelli A, Dunham C, Santi M, Negri GL, Triscott J, Zheludkova O, Golanov A, Ryzhova M, Okonechnikov K, Schrimpf D, Stichel D, Ellison DW, von Deimling A, Kool M, Pfister SM, Ramaswamy V, Korshunov A, Taylor MD, Sorensen PH. Clinically Tractable Outcome Prediction of non-WNT/non-SHH Medulloblastoma Based on TPD52 Immunohistochemistry in a Multicohort Study. Clin Cancer Res 2021; 28:116-128. [PMID: 34702771 DOI: 10.1158/1078-0432.ccr-21-2057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/12/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE International consensus and the 2021 WHO classification recognize eight molecular subgroups among non-WNT/non-SHH (Group 3/4) medulloblastoma, representing ~60% of tumors. However, very few clinical centers worldwide possess the technical capabilities to determine DNA-methylation profiles or other molecular parameters of high-risk for Group 3/4 tumors. As a result, biomarker-driven risk stratification and therapy assignment constitutes a major challenge in medulloblastoma research. Here, we identify an immunohistochemistry (IHC) marker as a clinically tractable method for improved medulloblastoma risk stratification. EXPERIMENTAL DESIGN We bioinformatically analyzed published medulloblastoma transcriptomes and proteomes identifying as a potential biomarker TPD52, whose IHC prognostic value was validated across three Group 3/4 medulloblastoma clinical cohorts (n = 387) treated with conventional therapies. RESULTS TPD52 IHC positivity represented a significant independent predictor of early relapse and death for Group 3/4 medulloblastoma (HRs between 3.67-26.7 [95% CIs between 1.00-706.23], p = 0.05, 0.017 and 0.0058). Cross-validated survival models incorporating TPD52 IHC with clinical features outperformed existing state-of-the-art risk stratification schemes, and reclassified ~50% of patients into more appropriate risk categories. Finally, TPD52 immunopositivity was a predictive indicator of poor response to chemotherapy (HR 12.66 [95% CI 3.53-45.40], p < 0.0001), suggesting important implication for therapeutic choices. CONCLUSIONS The current study redefines the approach to risk stratification in Group 3/4 medulloblastoma in global practice. Since integration of TPD52 IHC in classification algorithms significantly improved outcome prediction, this test could be rapidly adopted for risk stratification on a global scale, independently of advanced but technically challenging molecular profiling techniques.
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Affiliation(s)
- Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, and University of British Columbia, Vancouver, British Columbia, Canada
| | - Mariarita Santi
- Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Joanna Triscott
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Olga Zheludkova
- St Luka's Clinical Research Center for Children, Moscow, Russian Federation
| | - Andrey Golanov
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | - Marina Ryzhova
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)
| | - Daniel Schrimpf
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andreas von Deimling
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrey Korshunov
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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19
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Zheng T, Ghasemi DR, Okonechnikov K, Korshunov A, Sill M, Maass KK, Benites Goncalves da Silva P, Ryzhova M, Gojo J, Stichel D, Arabzade A, Kupp R, Benzel J, Taya S, Adachi T, Shiraishi R, Gerber NU, Sturm D, Ecker J, Sievers P, Selt F, Chapman R, Haberler C, Figarella-Branger D, Reifenberger G, Fleischhack G, Rutkowski S, Donson AM, Ramaswamy V, Capper D, Ellison DW, Herold-Mende CC, Schüller U, Brandner S, Driever PH, Kros JM, Snuderl M, Milde T, Grundy RG, Hoshino M, Mack SC, Gilbertson RJ, Jones DTW, Kool M, von Deimling A, Pfister SM, Sahm F, Kawauchi D, Pajtler KW. Cross-Species Genomics Reveals Oncogenic Dependencies in ZFTA/C11orf95 Fusion-Positive Supratentorial Ependymomas. Cancer Discov 2021; 11:2230-2247. [PMID: 33879448 DOI: 10.1158/2159-8290.cd-20-0963] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/16/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022]
Abstract
Molecular groups of supratentorial ependymomas comprise tumors with ZFTA-RELA or YAP1-involving fusions and fusion-negative subependymoma. However, occasionally supratentorial ependymomas cannot be readily assigned to any of these groups due to lack of detection of a typical fusion and/or ambiguous DNA methylation-based classification. An unbiased approach with a cohort of unprecedented size revealed distinct methylation clusters composed of tumors with ependymal but also various other histologic features containing alternative translocations that shared ZFTA as a partner gene. Somatic overexpression of ZFTA-associated fusion genes in the developing cerebral cortex is capable of inducing tumor formation in vivo, and cross-species comparative analyses identified GLI2 as a key downstream regulator of tumorigenesis in all tumors. Targeting GLI2 with arsenic trioxide caused extended survival of tumor-bearing animals, indicating a potential therapeutic vulnerability in ZFTA fusion-positive tumors. SIGNIFICANCE: ZFTA-RELA fusions are a hallmark feature of supratentorial ependymoma. We find that ZFTA acts as a partner for alternative transcriptional activators in oncogenic fusions of supratentorial tumors with various histologic characteristics. Establishing representative mouse models, we identify potential therapeutic targets shared by ZFTA fusion-positive tumors, such as GLI2.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Tuyu Zheng
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - David R Ghasemi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kendra K Maass
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Patricia Benites Goncalves da Silva
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Johannes Gojo
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Amir Arabzade
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Robert Kupp
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Julia Benzel
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Shinichiro Taya
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Toma Adachi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Ryo Shiraishi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Nicolas U Gerber
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Rebecca Chapman
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | | | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Duesseldorf, Germany
| | - Gudrun Fleischhack
- Pediatric Oncology and Hematology, Pediatrics III, University Hospital of Essen, Essen, Germany
| | - Stefan Rutkowski
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrew M Donson
- University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Vijay Ramaswamy
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Capper
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Ulrich Schüller
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sebastian Brandner
- Division of Neuropathology, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, United Kingdom
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Pablo Hernáiz Driever
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Matija Snuderl
- Division of Neuropathology, Department of Pathology, NYU Langone Health, New York, New York
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Stephen C Mack
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Centre for Paediatric Oncology, Utrecht, the Netherlands
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daisuke Kawauchi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
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20
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Korshunov A, Okonechnikov K, Stichel D, Ryzhova M, Schrimpf D, Sahm F, Sievers P, Absalyamova O, Zheludkova O, Golanov A, Jones DTW, Pfister SM, von Deimling A, Kool M. Integrated molecular analysis of adult sonic hedgehog (SHH)-activated medulloblastomas reveals two clinically relevant tumor subsets with VEGFA as potent prognostic indicator. Neuro Oncol 2021; 23:1576-1585. [PMID: 33589929 PMCID: PMC8408884 DOI: 10.1093/neuonc/noab031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Up to now, adult medulloblastoma (MB) patients are treated according to the protocols elaborated for pediatric MB although these tumors are different in terms of clinical outcomes and biology. Approximately 70% of adult MB disclose a sonic hedgehog (SHH) molecular signature in contrast to about 30% in pediatric cohorts. In addition, adult SHH-MB (aSHH-MB) are clinically heterogeneous but there is consensus neither on their optimal treatment nor on risk stratification. Thus, the identification of clinically relevant molecular subsets of aSHH-MB and identification of potential treatment targets remains inconclusive. METHODS We analyzed 96 samples of institutionally diagnosed aSHH-MB through genome-wide DNA methylation profiling, targeted DNA sequencing, and RNA sequencing to identify molecular subcategories of these tumors and assess their prognostic significance. RESULTS We defined two aSHH-MB numerically comparable epigenetic subsets with clinical and molecular variability. The subset "aSHH-MBI" (46%/48%) was associated with PTCH1/SMO (54%/46%) mutations, "neuronal" transcriptional signatures, and favorable outcomes after combined radio-chemotherapy (5-year PFS = 80% and OS = 92%). The clinically unfavorable "aSHH-MBII" subset (50%/52%; 5-year PFS = 24% and OS = 45%) disclosed GLI2 amplifications (8%), loss of 10q (22%), and gene expression signatures associated with angiogenesis and embryonal development. aSHH-MBII tumors revealed strong and ubiquitous expression of VEGFA both at transcript and protein levels that was correlated with unfavorable outcome. CONCLUSIONS (1) The histologically uniform aSHH-MB cohort exhibits clear molecular heterogeneity separating these tumors into two molecular subsets (aSHH-MBI and aSHH-MBII), which are associated with different cytogenetics, mutational landscapes, gene expression signatures, and clinical course. (2) VEGFA appears to be a promising biomarker to predict clinical course, which needs further prospective validation as its potential role in the pathogenesis of this subset.
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Affiliation(s)
- Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | - Marina Ryzhova
- N.N. Burdenko Neurosurgical Research Centre, Moscow, Russia
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | | | - Olga Zheludkova
- Department of Neuro-Oncology, Russian Scientific Center of Radiology, Moscow, Russia
| | - Andrey Golanov
- N.N. Burdenko Neurosurgical Research Centre, Moscow, Russia
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group (B360), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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21
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Sarropoulos I, Sepp M, Frömel R, Leiss K, Trost N, Leushkin E, Okonechnikov K, Joshi P, Giere P, Kutscher LM, Cardoso-Moreira M, Pfister SM, Kaessmann H. Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells. Science 2021; 373:eabg4696. [PMID: 34446581 PMCID: PMC7611596 DOI: 10.1126/science.abg4696] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/14/2021] [Indexed: 12/13/2022]
Abstract
Organ development is orchestrated by cell- and time-specific gene regulatory networks. In this study, we investigated the regulatory basis of mouse cerebellum development from early neurogenesis to adulthood. By acquiring snATAC-seq (single-nucleus assay for transposase accessible chromatin using sequencing) profiles for ~90,000 cells spanning 11 stages, we mapped cerebellar cell types and identified candidate cis-regulatory elements (CREs). We detected extensive spatiotemporal heterogeneity among progenitor cells and a gradual divergence in the regulatory programs of cerebellar neurons during differentiation. Comparisons to vertebrate genomes and snATAC-seq profiles for ∼20,000 cerebellar cells from the marsupial opossum revealed a shared decrease in CRE conservation during development and differentiation as well as differences in constraint between cell types. Our work delineates the developmental and evolutionary dynamics of gene regulation in cerebellar cells and provides insights into mammalian organ development.
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Affiliation(s)
- Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany.
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany.
| | - Robert Frömel
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Nils Trost
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), and German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Piyush Joshi
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), and German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Peter Giere
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Lena M Kutscher
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Developmental Origins of Pediatric Cancer Group, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - Margarida Cardoso-Moreira
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
- Evolutionary Developmental Biology Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), and German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany.
