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Clavreul A, Guette C, Lasla H, Rousseau A, Blanchet O, Henry C, Boissard A, Cherel M, Jézéquel P, Guillonneau F, Menei P, Lemée JM. Proteomics of tumor and serum samples from isocitrate dehydrogenase-wildtype glioblastoma patients: is the detoxification of reactive oxygen species associated with shorter survival? Mol Oncol 2024. [PMID: 38803161 DOI: 10.1002/1878-0261.13668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/12/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Proteomics has been little used for the identification of novel prognostic and/or therapeutic markers in isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GB). In this study, we analyzed 50 tumor and 30 serum samples from short- and long-term survivors of IDH-wildtype GB (STS and LTS, respectively) by data-independent acquisition mass spectrometry (DIA-MS)-based proteomics, with the aim of identifying such markers. DIA-MS identified 5422 and 826 normalized proteins in tumor and serum samples, respectively, with only three tumor proteins and 26 serum proteins displaying significant differential expression between the STS and LTS groups. These dysregulated proteins were principally associated with the detoxification of reactive oxygen species (ROS). In particular, GB patients in the STS group had high serum levels of malate dehydrogenase 1 (MDH1) and ribonuclease inhibitor 1 (RNH1) and low tumor levels of fatty acid-binding protein 7 (FABP7), which may have enabled them to maintain low ROS levels, counteracting the effects of the first-line treatment with radiotherapy plus concomitant and adjuvant temozolomide. A blood score built on the levels of MDH1 and RNH1 expression was found to be an independent prognostic factor for survival based on the serum proteome data for a cohort of 96 IDH-wildtype GB patients. This study highlights the utility of circulating MDH1 and RNH1 biomarkers for determining the prognosis of patients with IDH-wildtype GB. Furthermore, the pathways driven by these biomarkers, and the tumor FABP7 pathway, may constitute promising therapeutic targets for blocking ROS detoxification to overcome resistance to chemoradiotherapy in potential GB STS.
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Affiliation(s)
- Anne Clavreul
- Département de Neurochirurgie, CHU d'Angers, France
- Inserm UMR 1307, CNRS UMR 6075, Université de Nantes, CRCI2NA, Université d'Angers, France
| | - Catherine Guette
- Inserm UMR 1307, CNRS UMR 6075, Université de Nantes, CRCI2NA, Université d'Angers, France
- PROT'ICO - Plateforme Oncoprotéomique, Institut de Cancérologie de l'Ouest (ICO), Angers, France
| | - Hamza Lasla
- Omics Data Science Unit, Institut de Cancérologie de l'Ouest (ICO), Nantes, France
- SIRIC ILIAD, Institut de Recherche en Santé, Université de Nantes, France
| | - Audrey Rousseau
- Inserm UMR 1307, CNRS UMR 6075, Université de Nantes, CRCI2NA, Université d'Angers, France
- Département de Pathologie, CHU d'Angers, France
| | - Odile Blanchet
- Centre de Ressources Biologiques, BB-0033-00038, CHU d'Angers, France
| | - Cécile Henry
- PROT'ICO - Plateforme Oncoprotéomique, Institut de Cancérologie de l'Ouest (ICO), Angers, France
| | - Alice Boissard
- PROT'ICO - Plateforme Oncoprotéomique, Institut de Cancérologie de l'Ouest (ICO), Angers, France
| | - Mathilde Cherel
- Département de Biologie Médicale, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Pascal Jézéquel
- Inserm UMR 1307, CNRS UMR 6075, Université de Nantes, CRCI2NA, Université d'Angers, France
- Omics Data Science Unit, Institut de Cancérologie de l'Ouest (ICO), Nantes, France
- SIRIC ILIAD, Institut de Recherche en Santé, Université de Nantes, France
| | - François Guillonneau
- Inserm UMR 1307, CNRS UMR 6075, Université de Nantes, CRCI2NA, Université d'Angers, France
- PROT'ICO - Plateforme Oncoprotéomique, Institut de Cancérologie de l'Ouest (ICO), Angers, France
| | - Philippe Menei
- Département de Neurochirurgie, CHU d'Angers, France
- Inserm UMR 1307, CNRS UMR 6075, Université de Nantes, CRCI2NA, Université d'Angers, France
| | - Jean-Michel Lemée
- Département de Neurochirurgie, CHU d'Angers, France
- Inserm UMR 1307, CNRS UMR 6075, Université de Nantes, CRCI2NA, Université d'Angers, France
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2
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Seffernick AE, Archer KJ. Penalized Bayesian forward continuation ratio model with application to high-dimensional data with discrete survival outcomes. PLoS One 2024; 19:e0300638. [PMID: 38547174 PMCID: PMC10977717 DOI: 10.1371/journal.pone.0300638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/03/2024] [Indexed: 04/02/2024] Open
Abstract
While time-to-event data are often continuous, there are several instances where discrete survival data, which are inherently ordinal, may be available or are more appropriate or useful. Several discrete survival models exist, but the forward continuation ratio model with a complementary log-log link has a survival interpretation and is closely related to the Cox proportional hazards model, despite being an ordinal model. This model has previously been implemented in the high-dimensional setting using the ordinal generalized monotone incremental forward stagewise algorithm. Here, we propose a Bayesian penalized forward continuation ratio model with a complementary log-log link and explore different priors to perform variable selection and regularization. Through simulations, we show that our Bayesian model outperformed the existing frequentist method in terms of variable selection performance, and that a 10% prior inclusion probability performed better than 1% or 50%. We also illustrate our model on a publicly available acute myeloid leukemia dataset to identify genomic features associated with discrete survival. We identified nine features that map to ten unique genes, five of which have been previously associated with leukemia in the literature. In conclusion, our proposed Bayesian model is flexible, allows simultaneous variable selection and uncertainty quantification, and performed well in simulation studies and application to real data.
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Affiliation(s)
- Anna Eames Seffernick
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
- Division of Biostatistics, College of Public Health, Ohio State University, Columbus, OH, United States of America
| | - Kellie J. Archer
- Division of Biostatistics, College of Public Health, Ohio State University, Columbus, OH, United States of America
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3
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Spoor JKH, den Braber M, Dirven CMF, Pennycuick A, Bartkova J, Bartek J, van Dis V, van den Bosch TPP, Leenstra S, Venkatesan S. Investigating chromosomal instability in long-term survivors with glioblastoma and grade 4 astrocytoma. Front Oncol 2024; 13:1218297. [PMID: 38260852 PMCID: PMC10800987 DOI: 10.3389/fonc.2023.1218297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Background Only a small group of patients with glioblastoma multiforme (GBM) survives more than 36 months, so-called long-term survivors. Recent studies have shown that chromosomal instability (CIN) plays a prognostic and predictive role among different cancer types. Here, we compared histological (chromosome missegregation) and bioinformatic metrics (CIN signatures) of CIN in tumors of GBM typical survivors (≤36 months overall survival), GBM long-term survivors and isocitrate dehydrogenase (IDH)-mutant grade 4 astrocytomas. Methods Tumor sections of all gliomas were examined for anaphases and chromosome missegregation. Further CIN signature activity analysis in the The Cancer Genome Atlas (TCGA)-GBM cohort was performed. Results Our data show that chromosome missegregation is pervasive in high grade gliomas and is not different between the 3 groups. We find only limited evidence of altered CIN levels in tumors of GBM long-term survivors relative to the other groups, since a significant depletion in CIN signature 11 relative to GBM typical survivors was the only alteration detected. In contrast, within IDH-mutant grade 4 astrocytomas we detected a significant enrichment of CIN signature 5 and 10 activities and a depletion of CIN signature 1 activity relative to tumors of GBM typical survivors. Conclusions Our data suggest that CIN is pervasive in high grade gliomas, however this is unlikely to be a major contributor to the phenomenon of long-term survivorship in GBM. Nevertheless, further evaluation of specific types of CIN (signatures) could have prognostic value in patients suffering from grade 4 gliomas.
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Affiliation(s)
- Jochem K. H. Spoor
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Paediatric Neurosurgery, Erasmus Medical Center Sophia Children’s Hospital, Rotterdam, Netherlands
| | - May den Braber
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Clemens M. F. Dirven
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Adam Pennycuick
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Jirina Bartkova
- Genome Integrity Group, Danish Cancer Institute, Danish Cancer Society, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, Danish Cancer Society, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Vera van Dis
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Sieger Leenstra
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Subramanian Venkatesan
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Oncology, University College London, London, United Kingdom
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Weller M, Felsberg J, Hentschel B, Gramatzki D, Kubon N, Wolter M, Reusche M, Roth P, Krex D, Herrlinger U, Westphal M, Tonn JC, Regli L, Maurage CA, von Deimling A, Pietsch T, Le Rhun E, Reifenberger G. Improved prognostic stratification of patients with isocitrate dehydrogenase-mutant astrocytoma. Acta Neuropathol 2024; 147:11. [PMID: 38183430 PMCID: PMC10771615 DOI: 10.1007/s00401-023-02662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 01/08/2024]
Abstract
Prognostic factors and standards of care for astrocytoma, isocitrate dehydrogenase (IDH)-mutant, CNS WHO grade 4, remain poorly defined. Here we sought to explore disease characteristics, prognostic markers, and outcome in patients with this newly defined tumor type. We determined molecular biomarkers and assembled clinical and outcome data in patients with IDH-mutant astrocytomas confirmed by central pathology review. Patients were identified in the German Glioma Network cohort study; additional cohorts of patients with CNS WHO grade 4 tumors were identified retrospectively at two sites. In total, 258 patients with IDH-mutant astrocytomas (114 CNS WHO grade 2, 73 CNS WHO grade 3, 71 CNS WHO grade 4) were studied. The median age at diagnosis was similar for all grades. Karnofsky performance status at diagnosis inversely correlated with CNS WHO grade (p < 0.001). Despite more intensive treatment upfront with higher grade, CNS WHO grade was strongly prognostic: median overall survival was not reached for grade 2 (median follow-up 10.4 years), 8.1 years (95% CI 5.4-10.8) for grade 3, and 4.7 years (95% CI 3.4-6.0) for grade 4. Among patients with CNS WHO grade 4 astrocytoma, median overall survival was 5.5 years (95% CI 4.3-6.7) without (n = 58) versus 1.8 years (95% CI 0-4.1) with (n = 12) homozygous CDKN2A deletion. Lower levels of global DNA methylation as detected by LINE-1 methylation analysis were strongly associated with CNS WHO grade 4 (p < 0.001) and poor outcome. MGMT promoter methylation status was not prognostic for overall survival. Histomolecular stratification based on CNS WHO grade, LINE-1 methylation level, and CDKN2A status revealed four subgroups of patients with significantly different outcomes. In conclusion, CNS WHO grade, global DNA methylation status, and CDKN2A homozygous deletion are prognostic in patients with IDH-mutant astrocytoma. Combination of these parameters allows for improved prediction of outcome. These data aid in designing upcoming trials using IDH inhibitors.
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Affiliation(s)
- Michael Weller
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland.
- Department of Neurology, University of Zurich, Zurich, Switzerland.
| | - Jörg Felsberg
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Bettina Hentschel
- Institute for Medical Informatics, Statistics and Epidemiology, University Leipzig, Leipzig, Germany
| | - Dorothee Gramatzki
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
| | - Nadezhda Kubon
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marietta Wolter
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Matthias Reusche
- Institute for Medical Informatics, Statistics and Epidemiology, University Leipzig, Leipzig, Germany
| | - Patrick Roth
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurology, University of Zurich, Zurich, Switzerland
| | - Dietmar Krex
- Faculty of Medicine, Department of Neurosurgery, Technische Universität Dresden, University Hospital Carl Gustav Carus, Dresden, Germany
| | | | - Manfred Westphal
- Department of Neurosurgery, University of Hamburg, Hamburg, Germany
| | - Joerg C Tonn
- Department of Neurosurgery, Ludwig-Maximilians-University Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Luca Regli
- Department of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Neurosurgery, University of Zurich, Zurich, Switzerland
| | - Claude-Alain Maurage
- Department of Pathology, Centre Biologie Pathologie, Lille University Hospital, Hopital Nord, Lille, France
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Center (DKFZ), and German Cancer Consortium (DKTK), Partner Site Heidelberg, Heidelberg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical Center, DGNN Brain Tumor Reference Center, Bonn, Germany
| | - Emilie Le Rhun
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091, Zurich, Switzerland
- Department of Neurology, University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Neurosurgery, University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, Lille University Hospital, Lille, France
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, and University Hospital Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Düsseldorf, Germany
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5
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van der Meulen M, Ramos RC, Voisin MR, Patil V, Wei Q, Singh O, Climans SA, Kalidindi N, Or R, Aldape K, Diamandis P, Munoz DG, Zadeh G, Mason WP. Differences in methylation profiles between long-term survivors and short-term survivors of IDH-wild-type glioblastoma. Neurooncol Adv 2024; 6:vdae001. [PMID: 38312227 PMCID: PMC10838123 DOI: 10.1093/noajnl/vdae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024] Open
Abstract
Background Patients with glioblastoma (GBM) have a median overall survival (OS) of approximately 16 months. However, approximately 5% of patients survive >5 years. This study examines the differences in methylation profiles between long-term survivors (>5 years, LTS) and short-term survivors (<1 year, STS) with isocitrate dehydrogenase (IDH)-wild-type GBMs. Methods In a multicenter retrospective analysis, we identified 25 LTS with a histologically confirmed GBM. They were age- and sex-matched to an STS. The methylation profiles of all 50 samples were analyzed with EPIC 850k, classified according to the DKFZ methylation classifier, and the methylation profiles of LTS versus STS were compared. Results After methylation profiling, 16/25 LTS and 23/25 STS were confirmed to be IDH-wild-type GBMs, all with +7/-10 signature. LTS had significantly increased O6-methylguanine methyltransferase (MGMT) promoter methylation and higher prevalence of FGFR3-TACC3 fusion (P = .03). STS were more likely to exhibit CDKN2A/B loss (P = .01) and higher frequency of NF1 (P = .02) mutation. There were no significant CpGs identified between LTS versus STS at an adjusted P-value of .05. Unadjusted analyses identified key pathways involved in both LTS and STS. The most common pathways were the Hippo signaling pathway and the Wnt pathway in LTS, and GPCR ligand binding and cell-cell signaling in STS. Conclusions A small group of patients with IDH-wild-type GBM survive more than 5 years. While there are few differences in the global methylation profiles of LTS compared to STS, our study highlights potential pathways involved in GBMs with a good or poor prognosis.
