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Adeberg S, Knoll M, Koelsche C, Bernhardt D, Schrimpf D, Sahm F, König L, Harrabi SB, Hörner-Rieber J, Verma V, Bewerunge-Hudler M, Unterberg A, Sturm D, Jungk C, Herold-Mende C, Wick W, von Deimling A, Debus J, Rieken S, Abdollahi A. DNA-methylome-assisted classification of patients with poor prognostic subventricular zone associated IDH-wildtype glioblastoma. Acta Neuropathol 2022; 144:129-142. [PMID: 35660939 PMCID: PMC9217840 DOI: 10.1007/s00401-022-02443-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/04/2022] [Accepted: 05/21/2022] [Indexed: 11/25/2022]
Abstract
Glioblastoma (GBM) derived from the “stem cell” rich subventricular zone (SVZ) may constitute a therapy-refractory subgroup of tumors associated with poor prognosis. Risk stratification for these cases is necessary but is curtailed by error prone imaging-based evaluation. Therefore, we aimed to establish a robust DNA methylome-based classification of SVZ GBM and subsequently decipher underlying molecular characteristics. MRI assessment of SVZ association was performed in a retrospective training set of IDH-wildtype GBM patients (n = 54) uniformly treated with postoperative chemoradiotherapy. DNA isolated from FFPE samples was subject to methylome and copy number variation (CNV) analysis using Illumina Platform and cnAnalysis450k package. Deep next-generation sequencing (NGS) of a panel of 130 GBM-related genes was conducted (Agilent SureSelect/Illumina). Methylome, transcriptome, CNV, MRI, and mutational profiles of SVZ GBM were further evaluated in a confirmatory cohort of 132 patients (TCGA/TCIA). A 15 CpG SVZ methylation signature (SVZM) was discovered based on clustering and random forest analysis. One third of CpG in the SVZM were associated with MAB21L2/LRBA. There was a 14.8% (n = 8) discordance between SVZM vs. MRI classification. Re-analysis of these patients favored SVZM classification with a hazard ratio (HR) for OS of 2.48 [95% CI 1.35–4.58], p = 0.004 vs. 1.83 [1.0–3.35], p = 0.049 for MRI classification. In the validation cohort, consensus MRI based assignment was achieved in 62% of patients with an intraclass correlation (ICC) of 0.51 and non-significant HR for OS (2.03 [0.81–5.09], p = 0.133). In contrast, SVZM identified two prognostically distinct subgroups (HR 3.08 [1.24–7.66], p = 0.016). CNV alterations revealed loss of chromosome 10 in SVZM– and gains on chromosome 19 in SVZM– tumors. SVZM– tumors were also enriched for differentially mutated genes (p < 0.001). In summary, SVZM classification provides a novel means for stratifying GBM patients with poor prognosis and deciphering molecular mechanisms governing aggressive tumor phenotypes.
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Affiliation(s)
- Sebastian Adeberg
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Maximilian Knoll
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Christian Koelsche
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Denise Bernhardt
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Radiation Oncology, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Laila König
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Semi Ben Harrabi
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Juliane Hörner-Rieber
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Vivek Verma
- Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center Houston, Houston, TX, USA
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Andreas Unterberg
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Dominik Sturm
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Angelika Lautenschläger Children's Hospital, University Medical Center for Children and Adolescents, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Christine Jungk
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Christel Herold-Mende
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Wolfgang Wick
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neurooncology, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Andreas von Deimling
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Juergen Debus
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan Rieken
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
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Carrano A, Zarco N, Phillipps J, Lara-Velazquez M, Suarez-Meade P, Norton ES, Chaichana KL, Quiñones-Hinojosa A, Asmann YW, Guerrero-Cázares H. Human Cerebrospinal Fluid Modulates Pathways Promoting Glioblastoma Malignancy. Front Oncol 2021; 11:624145. [PMID: 33747938 PMCID: PMC7969659 DOI: 10.3389/fonc.2021.624145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/05/2021] [Indexed: 01/07/2023] Open
Abstract
Glioblastoma (GBM) is the most common and devastating primary cancer of the central nervous system in adults. High grade gliomas are able to modify and respond to the brain microenvironment. When GBM tumors infiltrate the Subventricular zone (SVZ) they have a more aggressive clinical presentation than SVZ-distal tumors. We suggest that cerebrospinal fluid (CSF) contact contributes to enhance GBM malignant characteristics in these tumors. We evaluated the impact of human CSF on GBM, performing a transcriptome analysis on human primary GBM cells exposed to CSF to measure changes in gene expression profile and their clinical relevance on disease outcome. In addition we evaluated the proliferation and migration changes of CSF-exposed GBM cells in vitro and in vivo. CSF induced transcriptomic changes in pathways promoting cell malignancy, such as apoptosis, survival, cell motility, angiogenesis, inflammation, and glucose metabolism. A genetic signature extracted from the identified transcriptional changes in response to CSF proved to be predictive of GBM patient survival using the TCGA database. Furthermore, CSF induced an increase in viability, proliferation rate, and self-renewing capacity, as well as the migratory capabilities of GBM cells in vitro. In vivo, GBM cells co-injected with human CSF generated larger and more proliferative tumors compared to controls. Taken together, these results provide direct evidence that CSF is a key player in determining tumor growth and invasion through the activation of complex gene expression patterns characteristic of a malignant phenotype. These findings have diagnostic and therapeutic implications for GBM patients. The changes induced by CSF contact might play a role in the increased malignancy of SVZ-proximal GBM.
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Affiliation(s)
- Anna Carrano
- Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, United States
| | - Natanael Zarco
- Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, United States
| | - Jordan Phillipps
- Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, United States
| | | | - Paola Suarez-Meade
- Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, United States
| | - Emily S Norton
- Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, United States.,Neuroscience Graduate Program, Mayo Clinic Graduate School of Biochemical Sciences, Mayo Clinic, Jacksonville, FL, United States.,Regenerative Sciences Training Program, Center for Regenerative Medicine, Mayo Clinic, Jacksonville, FL, United States
| | - Kaisorn L Chaichana
- Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, United States
| | | | - Yan W Asmann
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, United States
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