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22
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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: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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von Hoff K, Haberler C, Schmitt-Hoffner F, Schepke E, de Rojas T, Jacobs S, Zapotocky M, Sumerauer D, Perek-Polnik M, Dufour C, van Vuurden D, Slavc I, Gojo J, Pickles JC, Gerber NU, Massimino M, Gil-da-Costa MJ, Garami M, Kumirova E, Sehested A, Scheie D, Cruz O, Moreno L, Cho J, Zeller B, Bovenschen N, Grotzer M, Alderete D, Snuderl M, Zheludkova O, Golanov A, Okonechnikov K, Mynarek M, Juhnke BO, Rutkowski S, Schüller U, Pizer B, Zezschwitz BV, Kwiecien R, Wechsung M, Konietschke F, Hwang EI, Sturm D, Pfister SM, von Deimling A, Rushing EJ, Ryzhova M, Hauser P, Łastowska M, Wesseling P, Giangaspero F, Hawkins C, Figarella-Branger D, Eberhart C, Burger P, Gessi M, Korshunov A, Jacques TS, Capper D, Pietsch T, Kool M. Therapeutic implications of improved molecular diagnostics for rare CNS-embryonal tumor entities: results of an international, retrospective study. Neuro Oncol 2021; 23:1597-1611. [PMID: 34077956 DOI: 10.1093/neuonc/noab136] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Only few data are available on treatment-associated behavior of distinct rare CNS-embryonal tumor entities previously treated as "CNS-primitive neuroectodermal tumors" (CNS-PNET). Respective data on specific entities, including CNS neuroblastoma, FOXR2 activated (CNS NB-FOXR2), and embryonal tumor with multi-layered rosettes (ETMR) are needed for development of differentiated treatment strategies. METHODS Within this retrospective, international study, tumor samples of clinically well-annotated patients with the original diagnosis of CNS-PNET were analyzed using DNA methylation arrays (n=307). Additional cases (n=66) with DNA methylation pattern of CNS NB-FOXR2 were included irrespective of initial histological diagnosis. Pooled clinical data (n=292) were descriptively analyzed. RESULTS DNA methylation profiling of "CNS-PNET" classified 58(19%) cases as ETMR, 57(19%) as HGG, 36(12%) as CNS NB-FOXR2, and 89(29%) cases were classified into 18 other entities. Sixty-seven (22%) cases did not show DNA methylation patterns similar to established CNS tumor reference classes. Best treatment results were achieved for CNS NB-FOXR2 patients (5-year PFS: 63%±7%, OS: 85%±5%, n=63), with 35/42 progression-free survivors after upfront craniospinal irradiation (CSI) and chemotherapy. The worst outcome was seen for ETMR and HGG patients with 5-year PFS of 18%±6% and 22%±7%, and 5-year OS of 24%±6% and 25%±7%, respectively. CONCLUSION The historically reported poor outcome of CNS-PNET patients becomes highly variable when tumors are molecularly classified based on DNA methylation profiling. Patients with CNS NB-FOXR2 responded well to current treatments and a standard-risk-CSI based regimen may be prospectively evaluated. The poor outcome of ETMR across applied treatment strategies substantiates the necessity for evaluation of novel treatments.
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Affiliation(s)
- Katja von Hoff
- Department of Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Austria
| | - Felix Schmitt-Hoffner
- 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
| | - Elizabeth Schepke
- The Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Teresa de Rojas
- Pediatric OncoGenomics Unit, Children's University Hospital Niño Jesús, Madrid, Spain
| | - Sandra Jacobs
- Department of Pediatrics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Michal Zapotocky
- Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - David Sumerauer
- Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Marta Perek-Polnik
- Department of Oncology, The Children's Memorial Health Institute, University of Warsaw, Warsaw, Poland
| | - Christelle Dufour
- Gustave Roussy Cancer Center, Department of Pediatric and Adolescent Oncology, Villejuif, France.,Paris-Saclay University, INSERM, Molecular predictors and New targets in Oncology, Villejuif, France
| | | | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Jessica C Pickles
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Nicolas U Gerber
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - Maura Massimino
- Pediatric Unit, Fondazione IRCCS Istituto Nazionale die Tumori, Milan, Italy
| | | | - Miklos Garami
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Ella Kumirova
- Department of Neuro-Oncology, Dmitry Rogachev National Medical Research Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Astrid Sehested
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Frederik Vs vej 11, 2100 Copenhagen, Denmark
| | - Ofelia Cruz
- Pediatric Oncology Department. Hospital Sant Joan de Deu. Barcelona, Spain
| | - Lucas Moreno
- Paediatric Haematology & Oncology Division, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Jaeho Cho
- Dept. of Radiation Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Bernward Zeller
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Niels Bovenschen
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Michael Grotzer
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - Daniel Alderete
- Service of Hematology/Oncology, Hospital JP Garrahan, Buenos Aires, Argentina
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health and School of Medicine, New York, NY, USA
| | - Olga Zheludkova
- Department of Neurooncology, Russian Scientific Center of Radiology, Moscow, Russia
| | - Andrey Golanov
- Department of Neuroradiology, Burdenko Neurosurgical Institute, Moscow, Russia
| | - 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
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg
| | - B Ole Juhnke
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Barry Pizer
- Institute of Translational Research, University of Liverpool, UK
| | - Barbara V Zezschwitz
- Department of Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany
| | - Robert Kwiecien
- Institute of Biostatistics and Clinical Research, University of Muenster, Muenster, Germany
| | - Maximilian Wechsung
- Institute of Biometry and Clinical Epidemiology, Charité University Medicine and Berlin Institute of Health, Berlin, Germany
| | - Frank Konietschke
- Institute of Biometry and Clinical Epidemiology, Charité University Medicine and Berlin Institute of Health, Berlin, Germany
| | - Eugene I Hwang
- Department of Pediatric Hematology-Oncology, Center for Cancer and Immunology Research and Neuroscience Research, Children's National Medical Center, Washington DC, USA
| | - Dominik Sturm
- Hopp Children´s Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - 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 & Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisabeth J Rushing
- Institute of Neuropathology, University Medical Center Zurich, Zurich, Switzerland
| | - Marina Ryzhova
- Department of Neuropathology, Burdenko Neurosurgical Institute, Moscow, Russia
| | - Peter Hauser
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Maria Łastowska
- Department of Pathomorphology, Children's Memorial Health Institute, Warsaw, Poland
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Amsterdam University Medical Center / VUmc, Amsterdam, The Netherlands
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomopathological Sciences, Sapienza University of Rome, Rome, Italy.,IRCCS Neuromed, Pozzilli (IS), Italy
| | - Cynthia Hawkins
- Division of Pathology, The Hospital for Sick Children, Toronto, Canada
| | - Dominique Figarella-Branger
- Aix-Marseille Univ, APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Marseille, France
| | - Charles Eberhart
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Peter Burger
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Marco Gessi
- Neuropathology Unit, Division of Pathology, Fondazione Policlinico Universitario "A.Gemelli" IRCCS, Università Cattolica S.Cuore, Rome, Italy
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tom S Jacques
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - David Capper
- Department of Neuropathology, Charité University Medicine, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, DZNE German Center for Neurodegenerative Diseases, Bonn, Germany
| | - 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
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24
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Ballabio C, Gianesello M, Lago C, Okonechnikov K, Anderle M, Aiello G, Antonica F, Zhang T, Gianno F, Giangaspero F, Hassan BA, Pfister SM, Tiberi L. Notch1 switches progenitor competence in inducing medulloblastoma. Sci Adv 2021; 7:7/26/eabd2781. [PMID: 34162555 PMCID: PMC8221631 DOI: 10.1126/sciadv.abd2781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 05/07/2021] [Indexed: 05/13/2023]
Abstract
The identity of the cell of origin is a key determinant of cancer subtype, progression, and prognosis. Group 3 medulloblastoma (MB) is a malignant childhood brain cancer with poor prognosis and few candidates as putative cell of origin. We overexpressed the group 3 MB genetic drivers MYC and Gfi1 in different candidate cells of origin in the postnatal mouse cerebellum. We found that S100b+ cells are competent to initiate group 3 MB, and we observed that S100b+ cells have higher levels of Notch1 pathway activity compared to Math1+ cells. We found that additional activation of Notch1 in Math1+ and Sox2+ cells was sufficient to induce group 3 MB upon MYC/Gfi1 expression. Together, our data suggest that the Notch1 pathway plays a critical role in group 3 MB initiation.
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Affiliation(s)
- Claudio Ballabio
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Matteo Gianesello
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Chiara Lago
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Marica Anderle
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Giuseppe Aiello
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Francesco Antonica
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Tingting Zhang
- Paris Brain Institute-Institut du Cerveau, Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, 8, Paris, France
| | - Francesca Gianno
- Dept. of Radiologic, Oncologic and Anatomo Pathological Sciences, University Sapienza of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Felice Giangaspero
- Dept. of Radiologic, Oncologic and Anatomo Pathological Sciences, University Sapienza of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Bassem A Hassan
- Paris Brain Institute-Institut du Cerveau, Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, 8, Paris, France
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Luca Tiberi
- Armenise-Harvard Laboratory of Brain Cancer, Department CIBIO, University of Trento, Via Sommarive 9, 38123 Trento, Italy.
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25
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Zheng T, Ghasemi DR, Okonechnikov K, Korshunov A, Maaß KK, Sill M, Gojo J, Schüller U, Milde T, Mack SC, Gilbertson RJ, von Deimling A, Jones DTW, Kool M, Pfister SM, Sahm F, Kawauchi D, Pajtler KW. EPEN-03. ZFTA/C11ORF95 FUSIONS DRIVE SUPRATENTORIAL EPENDYMOMA VIA SHARED ONCOGENIC MECHANISMS. Neuro Oncol 2021. [PMCID: PMC8168100 DOI: 10.1093/neuonc/noab090.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The majority of supratentorial ependymomas (ST-EPN) are driven by fusion genes between RELA and zinc finger translocation associated, ZFTA, previously named C11orf95. Apart from fusions with a portion of the Hippo effector YAP1, which affects a small group of infant patients, the oncogenic mechanism of remaining ST-EPNs remains unclear. Aiming at refining the molecular classification of ST-EPNs, we have analyzed methylation profiles, RNA and DNA sequencing results as well as clinical data in a cohort of 613 ST-EPNs. An unbiased approach revealed distinct methylation clusters composed of tumors with ependymal but also various other histological features containing alternative translocations that shared ZFTA as a partner gene. Tumors within these additional clusters were characterized by fusions of ZFTA to numerous fusion partners different from RELA, e.g. MAML2, MAML3, NCOA2 and SS18, implying a general role of ZFTA in tumorigenesis of ST-EPN. Indeed, the transforming capacity of newly identified fusion genes was validated using an electroporation-based in vivo gene transfer technology in mice. All fusion genes themselves were sufficient to drive malignant transformation in the developing cerebral cortex and resulting tumors faithfully recapitulated molecular characteristics of their human counterparts. We found that both, the partner gene and the zinc finger DNA binding domain of ZFTA, were essential to exert tumorigenesis. Together with two additional studies, we performed a comprehensive analysis across datasets to derive a 93 gene signature of ZFTA-RELA-driven tumors, in which the Sonic Hedgehog effector gene GLI2 was identified as a promising downstream target. Subsequent co-expression of ZFTA:RELA and a dominant negative form of Gli2 indeed hampered tumorigenesis. Targeting GLI2 with arsenic trioxide caused extended survival of tumor-bearing animals, indicating GLI2 as a critical regulator of ZFTA fusion-positive tumorigenesis as well as a potential therapeutic vulnerability in these tumors.