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Affiliation(s)
- Matthijs van der Meulen
- Department of Medicine, Divisions of Neurology and Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Neurology, Medisch Spectrum Twente, Enschede, The Netherlands
| | - Ronald C Ramos
- Department of Medicine, Divisions of Neurology and Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Mathew R Voisin
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Vikas Patil
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Qingxia Wei
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olivia Singh
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Seth A Climans
- Department of Medicine, Divisions of Neurology and Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Oncology, London Regional Cancer Program, London, Ontario, Canada
| | - Navya Kalidindi
- Division of Neurology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Rosemarylin Or
- Department of Neurology, The Medical City, Pasig, Philippines
| | - Ken Aldape
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Health, Bethesda, Maryland, USA
| | - Phedias Diamandis
- Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - David G Munoz
- Department of Laboratory Medicine, St. Michaels Hospital, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Warren P Mason
- Department of Medicine, Divisions of Neurology and Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
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6
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Hertler C, Felsberg J, Gramatzki D, Le Rhun E, Clarke J, Soffietti R, Wick W, Chinot O, Ducray F, Roth P, McDonald K, Hau P, Hottinger AF, Reijneveld J, Schnell O, Marosi C, Glantz M, Darlix A, Lombardi G, Krex D, Glas M, Reardon DA, van den Bent M, Lefranc F, Herrlinger U, Razis E, Carpentier AF, Phillips S, Rudà R, Wick A, Tabouret E, Meyronet D, Maurage CA, Rushing E, Rapkins R, Bumes E, Hegi M, Weyerbrock A, Aregawi D, Gonzalez-Gomez C, Pellerino A, Klein M, Preusser M, Bendszus M, Golfinopoulos V, von Deimling A, Gorlia T, Wen PY, Reifenberger G, Weller M. Long-term survival with IDH wildtype glioblastoma: first results from the ETERNITY Brain Tumor Funders' Collaborative Consortium (EORTC 1419). Eur J Cancer 2023; 189:112913. [PMID: 37277265 DOI: 10.1016/j.ejca.2023.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 06/07/2023]
Abstract
BACKGROUND Median survival with glioblastoma remains in the range of 12 months on population levels. Only few patients survive for more than 5 years. Patient and disease features associated with long-term survival remain poorly defined. METHODS European Organization for Research and Treatment of Cancer (EORTC) 1419 (ETERNITY) is a registry study supported by the Brain Tumor Funders Collaborative in the US and the EORTC Brain Tumor Group. Patients with glioblastoma surviving at least 5 years from diagnosis were identified at 24 sites in Europe, US, and Australia. In patients with isocitrate dehydrogenase (IDH) wildtype tumours, prognostic factors were analysed using the Kaplan-Meier method and the Cox proportional hazards model. A population-based reference cohort was obtained from the Cantonal cancer registry Zurich. RESULTS At the database lock of July 2020, 280 patients with histologically centrally confirmed glioblastoma (189 IDH wildtype, 80 IDH mutant, 11 incompletely characterised) had been registered. In the IDH wildtype population, median age was 56 years (range 24-78 years), 96 patients (50.8%) were female, 139 patients (74.3%) had tumours with O6-methylguanine DNA methyltransferase (MGMT) promoter methylation. Median overall survival was 9.9 years (95% confidence interval [95% CI] 7.9-11.9). Patients without recurrence experienced longer median survival (not reached) than patients with one or more recurrences (8.92 years) (p < 0.001) and had a high rate (48.8%) of MGMT promoter-unmethylated tumours. CONCLUSIONS Freedom from progression is a powerful predictor of overall survival in long-term survivors with glioblastoma. Patients without relapse often have MGMT promoter-unmethylated glioblastoma and may represent a distinct subtype of glioblastoma.
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Affiliation(s)
- Caroline Hertler
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland; Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Jörg Felsberg
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Dorothee Gramatzki
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland; Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Emilie Le Rhun
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland; Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland; Service de neurochirurgie, CHU Lille, F-59000 Lille, France; Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Jennifer Clarke
- UCSF Department of Neurological Surgery, Division of Neuro-Oncology, 400 Parnassus Avenue, A-808 San Francisco, CA, USA
| | - Riccardo Soffietti
- Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science Hospital, Turin, Italy
| | - Wolfgang Wick
- Neurology Clinic, University of Heidelberg, Heidelberg, Germany; CCU Neurooncology, DKFZ, Heidelberg, Germany
| | - Olivier Chinot
- Aix-Marseille Univ, APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service de Neuro-Oncologie, Marseille, France
| | - François Ducray
- Departments of Neuro-Oncology, Hospices Civils de Lyon, Centre de recherche en Cancérologie de Lyon, Lyon, France; INSERM U1052, CNRS UMR 5286, Université Lyon 1, Lyon, France
| | - Patrick Roth
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland; Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Kerrie McDonald
- Cure Brain Cancer Neuro-Oncology group, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Peter Hau
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, Regensburg, Germany
| | - Andreas F Hottinger
- Lundin Family Brain Tumor Center, Departments of Oncology & Clinical Neurosciences, CHUV Lausanne University Hospital, Lausanne, Switzerland
| | - Jaap Reijneveld
- Amsterdam UMC location Vrije Universiteit Amsterdam, Neurology, Brain Tumor Center Amsterdam, Amsterdam, the Netherlands; Department of Neurology, Stichting Epilepsie Instellingen Nederland, Heemstede, the Netherlands
| | - Oliver Schnell
- Department of Neurosurgery, Medical Center- University of Freiburg, Freiburg, Germany
| | - Christine Marosi
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Michael Glantz
- Departments of Neurosurgery and Oncology, Penn State College of Medicine - Hershey Medical Center, Hershey, PA, USA
| | - Amélie Darlix
- Department of Medical Oncology, Institut régional du Cancer de Montpellier, University of Montpellier, Montpellier, France; Institut de Génomique Fonctionnelle, INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Giuseppe Lombardi
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Via Gattamelata 64, 35128 Padua, Italy
| | - Dietmar Krex
- Department of Neurosurgery, University Hospital Carl Gustav Carus, TU, Dresden, Germany; German Cancer Consortium (DKTK), Partner Site Dresden, Germany
| | - Martin Glas
- Division of Clinical Neurooncology, Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Medicine Essen, University Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site University Medicine Essen, Essen, Germany
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, USA; Harvard Medical School, Boston, USA
| | - Martin van den Bent
- Brain Tumor Center at ErasmusMC Cancer Institute, Erasmus University Hospital Rotterdam, Rotterdam, the Netherlands
| | - Florence Lefranc
- Department of Neurosurgery, Hôpital Universitaire de Bruxelles HUB, Brussels, Belgium
| | - Ulrich Herrlinger
- Division of Clinical Neurooncology, Department of Neurology and Center of Integrated Oncology, University of Bonn, Bonn, Germany
| | | | - Antoine F Carpentier
- Department of Neurology, Hôpital Saint-Louis, Université Paris Cité, APHP, Paris, France
| | - Samuel Phillips
- UCSF Department of Neurological Surgery, Division of Neuro-Oncology, 400 Parnassus Avenue, A-808 San Francisco, CA, USA
| | - Roberta Rudà
- Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science Hospital, Turin, Italy
| | - Antje Wick
- Neurology Clinic, University of Heidelberg, Heidelberg, Germany
| | - Emeline Tabouret
- Aix-Marseille Univ, APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service de Neuro-Oncologie, Marseille, France
| | - David Meyronet
- INSERM U1052, CNRS UMR 5286, Université Lyon 1, Lyon, France; Neuropathology, Hospices Civils de Lyon, Centre de recherche en Cancérologie de Lyon, Lyon, France
| | | | - Elisabeth Rushing
- Department of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Robert Rapkins
- Cure Brain Cancer Neuro-Oncology group, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Elisabeth Bumes
- Department of Neurology and Wilhelm Sander-NeuroOncology Unit, University Hospital Regensburg, Regensburg, Germany
| | - Monika Hegi
- Neuroscience Research Center and Service of Neurosurgery & Lundin Family Brain Tumor Center, Lausanne University Hospital and University of Lausanne, 1066 Epalinges, Switzerland
| | - Astrid Weyerbrock
- Department of Neurology, Stichting Epilepsie Instellingen Nederland, Heemstede, the Netherlands
| | - Dawit Aregawi
- Departments of Neurosurgery and Oncology, Penn State College of Medicine - Hershey Medical Center, Hershey, PA, USA
| | - Christian Gonzalez-Gomez
- UCSF Department of Neurological Surgery, Division of Neuro-Oncology, 400 Parnassus Avenue, A-808 San Francisco, CA, USA
| | - Alessia Pellerino
- Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science Hospital, Turin, Italy
| | - Martin Klein
- Amsterdam UMC location Vrije Universiteit Amsterdam, Medical Psychology, Amsterdam, the Netherlands
| | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Martin Bendszus
- Department of Neuroradiology, University Hospital of Heidelberg, Heidelberg, Germany
| | | | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany; CCU Neuropathology, German Cancer Center (DKFZ), Heidelberg, Germany
| | | | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, USA; Harvard Medical School, Boston, USA
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University and University Hospital Düsseldorf, Düsseldorf, Germany; German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland; Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland.
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7
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Qi D, Geng Y, Cardenas J, Gu J, Yi SS, Huang JH, Fonkem E, Wu E. Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers. NPJ Genom Med 2023; 8:2. [PMID: 36697401 PMCID: PMC9877004 DOI: 10.1038/s41525-022-00348-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023] Open
Abstract
Peripheral blood is gaining prominence as a noninvasive alternative to tissue biopsy to develop biomarkers for glioblastoma (GBM); however, widely utilized blood-based biomarkers in clinical settings have not yet been identified due to the lack of a robust detection approach. Here, we describe the application of globin reduction in RNA sequencing of whole blood (i.e., WBGR) and perform transcriptomic analysis to identify GBM-associated transcriptomic changes. By using WBGR, we improved the detection sensitivity of informatic reads and identified differential gene expression in GBM blood. By analyzing tumor tissues, we identified transcriptomic traits of GBM blood. Further functional enrichment analyses retained the most changed genes in GBM. Subsequent validation elicited a 10-gene panel covering mRNA, long noncoding RNA, and microRNA (i.e., GBM-Dx panel) that has translational potential to aid in the early detection or clinical management of GBM. Here, we report an integrated approach, WBGR, with comprehensive analytic capacity for blood-based marker identification.
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Affiliation(s)
- Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
| | - Yiqun Geng
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
- Laboratory of Molecular Pathology, Shantou University Medical College, 515041, Shantou, China
| | - Jacob Cardenas
- Baylor Scott & White Research Institute, Dallas, TX, 75204, USA
| | - Jinghua Gu
- Baylor Scott & White Research Institute, Dallas, TX, 75204, USA
| | - S Stephen Yi
- Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Oncology, LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jason H Huang
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
- Texas A & M University School of Medicine, Temple, TX, 76508, USA.
| | - Ekokobe Fonkem
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
- Texas A & M University School of Medicine, Temple, TX, 76508, USA.
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
- Department of Oncology, LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA.
- Texas A & M University School of Medicine, Temple, TX, 76508, USA.
- Texas A & M University School of Pharmacy, College Station, TX, 77843, USA.
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8
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González Bonet LG, Piqueras-Sánchez C, Roselló-Sastre E, Broseta-Torres R, de las Peñas R. Glioblastomas de larga supervivencia: un análisis sistemático de la literatura a propósito de un caso. Neurocirugia (Astur) 2022. [DOI: 10.1016/j.neucir.2021.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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González Bonet LG, Piqueras-Sánchez C, Roselló-Sastre E, Broseta-Torres R, de Las Peñas R. Long-term survival of glioblastoma: A systematic analysis of literature about a case. NEUROCIRUGIA (ENGLISH EDITION) 2022; 33:227-236. [PMID: 34802981 DOI: 10.1016/j.neucie.2021.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/05/2021] [Indexed: 06/13/2023]
Abstract
INTRODUCTION In spite of the changes for the treatment of glioblastoma since 2005, we have not seen differences between long-survival patients of more than 10 years showing a value minor than 1%. MATERIAL AND METHOD We realize a systematic analysis and identify important factors for long survivor patients. We also show an own case with more of 20 years of survival. We make a new pathological study of the old paraffin block of this patient. RESULTS The most important variable associated with long-survival between all multivariant studies is the age. When we try to find genetic and molecular alterations in glioblastoma associated with prolongated survival, the MGMT promoter methylation play the most important role. We find a correct diagnosis in the current analysis of our patient's sample with very long survival. CONCLUSIONS Multiple variables are found that affect long survival of glioblastoma series but analyzed studies are very heterogeneous and it is very difficult comparation between them. Most articles we review are obtained from databases of different countries with hundreds of patients. It would be very interesting to promote the use of a single database in Spain that allows us to study these long-term glioblastoma survivors.
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Affiliation(s)
- Luis Germán González Bonet
- Servicio de Neurocirugía, Hospital General Universitario de Castellón, Castellón, Spain; Facultad de Ciencias de la Salud, Universidad Jaume I de Castellón, Castellón, Spain.
| | | | - Esther Roselló-Sastre
- Facultad de Ciencias de la Salud, Universidad Jaume I de Castellón, Castellón, Spain; Servicio de Anatomía Patológica, Hospital General Universitario de Castellón, Castellón, Spain
| | | | - Ramón de Las Peñas
- Servicio de Oncología Médica, Hospital Provincial de Castellón, Castellón, Spain
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10
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Recurrent glioblastoma: which treatment? A real-world study from the Neuro-oncology Unit “Regina Elena” National Cancer Institute. Neurol Sci 2022; 43:5533-5541. [DOI: 10.1007/s10072-022-06172-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/22/2022] [Indexed: 10/18/2022]
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11
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Shi D, Zhong W, Liu D, Sun X, Hao S, Yang Y, Ao L, Zhou J, Xia Y, Zhou Y, Yu H, Xia H. Computational identification of immune-related lncRNA signature for predicting the prognosis and immune landscape of human glioblastoma multiforme. Front Immunol 2022; 13:932938. [PMID: 36032137 PMCID: PMC9412749 DOI: 10.3389/fimmu.2022.932938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Emerging evidence shows immune-related long noncoding RNAs (ir-lncRNAs) perform critical roles in tumor progression and prognosis assessment. However, the identification of ir-lncRNAs and their clinical significance in human glioblastoma multiforme (GBM) remain largely unexplored. Here, a designed computational frame based on immune score was used to identify differentially expressed ir-lncRNAs (DEir-lncRNAs) from The Cancer Genome Atlas (TCGA) GBM program. The immune-related lncRNA signature (IRLncSig) composed of prognosis-related DEir-lncRNAs selected by Cox regression analysis and its clinical predictive values were verified, which was further validated by another dataset from the Gene Expression Omnibus database (GEO). Subsequently, the association between IRLncSig and immune cell infiltration, immune checkpoint inhibitor (ICI) biomarkers, O6-methylguanine-DNA methyltransferase (MGMT) gene expression, and biological function were also analyzed. After calculation, five prognosis-related ir-lncRNAs were included in the establishment of IRLncSig. The risk assessment based on IRLncSig indicated that the high-IRLncSig-score group was significantly associated with poor prognosis (p < 0.001), significant aggregation of macrophages (p < 0.05), higher ICI biomarker expression, and MGMT gene expression (p < 0.05). Signature-related lncRNAs may be involved in immune activities in the tumorigenesis and progression of GBM. In summary, the novel IRLncSig shows a promising clinical value in predicting the prognosis and immune landscape of GBM.
