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Mirian C, Thastrup M, Mathiasen R, Schmiegelow K, Olsen JV, Østergaard O. Mass spectrometry-based proteomics of cerebrospinal fluid in pediatric central nervous system malignancies: a systematic review with meta-analysis of individual patient data. Fluids Barriers CNS 2024; 21:14. [PMID: 38350915 PMCID: PMC10863112 DOI: 10.1186/s12987-024-00515-x] [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: 09/21/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The cerebrospinal fluid (CSF) proteome could offer important insights into central nervous system (CNS) malignancies. To advance proteomic research in pediatric CNS cancer, the current study aims to (1) evaluate past mass spectrometry-based workflows and (2) synthesize previous CSF proteomic data, focusing on both qualitative summaries and quantitative re-analysis. MAIN: In our analysis of 11 studies investigating the CSF proteome in pediatric patients with acute lymphoblastic leukemia (ALL) or primary brain tumors, we observed significant methodological variability. This variability negatively affects comparative analysis of the included studies, as per GRADE criteria for quality of evidence. The qualitative summaries covered 161 patients and 134 non-tumor controls, while the application of validation cohort varied among the studies. The quantitative re-analysis comprised 15 B-ALL vs 6 "healthy" controls and 15 medulloblastoma patients vs 22 non-tumor controls. Certain CSF proteins were identified as potential indicators of specific malignancies or stages of neurotoxicity during chemotherapy, yet definitive conclusions were impeded by inconsistent data. There were no proteins with statistically significant differences when comparing cases versus controls that were corroborated across studies where quantitative reanalysis was feasible. From a gene ontology enrichment, we observed that age disparities between unmatched case and controls may mislead to protein correlations more indicative of age-related CNS developmental stages rather than neuro-oncological disease. Despite efforts to batch correct (HarmonizR) and impute missing values, merging of dataset proved unfeasible and thereby limited meaningful data integration across different studies. CONCLUSION Infrequent publications on rare pediatric cancer entities, which often involve small sample sizes, are inherently prone to result in heterogeneous studies-particularly when conducted within a rapidly evolving field like proteomics. As a result, obtaining clear evidence, such as CSF proteome biomarkers for CNS dissemination or early-stage neurotoxicity, is currently impractical. Our general recommendations comprise the need for standardized methodologies, collaborative efforts, and improved data sharing in pediatric CNS malignancy research. We specifically emphasize the possible importance of considering natural age-related variations in CSF due to different CNS development stages when matching cases and controls in future studies.
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Affiliation(s)
- Christian Mirian
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Maria Thastrup
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - René Mathiasen
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Velgaard Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Østergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Fiaschetti G, Abela L, Nonoguchi N, Dubuc AM, Remke M, Boro A, Grunder E, Siler U, Ohgaki H, Taylor MD, Baumgartner M, Shalaby T, Grotzer MA. Epigenetic silencing of miRNA-9 is associated with HES1 oncogenic activity and poor prognosis of medulloblastoma. Br J Cancer 2013; 110:636-47. [PMID: 24346283 PMCID: PMC3915127 DOI: 10.1038/bjc.2013.764] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/31/2013] [Accepted: 11/13/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND microRNA-9 is a key regulator of neuronal development aberrantly expressed in brain malignancies, including medulloblastoma. The mechanisms by which microRNA-9 contributes to medulloblastoma pathogenesis remain unclear, and factors that regulate this process have not been delineated. METHODS Expression and methylation status of microRNA-9 in medulloblastoma cell lines and primary samples were analysed. The association of microRNA-9 expression with medulloblastoma patients' clinical outcome was assessed, and the impact of microRNA-9 restoration was functionally validated in medulloblastoma cells. RESULTS microRNA-9 expression is repressed in a large subset of MB samples compared with normal fetal cerebellum. Low microRNA-9 expression correlates significantly with the diagnosis of unfavourable histopathological variants and with poor clinical outcome. microRNA-9 silencing occurs via cancer-specific CpG island hypermethylation. HES1 was identified as a direct target of microRNA-9 in medulloblastoma, and restoration of microRNA-9 was shown to trigger cell cycle arrest, to inhibit clonal growth and to promote medulloblastoma cell differentiation. CONCLUSIONS microRNA-9 is a methylation-silenced tumour suppressor that could be a potential candidate predictive marker for poor prognosis of medulloblastoma. Loss of microRNA-9 may confer a proliferative advantage to tumour cells, and it could possibly contribute to disease pathogenesis. Thus, re-expression of microRNA-9 may constitute a novel epigenetic regulation strategy against medulloblastoma.