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Affiliation(s)
- Tuyu Zheng
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David R Ghasemi
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kendra K Maaß
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes Gojo
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Ulrich Schüller
- Research Institute, Children’s Cancer Center Hamburg, Hamburg, Germany
- nstitute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Milde
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - 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, TX, USA
- Therapeutic Innovation Center at BCM, Houston, TX, USA
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, UK
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Centre for Paediatric Oncology, Utrecht, Netherlands
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daisuke Kawauchi
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Bicochemistry and Celllar Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
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26
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Morcavallo A, Barker K, Adachi T, Boult JKR, Kwok C, da Silva PBG, Okonechnikov K, Hitchen L, Robinson SP, Clifford SC, Pfister SM, Kawauchi D, Chesler L. TMOD-03. A NOVEL MB GR3 TRANSGENIC MOUSE MODEL IS GENERATED BY MYCN AND P53 DEFECTS IN VENTRICULAR ZONE PROGENITORS. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab090.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Medulloblastoma (MB) represents the most common embryonal tumour of the Central Nervous System in childhood. MB occurs in the cerebellum and molecular features dictate the classification into four subgroups. Although Group3 (Gr3) MB tumours are dominated by primitive progenitor-like cells, the cells of origin remain unidentified. Gr3 MB is associated with relatively common MYC family member amplification and overexpression, often combined with p53 pathway defects at relapse. Molecularly stratified treatment is not yet available, causing Gr3 MB and its subsequent relapse to often represent an unstoppable progressive disease. The limited understanding of Gr3 tumorigenesis and targeted therapy development is also due to the lack of faithful in vivo models and consequently, their use in preclinical studies. We have now developed a new germline genetically engineered mouse model (GEMM), harbouring MYCN amplification in a p53 inactive background (tamoxifen-inducible p53 activation, Trp53ERTAM). The purpose of the GEMM is to investigate the developmental significance of MYC aberration in putative Gr3 MB cells of origin and exploit it in preclinical studies. A LSL-MYCN-Luciferase strain was crossed with mice expressing Cre recombinase under the Blbp promoter and subsequently to Trp53ERTAM inducible mice. As result, the MYCN overexpression alone did not generate tumours, conversely to the combination of MYCN with p53 deregulation. Tumours arise exclusively in the hindbrain of homozygote mice, with a penetrance of 100% and a latency of ~135 days. Pathology report suggests tumours are Gr3 MB with large cell/anaplastic (LCA) histology. Preliminary transcriptional profiling data analysis reveals that tumours share molecular features with human counterparts, clustering with Gr3 MB. Ongoing analysis will explore the tumour cells of origin, followed by tumour progression alteration restoring p53 activity and blood-brain barrier integrity status. In conclusion, we have developed a MYCN/Trp53ERTAM Gr3 MB GEMM arising from ventricular zone progenitor cells and resembling human cancer characteristics.
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Affiliation(s)
- Alaide Morcavallo
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton, Surrey, UK
| | - Karen Barker
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton, Surrey, UK
| | - Toma Adachi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), National Institute of Neuroscience, Tokyo, Japan
| | - Jessica K R Boult
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Colin Kwok
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton, Surrey, UK
| | - Patricia Benites Goncalves da Silva
- Hopp Children′s Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), and Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children′s Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), and Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Luke Hitchen
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton, Surrey, UK
| | - Simon P Robinson
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle Upon Tyne, UK
| | - Stefan M Pfister
- Hopp Children′s Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), and Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), National Institute of Neuroscience, Tokyo, Japan
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, and The Royal Marsden NHS Trust, Sutton, Surrey, UK
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27
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Delaidelli A, Dunham C, Santi MR, Negri GL, Triscott J, Zheludkova O, Golanov A, Ryzhova M, Okonechnikov K, Schrimpf D, Stichel D, von Deimling A, Kool M, Pfister S, Ramaswamy V, Korshunov A, Taylor M, Sorensen P. EMBR-21. CLINICALLY TRACTABLE OUTCOME PREDICTION OF GROUP 3/4 MEDULLOBLASTOMA BASED ON TPD52 IMMUNOHISTOCHEMISTRY: A MULTICOHORT STUDY. Neuro Oncol 2021. [PMCID: PMC8168220 DOI: 10.1093/neuonc/noab090.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background International consensus and the 2021 WHO classification recognize eight molecular subtypes among Group 3/4 medulloblastoma (representing ~60% of tumors). However, very few clinical centers worldwide possess the technical capabilities to determine DNA-methylation patterns or other molecular parameters of high-risk for Group 3/4 tumors. As a result, biomarker-driven risk stratification and therapy assignment constitutes a major challenge in medulloblastoma research. Here, we identify an immunohistochemistry (IHC) marker as a clinically tractable method for improved medulloblastoma risk-stratification. Patients and Methods We bioinformatically analyzed published medulloblastoma transcriptomes and proteomes identifying as a potential biomarker TPD52, whose IHC prognostic value was validated across three Group 3/4 medulloblastoma clinical cohorts (n = 387) treated with conventional therapies. Risk stratification and prediction capability were computed utilizing uni- and multivariate survival analysis. Newly developed risk classifiers including TPD52 IHC were compared to state-of-the-art risk stratification schemes in terms of prediction error, area under the time-dependent receiver operating characteristic (ROC) curves and C-statistic. Biomarker-driven prognostic stratification models identified were cross validated in different cohorts. Results TPD52 IHC positivity represents a significant independent predictor of early relapse and death for Group 3/4 medulloblastoma (HRs between 3.67–26.7 [95% CIs between 1.00–706.23], p = 0.05, 0.017 and 0.0058). Cross-validated survival models incorporating TPD52 IHC with clinical features outperformed existing disease risk-stratification schemes, and reclassified ~50% of patients into more appropriate risk categories. Finally, TPD52 immunopositivity is a predictive indicator of poor response to chemotherapy (HR 12.66 [95% CI 3.53–45.40], p < 0.0001), suggesting important implication for therapeutic choices. Conclusion The current study redefines the approach to risk-stratification in Group 3/4 medulloblastoma. Integration of TPD52 IHC in classification algorithms significantly improves outcome prediction and can be rapidly adopted for risk stratification on a global scale, independently of advanced but technically challenging molecular profiling techniques.
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Affiliation(s)
| | | | | | | | | | - Olga Zheludkova
- St Luka’s Clinical Research Center for Children, Moscow, Russian Federation
| | - Andrey Golanov
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | - Marina Ryzhova
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | | | | | - Damian Stichel
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Marcel Kool
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Pfister
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada
| | | | - Michael Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada
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28
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Thomas C, Soschinski P, Zwaig M, Oikonomopoulos S, Okonechnikov K, Pajtler KW, Sill M, Schweizer L, Koch A, Neumann J, Schüller U, Sahm F, Rauschenbach L, Keyvani K, Proescholdt M, Riemenschneider MJ, Segewiß J, Ruckert C, Grauer O, Monoranu CM, Lamszus K, Patrizi A, Kordes U, Siebert R, Kool M, Ragoussis J, Foulkes WD, Paulus W, Rivera B, Hasselblatt M. The genetic landscape of choroid plexus tumors in children and adults. Neuro Oncol 2021; 23:650-660. [PMID: 33249490 DOI: 10.1093/neuonc/noaa267] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Choroid plexus tumors (CPTs) are intraventricular brain tumors predominantly arising in children but also affecting adults. In most cases, driver mutations have not been identified, although there are reports of frequent chromosome-wide copy-number alterations and TP53 mutations, especially in choroid plexus carcinomas (CPCs). METHODS DNA methylation profiling and RNA-sequencing was performed in a series of 47 CPTs. Samples comprised 35 choroid plexus papillomas (CPPs), 6 atypical choroid plexus papillomas (aCPPs) and 6 CPCs plus three recurrences thereof. Targeted TP53 and TERT promotor sequencing was performed in all samples. Whole exome sequencing (WES) and linked-read whole genome sequencing (WGS) was performed in 25 and 4 samples, respectively. RESULTS Tumors comprised the molecular subgroups "pediatric A" (N=11), "pediatric B" (N=12) and "adult" (N=27). Copy-number alterations mainly represented whole-chromosomal alterations with subgroup-specific enrichments (gains of Chr1, 2 and 21q in "pediatric B" and gains of Chr5 and 9 and loss of Chr21q in "adult"). RNA sequencing yielded a novel CCDC47-PRKCA fusion transcript in one adult choroid plexus papilloma patient with aggressive clinical course; an underlying Chr17 inversion was demonstrated by linked-read WGS. WES and targeted sequencing showed TP53 mutations in 7/47 CPTs (15%), five of which were children. On the contrary, TERT promoter mutations were encountered in 7/28 adult patients (25%) and associated with shorter progression-free survival (log-rank test, p=0.015). CONCLUSION Pediatric CPTs lack recurrent driver alterations except for TP53, whereas CPTs in adults show TERT promoter mutations or a novel CCDC47-PRKCA gene fusion, being associated with a more unfavorable clinical course.
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Affiliation(s)
- Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Patrick Soschinski
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Melissa Zwaig
- McGill University Genome Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - Spyridon Oikonomopoulos
- McGill University Genome Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - 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
| | - 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, University Hospital, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Leonille Schweizer
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany, Partner Site Charité Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Arend Koch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany, Partner Site Charité Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Julia Neumann
- Department of Neuropathology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Neuropathology, University Hospital 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
| | - 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
| | - Laurèl Rauschenbach
- Department of Neurosurgery and Spine Surgery, University Hospital Essen, University Duisburg-Essen, Essen, Germany.,DKFZ Division Translational Neurooncology, DKTK partner site, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Kathy Keyvani
- Institute of Neuropathology, University of Duisburg-Essen, Essen, Germany
| | - Martin Proescholdt
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Neurosurgery, Regensburg University Hospital, Regensburg, Germany
| | | | - Jochen Segewiß
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
| | - Christian Ruckert
- Institute of Human Genetics, University Hospital Münster, Münster, Germany
| | - Oliver Grauer
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | | | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annarita Patrizi
- Schaller Research Group Leader at the German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Kordes
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - 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
| | - Jiannis Ragoussis
- McGill University Genome Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Barbara Rivera
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
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29
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Afanasyeva EA, Gartlgruber M, Ryl T, Decaesteker B, Denecker G, Mönke G, Toprak UH, Florez A, Torkov A, Dreidax D, Herrmann C, Okonechnikov K, Ek S, Sharma AK, Sagulenko V, Speleman F, Henrich KO, Westermann F. Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma. Life Sci Alliance 2021; 4:e201900332. [PMID: 33658318 PMCID: PMC8017594 DOI: 10.26508/lsa.201900332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The migrational propensity of neuroblastoma is affected by cell identity, but the mechanisms behind the divergence remain unknown. Using RNAi and time-lapse imaging, we show that ADRN-type NB cells exhibit RAC1- and kalirin-dependent nucleokinetic (NUC) migration that relies on several integral components of neuronal migration. Inhibition of NUC migration by RAC1 and kalirin-GEF1 inhibitors occurs without hampering cell proliferation and ADRN identity. Using three clinically relevant expression dichotomies, we reveal that most of up-regulated mRNAs in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells are associated with low-risk characteristics. The computational analysis shows that, in a context of overall gene set poverty, the upregulomes in RAC1- and kalirin-GEF1-suppressed ADRN-type cells are a batch of AU-rich element-containing mRNAs, which suggests a link between NUC migration and mRNA stability. Gene set enrichment analysis-based search for vulnerabilities reveals prospective weak points in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells, including activities of H3K27- and DNA methyltransferases. Altogether, these data support the introduction of NUC inhibitors into cancer treatment research.