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Affiliation(s)
- Dongjie Shi
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wenjie Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dan Liu
- Department of Pharmacy, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Xiaochuan Sun
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shilei Hao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Yaying Yang
- Department of Pathology, Molecular Medicine and Tumor Center, Chongqing Medical University, Chongqing, China
| | - Lei Ao
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Junjie Zhou
- Department of Pathology, Molecular Medicine and Tumor Center, Chongqing Medical University, Chongqing, China
| | - Yongzhi Xia
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yudong Zhou
- Department of Neurosurgery, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Hua Yu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haijian Xia
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Haijian Xia,
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12
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Vo VTA, Kim S, Hua TNM, Oh J, Jeong Y. Iron commensalism of mesenchymal glioblastoma promotes ferroptosis susceptibility upon dopamine treatment. Commun Biol 2022; 5:593. [PMID: 35710828 PMCID: PMC9203457 DOI: 10.1038/s42003-022-03538-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
The heterogeneity of glioblastoma multiforme (GBM) leads to poor patient prognosis. Here, we aim to investigate the mechanism through which GBM heterogeneity is coordinated to promote tumor progression. We find that proneural (PN)-GBM stem cells (GSCs) secreted dopamine (DA) and transferrin (TF), inducing the proliferation of mesenchymal (MES)-GSCs and enhancing their susceptibility toward ferroptosis. PN-GSC-derived TF stimulates MES-GSC proliferation in an iron-dependent manner. DA acts in an autocrine on PN-GSC growth in a DA receptor D1-dependent manner, while in a paracrine it induces TF receptor 1 expression in MES-GSCs to assist iron uptake and thus enhance ferroptotic vulnerability. Analysis of public datasets reveals worse prognosis of patients with heterogeneous GBM with high iron uptake than those with other GBM subtypes. Collectively, the findings here provide evidence of commensalism symbiosis that causes MES-GSCs to become iron-addicted, which in turn provides a rationale for targeting ferroptosis to treat resistant MES GBM. Glioblastoma stem-cell derived mesenchymal cells become reliant on iron but vulnerable to ferroptosis and within patients of heterogeneous glioblastoma multiforme prognosis for those with high iron uptake is poorer than other subtypes.
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Affiliation(s)
- Vu T A Vo
- Department of Biochemistry, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea.,Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea.,Mitohormesis Research Center, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea
| | - Sohyun Kim
- Department of Physiology, Yonsei University College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Tuyen N M Hua
- Department of Biochemistry, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea.,Mitohormesis Research Center, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea
| | - Jiwoong Oh
- Department of Neurosurgery, Severance Hospital, Yonsei University, Seoul, Republic of Korea
| | - Yangsik Jeong
- Department of Biochemistry, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea. .,Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea. .,Mitohormesis Research Center, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea. .,Institute of Lifestyle Medicine, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea. .,Institute of Mitochondrial Medicine, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, Republic of Korea.
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13
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Translational landscape of glioblastoma immunotherapy for physicians: guiding clinical practice with basic scientific evidence. J Hematol Oncol 2022; 15:80. [PMID: 35690784 PMCID: PMC9188021 DOI: 10.1186/s13045-022-01298-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/10/2022] [Indexed: 02/06/2023] Open
Abstract
Despite recent advances in cancer therapeutics, glioblastoma (GBM) remains one of the most difficult cancers to treat in both the primary and recurrent settings. GBM presents a unique therapeutic challenge given the immune-privileged environment of the brain and the aggressive nature of the disease. Furthermore, it can change phenotypes throughout the course of disease—switching between mesenchymal, neural, and classic gene signatures, each with specific markers and mechanisms of resistance. Recent advancements in the field of immunotherapy—which utilizes strategies to reenergize or alter the immune system to target cancer—have shown striking results in patients with many types of malignancy. Immune checkpoint inhibitors, adoptive cellular therapy, cellular and peptide vaccines, and other technologies provide clinicians with a vast array of tools to design highly individualized treatment and potential for combination strategies. There are currently over 80 active clinical trials evaluating immunotherapies for GBM, often in combination with standard secondary treatment options including re-resection and anti-angiogenic agents, such as bevacizumab. This review will provide a clinically focused overview of the immune environment present in GBM, which is frequently immunosuppressive and characterized by M2 macrophages, T cell exhaustion, enhanced transforming growth factor-β signaling, and others. We will also outline existing immunotherapeutic strategies, with a special focus on immune checkpoint inhibitors, chimeric antigen receptor therapy, and dendritic cell vaccines. Finally, we will summarize key discoveries in the field and discuss currently active clinical trials, including combination strategies, burgeoning technology like nucleic acid and nanoparticle therapy, and novel anticancer vaccines. This review aims to provide the most updated summary of the field of immunotherapy for GBM and offer both historical perspective and future directions to help inform clinical practice.
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14
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Integrated Multi-Omics Maps of Lower-Grade Gliomas. Cancers (Basel) 2022; 14:cancers14112797. [PMID: 35681780 PMCID: PMC9179546 DOI: 10.3390/cancers14112797] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/18/2022] [Accepted: 05/31/2022] [Indexed: 02/01/2023] Open
Abstract
Multi-omics high-throughput technologies produce data sets which are not restricted to only one but consist of multiple omics modalities, often as patient-matched tumour specimens. The integrative analysis of these omics modalities is essential to obtain a holistic view on the otherwise fragmented information hidden in this data. We present an intuitive method enabling the combined analysis of multi-omics data based on self-organizing maps machine learning. It "portrays" the expression, methylation and copy number variations (CNV) landscapes of each tumour using the same gene-centred coordinate system. It enables the visual evaluation and direct comparison of the different omics layers on a personalized basis. We applied this combined molecular portrayal to lower grade gliomas, a heterogeneous brain tumour entity. It classifies into a series of molecular subtypes defined by genetic key lesions, which associate with large-scale effects on DNA methylation and gene expression, and in final consequence, drive with cell fate decisions towards oligodendroglioma-, astrocytoma- and glioblastoma-like cancer cell lineages with different prognoses. Consensus modes of concerted changes of expression, methylation and CNV are governed by the degree of co-regulation within and between the omics layers. The method is not restricted to the triple-omics data used here. The similarity landscapes reflect partly independent effects of genetic lesions and DNA methylation with consequences for cancer hallmark characteristics such as proliferation, inflammation and blocked differentiation in a subtype specific fashion. It can be extended to integrate other omics features such as genetic mutation, protein expression data as well as extracting prognostic markers.
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15
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Dang TT, Lerner M, Saunders D, Smith N, Gulej R, Zalles M, Towner RA, Morales JC. XRN2 Is Required for Cell Motility and Invasion in Glioblastomas. Cells 2022; 11:1481. [PMID: 35563787 PMCID: PMC9100175 DOI: 10.3390/cells11091481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
One of the major obstacles in treating brain cancers, particularly glioblastoma multiforme, is the occurrence of secondary tumor lesions that arise in areas of the brain and are inoperable while obtaining resistance to current therapeutic agents. Thus, gaining a better understanding of the cellular factors that regulate glioblastoma multiforme cellular movement is imperative. In our study, we demonstrate that the 5'-3' exoribonuclease XRN2 is important to the invasive nature of glioblastoma. A loss of XRN2 decreases cellular speed, displacement, and movement through a matrix of established glioblastoma multiforme cell lines. Additionally, a loss of XRN2 abolishes tumor formation in orthotopic mouse xenograft implanted with G55 glioblastoma multiforme cells. One reason for these observations is that loss of XRN2 disrupts the expression profile of several cellular factors that are important for tumor invasion in glioblastoma multiforme cells. Importantly, XRN2 mRNA and protein levels are elevated in glioblastoma multiforme patient samples. Elevation in XRN2 mRNA also correlates with poor overall patient survival. These data demonstrate that XRN2 is an important cellular factor regulating one of the major obstacles in treating glioblastomas and is a potential molecular target that can greatly enhance patient survival.
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Affiliation(s)
- Tuyen T. Dang
- Department of Neurosurgery, Sttephenson Cancer Center University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA;
| | - Megan Lerner
- Department of Surgery, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA;
| | - Debra Saunders
- Department of Pathology, University of Oklahoma Health Science Center, Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (D.S.); (N.S.); (R.G.); (M.Z.); (R.A.T.)
| | - Nataliya Smith
- Department of Pathology, University of Oklahoma Health Science Center, Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (D.S.); (N.S.); (R.G.); (M.Z.); (R.A.T.)
| | - Rafal Gulej
- Department of Pathology, University of Oklahoma Health Science Center, Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (D.S.); (N.S.); (R.G.); (M.Z.); (R.A.T.)
| | - Michelle Zalles
- Department of Pathology, University of Oklahoma Health Science Center, Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (D.S.); (N.S.); (R.G.); (M.Z.); (R.A.T.)
| | - Rheal A. Towner
- Department of Pathology, University of Oklahoma Health Science Center, Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (D.S.); (N.S.); (R.G.); (M.Z.); (R.A.T.)
| | - Julio C. Morales
- Department of Neurosurgery, Sttephenson Cancer Center University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA;
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16
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LPPR5 Expression in Glioma Affects Growth, Vascular Architecture, and Sunitinib Resistance. Int J Mol Sci 2022; 23:ijms23063108. [PMID: 35328529 PMCID: PMC8952597 DOI: 10.3390/ijms23063108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 12/21/2022] Open
Abstract
Despite intensive research, glioblastoma remains almost invariably fatal. Various promising drugs targeting specific aspects of glioma biology, in addition to or as an alternative to antiproliferative chemotherapy, were not successful in larger clinical trials. Further insights into the biology of glioma and the mechanisms behind the evasive-adaptive response to targeted therapies is needed to help identify new therapeutic targets, prognostics, or predictive biomarkers. As a modulator of the canonically oncogenic Rho-GTPase pathway, Lipid phosphate phosphatase-related protein type 5 (LPPR5) is pivotal in influencing growth, angiogenesis, and therapeutic resistance. We used a GL261 murine orthotopic allograft glioma model to quantify the tumor growth and to obtain tissue for histological and molecular analysis. Epicortical intravital epi-illumination fluorescence video microscopy of the tumor cell spheroids was used to characterize the neovascular architecture and hemodynamics. GL261-glioma growth was delayed and decelerated after LPPR5 overexpression (LPPR5OE). We observed increased tumor cell apoptosis and decreased expression and secretion of vascular endothelial growth factor A in LPPR5OE glioma. Hence, an altered micro-angioarchitecture consisting of dysfunctional small blood vessels was discovered in the LPPR5OE tumors. Sunitinib therapy eliminated these vessels but had no effect on tumor growth or apoptosis. In general, LPPR5 overexpression generated a more benign, proapoptotic glioma phenotype with delayed growth and a dysfunctional vascular architecture.
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17
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Wang G, Du W, Che L, Gao X, Zhao R, Duan J, Gu Z, Ma Q. High Expression of PLAGL2 is Associated With Poor Prognosis in High-Grade Glioma. Front Genet 2022; 12:787746. [PMID: 35222518 PMCID: PMC8863765 DOI: 10.3389/fgene.2021.787746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022] Open
Abstract
Pleomorphic adenoma gene like-2 (PLAGL2) has been implicated in the development and progression of diverse malignancies, including glioblastoma. An increasing number of studies have reported that dysregulated expression of PLAGL2 is a common phenomenon in different malignancies. However, the mechanism and biological functions of PLAGL2 in patients with high-grade glioma (HGG) remain unclear. In addition, the expression and clinical significance of PLAGL2 in HGG have not yet been reported. Herein, we investigated the expression patterns and prognostic values of PLAGL2 in patients with HGG by using various databases, including Tumor Immune Estimation Resource 2.0 (TIMER2.0), GENT2, ONCOMINE, GEPIA, Human Protein Atlas, and Gene Expression Omnibus datasets. In the present study, we analyzed the relationship between PLAGL2 mRNA expression and clinical parameters in 184 HGG cases and found that PLAGL2 presented positively high expression and was relevant to poor prognosis. Immunohistochemistry analysis confirmed the overexpression of PLAGL2 protein, which is mainly expressed in the nucleus of glioma. Additionally, a high level of expression of the PLAGL2 gene was associated with lower survival in progression-free survival and overall survival in GBM patients. The correlation analysis between PLAGL2 and immune infiltration related to the abundance of B cells, CD8+ T cells, CD4+ T cells, macrophages, DCs, and neutrophils was also performed using TIMER2.0. GSEA results showed that high PLAGL2 expression was associated with cell migration, proliferation, actin cytoskeletal, and angiogenesis. To sum up, our findings indicated that PLAGL2 could serve as an independent prognostic biomarker and might be a potential therapeutic target for HGG, which should be further investigated.
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Affiliation(s)
- Gang Wang
- Department of Rehabilitation, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Wei Du
- Department of Neurosurgery, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Lingyi Che
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xianzheng Gao
- Department of Pathology, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ruihua Zhao
- Department of Medical Oncology, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Juan Duan
- Department of Cardiology, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Zhuoyu Gu
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Qian Ma, ; Zhuoyu Gu,
| | - Qian Ma
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
- *Correspondence: Qian Ma, ; Zhuoyu Gu,
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18
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Wang S, Xiao F, Sun W, Yang C, Ma C, Huang Y, Xu D, Li L, Chen J, Li H, Xu H. Radiomics Analysis Based on Magnetic Resonance Imaging for Preoperative Overall Survival Prediction in Isocitrate Dehydrogenase Wild-Type Glioblastoma. Front Neurosci 2022; 15:791776. [PMID: 35153659 PMCID: PMC8833841 DOI: 10.3389/fnins.2021.791776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/15/2021] [Indexed: 01/24/2023] Open
Abstract
PurposeThis study aimed to develop a radiomics signature for the preoperative prognosis prediction of isocitrate dehydrogenase (IDH)-wild-type glioblastoma (GBM) patients and to provide personalized assistance in the clinical decision-making for different patients.Materials and MethodsA total of 142 IDH-wild-type GBM patients classified using the new classification criteria of WHO 2021 from two centers were included in the study and randomly divided into a training set and a test set. Firstly, their clinical characteristics were screened using univariate Cox regression. Then, the radiomics features were extracted from the tumor and peritumoral edema areas on their contrast-enhanced T1-weighted image (CE-T1WI), T2-weighted image (T2WI), and T2-weighted fluid-attenuated inversion recovery (T2-FLAIR) magnetic resonance imaging (MRI) images. Subsequently, inter- and intra-class correlation coefficient (ICC) analysis, Spearman’s correlation analysis, univariate Cox, and the least absolute shrinkage and selection operator (LASSO) Cox regression were used step by step for feature selection and the construction of a radiomics signature. The combined model was established by integrating the selected clinical factors. Kaplan–Meier analysis was performed for the validation of the discrimination ability of the model, and the C-index was used to evaluate consistency in the prediction. Finally, a Radiomics + Clinical nomogram was generated for personalized prognosis analysis and then validated using the calibration curve.ResultsAnalysis of the clinical characteristics resulted in the screening of four risk factors. The combination of ICC, Spearman’s correlation, and univariate and LASSO Cox resulted in the selection of eight radiomics features, which made up the radiomics signature. Both the radiomics and combined models can significantly stratify high- and low-risk patients (p < 0.001 and p < 0.05 for the training and test sets, respectively) and obtained good prediction consistency (C-index = 0.74–0.86). The calibration plots exhibited good agreement in both 1- and 2-year survival between the prediction of the model and the actual observation.ConclusionRadiomics is an independent preoperative non-invasive prognostic tool for patients who were newly classified as having IDH-wild-type GBM. The constructed nomogram, which combined radiomics features with clinical factors, can predict the overall survival (OS) of IDH-wild-type GBM patients and could be a new supplement to treatment guidelines.
