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Cidre-Aranaz F, Li J, Hölting TLB, Orth MF, Imle R, Kutschmann S, Ammirati G, Ceranski K, Carreño-Gonzalez MJ, Kasan M, Marchetto A, Funk CM, Bestvater F, Bersini S, Arrigoni C, Moretti M, Thiel U, Baumhoer D, Sahm F, Pfister SM, Hartmann W, Dirksen U, Romero-Pérez L, Banito A, Ohmura S, Musa J, Kirchner T, Knott MML, Grünewald TGP. Integrative gene network and functional analyses identify a prognostically relevant key regulator of metastasis in Ewing sarcoma. Mol Cancer 2022; 21:1. [PMID: 34980141 PMCID: PMC8722160 DOI: 10.1186/s12943-021-01470-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/24/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Florencia Cidre-Aranaz
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany
| | - Jing Li
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany
| | - Tilman L B Hölting
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Roland Imle
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Soft-Tissue Sarcoma Junior Research Group, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Pediatric Surgery, Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefanie Kutschmann
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany
| | - Giulia Ammirati
- Regenerative Medicine Technologies Laboratory, Ente Ospedaliero Cantonale (EOC), Lugano, Switzerland
| | - Katharina Ceranski
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany
| | - Martha Julia Carreño-Gonzalez
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany
| | - Merve Kasan
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Aruna Marchetto
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Cornelius M Funk
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany
| | - Felix Bestvater
- Light Microscopy Facility (W210), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Simone Bersini
- Regenerative Medicine Technologies Laboratory, Ente Ospedaliero Cantonale (EOC), Lugano, Switzerland
| | - Chiara Arrigoni
- Regenerative Medicine Technologies Laboratory, Ente Ospedaliero Cantonale (EOC), Lugano, Switzerland
| | - Matteo Moretti
- Regenerative Medicine Technologies Laboratory, Ente Ospedaliero Cantonale (EOC), Lugano, Switzerland
- Biomedical Sciences Faculty, Università della Svizzera Italiana (USI), Lugano, Switzerland
| | - Uwe Thiel
- Technical University of Munich, School of Medicine, Department of Pediatrics and Children's Cancer Research Center, Munich, Germany
| | - Daniel Baumhoer
- Bone Tumor Reference Center, Institute of Pathology of the University Hospital of Basel, Basel, Switzerland
| | - Felix Sahm
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit (CCU) Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk-Institute for Pathology, University Hospital Münster, Münster, Germany
| | - Uta Dirksen
- Pediatrics III, AYA Unit, West German Cancer Centre, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen, Essen, Germany
| | - Laura Romero-Pérez
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany
| | - Ana Banito
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Soft-Tissue Sarcoma Junior Research Group, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Shunya Ohmura
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany
| | - Julian Musa
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Kirchner
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Maximilian M L Knott
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas G P Grünewald
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Translational Pediatric Sarcoma Research (B410), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69210, Heidelberg, Germany.
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany.
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
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Schmid D, Warnken U, Latzer P, Hoffmann DC, Roth J, Kutschmann S, Jaschonek H, Rübmann P, Foltyn M, Vollmuth P, Winkler F, Seliger C, Felix M, Sahm F, Haas J, Reuss D, Bendszus M, Wildemann B, von Deimling A, Wick W, Kessler T. Diagnostic biomarkers from proteomic characterization of cerebrospinal fluid in patients with brain malignancies. J Neurochem 2021; 158:522-538. [PMID: 33735443 DOI: 10.1111/jnc.15350] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 12/23/2022]
Abstract
Recent technological advances in molecular diagnostics through liquid biopsies hold the promise to repetitively monitor tumor evolution and treatment response of brain malignancies without the need of invasive surgical tissue accrual. Here, we implemented a mass spectrometry-based protein analysis pipeline which identified hundreds of proteins in 251 cerebrospinal fluid (CSF) samples from patients with four types of brain malignancies (glioblastoma, lymphoma, brain metastasis, and leptomeningeal disease [LMD]) and from healthy individuals with a focus on glioblastoma in a retrospective and confirmatory prospective observational study. CSF proteome deregulation via disruption of the blood brain barrier appeared to be largely conserved across brain tumor entities. CSF analysis of glioblastoma patients identified two proteomic clusters that correlated with tumor size and patient survival. By integrating CSF data with proteomic analyses of matching glioblastoma tumor tissue and primary glioblastoma cells, we identified potential CSF biomarkers for glioblastoma, in particular chitinase-3-like protein 1 (CHI3L1) and glial fibrillary acidic protein (GFAP). Key findings were validated in a prospective cohort consisting of 35 glioma patients. Finally, in LMD patients who frequently undergo repeated CSF work-up, we explored our proteomic pipeline as a mean to profile consecutive CSF samples. Therefore, proteomic analysis of CSF in brain malignancies has the potential to reveal biomarkers for diagnosis and therapy monitoring.
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Affiliation(s)
- Dominic Schmid
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Uwe Warnken
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Functional Proteome Analysis, DKFZ, Heidelberg, Germany
| | - Pauline Latzer
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk C Hoffmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Judith Roth
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Kutschmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hannah Jaschonek
- Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Petra Rübmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martha Foltyn
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Vollmuth
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Winkler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Corinna Seliger
- Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marius Felix
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jürgen Haas
- Molecular Neuroimmunology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Reuss
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Brigitte Wildemann
- Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Neuroimmunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Tobias Kessler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
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