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Affiliation(s)
- Elena A Afanasyeva
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Moritz Gartlgruber
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Tatsiana Ryl
- Department of Neurosurgery, University of Duisburg Essen, Essen, Germany
| | - Bieke Decaesteker
- Center for Medical Genetics, Ghent University, and Cancer Research Institute Ghent, Ghent, Belgium
| | - Geertrui Denecker
- Center for Medical Genetics, Ghent University, and Cancer Research Institute Ghent, Ghent, Belgium
| | - Gregor Mönke
- European Molecular Biology Laboratories, Heidelberg, Germany
| | - Umut H Toprak
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Andres Florez
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
- Center for Systems Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Alica Torkov
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Daniel Dreidax
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Carl Herrmann
- Group of Cancer Regulatory Genomics B086, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Department of Pediatric Neurooncology, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Sara Ek
- Department of Immunotechnology, CREATE Health, Faculty of Engineering, Lund University, Lund, Sweden
| | - Ashwini Kumar Sharma
- Institute for Pharmacy and Molecular Biotechnology and BioQuant, Heidelberg University, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vitaliya Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, and Cancer Research Institute Ghent, Ghent, Belgium
| | - Kai-Oliver Henrich
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Frank Westermann
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
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30
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Hartlieb SA, Sieverling L, Nadler-Holly M, Ziehm M, Toprak UH, Herrmann C, Ishaque N, Okonechnikov K, Gartlgruber M, Park YG, Wecht EM, Savelyeva L, Henrich KO, Rosswog C, Fischer M, Hero B, Jones DTW, Pfaff E, Witt O, Pfister SM, Volckmann R, Koster J, Kiesel K, Rippe K, Taschner-Mandl S, Ambros P, Brors B, Selbach M, Feuerbach L, Westermann F. Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome. Nat Commun 2021; 12:1269. [PMID: 33627664 PMCID: PMC7904810 DOI: 10.1038/s41467-021-21247-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023] Open
Abstract
Telomere maintenance by telomerase activation or alternative lengthening of telomeres (ALT) is a major determinant of poor outcome in neuroblastoma. Here, we screen for ALT in primary and relapsed neuroblastomas (n = 760) and characterize its features using multi-omics profiling. ALT-positive tumors are molecularly distinct from other neuroblastoma subtypes and enriched in a population-based clinical sequencing study cohort for relapsed cases. They display reduced ATRX/DAXX complex abundance, due to either ATRX mutations (55%) or low protein expression. The heterochromatic histone mark H3K9me3 recognized by ATRX is enriched at the telomeres of ALT-positive tumors. Notably, we find a high frequency of telomeric repeat loci with a neuroblastoma ALT-specific hotspot on chr1q42.2 and loss of the adjacent chromosomal segment forming a neo-telomere. ALT-positive neuroblastomas proliferate slowly, which is reflected by a protracted clinical course of disease. Nevertheless, children with an ALT-positive neuroblastoma have dismal outcome.
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Affiliation(s)
- Sabine A Hartlieb
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Lina Sieverling
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Applied Bioinformatics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Michal Nadler-Holly
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Matthias Ziehm
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Umut H Toprak
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty Heidelberg and BioQuant, Heidelberg, Germany
| | - Naveed Ishaque
- Digital Health Centre, Berlin Institute of Health (BIH), Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Moritz Gartlgruber
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Young-Gyu Park
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisa Maria Wecht
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Larissa Savelyeva
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University of Cologne, Cologne, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elke Pfaff
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Richard Volckmann
- Department of Oncogenomics Amsterdam University Medical Centers (AUMC), Amsterdam, the Netherlands
| | - Jan Koster
- Department of Oncogenomics Amsterdam University Medical Centers (AUMC), Amsterdam, the Netherlands
| | - Katharina Kiesel
- Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Karsten Rippe
- Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | | | - Peter Ambros
- CCRI, St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Benedikt Brors
- Applied Bioinformatics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lars Feuerbach
- Applied Bioinformatics, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Korshunov A, Okonechnikov K, Schmitt-Hoffner F, Ryzhova M, Sahm F, Stichel D, Schrimpf D, Reuss DE, Sievers P, Suwala AK, Kumirova E, Zheludkova O, Golanov A, Jones DTW, Pfister SM, Kool M, von Deimling A. Molecular analysis of pediatric CNS-PNET revealed nosologic heterogeneity and potent diagnostic markers for CNS neuroblastoma with FOXR2-activation. Acta Neuropathol Commun 2021; 9:20. [PMID: 33536079 PMCID: PMC7860633 DOI: 10.1186/s40478-021-01118-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022] Open
Abstract
Primitive neuroectodermal tumors of the central nervous system (CNS-PNETs) are highly malignant neoplasms posing diagnostic challenge due to a lack of defining molecular markers. CNS neuroblastoma with forkhead box R2 (FOXR2) activation (CNS_NBL) emerged as a distinct pediatric brain tumor entity from a pool previously diagnosed as primitive neuroectodermal tumors of the central nervous system (CNS-PNETs). Current standard of identifying CNS_NBL relies on molecular analysis. We set out to establish immunohistochemical markers allowing safely distinguishing CNS_NBL from morphological mimics. To this aim we analyzed a series of 84 brain tumors institutionally diagnosed as CNS-PNET. As expected, epigenetic analysis revealed different methylation groups corresponding to the (1) CNS-NBL (24%), (2) glioblastoma IDH wild-type subclass H3.3 G34 (26%), (3) glioblastoma IDH wild-type subclass MYCN (21%) and (4) ependymoma with RELA_C11orf95 fusion (29%) entities. Transcriptome analysis of this series revealed a set of differentially expressed genes distinguishing CNS_NBL from its mimics. Based on RNA-sequencing data we established SOX10 and ANKRD55 expression as genes discriminating CNS_NBL from other tumors exhibiting CNS-PNET. Immunohistochemical detection of combined expression of SOX10 and ANKRD55 clearly identifies CNS_NBL discriminating them to other hemispheric CNS neoplasms harboring “PNET-like” microscopic appearance. Owing the rarity of CNS_NBL, a confirmation of the elaborated diagnostic IHC algorithm will be necessary in prospective patient series.
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Vouri M, Mercier A, da Silva PBG, Okonechnikov K, Forget A, Yu H, Chivet A, Kool M, Pfister S, Ayrault O, Kawauchi D. MBRS-51. MUTATIONS IN BRPF1 FOUND IN SHH MEDULLOBLASTOMA PREVENT INTERACTION WITH TP53 AND LEADS TO RADIORESISTANCE IN VITRO. Neuro Oncol 2020. [PMCID: PMC7715508 DOI: 10.1093/neuonc/noaa222.558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Medulloblastoma (MB) is one of the most common pediatric tumors in children. Among them, SHH subgroups of MB (MBSHH) is characterized by constitutive activation of SHH pathway. Somatic mutations in BRPF1, a chromatin modifier, is found in more than 5% of MBSHH and accounts for almost 20% of adult MBSHH but its potential role in MBSHH pathophysiology is still unknown. In this study, we first examined the function of Brpf1 on pro-tumorigenic features of MBSHH and evaluated molecular pathways regulated by Brpf1 using Brpf1floxed::Atoh1-Cre conditional knockout mice, in which Brpf1 is conditionally deleted in cerebellar granule neuron progenitors (GNPs). While RNA-seq analysis on GNPs from Brpf1 WT and KO mice showed significant differences in the pathways related with cell cycle and cell death, deletion of Brpf1 did not cause acceleration of tumorigenesis in the Ptch1 heterozygous tumor-prone. Background: Co-immunoprecipitation followed by mass spectrometry analysis identified interaction partners of BRPF1 including MOZ, MORF and ING5, known partners of BRPF1. Gene ontology analysis also depicted pathways important for cell cycle progression, cell death and response to DNA damage. Consistent with these observations, TP53 was identified as a novel co-factor of BRPF1. Of note, some of MBSHH-relevant BRPF1 mutations prevented interaction with TP53. According to the previous finding that cytosolic TP53 is required for apoptotic cell death, GNPs expressing the BRPF1-R600X mutant gene exhibited the resistance to irradiation-induced cell death. In conclusion, our data revealed that BRPF1 mutants found in MBSHH could prevent the complex formation with TP53, leading to enhanced resistance to cell apoptosis.
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Affiliation(s)
- Mikaela Vouri
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center, Heidelberg, Germany
| | | | | | - Konstantin Okonechnikov
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center, Heidelberg, Germany
| | | | - Hua Yu
- Institut Curie, INSERM, Orsay, France
| | | | - Marcel Kool
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center, Heidelberg, Germany
| | - Stefan Pfister
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center, Heidelberg, Germany
| | | | - Daisuke Kawauchi
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center, Heidelberg, Germany
- National Center of Neurology and Psychiatry, Tokyo, Japan
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Zheng T, Ghasemi DR, Okonechnikov K, Korshunov A, Sill M, Hübner JM, Maaß KK, Snuderl M, Gojo J, Schüller U, Gerber NU, Hernáiz-Driever P, Milde T, Sturm D, Chapman R, Grundy RG, von Deimling A, Jones DTW, Kool M, Pfister SM, Sahm F, Kawauchi D, Pajtler KW. EPEN-18. CROSS-SPECIES GENOMICS IDENTIFIES GLI2 AS AN ONCOGENE OF C11orf95 FUSION-POSITIVE SUPRATENTORIAL EPENDYMOMA. Neuro Oncol 2020. [PMCID: PMC7715864 DOI: 10.1093/neuonc/noaa222.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The majority of supratentorial ependymomas (ST-EPN) are driven by fusions between RELA and a zinc finger containing gene, C11orf95. Apart from fusions to the Hippo effector YAP1, which affects a small group of infant patients, the oncogenic mechanism of remaining ST-EPNs is unclear. Aiming at refining the molecular classification of ST-EPNs, we analyzed methylation profiles, RNA and DNA sequencing results as well as clinical data in a cohort of 617 ST-EPNs. Unsupervised clustering analysis of DNA methylation data revealed four distinct clusters that formed in addition to the known molecular groups ST-EPN-RELA and –YAP1. Tumors within these additional clusters were characterized by fusions of C11orf95 to numerous fusion partners different from RELA, e.g. MAML2, MAML3, NCOA2 and SS18, suggesting a general role of C11orf95 in tumorigenesis of ST-EPN. Transforming capacity of newly identified fusion genes was validated using an electroporation-based in vivo gene transfer technology. All fusion genes were sufficient to drive malignant transformation in the cerebral cortex of mice and resulting tumors faithfully recapitulated molecular characteristics of their human counterparts. We found that both, the partner gene and the zinc finger DNA binding domain of C11orf95, were essential to exert tumorigenesis. When exploring genes commonly upregulated in C11orf95 fusion-expressing tumors of human and murine origin, the Sonic Hedgehog effector gene Gli2 was identified as a promising downstream target. Subsequent co-expression of C11orf95:RELA and a dominant negative form of Gli2 indeed hampered tumorigenesis. We thus propose GLI2 as a potential therapeutic downstream target of C11orf95 fusion-dependent oncogenic signaling in ST-EPN.
