Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
Summary Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB subtypes emerged, that could be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3-Myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis revealed different conservation levels of proteome features across MB subtypes at the DNA-methylation level. Aggressive pGroup3-Myc MBs and favorable pWNT MBs were most similar in cluster hierarchies concerning overall proteome patterns but showed different protein abundances of the vincristine resistance associated multiprotein complex TriC/CCT and of N-glycan turnover associated factors. The N-glycome reflected proteome subtypes and complex-bisecting N-glycans characterized pGroup3-Myc tumors. Our results shed light on new targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures. Significance Whereas the application of omics technologies has significantly improved MB tumor classification and treatment stratification, it is still of debate, which features predict best clinical outcome. Moreover, treatment options - especially for high-risk groups - are still unsatisfactory. In contrast to nucleic acids, the proteome and their N-glycans may reflect the phenotype of a tumor in a more direct way and thus hold the potential to discover clinically relevant phenotypes and potentially targetable pathways. We show that these analyses are feasible on formalin fixed and paraffine embedded tissue. Compiling a comprehensive MB dataset, we detected new biomarkers and characteristics for high- and low-risk MB subtypes that were not reflected by other omic data modalities before. Specifically, we identified subtype specific abundance differences in proteins of the vincristine resistance associated multiprotein complex TriC/CCT and in proteins involved in N-glycan turnover. Changes in the N-glycans are considered as potential hallmarks of cancer and we show that N-glycan profiles can distinguish MB subtypes. These tumor-specific N-glycan structures hold a strong potential as new biomarkers, as well as immunotherapy targets. Highlights - Integration of in-house proteome data on formalin fixated paraffine embedded medulloblastoma (MB) and publicly available datasets enables large scale proteome analysis of MB - Six proteome MB subtypes can be assigned to two main molecular programs: replication/ translation versus synapse/immune system - Identification and validation of IHC compatible protein-biomarkers for high and low risk MB subtypes, such as TNC and PALMD. - Subtype specific correlation of the DNA methylome and the proteome reveals different conserved molecular characteristics across MB subtypes. - pGroup3-Myc subtype MBs are associated with high-risk features including high abundances of vincristine resistance associated TriC/CCT member proteins - Proteome MB subtypes show differential N-glycosylation patterns, revealing complex-bisecting glycans as potentially immunotargetable hallmarks of the high risk pGroup3-Myc subtype.
Authors 20
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Affiliation as printed
Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
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Affiliation as printed
Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
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Universität Hamburg · University Medical Center Hamburg-Eppendorf
Affiliation as printed
Department of Pediatric Hematoloy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
Department of Pediatric Hematoloy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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German Center for Neurodegenerative Diseases · Institut für Neuropathologie · Ludwig-Maximilians-Universität München
Affiliation as printed
Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
German Center for Neurodegenerative Diseases, Munich, Germany
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German Cancer Research Center · University Hospital Heidelberg · Deutsches Konsortium für Translationale Krebsforschung
Affiliation as printed
Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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German Cancer Research Center · Heidelberg University · University Hospital Heidelberg · National Center for Tumor Diseases · Hopp Children's Cancer Center Heidelberg · Deutsches Konsortium für Translationale Krebsforschung
Affiliation as printed
Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
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Affiliation as printed
Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
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Medizinische Hochschule Hannover
Affiliation as printed
Department of Neuropathology, Hannover Medical School (MHH), Hannover, Germany
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Universitätsklinikum Aachen · RWTH Aachen University
Affiliation as printed
Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
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University of Augsburg · University Hospital Augsburg
Affiliation as printed
Institute of Pathology and Molecular Diagnostics, University Medical Center Augsburg, Augsburg, Germany
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Universität Hamburg · University Medical Center Hamburg-Eppendorf · Kinderkrebs-Zentrum Hamburg
Affiliation as printed
Department of Pediatric Hematoloy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Julia E. Neumann corresponding
Universität Hamburg · University Medical Center Hamburg-Eppendorf
Affiliation as printed
Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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