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Affiliation(s)
- Shouchao Wang
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Feng Xiao
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wenbo Sun
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chao Yang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chao Ma
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yong Huang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Dan Xu
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lanqing Li
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jun Chen
- Precision Health Institute, GE Healthcare, Shanghai, China
| | - Huan Li
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Huan Li,
| | - Haibo Xu
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Haibo Xu,
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19
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Yearley AG, Iorgulescu JB, Chiocca EA, Peruzzi PP, Smith TR, Reardon DA, Mooney MA. The current state of glioma data registries. Neurooncol Adv 2022; 4:vdac099. [DOI: 10.1093/noajnl/vdac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The landscape of glioma research has evolved in the past 20 years to include numerous large, multi-institutional, database efforts compiling either clinical data on glioma patients, molecular data on glioma specimens, or a combination of both. While these strategies can provide a wealth of information for glioma research, obtaining information regarding data availability and access specifications can be challenging.
Methods
We reviewed the literature for ongoing clinical, molecular, and combined database efforts related to glioma research to provide researchers with a curated overview of the current state of glioma database resources.
Results
We identified and reviewed a total of 20 databases with data collection spanning from 1975 to 2022. Surveyed databases included both low- and high-grade gliomas, and data elements included over 100 clinical variables and 12 molecular data types. Select database strengths included large sample sizes and a wide variety of variables available, while limitations of some databases included complex data access requirements and a lack of glioma-specific variables.
Conclusions
This review highlights current databases and registries and their potential utility in clinical and genomic glioma research. While many high-quality resources exist, the fluid nature of glioma taxonomy makes it difficult to isolate a large cohort of patients with a pathologically confirmed diagnosis. Large, well-defined, and publicly available glioma datasets have the potential to expand the reach of glioma research and drive the field forward.
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Affiliation(s)
- Alexander G Yearley
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
| | - Julian Bryan Iorgulescu
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
- Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, Massachusetts , USA
| | - Ennio Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
| | - Pier Paolo Peruzzi
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
| | - Timothy R Smith
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute , Boston, Massachusetts , USA
| | - Michael A Mooney
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School , Boston, Massachusetts , USA
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20
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Lopes-Ramos CM, Belova T, Brunner TH, Ben Guebila M, Osorio D, Quackenbush J, Kuijjer ML. Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme. Cancer Res 2021; 81:5401-5412. [PMID: 34493595 PMCID: PMC8563450 DOI: 10.1158/0008-5472.can-21-0730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/20/2021] [Accepted: 09/02/2021] [Indexed: 01/07/2023]
Abstract
Glioblastoma is an aggressive cancer of the brain and spine. While analysis of glioblastoma 'omics data has somewhat improved our understanding of the disease, it has not led to direct improvement in patient survival. Cancer survival is often characterized by differences in gene expression, but the mechanisms that drive these differences are generally unknown. We therefore set out to model the regulatory mechanisms associated with glioblastoma survival. We inferred individual patient gene regulatory networks using data from two different expression platforms from The Cancer Genome Atlas. We performed comparative network analysis between patients with long- and short-term survival. Seven pathways were identified as associated with survival, all of them involved in immune signaling; differential regulation of PD1 signaling was validated to correspond with outcome in an independent dataset from the German Glioma Network. In this pathway, transcriptional repression of genes for which treatment options are available was lost in short-term survivors; this was independent of mutational burden and only weakly associated with T-cell infiltration. Collectively, these results provide a new way to stratify patients with glioblastoma that uses network features as biomarkers to predict survival. They also identify new potential therapeutic interventions, underscoring the value of analyzing gene regulatory networks in individual patients with cancer. SIGNIFICANCE: Genome-wide network modeling of individual glioblastomas identifies dysregulation of PD1 signaling in patients with poor prognosis, indicating this approach can be used to understand how gene regulation influences cancer progression.
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Affiliation(s)
- Camila M. Lopes-Ramos
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Tatiana Belova
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | | | - Marouen Ben Guebila
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Daniel Osorio
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Channing Division of Network Medicine, Harvard Medical School, Boston, Massachusetts
| | - Marieke L. Kuijjer
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.,Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.,Corresponding Author: Marieke L. Kuijjer, Centre for Molecular Medicine Norway, University of Oslo, Guastadalléen 21, Oslo 0318, Norway. Phone: 47-22840528; E-mail:
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21
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Zhang X, Katsakhyan L, LiVolsi VA, Roth JJ, Rassekh CH, Bagley SJ, Nasrallah MP. TP53 Mutation and Extraneural Metastasis of Glioblastoma: Insights From an Institutional Experience and Comprehensive Literature Review. Am J Surg Pathol 2021; 45:1516-1526. [PMID: 34366423 DOI: 10.1097/pas.0000000000001762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Extraneural metastases of glioblastoma (GBM), although rare, are becoming an increasingly recognized occurrence. Currently, the biological mechanism underlying this rare occurrence is not understood. To explore the potential genomic drivers of extraneural metastasis in GBM, we present the molecular features of 4 extraneural metastatic GBMs, along with a comprehensive review and analysis of previously reported cases that had available molecular characterization. In addition to our 4 cases, 42 patients from 35 publications are reviewed. To compare the molecular profiles between GBM cases with extraneural metastasis and the general GBM population, genomic data from GBM samples in The Cancer Genome Atlas (TCGA) database were also analyzed. We found that 64.5% (20/31) of the cases with extraneural metastasis that were tested for TP53 changes had at least 1 TP53 pathogenic variant detected in either 1 or both primary and metastatic tumors. In contrast, TP53 mutation was significantly less frequent in the unselected GBM from TCGA (22.6%, 56/248) (P=0.000). In addition, O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation was more common in unselected TCGA GBM cases (48.6%, 170/350) than in cases with extraneural metastasis (31.8%, 7/22), although not statistically significant. Although isocitrate dehydrogenase (IDH) mutation is a rare occurrence in high-grade astrocytomas, IDH-mutant grade 4 astrocytomas are at least as likely to metastasize as IDH wild-type GBMs; 3 metastatic cases definitively harbored an IDH1 (p.R132H) mutation in our analysis. Our findings not only provide potential biomarkers for earlier screening of extraneural metastasis, but could also suggest clues to understanding biological mechanisms underlying GBM metastasis, and for the development of therapeutic modalities.
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Affiliation(s)
| | | | | | | | | | - Stephen J Bagley
- Hematology Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA
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22
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Ahmadov U, Picard D, Bartl J, Silginer M, Trajkovic-Arsic M, Qin N, Blümel L, Wolter M, Lim JKM, Pauck D, Winkelkotte AM, Melcher M, Langini M, Marquardt V, Sander F, Stefanski A, Steltgens S, Hassiepen C, Kaufhold A, Meyer FD, Seibt A, Kleinesudeik L, Hain A, Münk C, Knobbe-Thomsen CB, Schramm A, Fischer U, Leprivier G, Stühler K, Fulda S, Siveke JT, Distelmaier F, Borkhardt A, Weller M, Roth P, Reifenberger G, Remke M. The long non-coding RNA HOTAIRM1 promotes tumor aggressiveness and radiotherapy resistance in glioblastoma. Cell Death Dis 2021; 12:885. [PMID: 34584066 PMCID: PMC8478910 DOI: 10.1038/s41419-021-04146-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 06/18/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022]
Abstract
Glioblastoma is the most common malignant primary brain tumor. To date, clinically relevant biomarkers are restricted to isocitrate dehydrogenase (IDH) gene 1 or 2 mutations and O6-methylguanine DNA methyltransferase (MGMT) promoter methylation. Long non-coding RNAs (lncRNAs) have been shown to contribute to glioblastoma pathogenesis and could potentially serve as novel biomarkers. The clinical significance of HOXA Transcript Antisense RNA, Myeloid-Specific 1 (HOTAIRM1) was determined by analyzing HOTAIRM1 in multiple glioblastoma gene expression data sets for associations with prognosis, as well as, IDH mutation and MGMT promoter methylation status. Finally, the role of HOTAIRM1 in glioblastoma biology and radiotherapy resistance was characterized in vitro and in vivo. We identified HOTAIRM1 as a candidate lncRNA whose up-regulation is significantly associated with shorter survival of glioblastoma patients, independent from IDH mutation and MGMT promoter methylation. Glioblastoma cell line models uniformly showed reduced cell viability, decreased invasive growth and diminished colony formation capacity upon HOTAIRM1 down-regulation. Integrated proteogenomic analyses revealed impaired mitochondrial function and determination of reactive oxygen species (ROS) levels confirmed increased ROS levels upon HOTAIRM1 knock-down. HOTAIRM1 knock-down decreased expression of transglutaminase 2 (TGM2), a candidate protein implicated in mitochondrial function, and knock-down of TGM2 mimicked the phenotype of HOTAIRM1 down-regulation in glioblastoma cells. Moreover, HOTAIRM1 modulates radiosensitivity of glioblastoma cells both in vitro and in vivo. Our data support a role for HOTAIRM1 as a driver of biological aggressiveness, radioresistance and poor outcome in glioblastoma. Targeting HOTAIRM1 may be a promising new therapeutic approach.
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Affiliation(s)
- Ulvi Ahmadov
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Picard
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Jasmin Bartl
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Manuela Silginer
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Marija Trajkovic-Arsic
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Medicine Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), partner site Essen, Heidelberg, Germany
| | - Nan Qin
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Lena Blümel
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Marietta Wolter
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Jonathan K M Lim
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - David Pauck
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Alina Marie Winkelkotte
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Medicine Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), partner site Essen, Heidelberg, Germany
| | - Marlen Melcher
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Maike Langini
- Institute for Molecular Medicine I, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Molecular Proteomics Laboratory (MPL), Biological-Medical Research Center (BMFZ), Heinrich Heine University, Düsseldorf, Germany
| | - Viktoria Marquardt
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Felix Sander
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Anja Stefanski
- Institute for Molecular Medicine I, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Molecular Proteomics Laboratory (MPL), Biological-Medical Research Center (BMFZ), Heinrich Heine University, Düsseldorf, Germany
| | - Sascha Steltgens
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Christina Hassiepen
- Department of Molecular Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Anna Kaufhold
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Frauke-Dorothee Meyer
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Annette Seibt
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Lara Kleinesudeik
- Institute for Experimental Cancer Research in Pediatrics, Goethe University Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anika Hain
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | | | - Alexander Schramm
- Department of Molecular Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Gabriel Leprivier
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Kai Stühler
- Institute for Molecular Medicine I, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Molecular Proteomics Laboratory (MPL), Biological-Medical Research Center (BMFZ), Heinrich Heine University, Düsseldorf, Germany
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe University Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens T Siveke
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Medicine Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), partner site Essen, Heidelberg, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Arndt Borkhardt
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Patrick Roth
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Guido Reifenberger
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Marc Remke
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Consortium for Translational Cancer Research (DKTK), partner site Essen/Düsseldorf, Düsseldorf, Germany.
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany.
- Department of Neuropathology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
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23
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Yılmaz H, Toy HI, Marquardt S, Karakülah G, Küçük C, Kontou PI, Logotheti S, Pavlopoulou A. In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia. Int J Mol Sci 2021; 22:ijms22179601. [PMID: 34502522 PMCID: PMC8431757 DOI: 10.3390/ijms22179601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Acute myeloid leukemia (AML), the most common type of acute leukemia in adults, is mainly asymptomatic at early stages and progresses/recurs rapidly and frequently. These attributes necessitate the identification of biomarkers for timely diagnosis and accurate prognosis. In this study, differential gene expression analysis was performed on large-scale transcriptomics data of AML patients versus corresponding normal tissue. Weighted gene co-expression network analysis was conducted to construct networks of co-expressed genes, and detect gene modules. Finally, hub genes were identified from selected modules by applying network-based methods. This robust and integrative bioinformatics approach revealed a set of twenty-four genes, mainly related to cell cycle and immune response, the diagnostic significance of which was subsequently compared against two independent gene expression datasets. Furthermore, based on a recent notion suggesting that molecular characteristics of a few, unusual patients with exceptionally favorable survival can provide insights for improving the outcome of individuals with more typical disease trajectories, we defined groups of long-term survivors in AML patient cohorts and compared their transcriptomes versus the general population to infer favorable prognostic signatures. These findings could have potential applications in the clinical setting, in particular, in diagnosis and prognosis of AML.
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Affiliation(s)
- Hande Yılmaz
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany;
| | - Halil Ibrahim Toy
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
| | - Stephan Marquardt
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany;
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
| | - Can Küçük
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
| | - Panagiota I. Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece;
| | - Stella Logotheti
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany;
- Correspondence: (S.L.); (A.P.)
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
- Correspondence: (S.L.); (A.P.)
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24
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Willscher E, Hopp L, Kreuz M, Schmidt M, Hakobyan S, Arakelyan A, Hentschel B, Jones DTW, Pfister SM, Loeffler M, Loeffler-Wirth H, Binder H. High-Resolution Cartography of the Transcriptome and Methylome Landscapes of Diffuse Gliomas. Cancers (Basel) 2021; 13:3198. [PMID: 34206856 PMCID: PMC8268631 DOI: 10.3390/cancers13133198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/01/2023] Open
Abstract
Molecular mechanisms of lower-grade (II-III) diffuse gliomas (LGG) are still poorly understood, mainly because of their heterogeneity. They split into astrocytoma- (IDH-A) and oligodendroglioma-like (IDH-O) tumors both carrying mutations(s) at the isocitrate dehydrogenase (IDH) gene and into IDH wild type (IDH-wt) gliomas of glioblastoma resemblance. We generated detailed maps of the transcriptomes and DNA methylomes, revealing that cell functions divided into three major archetypic hallmarks: (i) increased proliferation in IDH-wt and, to a lesser degree, IDH-O; (ii) increased inflammation in IDH-A and IDH-wt; and (iii) the loss of synaptic transmission in all subtypes. Immunogenic properties of IDH-A are diverse, partly resembling signatures observed in grade IV mesenchymal glioblastomas or in grade I pilocytic astrocytomas. We analyzed details of coregulation between gene expression and DNA methylation and of the immunogenic micro-environment presumably driving tumor development and treatment resistance. Our transcriptome and methylome maps support personalized, case-by-case views to decipher the heterogeneity of glioma states in terms of data portraits. Thereby, molecular cartography provides a graphical coordinate system that links gene-level information with glioma subtypes, their phenotypes, and clinical context.