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Affiliation(s)
- Tuyu Zheng
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David R Ghasemi
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens-Martin Hübner
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kendra K Maaß
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Matija Snuderl
- Division of Neuropathology, Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Ulrich Schüller
- Research Institute, Children’s Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicolas U Gerber
- Department of Oncology, University Children’s Hospital, Zurich, Switzerland
| | - Pablo Hernáiz-Driever
- Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Till Milde
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Rebecca Chapman
- Children’s Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Richard G Grundy
- Children’s Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daisuke Kawauchi
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Bicochemistry and Celllar Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
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Ghasemi DN, Okonechnikov K, Malm JP, Lappalainen K, Bauer K, Liberio MS, Giese L, Maass KK, Kool M, Jones DTW, von Deimling A, Pfister SM, Korshunov A, Pajtler KW. MBRS-68. SINGLE NUCLEUS RNA-SEQUENCING DECIPHERS INTRATUMORAL HETEROGENEITY IN MEDULLOBLASTOMA WITH EXTENSIVE NODULARITY (MBEN). Neuro Oncol 2020. [PMCID: PMC7715174 DOI: 10.1093/neuonc/noaa222.572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Medulloblastoma (MB) with extensive nodularity (MBEN) represent a rare subtype of cerebellar tumors of infancy which comprise two histologically distinct components, nodular reticulin-free zones and inter-nodular reticulin-rich regions. We applied single nucleus RNA-sequencing (snRNA-seq) using the 10X Genomics and the SMARTseq V2 protocols, bulk RNA-sequencing, DNA-methylation profiling and DNA-panel sequencing to ten histologically confirmed MBEN specimens. All tumors were classified as sonic hedgehog (SHH) MB based on DNA methylation. Somatic mutations within the SHH-pathway were detected in seven samples (3x SUFU, 2x PTCH1, 2x SMO) by DNA panel sequencing. The combined snRNAseq approach resulted in data on ~30.000 single cells. Several non-malignant cell types were identified, e.g. endothelial cells, astrocytes, and microglia. Amongst malignant cell populations SHH-pathway activation and mitotic activity differed revealing actively cycling embryonic stem (ES) cell-like and more differentiated neuronal-like cell types. In addition, distinct histological components of these tumours were subjected to bulk RNA sequencing following microdissection. This approach was repeated for DNA methylation profiling in an independent paraffin embedded MBEN cohort. However, these analyses did not reveal significant transcriptomic differences or differential methylation patterns between the two histological components. In summary, snRNA-seq identified a strongly proliferating, ES-like subset of cells in MBEN, which might represent the driving cell population in these malignancies, while direct analyses of nodular and inter-nodular regions did not reveal any significant differences. These findings suggest that both components originate from the same cell of origin but represent different cellular developmental stages.
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Affiliation(s)
- David N Ghasemi
- Hopp-Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp-Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan-Philipp Malm
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Heidelberg, Germany
| | - Kati Lappalainen
- Hopp-Children’s Cancer Center Heidelberg (KiTZ) and Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katharina Bauer
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle S Liberio
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laura Giese
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kendra K Maass
- Hopp-Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp-Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - David T W Jones
- Hopp-Children’s Cancer Center Heidelberg (KiTZ) and Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp-Children’s Cancer Center Heidelberg (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
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Okonechnikov K, Sepp M, Leiss K, Kutscher L, Ernst K, Jones D, Jäger N, Pajtler KW, Kaessmann H, Pfister SM. MBRS-03. SINGLE NUCLEUS TRANSCRIPTOME PROFILES FROM HUMAN DEVELOPING CEREBELLUM REVEAL POTENTIAL CELLULAR ORIGINS OF MEDULLOBLASTOMA BRAIN TUMORS. Neuro Oncol 2020. [PMCID: PMC7715804 DOI: 10.1093/neuonc/noaa222.524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Medulloblastoma (MB) is a highly malignant pediatric brain tumor originating from the cerebellum and brainstem. Identification of molecular subgroups forming this heterogeneous tumor entity was initially achieved from transcriptome characterization and further strengthened using DNA methylation profiling. While subgroup classification improved clinical diagnosis and treatment options, the lack of knowledge of the cell-of-origin for some of the subgroups hinders further treatment improvements. In addition identification of the precise cells of origin for each subgroup could help to understand tumor cell biology. Single cell sequencing is the optimal way to solve this task; recently, there were attempts to uncover putative MB cell-of-origin by using such information obtained from mouse embryonic cerebellum. However, such a comparative strategy can miss important results due to the differences between mouse and human. To solve this issue, we performed global single nucleus sequencing on human cerebellum pre- and postnatal materials across several developmental time points and generated transcriptome profiles from ~200k single cells. We identified known cell types forming the human cerebellum and performed detailed comparison of normal cells to RNA-seq bulk data from MB brain tumors across all subgroups. By selecting an optimal analysis strategy, we verified granule neuron precursors as cells of origin for the SHH MB subgroup. Additionally, we also found other cell types in conjunction with the remaining MB subgroups, suggesting new potential targets for investigation. Notably, this strategy can be further applied to the examination of other brain tumors and has perspectives in medical application.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Lena Kutscher
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kati Ernst
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Jones
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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36
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Okonechnikov K, Hübner JM, Chapman O, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Hidalgo RA, Mundlos S, Wechsler-Reya R, Juarez EF, Coufal N, Levy M, Crawford J, Pajtler K, Reid D, Schmitt A, Carter H, Ay F, Dixon J, Mesirov J, Pfister SM, Kool M, Chavez L. EPEN-04. ONCOGENIC 3D TUMOR GENOME ORGANIZATION IDENTIFIES NEW THERAPEUTIC TARGETS IN EPENDYMOMA. Neuro Oncol 2020. [PMCID: PMC7715851 DOI: 10.1093/neuonc/noaa222.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
By profiling enhancers in primary ependymoma tumors, we have recently identified putative oncogenes, molecular targets, and functional pathways. Inhibition of selected targets diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymoma. While enhancers frequently regulate the nearest gene, identification of enhancer target genes remains to be a challenge in the absence of chromosome conformation information. Consequently, we have now used HiC to map the 3-dimensional organization of tumor chromatin in the two most common and aggressive ependymoma subgroups: posterior fossa group A (PF-EPN-A) and supratentorial ependymomas with gene fusions involving the NF-κB subunit gene RELA (ST-EPN-RELA). By an integrative analysis of enhancer and gene expression in the context of the newly derived HiC data, we find that a large number of the predicted enhancer target genes are enriched for strong physical interactions. Importantly, we also identify many new putative tumor-dependency genes activated by long-range promoter-enhancer interactions and complex tumor-specific chromatin clusters of regulatory elements. Complementary to the analysis of gene-enhancer interactions, we have also leveraged the HiC data for resolving structural rearrangements underlying copy number alterations. Copy number gains of the 1q arm of chromosome 1 are especially associated with poor survival. Our preliminary results in PFA relapse samples show complex structural variants underlying 1q gain that lead to inter-chromosomal rearrangements and affect several genes that potentially contribute to poor survival. In ongoing work we are testing the relevance of the novel candidate genes for tumor cell growth and proliferation in-patient derived ependymoma models.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens-Martin Hübner
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Owen Chapman
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Abhijit Chakraborty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, San Diego, CA, USA
| | - Meghana Pagadala
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Rosalind Bump
- Salk Institute for Biological Studies, San Diego, CA, USA
| | | | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | | | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Robert Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Research Discovery Institute, San Diego, USA
| | - Edwin F Juarez
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Nicole Coufal
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Michael Levy
- Department of Neurosurgery, University of California San Diego – Rady Children’s Hospital, San Diego, CA, USA
| | - John Crawford
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
- Department of Neurosciences, University of California San Diego – Rady Children’s Hospital, San Diego, CA, USA
| | - Kristian Pajtler
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | - Hannah Carter
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Ferhat Ay
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, San Diego, CA, USA
| | - Jesse Dixon
- Salk Institute for Biological Studies, San Diego, CA, USA
| | - Jill Mesirov
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
| | - Stefan M Pfister
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lukas Chavez
- Department of Medicine, University of California San Diego (UCSD), San Diego, CA, USA
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Johann P, Büllesbach A, Ernst K, Okonechnikov K, Jones DTW, Pfister SM, Hasselblatt M, Kool M. ATRT-28. SINGLE NUCLEI SEQUENCING REVEALS THE DIFFERENT PHENOTYPIC COMPOSITION OF THE ATRT SUBGROUPS. Neuro Oncol 2020. [PMCID: PMC7715748 DOI: 10.1093/neuonc/noaa222.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Atypical teratoid/rhabdoid tumors (ATRT) represents a genomically homogeneous disease characterized by loss of SMARCB1 protein in the vast majority of cases. In recent years, it has become clear that these tumors display a high degree of intertumoral heterogeneity with three molecularly distinct subgroups. However, the degree of intratumoral heterogeneity and the information on cellular subpopulations currently remains largely an unchartered territory. To explore the transcriptomic composition of ATRTs, we performed single nuclei RNA sequencing for 16 ATRTs representing all three molecular subgroups (5 ATRT-TYR, 7 ATRT-SHH, 4 ATRT-MYC). By performing tSNE cluster analyses of all the single cell data (~50.000 cells have been sequenced), we were able to gain unprecedented insights into the phenotypic composition of ATRTs and unravelled substantial differences between the three subgroups. Integrating transcriptomic information from non-neoplastic brain cells and the data derived from single nuclei sequencing, we found an OPC like gene signature in ATRT-SHH. In contrast, ATRT-TYR subpopulations overexpressed more markers of neuronal stem cells suggesting a larger fraction of undifferentiated cells in this subgroup. We also identified a subpopulation of cells with a clear overexpression of cell cycle associated genes (CDK4, CDKN3), predominantly present in ATRT-MYC samples, a finding which may harbour important consequences for a targeted therapy with e.g. CDK inhibitors. In summary, our analyses reveal different cellular compartments in ATRT and provide important insights into the cellular differentiation of the three ATRT-subgroups. Further analyses to achieve a specific mapping of ATRT to its physiological cell of origin are currently being pursued.
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Affiliation(s)
- Pascal Johann
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg, Germany
| | | | - Kati Ernst
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - David T W Jones
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg, Germany
| | | | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
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38
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Colmenero-Repiso A, Gómez-Muñoz MA, Rodríguez-Prieto I, Amador-Álvarez A, Henrich KO, Pascual-Vaca D, Okonechnikov K, Rivas E, Westermann F, Pardal R, Vega FM. Identification of VRK1 as a New Neuroblastoma Tumor Progression Marker Regulating Cell Proliferation. Cancers (Basel) 2020; 12:cancers12113465. [PMID: 33233777 PMCID: PMC7699843 DOI: 10.3390/cancers12113465] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/31/2022] Open
Abstract
Neuroblastoma (NB) is one of the most common pediatric cancers and presents a poor survival rate in affected children. Current pretreatment risk assessment relies on a few known molecular parameters, like the amplification of the oncogene MYCN. However, a better molecular knowledge about the aggressive progression of the disease is needed to provide new therapeutical targets and prognostic markers and to improve patients' outcomes. The human protein kinase VRK1 phosphorylates various signaling molecules and transcription factors to regulate cell cycle progression and other processes in physiological and pathological situations. Using neuroblastoma tumor expression data, tissue microarrays from fresh human samples and patient-derived xenografts (PDXs), we have determined that VRK1 kinase expression stratifies patients according to tumor aggressiveness and survival, allowing the identification of patients with worse outcome among intermediate risk. VRK1 associates with cell cycle signaling pathways in NB and its downregulation abrogates cell proliferation in vitro and in vivo. Through the analysis of ChIP-seq and methylation data from NB tumors, we show that VRK1 is a MYCN gene target, however VRK1 correlates with NB aggressiveness independently of MYCN gene amplification, synergizing with the oncogene to drive NB progression. Our study also suggests that VRK1 inhibition may constitute a novel cell-cycle-targeted strategy for anticancer therapy in neuroblastoma.