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Affiliation(s)
- G Fiaschetti
- Neuro-Oncology group, Experimental Infectious Diseases and Cancer Research, August-Forel Strasse 1, Zurich CH-8008, Switzerland
| | - L Abela
- Division of Oncology, University Children's Hospital of Zürich, Steinwiesstrasse 75, Zurich CH-8032, Switzerland
| | - N Nonoguchi
- International Agency for Research on Cancer, World Health Organization, Section of Molecular Pathology, 150 Cours Albert Thomas, 69372, Lyon Cedex 08, France
| | - A M Dubuc
- Arthur and Sonia Labatt Brain Tumour Research Centre, MaRS Centre - 11-401M, 101 College Street, Toronto, ON M5G1L7, Canada
| | - M Remke
- Brain Tumor Research Centre, 101 College Street, TMDT-11-401M, Toronto, ON M5G1L7, Canada
| | - A Boro
- Oncology group, Experimental Infectious Diseases and Cancer Research, August-Forel Strasse 1, Zurich CH-8008, Switzerland
| | - E Grunder
- Division of Oncology, University Children's Hospital of Zürich, Steinwiesstrasse 75, Zurich CH-8032, Switzerland
| | - U Siler
- Division of Immunology, University Children's Hospital of Zürich, Steinwiesstrasse 75, Zurich CH-8032, Switzerland
| | - H Ohgaki
- International Agency for Research on Cancer, World Health Organization, Section of Molecular Pathology, 150 Cours Albert Thomas, 69372, Lyon Cedex 08, France
| | - M D Taylor
- The Hospital for Sick Children, Division of Neurosurgery, Suite 1504, 555 University Avenue, Toronto, ON M5G1X8, Canada
| | - M Baumgartner
- Neuro-Oncology group, Experimental Infectious Diseases and Cancer Research, August-Forel Strasse 1, Zurich CH-8008, Switzerland
| | - T Shalaby
- Neuro-Oncology group, Experimental Infectious Diseases and Cancer Research, August-Forel Strasse 1, Zurich CH-8008, Switzerland
| | - M A Grotzer
- Division of Oncology, University Children's Hospital of Zürich, Steinwiesstrasse 75, Zurich CH-8032, Switzerland
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Rossi A, Russo G, Puca A, La Montagna R, Caputo M, Mattioli E, Lopez M, Giordano A, Pentimalli F. The antiretroviral nucleoside analogue Abacavir reduces cell growth and promotes differentiation of human medulloblastoma cells. Int J Cancer 2009; 125:235-43. [PMID: 19358275 DOI: 10.1002/ijc.24331] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Abacavir is one of the most efficacious nucleoside analogues, with a well-characterized inhibitory activity on reverse transcriptase enzymes of retroviral origin, and has been clinically approved for the treatment of AIDS. Recently, Abacavir has been shown to inhibit also the human telomerase activity. Telomerase activity seems to be required in essentially all tumours for the immortalization of a subset of cells, including cancer stem cells. In fact, many cancer cells are dependent on telomerase for their continued replication and therefore telomerase is an attractive target for cancer therapy. Telomerase expression is upregulated in primary primitive neuroectodermal tumours and in the majority of medulloblastomas suggesting that its activation is associated with the development of these diseases. Therefore, we decided to test Abacavir activity on human medulloblastoma cell lines with high telomerase activity. We report that exposure to Abacavir induces a dose-dependent decrease in the proliferation rate of medulloblastoma cells. This is associated with a cell accumulation in the G(2)/M phase of the cell cycle in the Daoy cell line, and with increased cell death in the D283-MED cell line, and is likely to be dependent on the inhibition of telomerase activity. Interestingly, both cell lines showed features of senescence after Abacavir treatment. Moreover, after Abacavir exposure we detected, by immunofluorescence staining, increased protein expression of the glial marker glial fibrillary acidic protein and the neuronal marker synaptophysin in both medulloblastoma cell lines. In conclusion, our results suggest that Abacavir reduces proliferation and induces differentiation of human medulloblastoma cells through the downregulation of telomerase activity. Thus, using Abacavir, alone or in combination with current therapies, might be an effective therapeutic strategy for the treatment of medulloblastoma.
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Affiliation(s)
- Alessandra Rossi
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia PA
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