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Affiliation(s)
- Edith Willscher
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Lydia Hopp
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Markus Kreuz
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Siras Hakobyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Arsen Arakelyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Bettina Hentschel
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - David T. W. Jones
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Stefan M. Pfister
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Markus Loeffler
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
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18F-FET PET Uptake Characteristics of Long-Term IDH-Wildtype Diffuse Glioma Survivors. Cancers (Basel) 2021; 13:cancers13133163. [PMID: 34202726 PMCID: PMC8268019 DOI: 10.3390/cancers13133163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 11/28/2022] Open
Abstract
Simple Summary IDH-wildtype (IDHwt) gliomas represent a tumor entity with poor overall survival. Only rare cases have an overall survival over several years. Dynamic and static 18F-FET PET is recommended as valuable complementary tool for glioma imaging in gliomas. This study shows that, besides molecular genetic prognosticators, long survival (≥36 months survival) in IDHwt gliomas is associated with a longer time-to-peak and smaller volume on 18F-FET PET at initial diagnosis compared to glioma patients with a short-term survival (≤15 months survival). 18F-FET uptake intensity and MRI-derived tumor size do not differ in patients with long-term survival compared to patient with a short-term survival. Abstract Background: IDHwt diffuse gliomas represent the tumor entity with one of the worst clinical outcomes. Only rare cases present with a long-term survival of several years. Here we aimed at comparing the uptake characteristics on dynamic 18F-FET PET, clinical and molecular genetic parameters of long-term survivors (LTS) versus short-term survivors (STS): Methods: Patients with de-novo IDHwt glioma (WHO grade III/IV) and 18F-FET PET prior to any therapy were stratified into LTS (≥36 months survival) and STS (≤15 months survival). Static and dynamic 18F-FET PET parameters (mean/maximal tumor-to-background ratio (TBRmean/max), biological tumor volume (BTV), minimal time-to-peak (TTPmin)), diameter and volume of contrast-enhancement on MRI, clinical parameters (age, sex, Karnofksy-performance-score), mode of surgery; initial treatment and molecular genetics were assessed and compared between LTS and STS. Results: Overall, 75 IDHwt glioma patients were included (26 LTS, 49 STS). LTS were significantly younger (p < 0.001), had a higher rate of WHO grade III glioma (p = 0.032), of O(6)-Methylguanine-DNA methyltransferase (MGMT) promoter methylation (p < 0.001) and missing Telomerase reverse transcriptase promoter (TERTp) mutations (p = 0.004) compared to STS. On imaging, LTS showed a smaller median BTV (p = 0.017) and a significantly longer TTPmin (p = 0.008) on 18F-FET PET than STS, while uptake intensity (TBRmean/max) did not differ. In contrast to the tumor-volume on PET, MRI-derived parameters such as tumor size as well as all other above-mentioned parameters did not differ between LTS and STS (p > 0.05 each). Conclusion: Besides molecular genetic prognosticators, a long survival time in IDHwt glioma patients is associated with a longer TTPmin as well as a smaller BTV on 18F-FET PET at initial diagnosis. 18F-FET uptake intensity as well as the MRI-derived tumor size (volume and maximal diameter) do not differ in patients with long-term survival.
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Kalya M, Kel A, Wlochowitz D, Wingender E, Beißbarth T. IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. Front Genet 2021; 12:670240. [PMID: 34211498 PMCID: PMC8239365 DOI: 10.3389/fgene.2021.670240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/06/2021] [Indexed: 01/01/2023] Open
Abstract
Only 2% of glioblastoma multiforme (GBM) patients respond to standard therapy and survive beyond 36 months (long-term survivors, LTS), while the majority survive less than 12 months (short-term survivors, STS). To understand the mechanism leading to poor survival, we analyzed publicly available datasets of 113 STS and 58 LTS. This analysis revealed 198 differentially expressed genes (DEGs) that characterize aggressive tumor growth and may be responsible for the poor prognosis. These genes belong largely to the Gene Ontology (GO) categories “epithelial-to-mesenchymal transition” and “response to hypoxia.” In this article, we applied an upstream analysis approach that involves state-of-the-art promoter analysis and network analysis of the dysregulated genes potentially responsible for short survival in GBM. Binding sites for transcription factors (TFs) associated with GBM pathology like NANOG, NF-κB, REST, FRA-1, PPARG, and seven others were found enriched in the promoters of the dysregulated genes. We reconstructed the gene regulatory network with several positive feedback loops controlled by five master regulators [insulin-like growth factor binding protein 2 (IGFBP2), vascular endothelial growth factor A (VEGFA), VEGF165, platelet-derived growth factor A (PDGFA), adipocyte enhancer-binding protein (AEBP1), and oncostatin M (OSMR)], which can be proposed as biomarkers and as therapeutic targets for enhancing GBM prognosis. A critical analysis of this gene regulatory network gives insights into the mechanism of gene regulation by IGFBP2 via several TFs including the key molecule of GBM tumor invasiveness and progression, FRA-1. All the observations were validated in independent cohorts, and their impact on overall survival has been investigated.
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Affiliation(s)
- Manasa Kalya
- Department of Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany.,geneXplain GmbH, Wolfenbüttel, Germany
| | - Alexander Kel
- geneXplain GmbH, Wolfenbüttel, Germany.,Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Darius Wlochowitz
- Department of Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany
| | | | - Tim Beißbarth
- Department of Medical Bioinformatics, University Medical Center Göttingen, Göttingen, Germany
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Kalya MP, Beisbarth T, Kel A. [Master regulators associated with poor prognosis in glioblastoma multiforme]. BIOMEDITSINSKAIA KHIMIIA 2021; 67:201-212. [PMID: 34142527 DOI: 10.18097/pbmc20216703201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glioblastoma multiforme (GBM) is a highly malignant brain tumor with average survival time of 15 months. Less than 2% of the patients survive beyond 36 months. To understand the molecular mechanism responsible for poor prognosis, we analyzed GBM samples of TCGA microarray (n=560) data. We have identified 720 genes that have a significant impact upon survival based on univariate cox regression. We applied the Genome Enhancer pipeline to analyze potential mechanisms of regulation of activity of these genes and to build gene regulatory networks. We identified 12 transcription factors enriched in the promoters of these genes including the key molecule of GBM - STAT3. We found that STAT3 had significant differential expression across extreme survivor groups (short-term survivors- survival 36 months) and also had a significant impact on survival. In the next step, we identified master regulators in the signal transduction network that regulate the activity of these transcription factors. Master regulators are filtered based on their differential expression across extreme survivors groups and impact on survival. This work validates our earlier report on master regulators IGFBP2, PDGFA, OSMR, and AEBP1 driving short survival. Additionally, we propose CD14, CD44, DUSP6, GRB10, IL1RAP, FGFR3, and POSTN as master regulators driving poor survival. These master regulators are proposed as promising therapeutic targets to counter poor prognosis in GBM. Finally, the algorithm has prioritized several drugs for the further study as potential remedies to conquer the aggressive forms of GBM and to extend survival of the patients.
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Affiliation(s)
- M P Kalya
- University Medical Center Göttingen, Göttingen, Germany; geneXplain GmbH, Wolfenbüttel, Germany
| | - T Beisbarth
- University Medical Center Göttingen, Göttingen, Germany
| | - A Kel
- geneXplain GmbH, Wolfenbüttel, Germany; Institute of Chemical Biology and Fundamental Medicine SBRAS, Novosibirsk, Russia
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28
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Peng D, Gleyzer R, Tai WH, Kumar P, Bian Q, Isaacs B, da Rocha EL, Cai S, DiNapoli K, Huang FW, Cahan P. Evaluating the transcriptional fidelity of cancer models. Genome Med 2021; 13:73. [PMID: 33926541 PMCID: PMC8086312 DOI: 10.1186/s13073-021-00888-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 04/15/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Cancer researchers use cell lines, patient-derived xenografts, engineered mice, and tumoroids as models to investigate tumor biology and to identify therapies. The generalizability and power of a model derive from the fidelity with which it represents the tumor type under investigation; however, the extent to which this is true is often unclear. The preponderance of models and the ability to readily generate new ones has created a demand for tools that can measure the extent and ways in which cancer models resemble or diverge from native tumors. METHODS We developed a machine learning-based computational tool, CancerCellNet, that measures the similarity of cancer models to 22 naturally occurring tumor types and 36 subtypes, in a platform and species agnostic manner. We applied this tool to 657 cancer cell lines, 415 patient-derived xenografts, 26 distinct genetically engineered mouse models, and 131 tumoroids. We validated CancerCellNet by application to independent data, and we tested several predictions with immunofluorescence. RESULTS We have documented the cancer models with the greatest transcriptional fidelity to natural tumors, we have identified cancers underserved by adequate models, and we have found models with annotations that do not match their classification. By comparing models across modalities, we report that, on average, genetically engineered mice and tumoroids have higher transcriptional fidelity than patient-derived xenografts and cell lines in four out of five tumor types. However, several patient-derived xenografts and tumoroids have classification scores that are on par with native tumors, highlighting both their potential as faithful model classes and their heterogeneity. CONCLUSIONS CancerCellNet enables the rapid assessment of transcriptional fidelity of tumor models. We have made CancerCellNet available as a freely downloadable R package ( https://github.com/pcahan1/cancerCellNet ) and as a web application ( http://www.cahanlab.org/resources/cancerCellNet_web ) that can be applied to new cancer models that allows for direct comparison to the cancer models evaluated here.
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Affiliation(s)
- Da Peng
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Rachel Gleyzer
- grid.21107.350000 0001 2171 9311Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Wen-Hsin Tai
- grid.21107.350000 0001 2171 9311Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Pavithra Kumar
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Qin Bian
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Bradley Isaacs
- grid.21107.350000 0001 2171 9311Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Edroaldo Lummertz da Rocha
- grid.411237.20000 0001 2188 7235Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, SC Brazil
| | - Stephanie Cai
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Kathleen DiNapoli
- grid.21107.350000 0001 2171 9311Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Franklin W. Huang
- grid.266102.10000 0001 2297 6811Division of Hematology/Oncology, Department of Medicine; Helen Diller Family Cancer Center; Bakar Computational Health Sciences Institute; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA USA
| | - Patrick Cahan
- grid.21107.350000 0001 2171 9311Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ,grid.21107.350000 0001 2171 9311Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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Rogers JL, Vera E, Acquaye A, Briceno N, Jammula V, King AL, Leeper H, Quezado MM, Gonzalez Alarcon J, Boris L, Burton E, Celiku O, Choi A, Christ A, Crandon S, Grajkowska E, Leggiero N, Lollo N, Penas-Prado M, Reyes J, Siegel C, Theeler BJ, Timmer M, Wall K, Wu J, Aldape K, Gilbert MR, Armstrong TS. Living with a central nervous system (CNS) tumor: findings on long-term survivorship from the NIH Natural History Study. Neurooncol Pract 2021; 8:460-474. [PMID: 34277024 DOI: 10.1093/nop/npab022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Primary central nervous system (CNS) tumors are often associated with high symptom burden and a poor prognosis from the time of diagnosis. The purpose of this study is to describe patient-reported outcomes (PRO) data from long-term survivors (LTS; ≥5-year survival post-diagnosis). Methods Clinical/treatment/molecular characteristics and PROs (symptom burden/interference (MDASI-BT/SP), perceived cognition (Neuro-QoL), anxiety/depression (PROMIS), and general health status (EQ-5D-3L)) were collected on 248 adult LTS between 9/2016 and 8/2019. Descriptive statistics and regression analysis were used to report results. Results Participants had a median age of 47 years (19-82) and were primarily White (83%) males (51%) with high-grade tumors (59%) and few mutations. Forty-two percent of the 222 brain tumor LTS reported no moderate-to-severe symptoms, whereas 45% reported three or more; most common symptoms were fatigue (40%), difficulty remembering (29%), and drowsiness (28%). Among spine tumor LTS (n = 42), nearly half reported moderate-to-severe weakness, pain, fatigue, and numbness/tingling, with 72% experiencing activity-related interference. Severe anxiety, depression, and cognitive symptoms were reported in up to 23% of the sample. Brain tumor LTS at higher risk for severe symptoms were more likely to be young, unemployed, and have poor KPS (Karnofsky Performance Status), whereas high symptom-risk spinal cord tumor LTS had poor KPS and received any tumor treatment. Conclusions Findings indicate LTS fall into distinct cohorts with no significant symptoms or very high symptom burden, regardless of tumor grade or mutational profile. These LTS data demonstrate the need for survivorship care programs and future studies to explore the symptom trajectory of all CNS tumor patients for prevention and early interventions.
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Affiliation(s)
- James L Rogers
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Elizabeth Vera
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alvina Acquaye
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicole Briceno
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Varna Jammula
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Amanda L King
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Heather Leeper
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Martha M Quezado
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Javier Gonzalez Alarcon
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa Boris
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland, USA
| | - Eric Burton
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Orieta Celiku
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anna Choi
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alexa Christ
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sonja Crandon
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ewa Grajkowska
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Nicole Lollo
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marta Penas-Prado
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennifer Reyes
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Christine Siegel
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland, USA
| | - Brett J Theeler
- Department of Neurology, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Michael Timmer
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kathleen Wall
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland, USA
| | - Jing Wu
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Terri S Armstrong
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Wirsching HG, Silginer M, Ventura E, Macnair W, Burghardt I, Claassen M, Gatti S, Wichmann J, Riemer C, Schneider H, Weller M. Negative allosteric modulators of metabotropic glutamate receptor 3 target the stem-like phenotype of glioblastoma. Mol Ther Oncolytics 2021; 20:166-174. [PMID: 33575479 PMCID: PMC7851500 DOI: 10.1016/j.omto.2020.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
Glioblastoma is an invariably deadly disease. A subpopulation of glioma stem-like cells (GSCs) drives tumor progression and treatment resistance. Two recent studies demonstrated that neurons form oncogenic glutamatergic electrochemical synapses with post-synaptic GSCs. This led us to explore whether glutamate signaling through G protein-coupled metabotropic receptors would also contribute to the malignancy of glioblastoma. We found that glutamate metabotropic receptor (Grm)3 is the predominantly expressed Grm in glioblastoma. Associations of GRM3 gene expression levels with survival are confined to the proneural gene expression subtype, which is associated with enrichment of GSCs. Using multiplexed single-cell qRT-PCR, GSC marker-based cell sorting, database interrogations, and functional assays in GSCs derived from patients' tumors, we establish Grm3 as a novel marker and potential therapeutic target in GSCs. We confirm that Grm3 inhibits adenylyl cyclase and regulates extracellular signal-regulated kinase. Targeting Grm3 disrupts self-renewal and promotes differentiation of GSCs. Thus, we hypothesize that Grm3 signaling may complement oncogenic functions of glutamatergic ionotropic receptor activity in neuroglial synapses, supporting a link between neuronal activity and the GSC phenotype. The novel class of highly specific Grm3 inhibitors that we characterize herein have been clinically tested as cognitive enhancers in humans with a favorable safety profile.