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Affiliation(s)
- Ana Colmenero-Repiso
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41013 Seville, Spain
| | - María A. Gómez-Muñoz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41013 Seville, Spain
| | - Ismael Rodríguez-Prieto
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41013 Seville, Spain
| | - Aida Amador-Álvarez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Kai-Oliver Henrich
- German Cancer Research Center (DKFZ), Division Neuroblastoma Genomics, 69120 Heidelberg, Germany; (K.-O.H.); (F.W.)
| | - Diego Pascual-Vaca
- Departamento de Anatomía Patológica, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain; (D.P.-V.); (E.R.)
| | | | - Eloy Rivas
- Departamento de Anatomía Patológica, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain; (D.P.-V.); (E.R.)
| | - Frank Westermann
- German Cancer Research Center (DKFZ), Division Neuroblastoma Genomics, 69120 Heidelberg, Germany; (K.-O.H.); (F.W.)
| | - Ricardo Pardal
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41013 Seville, Spain
- Correspondence: (R.P.); (F.M.V.)
| | - Francisco M. Vega
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013 Seville, Spain; (A.C.-R.); (M.A.G.-M.); (I.R.-P.); (A.A.-Á.)
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
- Correspondence: (R.P.); (F.M.V.)
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39
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Kutscher LM, Okonechnikov K, Batora NV, Clark J, Silva PBG, Vouri M, van Rijn S, Sieber L, Statz B, Gearhart MD, Shiraishi R, Mack N, Orr BA, Korshunov A, Gudenas BL, Smith KS, Mercier AL, Ayrault O, Hoshino M, Kool M, von Hoff K, Graf N, Fleischhack G, Bardwell VJ, Pfister SM, Northcott PA, Kawauchi D. Functional loss of a noncanonical BCOR-PRC1.1 complex accelerates SHH-driven medulloblastoma formation. Genes Dev 2020; 34:1161-1176. [PMID: 32820036 PMCID: PMC7462063 DOI: 10.1101/gad.337584.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022]
Abstract
In this study, Kutscher et al. investigated the transcriptional corepressor BCOR as a putative tumor suppressor and used a genetically engineered mouse model to delete exons 9/10 of Bcor in GNPs during development. Their data suggest that BCOR–PRC1.1 disruption leads to Igf2 overexpression, which transforms preneoplastic cells to malignant tumors. Medulloblastoma is a malignant childhood brain tumor arising from the developing cerebellum. In Sonic Hedgehog (SHH) subgroup medulloblastoma, aberrant activation of SHH signaling causes increased proliferation of granule neuron progenitors (GNPs), and predisposes these cells to tumorigenesis. A second, cooperating genetic hit is often required to push these hyperplastic cells to malignancy and confer mutation-specific characteristics associated with oncogenic signaling. Somatic loss-of-function mutations of the transcriptional corepressor BCOR are recurrent and enriched in SHH medulloblastoma. To investigate BCOR as a putative tumor suppressor, we used a genetically engineered mouse model to delete exons 9/10 of Bcor (BcorΔE9–10) in GNPs during development. This mutation leads to reduced expression of C-terminally truncated BCOR (BCORΔE9–10). While BcorΔE9–10 alone did not promote tumorigenesis or affect GNP differentiation, BcorΔE9–10 combined with loss of the SHH receptor gene Ptch1 resulted in fully penetrant medulloblastomas. In Ptch1+/−;BcorΔE9–10 tumors, the growth factor gene Igf2 was aberrantly up-regulated, and ectopic Igf2 overexpression was sufficient to drive tumorigenesis in Ptch1+/− GNPs. BCOR directly regulates Igf2, likely through the PRC1.1 complex; the repressive histone mark H2AK119Ub is decreased at the Igf2 promoter in Ptch1+/−;BcorΔE9–10 tumors. Overall, our data suggests that BCOR–PRC1.1 disruption leads to Igf2 overexpression, which transforms preneoplastic cells to malignant tumors.
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Affiliation(s)
- Lena M Kutscher
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Nadja V Batora
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Jessica Clark
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Patricia B G Silva
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Mikaella Vouri
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Sjoerd van Rijn
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Laura Sieber
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Britta Statz
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Micah D Gearhart
- Department of Genetics, Cell Biology, and Development, Masonic Cancer Center, Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ryo Shiraishi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-0031, Japan
| | - Norman Mack
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Brian L Gudenas
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kyle S Smith
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Audrey L Mercier
- Institut Curie, PSL Research University, UMR 3347, Centre National de la Recherche Scientifique (CNRS), U1021, Institut National de la Santé et de la Recherche Médicale (INSERM), Orsay 91405, France.,Université Paris Sud, Université, UMR 3347, CNRS, U1021, INSERM, Orsay 91405, France
| | - Olivier Ayrault
- Institut Curie, PSL Research University, UMR 3347, Centre National de la Recherche Scientifique (CNRS), U1021, Institut National de la Santé et de la Recherche Médicale (INSERM), Orsay 91405, France.,Université Paris Sud, Université, UMR 3347, CNRS, U1021, INSERM, Orsay 91405, France
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-0031, Japan
| | - Marcel Kool
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Katja von Hoff
- Department for Paediatric Oncology and Haematology, Charité University Medicine, 13354 Berlin, Germany
| | - Norbert Graf
- Department for Pediatric Oncology and Hematology, Universitätsklinikum des Saarlandes, 66421 Homburg, Germany
| | - Gudrun Fleischhack
- Pediatric Haematology and Oncology, Pediatrics III, University Hospital of Essen, 45147 Essen, Germany
| | - Vivian J Bardwell
- Department of Genetics, Cell Biology, and Development, Masonic Cancer Center, Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Daisuke Kawauchi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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40
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Ghasemi D, Okonechnikov K, Korshunov A, Sill M, Zheng T, Huebner J, Maass K, Benzel J, Snuderl M, Gojo J, Schüller U, Gerber N, Stoler I, Hernáiz-Driever P, Milde T, Sturm D, Chapman R, Grundy R, von Deimling A, Kawauchi D, Jones D, Kool M, Pfister S, Sahm F, Pajtler K. Abstract B71: Molecular heterogeneity and novel oncogenic fusions in RELA- and YAP1-negative supratentorial ependymoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-b71] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: One of the DNA methylation-based molecular subgroups of supratentorial ependymoma (ST-EPN), designated ST-EPN-RELA, mostly harbors fusions of the uncharacterized gene C11orf95 and RELA (ST-EPN-RELA). Rarely, no C11orf95-RELA fusion is detected in tumors predicted to belong to the ST-EPN-RELA group. With this study we aimed to refine the molecular classification of ST-EPN and to identify alternative oncogenic mechanisms in the absence of a classic fusion type.
Methods and Materials: In an unbiased approach, t-Distributed Stochastic Neighbor Embedding was applied to 53,468 DNA methylation profiles from brain tumors, other cancer types, and control tissues. Only samples clustering with a reference set of ST-EPN-RELA were selected for further analyses (n=614), including RNA- and/or DNA-panel sequencing, histopathologic reevaluation, and immunohistochemistry for L1CAM. Fusions were validated using RT-PCR on total RNA and Sanger sequencing. Clinical data were analyzed retrospectively for 150 patients.
Results: We identified one large and four satellite clusters. The large cluster (n=479; designated ST-EPN-RELA 1) and one of the satellite clusters (n=12; ST-EPN-RELA 2) predominantly contained samples with a calibrated score ≥ 0.9 for ST-EPN-RELA based on the current version of the Heidelberg Brain Tumor Classifier. Samples of the three other satellite clusters (n=41, n=17, and n=25 samples) contained 65.9%, 88.2%, and 96.0% of samples with a calibrated score < 0.9 for any methylation class, and were thus predicted as unclassifiable. These clusters were provisionally designated ST-EPN-RELA-like A, B, and C, and initial histologic diagnoses showed a wide spectrum of rare morphologies beside EPN, e.g., sarcoma and teratoma. Within clusters ST-EPN-RELA-like A and C, sequencing revealed fusions of C11orf95 with different partner genes, including MAML2 (n=14), MAML3 (n=2), and NCOA2 (n=7), while ST-EPN-RELA-like B included classic C11orf95-RELA fusions (n=11) in samples with initial diagnoses other than EPN. Copy number variation analysis showed clear differences between the clusters. L1CAM-positivity was observed in all groups. Within the cluster ST-EPN-RELA 1, samples separated according to fusion types, 1 versus 2/3. Analysis of clinical data showed significant differences in overall survival between cases with confirmed C11orf95-RELA fusion type 1 (n=25, median OS=88 months) and type 2/3 (n=20, median OS=67 months). Clinical data collection for the satellite clusters is currently ongoing.
Conclusion: Molecular refinement of ST-EPN-RELA revealed novel subgroups harboring fusions of C11orf95 with numerous fusion partners different from RELA, which will be included in the next update of the Heidelberg Classifier. Preliminary analysis suggests differences in clinical outcome related to the fusion type. Findings of this study will improve diagnostic accuracy and clinical management and need to be considered when developing targeted treatment strategies against ST-EPN.
Citation Format: D.R. Ghasemi, K. Okonechnikov, A. Korshunov, M. Sill, T. Zheng, J.M. Huebner, K.K. Maass, J. Benzel, M. Snuderl, J. Gojo, U. Schüller, N.U. Gerber, I. Stoler, P. Hernáiz-Driever, T. Milde, D. Sturm, R. Chapman, R.G. Grundy, A. von Deimling, D. Kawauchi, D.T.W. Jones, M. Kool, S.M. Pfister, F. Sahm, K.W. Pajtler. Molecular heterogeneity and novel oncogenic fusions in RELA- and YAP1-negative supratentorial ependymoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B71.
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Affiliation(s)
- D.R. Ghasemi
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - K. Okonechnikov
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - A. Korshunov
- 3Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany,
- 4Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,
| | - M. Sill
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - T. Zheng
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - J.M. Huebner
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - K.K. Maass
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
- 5Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany,
| | - J. Benzel
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - M. Snuderl
- 6Division of Neuropathology, Department of Pathology, NYU Langone Health, New York, NY,
| | - J. Gojo
- 7Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria,
| | - U. Schüller
- 8Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,
- 9Research Institute, Children’s Cancer Center Hamburg, Hamburg, Germany,
- 10Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,
| | - N.U. Gerber
- 11Department of Oncology, University Children’s Hospital, Zurich, Switzerland,
| | - I. Stoler
- 12Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, Berlin Institute of Health, Berlin, Germany,
| | - P. Hernáiz-Driever
- 12Department of Pediatric Oncology/Hematology, Charité Universitätsmedizin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, Berlin Institute of Health, Berlin, Germany,
| | - T. Milde
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 5Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany,
- 13CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany,
| | - D. Sturm
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 5Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany,
- 15Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - R. Chapman
- 14Children’s Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom,
| | - R.G. Grundy
- 14Children’s Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom,
| | - A. von Deimling
- 3Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany,
- 4Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,
| | - D. Kawauchi
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - D.T.W. Jones
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 15Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M. Kool
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
| | - S.M. Pfister
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
- 5Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany,
| | - F. Sahm
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 3Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany,
- 4Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,
| | - K.W. Pajtler
- 1Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany,
- 2Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany,
- 5Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany,
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Kawauchi D, Pajtler K, Wei Y, Okonechnikov K, Silva P, Jones D, Hoshino M, Pfister S, Kool M, Li W. TB-06 MOLECULAR MECHANISM OF BRAIN TUMOUR FORMATION DRIVEN BY SUPRATENTORIAL EPENDYMOMA-SPECIFIC YAP1 FUSION GENES. Neurooncol Adv 2019. [PMCID: PMC7213335 DOI: 10.1093/noajnl/vdz039.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
YAP1 fusion-positive supratentorial ependymomas predominantly occur in infants, but the molecular mechanisms of oncogenesis are unknown. Here we show YAP1-MAMLD1 fusions but not YAP1 wildtype are sufficient to drive malignant transformation of neural progenitors in the developing cerebral cortex in mice, and the resulting tumours share histo-molecular characteristics of human ependymomas. Nuclear localization of YAP1-MAMLD1 protein is associated with its oncogenicity and is mediated by the nuclear localization signal of MAMLD1 in a YAP1-Ser127 phosphorylation-independent manner. Chromatin immunoprecipitation-sequencing analyses of human YAP1-MAMLD1-positive ependymoma reveal enrichment of NFI and TEAD transcription factor binding site motifs in YAP1-bound regulatory elements, hypothesizing the important role of these transcription factors in YAP1-MAMLD1-driven tumourigenesis. Indeed, co-immunoprecipitation assays revealed physical interactions of TEADs and NFIA/B with the YAP1 and MAMLD1 domains of the fusion protein, respectively. Mutation of the TEAD binding site in the YAP1 fusion or repression of NFI targets prevents tumour induction in mice. Together, these results demonstrate that the YAP1-MAMLD1 fusion functions as an oncogenic driver of ependymoma through recruitment of TEADs and NFIs, indicating a rationale for preclinical studies to block the interaction between YAP1 fusions and NFI and TEAD transcription factors.
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Affiliation(s)
| | | | - Yiju Wei
- Hopp-Children’s Cancer Center Heidelberg (KiTZ)
| | | | | | - David Jones
- Hopp-Children’s Cancer Center Heidelberg (KiTZ)
| | | | | | - Marcel Kool
- Hopp-Children’s Cancer Center Heidelberg (KiTZ)
| | - Wei Li
- Hopp-Children’s Cancer Center Heidelberg (KiTZ)
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42
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Ghasemi DR, Sill M, Okonechnikov K, Korshunov A, Yip S, Schutz PW, Scheie D, Kruse A, Harter PN, Kastelan M, Wagner M, Hartmann C, Benzel J, Maass KK, Khasraw M, Sträter R, Thomas C, Paulus W, Kratz CP, Witt H, Kawauchi D, Herold-Mende C, Sahm F, Brandner S, Kool M, Jones DTW, von Deimling A, Pfister SM, Reuss DE, Pajtler KW. MYCN amplification drives an aggressive form of spinal ependymoma. Acta Neuropathol 2019; 138:1075-1089. [PMID: 31414211 PMCID: PMC6851394 DOI: 10.1007/s00401-019-02056-2] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/05/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022]
Abstract
Spinal ependymal tumors form a histologically and molecularly heterogeneous group of tumors with generally good prognosis. However, their treatment can be challenging if infiltration of the spinal cord or dissemination throughout the central nervous system (CNS) occurs and, in these cases, clinical outcome remains poor. Here, we describe a new and relatively rare subgroup of spinal ependymal tumors identified using DNA methylation profiling that is distinct from other molecular subgroups of ependymoma. Copy number variation plots derived from DNA methylation arrays showed MYCN amplification as a characteristic genetic alteration in all cases of our cohort (n = 13), which was subsequently validated using fluorescence in situ hybridization. The histological diagnosis was anaplastic ependymoma (WHO Grade III) in ten cases and classic ependymoma (WHO Grade II) in three cases. Histological re-evaluation in five primary tumors and seven relapses showed characteristic histological features of ependymoma, namely pseudorosettes, GFAP- and EMA positivity. Electron microscopy revealed cilia, complex intercellular junctions and intermediate filaments in a representative sample. Taking these findings into account, we suggest to designate this molecular subgroup spinal ependymoma with MYCN amplification, SP-EPN-MYCN. SP-EPN-MYCN tumors showed distinct growth patterns with intradural, extramedullary localization mostly within the thoracic and cervical spine, diffuse leptomeningeal spread throughout the whole CNS and infiltrative invasion of the spinal cord. Dissemination was observed in 100% of cases. Despite high-intensity treatment, SP-EPN-MYCN showed significantly worse median progression free survival (PFS) (17 months) and median overall survival (OS) (87 months) than all other previously described molecular spinal ependymoma subgroups. OS and PFS were similar to supratentorial ependymoma with RELA-fusion (ST-EPN-RELA) and posterior fossa ependymoma A (PF-EPN-A), further highlighting the aggressiveness of this distinct new subgroup. We, therefore, propose to establish SP-EPN-MYCN as a new molecular subgroup in ependymoma and advocate for testing newly diagnosed spinal ependymal tumors for MYCN amplification.
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Affiliation(s)
- David R Ghasemi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Martin Sill
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stephen Yip
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Peter W Schutz
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | - Anders Kruse
- Spine Section, Department of Orthopedic Surgery, Rigshospitalet, Copenhagen, Denmark
| | - Patrick N Harter
- 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
| | - Marina Kastelan
- Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia
- The Brain Cancer Group, Sydney, NSW, Australia
| | - Marlies Wagner
- LOEWE Center for Personalized Translational Epilepsy Research (CePTER), Frankfurt, Germany
- Institute of Neuroradiology, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Christian Hartmann
- Department of Neuropathology, Hannover Medical School, Hannover, Germany
| | - Julia Benzel
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kendra K Maass
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mustafa Khasraw
- Royal North Shore Hospital, The University of Sydney, Sydney, Australia
| | - Ronald Sträter
- Department of Pediatric Hematology/Oncology, University of Münster, Münster, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Hendrik Witt
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Daisuke Kawauchi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Felix Sahm
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sebastian Brandner
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Marcel Kool
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 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
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - David E Reuss
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
- Department of Neuropathology, Institute of Pathology, 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), German Cancer Consortium (DKTK), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany.
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Okonechnikov K, Hübner JM, Chapman O, Chakraborty A, Bump R, Chandran S, Kraft K, Acuna Hidalgo R, Mundlos S, Coufal N, Levy M, Crawford J, Ay F, Mesirov J, Pajtler K, Dixon J, Pfister S, Kool M, Chavez L. GENE-15. TARGETING OF EPENDYMOMA AS INFORMED BY ONCOGENIC 3D GENOME ORGANIZATION. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
By profiling enhancers in primary ependymoma tumors, we have recently identified putative oncogenes, molecular targets, and functional pathways. Inhibition of selected targets diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymoma. While enhancers frequently regulate the nearest gene, unambiguous identification of enhancer target genes remains to be a challenge in the absence of chromosome conformation information. Consequently, we have now used HiC to map the 3-dimensional organization of tumor chromatin in the two most common and aggressive ependymoma subgroups: posterior fossa group A (PF-EPN-A) and supratentorial ependymomas with gene fusions involving the NF-κB subunit gene RELA (ST-EPN-RELA). By an integrative analysis of enhancer and gene expression in the context of the newly derived HiC data, we find that a large amount of the previously predicted enhancer target genes can be confirmed by physical interactions. Importantly, we also identify many new putative tumor-dependency genes activated by long-range promoter-enhancer interactions. Complementary to the analysis of gene-enhancer interactions, we have also leveraged the HiC data for resolving structural rearrangements underlying copy number alterations frequently observed in PF-EPN-A tumors. Especially copy number gains of the 1q arm of chromosome 1 are associated with poor survival. Our preliminary results reveal complex structural variants that underlie 1q gains, which lead to inter-chromosomal rearrangements and affect several genes that potentially contribute to poor survival. We now aim to test the relevance of the novel candidate tumor-dependency genes for tumor cell growth and proliferation in patient derived ependymoma models.
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Affiliation(s)
| | - Jens-Martin Hübner
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | | | | | - Rosalind Bump
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | | | - Stefan Mundlos
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | | | | | | | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Kristian Pajtler
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Jesse Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Stefan Pfister
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
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44
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Okonechnikov K, Pfister SM, Kutscher LM. Probing Medulloblastoma Initiation at the Single-Cell Level. Trends Cancer 2019; 5:759-761. [PMID: 31813451 DOI: 10.1016/j.trecan.2019.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 10/25/2022]
Abstract
Medulloblastoma is a pediatric brain tumor arising from the developing cerebellum. Despite significant strides in classifying tumor subgroups and identifying underlying genetic mutations, progress in clinical outcomes has been notably slower. About 30% of patients experience relapse after treatment, possibly because of our inability to identify and eliminate the cancer stem cells. Zhang et al. recently investigated these cells in the SHH subgroup of medulloblastoma and identified drugs that may target them.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Lena M Kutscher
- Hopp-Children's Cancer Center Heidelberg (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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45
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Pajtler KW, Wei Y, Okonechnikov K, Silva PBG, Vouri M, Zhang L, Brabetz S, Sieber L, Gulley M, Mauermann M, Wedig T, Mack N, Imamura Kawasawa Y, Sharma T, Zuckermann M, Andreiuolo F, Holland E, Maass K, Körkel-Qu H, Liu HK, Sahm F, Capper D, Bunt J, Richards LJ, Jones DTW, Korshunov A, Chavez L, Lichter P, Hoshino M, Pfister SM, Kool M, Li W, Kawauchi D. YAP1 subgroup supratentorial ependymoma requires TEAD and nuclear factor I-mediated transcriptional programmes for tumorigenesis. Nat Commun 2019; 10:3914. [PMID: 31477715 PMCID: PMC6718408 DOI: 10.1038/s41467-019-11884-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/07/2019] [Indexed: 01/22/2023] Open
Abstract
YAP1 fusion-positive supratentorial ependymomas predominantly occur in infants, but the molecular mechanisms of oncogenesis are unknown. Here we show YAP1-MAMLD1 fusions are sufficient to drive malignant transformation in mice, and the resulting tumors share histo-molecular characteristics of human ependymomas. Nuclear localization of YAP1-MAMLD1 protein is mediated by MAMLD1 and independent of YAP1-Ser127 phosphorylation. Chromatin immunoprecipitation-sequencing analyses of human YAP1-MAMLD1-positive ependymoma reveal enrichment of NFI and TEAD transcription factor binding site motifs in YAP1-bound regulatory elements, suggesting a role for these transcription factors in YAP1-MAMLD1-driven tumorigenesis. Mutation of the TEAD binding site in the YAP1 fusion or repression of NFI targets prevents tumor induction in mice. Together, these results demonstrate that the YAP1-MAMLD1 fusion functions as an oncogenic driver of ependymoma through recruitment of TEADs and NFIs, indicating a rationale for preclinical studies to block the interaction between YAP1 fusions and NFI and TEAD transcription factors. The molecular mechanisms driving proliferation in the pediatric brain cancer epdendymoma are poorly understood. Here the authors show that a YAP1- MAMLD1 fusion drives tumor formation in mice and show that the fusion protein can collaborate with the TEAD and NFI transcription factors.