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Affiliation(s)
- Hans-Georg Wirsching
- Department of Neurology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Manuela Silginer
- Department of Neurology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Elisa Ventura
- Department of Neurology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Will Macnair
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Isabel Burghardt
- Department of Neurology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Manfred Claassen
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Silvia Gatti
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Jürgen Wichmann
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Claus Riemer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Hannah Schneider
- Department of Neurology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Michael Weller
- Department of Neurology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
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Richardson TE, Kumar A, Xing C, Hatanpaa KJ, Walker JM. Overcoming the Odds: Toward a Molecular Profile of Long-Term Survival in Glioblastoma. J Neuropathol Exp Neurol 2021; 79:1031-1037. [PMID: 32954439 DOI: 10.1093/jnen/nlaa102] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
For over a century, gliomas were characterized solely by histologic features. With the publication of the WHO Classification of Tumours of the Central Nervous System, Revised 4th Edition in 2016, integrated histologic and molecular diagnosis became the norm, providing improved tumor grading and prognosis with IDH1/2 (isocitrate dehydrogenase 1 and 2) mutation being the most significant prognostic feature in all grades of adult diffuse glioma. Since then, much work has been done to identify additional molecular prognostic features, but the bulk of the progress has been made in defining aggressive features in lower grade astrocytoma. Although there have been several large case series of glioblastomas with long-term survival (LTS; overall survival ≥36 months), less is known about the clinical and molecular features of these cases. Herein, we review 19 studies examining LTS glioblastoma patients from 2009 to 2020 that include variable molecular analysis, including 465 cases with survival of 36 months or more (total n = 2328). These studies suggest that while there is no definitive molecular signature of long survival, younger age, IDH mutation, and MGMT (methyl guanine methyl transferase) promoter hypermethylation are associated with longer overall survival, and in IDH-wildtype tumors, chromosome 19/20 co-gain and lack of EGFR amplification, chromosome 7 gain/10 loss, and TERT promoter mutation are associated with LTS.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, State University of New York, Upstate Medical University, Syracuse, New York
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth & Development
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development.,Department of Bioinformatics and Department of Population and Data Sciences
| | | | - Jamie M Walker
- University of Texas Southwestern Medical Center, Dallas, Texas; and Department of Pathology and Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, Texas
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Minasi S, Baldi C, Gianno F, Antonelli M, Buccoliero AM, Pietsch T, Massimino M, Buttarelli FR. Alternative lengthening of telomeres in molecular subgroups of paediatric high-grade glioma. Childs Nerv Syst 2021; 37:809-818. [PMID: 33128602 PMCID: PMC7875853 DOI: 10.1007/s00381-020-04933-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/16/2020] [Indexed: 11/18/2022]
Abstract
PURPOSE The maintenance of telomere length prevents cancer cell senescence and occurs via two mutually exclusive mechanisms: (a) reactivation of telomerase expression and (b) activation of alternative lengthening of telomeres (ALT). ALT is frequently related to alterations on ATRX, a chromatin-remodelling protein. Recent data have identified different molecular subgroups of paediatric high-grade glioma (pHGG) with mutations of H3F3A, TERTp and ATRX; however, differences in telomere length among these molecular subgroups were not thoroughly examined. METHODS We investigated which genetic alterations trigger the ALT mechanism in 52 IDH-wildtype, 1p/19q-wildtype pHGG. Samples were analysed for telomere length using Tel-FISH. ATRX nuclear loss of expression was assessed by IHC, H3F3A and TERTp mutations by DNA sequencing, and TERTp methylation by MS-PCR. RESULTS Mutant H3.3 was found in 21 cases (40.3%): 19.2% with K27M mutation and 21.1% with G34R mutation. All H3.3G34R-mutated cases showed the ALT phenotype (100%); on the opposite, only 40% of the H3.3K27M-mutated showed ALT activation. ATRX nuclear loss was seen in 16 cases (30.7%), associated sometimes with the G34R mutation, and never with the K27M mutation. ATRX nuclear loss was always related to telomere elongation. TERTp C250T mutations were rare (5.4%) and were not associated with high intensity Tel-FISH signals, as TERTp hyper-methylation detected in 21% of the cases. H3.3/ATRX/TERTp-wildtype pHGG revealed all basal levels of telomere length. CONCLUSION Our results show a strong association between H3.3 mutations and ALT, and highlight the different telomeric profiles in histone-defined subgroups: H3.3-G34R mutants always trigger ALT to maintain telomere length, irrespective of ATRX status, whereas only some H3.3-K27M tumours activate ALT. These findings suggest that acquiring the gly34 mutation on H3.3 might suffice to trigger the ALT mechanism.
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Affiliation(s)
- Simone Minasi
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
- Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy
| | - Caterina Baldi
- Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy
| | - Francesca Gianno
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Manila Antonelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumour Reference Centre, University of Bonn Medical Centre, Bonn, Germany
| | - Maura Massimino
- Paediatric Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Francesca Romana Buttarelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy.
- Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy.
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Telomerase reverse transcriptase promoter mutation- and O 6-methylguanine DNA methyltransferase promoter methylation-mediated sensitivity to temozolomide in isocitrate dehydrogenase-wild-type glioblastoma: is there a link? Eur J Cancer 2021; 147:84-94. [PMID: 33631540 DOI: 10.1016/j.ejca.2021.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/28/2020] [Accepted: 01/07/2021] [Indexed: 01/12/2023]
Abstract
AIM OF THE STUDY Benefit from temozolomide (TMZ) chemotherapy in the treatment of isocitrate dehydrogenase (IDH)-wild-type glioblastoma is essentially limited to patients with O6-methylguanine DNA methyltransferase (MGMT) promoter-methylated tumours. Recent studies suggested that telomerase reverse transcriptase (TERT) promoter hotspot mutations may have an impact on the prognostic role of the MGMT status in patients with glioblastoma. METHODS MGMT promoter methylation and TERT promoter mutation status were retrospectively assessed in a prospective cohort of patients with IDH-wild-type glioblastoma of the German Glioma Network (GGN) (n = 298) and an independent retrospective cohort from Düsseldorf, Germany, and Zurich, Switzerland (n = 302). RESULTS In the GGN cohort, but not in the Düsseldorf/Zurich cohort, TERT promoter mutation was moderately associated with inferior outcomes in patients with MGMT promoter-unmethylated tumours (hazard ratio 1.74; 95% confidence interval: 1.07-2.82; p = 0.026). TERT promoter mutations were not associated with better outcomes in patients with MGMT promoter-methylated tumours in either cohort. The two different TERT promoter hotspot mutations (C228T and C250T) were not linked to distinct outcomes. CONCLUSIONS Analysis of two independent cohorts of patients with glioblastoma did not confirm previous data, suggesting that TERT promoter mutations confer an enhanced benefit from TMZ in patients with MGMT promoter-methylated glioblastoma. Thus, diagnostic testing for TERT promoter mutations may not be required for prediction of TMZ sensitivity in patients with IDH-wild-type glioblastoma.
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Nørøxe DS, Yde CW, Østrup O, Michaelsen SR, Schmidt AY, Kinalis S, Torp MH, Skjøth‐Rasmussen J, Brennum J, Hamerlik P, Poulsen HS, Nielsen FC, Lassen U. Genomic profiling of newly diagnosed glioblastoma patients and its potential for clinical utility - a prospective, translational study. Mol Oncol 2020; 14:2727-2743. [PMID: 32885540 PMCID: PMC7607169 DOI: 10.1002/1878-0261.12790] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/29/2020] [Accepted: 08/27/2020] [Indexed: 12/27/2022] Open
Abstract
Glioblastoma (GBM) is an incurable brain tumor for which new treatment strategies are urgently needed. Next-generation sequencing of GBM has most often been performed retrospectively and on archival tissue from both diagnostic and relapse surgeries with limited knowledge of clinical information, including treatment given. We sought to investigate the genomic composition prospectively in treatment-naïve patients, searched for possible targetable aberrations, and investigated for prognostic and/or predictive factors. A total of 108 newly diagnosed GBM patients were included. Clinical information, progression-free survival, and overall survival (OS) were noted. Tissues were analyzed by whole-exome sequencing, single nucleotide polymorphism (SNP) and transcriptome arrays, and RNA sequencing; assessed for mutations, fusions, tumor mutational burden (TMB), and chromosomal instability (CI); and classified into GBM subgroups. Each genomic report was discussed at a multidisciplinary tumor board meeting to evaluate for matching trials. From 111 consecutive patients, 97.3% accepted inclusion in this study. Eighty-six (77%) were treated with radiation therapy/temozolomide (TMZ) and adjuvant TMZ. One NTRK2 and three FGFR3-TACC3 fusions were identified. Copy number alterations in GRB2 and SMYD4 were significantly correlated with worse median OS together with known clinical variables like age, performance status, steroid dose, and O6-methyl-guanine-DNA-methyl-transferase status. Patients with CI-median or TMB-high had significantly worse median OS compared to CI-low/high or TMB-low/median. In conclusion, performing genomic profiling at diagnosis enables evaluation of genomic-driven therapy at the first progression. Furthermore, TMB-high or CI-median patients had worse median OS, which can support the possibility of offering experimental treatment already at the first line for this group.
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Affiliation(s)
- Dorte S. Nørøxe
- Department of Radiation BiologyRigshospitaletCopenhagenDenmark
- Department of OncologyRigshospitaletCopenhagenDenmark
| | | | - Olga Østrup
- Center for Genomic MedicineRigshospitaletCopenhagenDenmark
| | - Signe R. Michaelsen
- Department of Radiation BiologyRigshospitaletCopenhagenDenmark
- Biotech, Research and Innovation Centre (BRIC)University of CopenhagenCopenhagenDenmark
| | - Ane Y. Schmidt
- Center for Genomic MedicineRigshospitaletCopenhagenDenmark
| | - Savvas Kinalis
- Center for Genomic MedicineRigshospitaletCopenhagenDenmark
| | | | | | | | | | - Hans S. Poulsen
- Department of Radiation BiologyRigshospitaletCopenhagenDenmark
- Department of OncologyRigshospitaletCopenhagenDenmark
| | | | - Ulrik Lassen
- Department of OncologyRigshospitaletCopenhagenDenmark
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The Effects of Age, Cigarette Smoking, Sex, and Race on the Qualitative Characteristics of Lung Transcriptome. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6418460. [PMID: 32802863 PMCID: PMC7424369 DOI: 10.1155/2020/6418460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022]
Abstract
The within-sample relative expression orderings (REOs) of genes, which are stable qualitative transcriptional characteristics, can provide abundant information for a disease. Methods based on REO comparisons have been proposed for identifying differentially expressed genes (DEGs) at the individual level and for detecting disease-associated genes based on one-phenotype disease data by reusing data of normal samples from other sources. Here, we evaluated the effects of common potential confounding factors, including age, cigarette smoking, sex, and race, on the REOs of gene pairs within normal lung tissues transcriptome. Our results showed that age has little effect on REOs within lung tissues. We found that about 0.23% of the significantly stable REOs of gene pairs in nonsmokers' lung tissues are reversed in smokers' lung tissues, introduced by 344 DEGs between the two groups of samples (RankCompV2, FDR <0.05), which are enriched in metabolism of xenobiotics by cytochrome P450, glutathione metabolism, and other pathways (hypergeometric test, FDR <0.05). Comparison between the normal lung tissue samples of males and females revealed fewer reversal REOs introduced by 24 DEGs between the sex groups, among which 19 DEGs are located on sex chromosomes and 5 DEGs involving in spermatogenesis and regulation of oocyte are located on autosomes. Between the normal lung tissue samples of white and black people, we identified 22 DEGs (RankCompV2, FDR <0.05) which introduced a few reversal REOs between the two races. In summary, the REO-based study should take into account the confounding factors of cigarette smoking, sex, and race.
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Feng X, Zhang L, Ke S, Liu T, Hao L, Zhao P, Tu W, Cang S. High expression of GPNMB indicates an unfavorable prognosis in glioma: Combination of data from the GEO and CGGA databases and validation in tissue microarray. Oncol Lett 2020; 20:2356-2368. [PMID: 32782553 PMCID: PMC7400985 DOI: 10.3892/ol.2020.11787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
Glycoprotein non-metastatic melanoma protein B (GPNMB), a transmembrane glycoprotein, has been reported to be involved in tumor progression, but its prognostic value for glioma and the mechanistic effects on glioma progression have not been clearly explored. The present study aimed to investigate the prognostic role of GPNMB in glioma and the potential mechanisms of how GPNMB mediates glioma progression. Differentially expressed genes between the four highest and four lowest GPNMB expression samples in the GSE53733 dataset were first determined. Gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis and Gene set enrichment analysis results demonstrated that the significantly enriched pathways in samples with high GPNMB expression compared with those with low GPNMB expression were associated with hypoxia, angiogenesis, migration and invasion. Pearson correlation analysis was conducted to investigate the correlations between GPNMB expression and the markers of hypoxia, angiogenesis, migration and invasion in GSE53733, which were further validated using another mRNA microarray dataset from the Chinese Glioma Genome Atlas (CGGA). In addition, using the CGGA dataset, high GPNMB expression was demonstrated to be significantly associated with advanced WHO grade and short survival time in patients with glioma. Of note, based on the immunohistochemical staining of the tissue microarrays, Kaplan-Meier analysis with the Renyi test and a Cox proportional hazards model were used to validate the unfavorable prognostic role of high GPNMB expression in glioma. In conclusion, high GPNMB expression may be associated with high tumor grade and unfavorable prognosis in glioma. GPNMB expression was demonstrated to correlate with the markers of hypoxia, angiogenesis, migration and invasion, which may be potential mechanisms through which GPNMB mediates glioma progression.
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Affiliation(s)
- Xiao Feng
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Lina Zhang
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Shanbao Ke
- Department of Radiotherapy, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Tao Liu
- Department of Radiotherapy, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Liuwei Hao
- Department of Physical Examination and Health Management, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Pan Zhao
- Department of Neurology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Wenzhi Tu
- Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, P.R. China
| | - Shundong Cang
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, Henan 450003, P.R. China
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Wu X, Ouyang Y, Wang B, Lin J, Bai Y. Hypermethylation of the IRAK3-Activated MAPK Signaling Pathway to Promote the Development of Glioma. Cancer Manag Res 2020; 12:7043-7059. [PMID: 32848462 PMCID: PMC7425661 DOI: 10.2147/cmar.s252772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/25/2020] [Indexed: 12/21/2022] Open
Abstract
Objective This study aimed to elucidate the molecular mechanism underlying the involvement of abnormal DNA methylation in the development of glioma and identify potential new targets for glioma therapy. Methods The GSE79122 chip achieved from the Gene Expression Omnibus (GEO) database containing 69 glioma samples and 9 normal samples was analyzed. Methylation-specific polymerase chain reaction (MS-PCR or MSP), reverse transcription-PCR, and Western blot analysis were used to confirm the methylation level and expression level of the interleukin receptor-associated kinase (IRAK3) gene in glioma cells, 36 glioma samples, and the corresponding normal samples. In vitro, the proliferation, apoptosis rate, migration, and invasion abilities of glioma cells were detected by Cell Counting Kit-8 assay, Transwell assay, enzyme-linked immunosorbent assay, and flow cytometry, respectively. Besides, the xenograft assay of nude mice was used to confirm the effect of the IRAK3 on glioma in vivo. Results Microarray analysis showed that the IRAK3 was one of the most hypermethylated genes in glioma, and the related mitogen-activated protein kinase (MAPK) signaling pathway was activated. More experiments supported the higher methylation level and lower expression level of the IRAK3 in glioma tissues and cell lines. The viability, migration, and invasion ability of glioma cells significantly reduced and the apoptosis rate increased with the overexpression and demethylation of the IRAK3 in vitro. Besides, treatment with the MAPK signaling pathway inhibitor PD325901 alone or the overexpression or demethylation of the IRAK3 had a similar effect as the overexpression or demethylation of the IRAK3 alone in glioma cells. In vivo, xenotransplantation experiments in nude mice confirmed that the overexpression and demethylation of the IRAK3 and suppression of the MAPK signaling pathway inhibited the development of glioma. Conclusion IRAK3 inhibited the development of glioma progression through the MAPK signaling pathway.