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Affiliation(s)
- Kristian W Pajtler
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Yiju Wei
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Patricia B G Silva
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Mikaella Vouri
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Lei Zhang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Sebastian Brabetz
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Laura Sieber
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Melissa Gulley
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Monika Mauermann
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Tatjana Wedig
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Norman Mack
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Yuka Imamura Kawasawa
- Department of Biochemistry and Molecular Biology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, 17033, USA.,Department of Pharmacology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Tanvi Sharma
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Marc Zuckermann
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Felipe Andreiuolo
- Department of Neuropathology, Ste. Anne Hospital, 75014, Paris, France
| | - Eric Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Kendra Maass
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Huiqin Körkel-Qu
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Hai-Kun Liu
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - David Capper
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens Bunt
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia
| | - Linda J Richards
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia
| | - David T W Jones
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Lukas Chavez
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Marcel Kool
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Wei Li
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, 17033, USA. .,Department of Biochemistry and Molecular Biology, Penn State Health Hershey Medical Center, Penn State College of Medicine, Hershey, PA, 17033, USA.
| | - Daisuke Kawauchi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany. .,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
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46
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Korshunov A, Okonechnikov K, Sahm F, Ryzhova M, Stichel D, Sievers P, Meyer J, Schrimpf D, Zheludkova O, Golanov A, Lichter P, Jones DTW, Pfister SM, von Deimling A, Kool M. Molecular progression of SHH-activated medulloblastomas. Acta Neuropathol 2019; 138:327-330. [PMID: 31030238 DOI: 10.1007/s00401-019-02022-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 12/11/2022]
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47
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Korshunov A, Sahm F, Okonechnikov K, Ryzhova M, Stichel D, Schrimpf D, Casalini B, Sievers P, Meyer J, Zheludkova O, Golanov A, Lichter P, Jones DTW, Pfister SM, Kool M, von Deimling A. Desmoplastic/nodular medulloblastomas (DNMB) and medulloblastomas with extensive nodularity (MBEN) disclose similar epigenetic signatures but different transcriptional profiles. Acta Neuropathol 2019; 137:1003-1015. [PMID: 30826918 DOI: 10.1007/s00401-019-01981-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 12/20/2022]
Abstract
Desmoplastic/nodular medulloblastomas (DNMB) and medulloblastomas with extensive nodularity (MBEN) were outlined in the current WHO classification of tumors of the nervous system as two distinct histological MB variants. However, they are often considered as cognate SHH MB entities, and it is a reason why some clinical MB trials do not separate the patients with DNMB or MBEN histology. In the current study, we performed an integrated DNA/RNA-based molecular analysis of 83 DNMB and 36 MBEN to assess the etiopathogenetic relationship between these SHH MB variants. Methylation profiling revealed "infant" and "children" SHH MB clusters but neither DNMB nor MBEN composed separate epigenetic cohorts, and their profiles were intermixed within the "infant" cluster. In contrast, RNA-based transcriptional profiling disclosed that expression signatures of all MBEN were clustered separately from most of DNMB and a set of differentially expressed genes was identified. MBEN transcriptomes were enriched with genes associated with synaptic transmission, neuronal differentiation and metabolism, whereas DNMB profiling signatures included sets of genes involved in phototransduction and NOTCH signaling pathways. Thus, DNMB and MBEN are distinct tumor entities within the SHH MB family whose biology is determined by different transcriptional programs. Therefore, we recommend a transcriptome analysis as an optimal molecular tool to discriminate between DNMB and MBEN, which may be of benefit for patients' risk stratification in clinical trials. Molecular events identified in DNMB by RNA sequencing could be considered in the future as potent molecular targets for novel therapeutic interventions in treatment-resistant cases.
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Affiliation(s)
- Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.
- Hopp Children'S Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children'S Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children'S Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology (B062), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Belen Casalini
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jochen Meyer
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olga Zheludkova
- Department of Neuro-Oncology, Russian Scientific Center of Radiology, Moscow, Russia
| | - Andrey Golanov
- Department of Neuroradiology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Peter Lichter
- Hopp Children'S Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Molecular Genetics (B060), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - David T W Jones
- Hopp Children'S Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group (B360), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children'S Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology (B062), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children'S Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology (B062), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children'S Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
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48
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Kutscher L, Batora N, Okonechnikov K, Clark J, Vouri M, Rijn SV, Gearhart M, Orr B, Korshunov A, Kool M, Bardwell V, Pfister SM, Northcott PA, Kawauchi D. MEDU-21. LOSS OF THE TRANSCRIPTIONAL CO-REPRESSOR BCOR LEADS TO OVEREXPRESSION OF THE GROWTH FACTOR IGF2 AND SHH MEDULLOBLASTOMA TUMOR FORMATION. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz036.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Lena Kutscher
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nadja Batora
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Clark
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mikaella Vouri
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sjoerd van Rijn
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Brent Orr
- St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Andrey Korshunov
- Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Stefan M Pfister
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Daisuke Kawauchi
- Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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49
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Tao R, Murad N, Xu Z, Zhang P, Okonechnikov K, Kool M, Rivero-Hinojosa S, Lazarski C, Zheng P, Liu Y, Eberhart CG, Rood BR, Packer R, Pei Y. MYC Drives Group 3 Medulloblastoma through Transformation of Sox2 + Astrocyte Progenitor Cells. Cancer Res 2019; 79:1967-1980. [PMID: 30862721 DOI: 10.1158/0008-5472.can-18-1787] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/07/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
A subset of group 3 medulloblastoma frequently harbors amplification or overexpression of MYC lacking additional focal aberrations, yet it remains unclear whether MYC overexpression alone can induce tumorigenesis and which cells give rise to these tumors. Here, we showed that astrocyte progenitors in the early postnatal cerebellum were susceptible to transformation by MYC. The resulting tumors specifically resembled human group 3 medulloblastoma based on histology and gene-expression profiling. Gene-expression analysis of MYC-driven medulloblastoma cells revealed altered glucose metabolic pathways with marked overexpression of lactate dehydrogenase A (LDHA). LDHA abundance correlated positively with MYC expression and was associated with poor prognosis in human group 3 medulloblastoma. Inhibition of LDHA significantly reduced growth of both mouse and human MYC-driven tumors but had little effect on normal cerebellar cells or SHH-associated medulloblastoma. By generating a new mouse model, we demonstrated for the first time that astrocyte progenitors can be transformed by MYC and serve as the cells of origin for group 3 medulloblastoma. Moreover, we identified LDHA as a novel, specific therapeutic target for this devastating disease. SIGNIFICANCE: Insights from a new model identified LDHA as a novel target for group 3 medulloblastoma, paving the way for the development of effective therapies against this disease.
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Affiliation(s)
- Ran Tao
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Najiba Murad
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Zhenhua Xu
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Peng Zhang
- Division of Immunotherapy, Institute of Human Virology, School of Medicine, University of Maryland, College Park, Maryland
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center, NCT, Heidelberg, Germany.,Division of Pediatric Neuro-oncology of the German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center, NCT, Heidelberg, Germany.,Division of Pediatric Neuro-oncology of the German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Samuel Rivero-Hinojosa
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Christopher Lazarski
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Pan Zheng
- Division of Immunotherapy, Institute of Human Virology, School of Medicine, University of Maryland, College Park, Maryland
| | - Yang Liu
- Division of Immunotherapy, Institute of Human Virology, School of Medicine, University of Maryland, College Park, Maryland
| | - Charles G Eberhart
- Division of Neuropathology, Johns Hopkins University, Baltimore, Maryland
| | - Brian R Rood
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Roger Packer
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC
| | - Yanxin Pei
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC.
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50
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Ackermann S, Cartolano M, Hero B, Welte A, Kahlert Y, Roderwieser A, Bartenhagen C, Walter E, Gecht J, Kerschke L, Volland R, Menon R, Heuckmann JM, Gartlgruber M, Hartlieb S, Henrich KO, Okonechnikov K, Altmüller J, Nürnberg P, Lefever S, de Wilde B, Sand F, Ikram F, Rosswog C, Fischer J, Theissen J, Hertwig F, Singhi AD, Simon T, Vogel W, Perner S, Krug B, Schmidt M, Rahmann S, Achter V, Lang U, Vokuhl C, Ortmann M, Büttner R, Eggert A, Speleman F, O'Sullivan RJ, Thomas RK, Berthold F, Vandesompele J, Schramm A, Westermann F, Schulte JH, Peifer M, Fischer M. A mechanistic classification of clinical phenotypes in neuroblastoma. Science 2019; 362:1165-1170. [PMID: 30523111 DOI: 10.1126/science.aat6768] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/26/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022]
Abstract
Neuroblastoma is a pediatric tumor of the sympathetic nervous system. Its clinical course ranges from spontaneous tumor regression to fatal progression. To investigate the molecular features of the divergent tumor subtypes, we performed genome sequencing on 416 pretreatment neuroblastomas and assessed telomere maintenance mechanisms in 208 of these tumors. We found that patients whose tumors lacked telomere maintenance mechanisms had an excellent prognosis, whereas the prognosis of patients whose tumors harbored telomere maintenance mechanisms was substantially worse. Survival rates were lowest for neuroblastoma patients whose tumors harbored telomere maintenance mechanisms in combination with RAS and/or p53 pathway mutations. Spontaneous tumor regression occurred both in the presence and absence of these mutations in patients with telomere maintenance-negative tumors. On the basis of these data, we propose a mechanistic classification of neuroblastoma that may benefit the clinical management of patients.
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Affiliation(s)
- Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Maria Cartolano
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Anne Welte
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Yvonne Kahlert
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Andrea Roderwieser
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Esther Walter
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Judith Gecht
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Laura Kerschke
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Ruth Volland
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | | | | | - Moritz Gartlgruber
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Sabine Hartlieb
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Division of Pediatric Neurooncology, German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Bram de Wilde
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Frederik Sand
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Fakhera Ikram
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Lahore, Pakistan
| | - Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Janina Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Jessica Theissen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Thorsten Simon
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Wenzel Vogel
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany
| | - Sven Perner
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany
| | - Barbara Krug
- Department of Diagnostic and Interventional Radiology, University Hospital of Cologne, Cologne, Germany
| | - Matthias Schmidt
- Department of Nuclear Medicine, University of Cologne, Cologne, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Computer Science, TU Dortmund, Dortmund, Germany
| | - Viktor Achter
- Computing Center, University of Cologne, Cologne, Germany
| | - Ulrich Lang
- Computing Center, University of Cologne, Cologne, Germany.,Department of Informatics, University of Cologne, Cologne, Germany
| | - Christian Vokuhl
- Kiel Pediatric Tumor Registry, Department of Pediatric Pathology, University of Kiel, Kiel, Germany
| | - Monika Ortmann
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute (UPCI), Hillman Cancer Center, Pittsburgh, PA, USA
| | - Roman K Thomas
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pathology, University of Cologne, Cologne, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Berthold
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alexander Schramm
- Department of Medical Oncology, West German Cancer Center Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Westermann
- Division of Neuroblastoma Genomics (B087), German Cancer Research Center, and Hopp Children's Cancer Center at NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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