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Affiliation(s)
- Xinghai Wu
- Department of Neurosurgery, Zhangye People's Hospital Affiliated to Hexi University, Gansu, People's Republic of China
| | - Yian Ouyang
- Department of Neurosurgery, First Affiliated Hospital of Gannan Medical College, Jiangxi, People's Republic of China
| | - Bin Wang
- Department of Neurosurgery, Zhangye People's Hospital Affiliated to Hexi University, Gansu, People's Republic of China
| | - Jian Lin
- Department of Neurosurgery, Zhangye People's Hospital Affiliated to Hexi University, Gansu, People's Republic of China
| | - Yun Bai
- Department of Neurosurgery, Zhangye People's Hospital Affiliated to Hexi University, Gansu, People's Republic of China
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Burgenske DM, Yang J, Decker PA, Kollmeyer TM, Kosel ML, Mladek AC, Caron AA, Vaubel RA, Gupta SK, Kitange GJ, Sicotte H, Youland RS, Remonde D, Voss JS, Fritcher EGB, Kolsky KL, Ida CM, Meyer FB, Lachance DH, Parney IJ, Kipp BR, Giannini C, Sulman EP, Jenkins RB, Eckel-Passow JE, Sarkaria JN. Molecular profiling of long-term IDH-wildtype glioblastoma survivors. Neuro Oncol 2020; 21:1458-1469. [PMID: 31346613 DOI: 10.1093/neuonc/noz129] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) represents an aggressive cancer type with a median survival of only 14 months. With fewer than 5% of patients surviving 5 years, comprehensive profiling of these rare patients could elucidate prognostic biomarkers that may confer better patient outcomes. We utilized multiple molecular approaches to characterize the largest patient cohort of isocitrate dehydrogenase (IDH)-wildtype GBM long-term survivors (LTS) to date. METHODS Retrospective analysis was performed on 49 archived formalin-fixed paraffin embedded tumor specimens from patients diagnosed with GBM at the Mayo Clinic between December 1995 and September 2013. These patient samples were subdivided into 2 groups based on survival (12 LTS, 37 short-term survivors [STS]) and subsequently examined by mutation sequencing, copy number analysis, methylation profiling, and gene expression. RESULTS Of the 49 patients analyzed in this study, LTS were younger at diagnosis (P = 0.016), more likely to be female (P = 0.048), and MGMT promoter methylated (UniD, P = 0.01). IDH-wildtype STS and LTS demonstrated classic GBM mutations and copy number changes. Pathway analysis of differentially expressed genes showed LTS enrichment for sphingomyelin metabolism, which has been linked to decreased GBM growth, invasion, and angiogenesis. STS were enriched for DNA repair and cell cycle control networks. CONCLUSIONS While our findings largely report remarkable similarity between these LTS and more typical STS, unique attributes were observed in regard to altered gene expression and pathway enrichment. These attributes may be valuable prognostic markers and are worth further examination. Importantly, this study also underscores the limitations of existing biomarkers and classification methods in predicting patient prognosis.
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Affiliation(s)
| | - Jie Yang
- Department of Radiation Oncology, NYU Langone School of Medicine, New York, New York
| | - Paul A Decker
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Thomas M Kollmeyer
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew L Kosel
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ann C Mladek
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Alissa A Caron
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Rachael A Vaubel
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Shiv K Gupta
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Gaspar J Kitange
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Hugues Sicotte
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ryan S Youland
- Department of Radiation Oncology, Gundersen Health System, La Crosse, Wisconsin
| | - Dioval Remonde
- Department of Radiation Oncology, Mays Cancer Center, University of Texas Health San Antonio, San Antonio, Texas
| | - Jesse S Voss
- Molecular Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Emily G Barr Fritcher
- Molecular Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kathryn L Kolsky
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Cristiane M Ida
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Fredric B Meyer
- Department of Neurosurgery, Mayo Clinic, Rochester, Minnesota
| | | | - Ian J Parney
- Department of Neurosurgery, Mayo Clinic, Rochester, Minnesota
| | - Benjamin R Kipp
- Molecular Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Caterina Giannini
- Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Erik P Sulman
- Department of Radiation Oncology, NYU Langone School of Medicine, New York, New York
| | - Robert B Jenkins
- Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
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Raviraj R, Nagaraja SS, Selvakumar I, Mohan S, Nagarajan D. The epigenetics of brain tumors and its modulation during radiation: A review. Life Sci 2020; 256:117974. [PMID: 32553924 DOI: 10.1016/j.lfs.2020.117974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/23/2020] [Accepted: 06/10/2020] [Indexed: 10/24/2022]
Abstract
The brain tumor is the abnormal growth of heterogeneous cells around the central nervous system and spinal cord. Most clinically prominent brain tumors affecting both adult and pediatric are glioblastoma, medulloblastoma, and ependymoma and they are classified according to their origin of tissue. Chemotherapy, radiotherapy, and surgery are important treatments available to date. However, these treatments fail due to multiple reasons, including chemoresistance and radiation resistance of cancer cells. Thus, there is a need of new therapeutic designs to target cell signaling and molecular events which are responsible for this resistance. Recently epigenetic changes received increased attention because it helps in understanding chromatin-mediated disease mechanism. The epigenetic modification alters chromatin structure that affects the docking site of many drugs which cause chemo-resistance of cancer therapy. This review centers the mechanism of how epigenetic changes affect the transcription repression and activation of various genes including Polycomb gene, V-Myc avian myelocytomatosis viral oncogene (MYCN). This review also put forth the pathway of radiation-induced reactive oxygen species generation and its role in epigenetic changes in the cellular level and its impact on tissue physiology. Additionally, there is a strong relationship between the behavior of an individual and environment-induced epigenetic regulation of gene expression. The review also discusses Transcriptome heterogeneity and role of tumor microenvironment in glioblastoma. Overall, this review emphasis important and novel epigenetic targets that could be of therapeutic benefit, which helps in overcoming the unsolved chromatin alteration in brain cancer.
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Affiliation(s)
- Raghavi Raviraj
- Radiation Biology Lab, 206, ASK-II, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - SunilGowda Sunnaghatta Nagaraja
- Radiation Biology Lab, 206, ASK-II, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Ilakya Selvakumar
- Radiation Biology Lab, 206, ASK-II, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Suma Mohan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Devipriya Nagarajan
- Radiation Biology Lab, 206, ASK-II, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India.
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Prognostic Value of C-Reactive Protein to Albumin Ratio in Glioblastoma Multiforme Patients Treated with Concurrent Radiotherapy and Temozolomide. Int J Inflam 2020; 2020:6947382. [PMID: 32566124 PMCID: PMC7298277 DOI: 10.1155/2020/6947382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/25/2020] [Indexed: 12/31/2022] Open
Abstract
Objective We investigated the prognostic impact of C-reactive protein to albumin ratio (CRP/Alb) on the survival outcomes of newly diagnosed glioblastoma multiforme (GBM) patients treated with radiotherapy (RT) and concurrent plus adjuvant temozolomide (TMZ). Methods The pretreatment CRP and Alb records of GBM patients who underwent RT and concurrent plus adjuvant TMZ were retrospectively analyzed. The CRP/Alb was calculated by dividing serum CRP level by serum Alb level obtained prior to RT. The availability of significant cutoff value for CRP/Alb that interacts with survival was assessed with the receiver-operating characteristic (ROC) curve analysis. The primary endpoint was the association between the CRP/Alb and the overall survival (OS). Results A total of 153 patients were analyzed. At a median follow-up of 14.7 months, median and 5-year OS rates were 16.2 months (95% CI: 12.5–19.7) and 9.5%, respectively, for the entire cohort. The ROC curve analysis identified a significant cutoff value at 0.75 point (area under the curve: 74.9%; sensitivity: 70.9%; specificity: 67.7%; P < 0.001) for CRP/Alb that interacts with OS and grouped the patients into two: CRP/Alb <0.75 (n = 61) and ≥0.75 (n = 92), respectively. Survival comparisons revealed that the CRP/Alb <0.75 was associated with a significantly superior median (22.5 versus 15.7 months; P < 0.001) and 5-year (20% versus 0%) rates than the CRP/Alb ≥0.75, which retained its independent significance in multivariate analysis (P < 0.001). Conclusion Present results suggested the pretreatment CRP/Alb as a significant and independent inflammation-based index which can be utilized for further prognostic lamination of GBM patients.
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Multiple Functions of Fubp1 in Cell Cycle Progression and Cell Survival. Cells 2020; 9:cells9061347. [PMID: 32481602 PMCID: PMC7349734 DOI: 10.3390/cells9061347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022] Open
Abstract
The discovery of novel and critical genes implicated in malignant development is a topic of high interest in cancer research. Intriguingly, a group of genes named “double-agent” genes were reported to have both oncogenic and tumor-suppressive functions. To date, less than 100 “double-agent” genes have been documented. Fubp1 is a master transcriptional regulator of a subset of genes by interacting with a far upstream element (FUSE). Mounting evidence has collectively demonstrated both the oncogenic and tumor suppressive roles of Fubp1 and the debate regarding its roles in tumorigenesis has been around for several years. Therefore, the detailed molecular mechanisms of Fubp1 need to be determined in each context. In the present study, we showed that the Fubp1 protein level was enriched in the S phase and we identified that Fubp1 deficiency altered cell cycle progression, especially in the S phase, by downregulating the mRNA expression levels of Ccna genes encoding cyclin A. Although this Fubp1-cyclin A axis appears to exist in several types of tumors, Fubp1 showed heterogeneous expression patterns among various cancer tissues, suggesting it exhibits multiple and complicated functions in cancer development. In addition, we showed that Fubp1 deficiency confers survival advantages to cells against metabolic stress and anti-cancer drugs, suggesting that Fubp1 may play both positive and negative roles in malignant development.
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Jane EP, Premkumar DR, Thambireddy S, Golbourn B, Agnihotri S, Bertrand KC, Mack SC, Myers MI, Chattopadhyay A, Taylor DL, Schurdak ME, Stern AM, Pollack IF. Targeting NAD + Biosynthesis Overcomes Panobinostat and Bortezomib-Induced Malignant Glioma Resistance. Mol Cancer Res 2020; 18:1004-1017. [PMID: 32238439 DOI: 10.1158/1541-7786.mcr-19-0669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 12/17/2019] [Accepted: 03/26/2020] [Indexed: 12/12/2022]
Abstract
To improve therapeutic responses in patients with glioma, new combination therapies that exploit a mechanistic understanding of the inevitable emergence of drug resistance are needed. Intratumoral heterogeneity enables a low barrier to resistance in individual patients with glioma. We reasoned that targeting two or more fundamental processes that gliomas are particularly dependent upon could result in pleiotropic effects that would reduce the diversity of resistant subpopulations allowing convergence to a more robust therapeutic strategy. In contrast to the cytostatic responses observed with each drug alone, the combination of the histone deacetylase inhibitor panobinostat and the proteasome inhibitor bortezomib synergistically induced apoptosis of adult and pediatric glioma cell lines at clinically achievable doses. Resistance that developed was examined using RNA-sequencing and pharmacologic screening of resistant versus drug-naïve cells. Quinolinic acid phosphoribosyltransferase (QPRT), the rate-determining enzyme for de novo synthesis of NAD+ from tryptophan, exhibited particularly high differential gene expression in resistant U87 cells and protein expression in all resistant lines tested. Reducing QPRT expression reversed resistance, suggesting that QPRT is a selective and targetable dependency for the panobinostat-bortezomib resistance phenotype. Pharmacologic inhibition of either NAD+ biosynthesis or processes such as DNA repair that consume NAD+ or their simultaneous inhibition with drug combinations, specifically enhanced apoptosis in treatment-resistant cells. Concomitantly, de novo vulnerabilities to known drugs were observed. IMPLICATIONS: These data provide new insights into mechanisms of treatment resistance in gliomas, hold promise for targeting recurrent disease, and provide a potential strategy for further exploration of next-generation inhibitors.
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Affiliation(s)
- Esther P Jane
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Daniel R Premkumar
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania. .,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,University of Pittsburgh Cancer Institute Brain Tumor Center, Pittsburgh, Pennsylvania
| | - Swetha Thambireddy
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brian Golbourn
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sameer Agnihotri
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,University of Pittsburgh Cancer Institute Brain Tumor Center, Pittsburgh, Pennsylvania
| | - Kelsey C Bertrand
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Stephen C Mack
- Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Max I Myers
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ansuman Chattopadhyay
- Molecular Biology Information Service, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - D Lansing Taylor
- Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Mark E Schurdak
- Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Andrew M Stern
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ian F Pollack
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, Pennsylvania. .,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,University of Pittsburgh Cancer Institute Brain Tumor Center, Pittsburgh, Pennsylvania
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Hallal S, Russell BP, Wei H, Lee MYT, Toon CW, Sy J, Shivalingam B, Buckland ME, Kaufman KL. Extracellular Vesicles from Neurosurgical Aspirates Identifies Chaperonin Containing TCP1 Subunit 6A as a Potential Glioblastoma Biomarker with Prognostic Significance. Proteomics 2020; 19:e1800157. [PMID: 30451371 DOI: 10.1002/pmic.201800157] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/01/2018] [Indexed: 12/13/2022]
Abstract
Glioblastoma, WHO-grade IV glioma, carries a dismal prognosis owing to its infiltrative growth and limited treatment options. Glioblastoma-derived extracellular vesicles (EVs; 30-1000 nm membranous particles) influence the microenvironment to mediate tumor aggressiveness and carry oncogenic cargo across the blood-brain barrier into the circulation. As such, EVs are biomarker reservoirs with enormous potential for assessing glioblastoma tumors in situ. Neurosurgical aspirates are rich sources of EVs, isolated directly from glioma microenvironments. EV proteomes enriched from glioblastoma (n = 15) and glioma grade II-III (n = 7) aspirates are compared and 298 differentially-abundant proteins (p-value < 0.00496) are identified using quantitative LC-MS/MS. Along with previously reported glioblastoma-associated biomarkers, levels of all eight subunits of the key molecular chaperone, T-complex protein 1 Ring complex (TRiC), are higher in glioblastoma-EVs, including CCT2, CCT3, CCT5, CCT6A, CCT7, and TCP1 (p < 0.00496). Analogous increases in TRiC transcript levels and DNA copy numbers are detected in silico; CCT6A has the greatest induction of expression and amplification in glioblastoma and shows a negative association with survival (p = 0.006). CCT6A is co-localized with EGFR at 7p11.2, with a strong tendency for co-amplification (p < 0.001). Immunohistochemistry corroborates the CCT6A proteomics measurements and indicated a potential link between EGFR and CCT6A tissue expression. Putative EV-biomarkers described here should be further assessed in peripheral blood.
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Affiliation(s)
- Susannah Hallal
- Brainstorm Brain Cancer Research, Brain and Mind Centre, University of Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia
| | | | - Heng Wei
- Brainstorm Brain Cancer Research, Brain and Mind Centre, University of Sydney, NSW, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Maggie Yuk T Lee
- Brainstorm Brain Cancer Research, Brain and Mind Centre, University of Sydney, NSW, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Joanne Sy
- Brainstorm Brain Cancer Research, Brain and Mind Centre, University of Sydney, NSW, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Brindha Shivalingam
- Brainstorm Brain Cancer Research, Brain and Mind Centre, University of Sydney, NSW, Australia.,Department of Neurosurgery, Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Michael E Buckland
- Brainstorm Brain Cancer Research, Brain and Mind Centre, University of Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, NSW, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Kimberley L Kaufman
- Brainstorm Brain Cancer Research, Brain and Mind Centre, University of Sydney, NSW, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,School of Life and Environmental Science, University of Sydney, NSW, Australia
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44
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González-Tablas M, Arandia D, Jara-Acevedo M, Otero Á, Vital AL, Prieto C, González-Garcia N, Nieto-Librero AB, Tao H, Pascual D, Ruiz L, Sousa P, Galindo-Villardón P, Orfao A, Tabernero MD. Heterogeneous EGFR, CDK4, MDM4, and PDGFRA Gene Expression Profiles in Primary GBM: No Association with Patient Survival. Cancers (Basel) 2020; 12:cancers12010231. [PMID: 31963499 PMCID: PMC7016708 DOI: 10.3390/cancers12010231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The prognostic impact of the expression profile of genes recurrently amplified in glioblastoma multiforme (GBM) remains controversial. METHODS We investigated the RNA gene expression profile of epidermal growth factor receptor (EGFR), cyclin-dependent kinase 4 (CDK4), murine doble minute 4 (MDM4), and platelet derived growth factor receptor alpha (PDGFRA) in 83 primary GBM tumors vs. 42 normal brain tissue samples. Interphase FISH (iFISH) analysis for the four genes, together with analysis of intragenic deletions in EGFR and PDGFRA, were evaluated in parallel at the DNA level. As validation cohort, publicly available RNA gene expression data on 293 samples from 10 different GBM patient series were also studied. RESULTS At the RNA level, CDK4 was the most frequently overexpressed gene (90%) followed by EGFR (58%) and PDGFRA (58%). Chromosome 7 copy number alterations, i.e., trisomy (49%) and polysomy (44%), showed no clear association with EGFR gene expression levels. In turn, intragenic EGFR deletions were found in 39 patients (47%), including EGFRvIII (46%) in association with EGFRvIVa (4%), EGFRvII (2%) or other EGFR deletions (3%) and PDGFRA deletion of exons 8-9 was found in only two tumors (2%). CONCLUSIONS Overall, none of the gene expression profiles and/or intragenic EGFR deletions showed a significant impact on overall survival of GBM supporting the notion that other still unraveled features of the disease might play a more relevant prognostic role in GBM.
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Affiliation(s)
- María González-Tablas
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Centre for Cancer Research (CIC-IBMCC, CSIC/USAL, IBSAL) and Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
| | - Daniel Arandia
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Neurosurgery Service of the University Hospital of Salamanca, 37007 Salamanca, Spain
| | - María Jara-Acevedo
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Biomedical Research Networking Centre on Cancer–CIBER-CIBERONC, Institute of Health Carlos III, 28029 Madrid, Spain
- Sequencing DNA Service (NUCLEUS), University of Salamanca, 37007 Salamanca, Spain
| | - Álvaro Otero
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Neurosurgery Service of the University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Ana-Luisa Vital
- Centre for Neuroscience and Cell Biology and Faculty of Pharmacy, University of Coimbra, 3004-561 Coimbra, Portugal;
| | - Carlos Prieto
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Bioinformatics Service (NUCLEUS), University of Salamanca, 37007 Salamanca, Spain
| | - Nerea González-Garcia
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Department of Statistics, University of Salamanca, 37007 Salamanca, Spain;
| | - Ana Belén Nieto-Librero
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Department of Statistics, University of Salamanca, 37007 Salamanca, Spain;
| | - Herminio Tao
- Neurosurgery Service, University Hospital of Coimbra, 3004-561 Coimbra, Portugal;
| | - Daniel Pascual
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Neurosurgery Service of the University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Laura Ruiz
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Neurosurgery Service of the University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Pablo Sousa
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Neurosurgery Service of the University Hospital of Salamanca, 37007 Salamanca, Spain
| | | | - Alberto Orfao
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Centre for Cancer Research (CIC-IBMCC, CSIC/USAL, IBSAL) and Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
- Biomedical Research Networking Centre on Cancer–CIBER-CIBERONC, Institute of Health Carlos III, 28029 Madrid, Spain
- Correspondence: (A.O.); (M.D.T.); Tel.: +34923-29-11-00 (M.D.T.)
| | - María Dolores Tabernero
- Instituto de Investigación Biomédica de Salamanca, IBSAL—University Hospital of Salamanca, 37007 Salamanca, Spain; (M.G.-T.); (D.A.); (M.J.-A.); (Á.O.); (C.P.); (N.G.-G.); (A.B.N.-L.); (D.P.); (L.R.); (P.S.)
- Centre for Cancer Research (CIC-IBMCC, CSIC/USAL, IBSAL) and Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
- Biomedical Research Networking Centre on Cancer–CIBER-CIBERONC, Institute of Health Carlos III, 28029 Madrid, Spain
- Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL-IBSAL), 37007 Salamanca, Spain
- Correspondence: (A.O.); (M.D.T.); Tel.: +34923-29-11-00 (M.D.T.)
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45
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Stetson LC, Ostrom QT, Schlatzer D, Liao P, Devine K, Waite K, Couce ME, Harris PLR, Kerstetter-Fogle A, Berens ME, Sloan AE, Islam MM, Rajaratnam V, Mirza SP, Chance MR, Barnholtz-Sloan JS. Proteins inform survival-based differences in patients with glioblastoma. Neurooncol Adv 2020; 2:vdaa039. [PMID: 32642694 PMCID: PMC7212893 DOI: 10.1093/noajnl/vdaa039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Improving the care of patients with glioblastoma (GB) requires accurate and reliable predictors of patient prognosis. Unfortunately, while protein markers are an effective readout of cellular function, proteomics has been underutilized in GB prognostic marker discovery. METHODS For this study, GB patients were prospectively recruited and proteomics discovery using liquid chromatography-mass spectrometry analysis (LC-MS/MS) was performed for 27 patients including 13 short-term survivors (STS) (≤10 months) and 14 long-term survivors (LTS) (≥18 months). RESULTS Proteomics discovery identified 11 941 peptides in 2495 unique proteins, with 469 proteins exhibiting significant dysregulation when comparing STS to LTS. We verified the differential abundance of 67 out of these 469 proteins in a small previously published independent dataset. Proteins involved in axon guidance were upregulated in STS compared to LTS, while those involved in p53 signaling were upregulated in LTS. We also assessed the correlation between LS MS/MS data with RNAseq data from the same discovery patients and found a low correlation between protein abundance and mRNA expression. Finally, using LC-MS/MS on a set of 18 samples from 6 patients, we quantified the intratumoral heterogeneity of more than 2256 proteins in the multisample dataset. CONCLUSIONS These proteomic datasets and noted protein variations present a beneficial resource for better predicting patient outcome and investigating potential therapeutic targets.
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Affiliation(s)
- L C Stetson
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Quinn T Ostrom
- Department of Medicine and Division of Hematology-Oncology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Daniela Schlatzer
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Peter Liao
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Karen Devine
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Kristin Waite
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences and Cleveland Center for Health Outcomes Research (CCHOR), Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Marta E Couce
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Peggy L R Harris
- Brain Tumor and Neuro-Oncology Center & Center of Excellence, Translational Neuro-Oncology, Department of Neurosurgery, Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Amber Kerstetter-Fogle
- Brain Tumor and Neuro-Oncology Center & Center of Excellence, Translational Neuro-Oncology, Department of Neurosurgery, Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Michael E Berens
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Brain Tumor and Neuro-Oncology Center & Center of Excellence, Translational Neuro-Oncology, Department of Neurosurgery, Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Mohammad M Islam
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Vilashini Rajaratnam
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Shama P Mirza
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Mark R Chance
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences and Cleveland Center for Health Outcomes Research (CCHOR), Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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46
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Brand F, Förster A, Christians A, Bucher M, Thomé CM, Raab MS, Westphal M, Pietsch T, von Deimling A, Reifenberger G, Claus P, Hentschel B, Weller M, Weber RG. FOCAD loss impacts microtubule assembly, G2/M progression and patient survival in astrocytic gliomas. Acta Neuropathol 2020; 139:175-192. [PMID: 31473790 DOI: 10.1007/s00401-019-02067-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/12/2019] [Accepted: 08/19/2019] [Indexed: 12/23/2022]
Abstract
In search of novel genes associated with glioma pathogenesis, we have previously shown frequent deletions of the KIAA1797/FOCAD gene in malignant gliomas, and a tumor suppressor function of the encoded focadhesin impacting proliferation and migration of glioma cells in vitro and in vivo. Here, we examined an association of reduced FOCAD gene copy number with overall survival of patients with astrocytic gliomas, and addressed the molecular mechanisms that govern the suppressive effect of focadhesin on glioma growth. FOCAD loss was associated with inferior outcome in patients with isocitrate dehydrogenase 1 or 2 (IDH)-mutant astrocytic gliomas of WHO grades II-IV. Multivariate analysis considering age at diagnosis as well as IDH mutation, MGMT promoter methylation, and CDKN2A/B homozygous deletion status confirmed reduced FOCAD gene copy number as a prognostic factor for overall survival. Using a yeast two-hybrid screen and pull-down assays, tubulin beta-6 and other tubulin family members were identified as novel focadhesin-interacting partners. Tubulins and focadhesin co-localized to centrosomes where focadhesin was enriched in proximity to centrioles. Focadhesin was recruited to microtubules via its interaction partner SLAIN motif family member 2 and reduced microtubule assembly rates, possibly explaining the focadhesin-dependent decrease in cell migration. During the cell cycle, focadhesin levels peaked in G2/M phase and influenced time-dependent G2/M progression potentially via polo like kinase 1 phosphorylation, providing a possible explanation for focadhesin-dependent cell growth reduction. We conclude that FOCAD loss may promote biological aggressiveness and worsen clinical outcome of diffuse astrocytic gliomas by enhancing microtubule assembly and accelerating G2/M phase progression.
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Affiliation(s)
- Frank Brand
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Alisa Förster
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Anne Christians
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Martin Bucher
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Carina M Thomé
- Neurology Clinic and National Center for Tumor Diseases, Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc S Raab
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical School, Bonn, 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
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Claus
- Department of Neuroanatomy and Cell Biology, Hannover Medical School, Hannover, Germany
- Center for Systems Neuroscience (ZSN), Hannover, Germany
| | - Bettina Hentschel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Ruthild G Weber
- Department of Human Genetics OE 6300, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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47
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Park CK, Bae JM, Park SH. Long-term survivors of glioblastoma are a unique group of patients lacking universal characteristic features. Neurooncol Adv 2019; 2:vdz056. [PMID: 33842887 PMCID: PMC8023190 DOI: 10.1093/noajnl/vdz056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
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48
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Infratentorial Glioblastoma Metastasis to Bone. World Neurosurg 2019; 131:90-94. [DOI: 10.1016/j.wneu.2019.07.142] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022]
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49
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Cantero D, Rodríguez de Lope Á, Moreno de la Presa R, Sepúlveda JM, Borrás JM, Castresana JS, D'Haene N, García JF, Salmon I, Mollejo M, Rey JA, Hernández-Laín A, Meléndez B. Molecular Study of Long-Term Survivors of Glioblastoma by Gene-Targeted Next-Generation Sequencing. J Neuropathol Exp Neurol 2019; 77:710-716. [PMID: 30010995 DOI: 10.1093/jnen/nly048] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glioblastoma (GBM) is the most common malignant adult primary brain tumor. Despite its high lethality, a small proportion of patients have a relatively long overall survival (OS). Here we report a study of a series of 74 GBM samples from 29 long-term survivors ([LTS] OS ≥36 months) and 45 non-LTS. Using next-generation sequencing, we analyzed genetic alterations in the genes most frequently altered in gliomas. Approximately 20% of LTS had a mutation in the IDH1 or IDH2 (IDH) genes, denoting the relevance of this molecular prognostic factor. A new molecular group of GBMs harbored alterations in ATRX or DAXX genes in the absence of driver IDH or H3F3A mutations. These patients tended to have a slightly better prognosis, to be younger at diagnosis, and to present frontal or temporal tumors, and, morphologically, to present giant tumor cells. A significant fraction of LTS GBM patients had tumors with 1 or more alterations in the relevant GBM signaling pathways (RTK/PI3K, TP53 and RB1). In these patients, the PDGFRA alteration is suggested to be a favorable molecular factor. Our findings here are relevant for developing future targeted therapies and for identifying molecular prognostic factors in GBM patients.
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Affiliation(s)
| | | | | | - Juan M Sepúlveda
- Department of Medical Oncology, 12 de Octubre University Hospital, Madrid, Spain
| | - José M Borrás
- Department of Neurosurgery, Ciudad Real University Hospital, Ciudad Real, Spain
| | - Javier S Castresana
- Department of Biochemistry and Genetics, University of Navarra School of Sciences, Pamplona, Spain
| | - Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Juan F García
- Department of Pathology, MD Anderson Cancer Center, Madrid, Spain
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Manuela Mollejo
- Department of Pathology, Virgen de la Salud Hospital, Toledo, Spain
| | - Juan A Rey
- IdiPaz Research Unit, La Paz University Hospital, Madrid, Spain
| | | | - Bárbara Meléndez
- Department of Pathology, Virgen de la Salud Hospital, Toledo, Spain
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Djuric U, Lam KHB, Kao J, Batruch I, Jevtic S, Papaioannou MD, Diamandis P. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry. Mol Cell Proteomics 2019; 18:2029-2043. [PMID: 31353322 PMCID: PMC6773564 DOI: 10.1074/mcp.ra119.001521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/09/2019] [Indexed: 12/18/2022] Open
Abstract
Molecular characterization of diffuse gliomas has thus far largely focused on genomic and transcriptomic interrogations. Here, we utilized mass spectrometry and overlay protein-level information onto genomically defined cohorts of diffuse gliomas to improve our downstream molecular understanding of these lethal malignancies. Bulk and macrodissected tissues were utilized to quantitate 5,496 unique proteins over three glioma cohorts subclassified largely based on their IDH and 1p19q codeletion status (IDH wild type (IDHwt), n = 7; IDH mutated (IDHmt), 1p19q non-codeleted, n = 7; IDH mutated, 1p19q-codeleted, n = 10). Clustering analysis highlighted proteome and systems-level pathway differences in gliomas according to IDH and 1p19q-codeletion status, including 287 differentially abundant proteins in macrodissection-enriched tumor specimens. IDHwt tumors were enriched for proteins involved in invasiveness and epithelial to mesenchymal transition (EMT), while IDHmt gliomas had increased abundances of proteins involved in mRNA splicing. Finally, these abundance changes were compared with IDH-matched GBM stem-like cells (GSCs) to better pinpoint protein patterns enriched in putative cellular drivers of gliomas. Using this integrative approach, we outline specific proteins involved in chloride transport (e.g. chloride intracellular channel 1, CLIC1) and EMT (e.g. procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3, PLOD3, and serpin peptidase inhibitor clade H member 1, SERPINH1) that showed concordant IDH-status-dependent abundance differences in both primary tissue and purified GSC cultures. Given the downstream position proteins occupy in driving biology and phenotype, understanding the proteomic patterns operational in distinct glioma subtypes could help propose more specific, personalized, and effective targets for the management of patients with these aggressive malignancies.
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Affiliation(s)
- Ugljesa Djuric
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada
| | - K H Brian Lam
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jennifer Kao
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ihor Batruch
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Stefan Jevtic
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada
| | - Michail-Dimitrios Papaioannou
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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