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Aubin RG, Troisi EC, Montelongo J, Alghalith AN, Nasrallah MP, Santi M, Camara PG. Pro-inflammatory cytokines mediate the epithelial-to-mesenchymal-like transition of pediatric posterior fossa ependymoma. Nat Commun 2022; 13:3936. [PMID: 35803925 PMCID: PMC9270322 DOI: 10.1038/s41467-022-31683-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/28/2022] [Indexed: 12/13/2022] Open
Abstract
Pediatric ependymoma is a devastating brain cancer marked by its relapsing pattern and lack of effective chemotherapies. This shortage of treatments is due to limited knowledge about ependymoma tumorigenic mechanisms. By means of single-nucleus chromatin accessibility and gene expression profiling of posterior fossa primary tumors and distal metastases, we reveal key transcription factors and enhancers associated with the differentiation of ependymoma tumor cells into tumor-derived cell lineages and their transition into a mesenchymal-like state. We identify NFκB, AP-1, and MYC as mediators of this transition, and show that the gene expression profiles of tumor cells and infiltrating microglia are consistent with abundant pro-inflammatory signaling between these populations. In line with these results, both TGF-β1 and TNF-α induce the expression of mesenchymal genes on a patient-derived cell model, and TGF-β1 leads to an invasive phenotype. Altogether, these data suggest that tumor gliosis induced by inflammatory cytokines and oxidative stress underlies the mesenchymal phenotype of posterior fossa ependymoma.
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Affiliation(s)
- Rachael G Aubin
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Emma C Troisi
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Javier Montelongo
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Adam N Alghalith
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maclean P Nasrallah
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pablo G Camara
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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2
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An Insight into Pathophysiological Features and Therapeutic Advances on Ependymoma. Cancers (Basel) 2021; 13:cancers13133221. [PMID: 34203272 PMCID: PMC8269186 DOI: 10.3390/cancers13133221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Although biological information and the molecular classification of ependymoma have been studied, the treatment systems for ependymoma are still insufficient. In addition, because the disease occurs infrequently, it is difficult to obtain sufficient data to conduct large-scale or randomized clinical trials. Therefore, this study is intended to emphasize the importance of understanding its pathological characteristics and prognosis as well as developing treatments for ependymoma through multilateral studies. Abstract Glial cells comprise the non-sensory parts of the central nervous system as well as the peripheral nervous system. Glial cells, also known as neuroglia, constitute a significant portion of the mammalian nervous system and can be viewed simply as a matrix of neural cells. Despite being the “Nervenkitt” or “glue of the nerves”, they aptly serve multiple roles, including neuron repair, myelin sheath formation, and cerebrospinal fluid circulation. Ependymal cells are one of four kinds of glial cells that exert distinct functions. Tumorigenesis of a glial cell is termed a glioma, and in the case of an ependymal cell, it is called an ependymoma. Among the various gliomas, an ependymoma in children is one of the more challenging brain tumors to cure. Children are afflicted more severely by ependymal tumors than adults. It has appeared from several surveys that ependymoma comprises approximately six to ten percent of all tumors in children. Presently, the surgical removal of the tumor is considered a standard treatment for ependymomas. It has been conspicuously evident that a combination of irradiation therapy and surgery is much more efficacious in treating ependymomas. The main purpose of this review is to present the importance of both a deep understanding and ongoing research into histopathological features and prognoses of ependymomas to ensure that effective diagnostic methods and treatments can be developed.
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3
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Tsangaris GT, Anastasoviti MC, Anagnostopoulos AK. Proteomics of pediatric ependymomas: a review. Childs Nerv Syst 2021; 37:767-770. [PMID: 32377827 DOI: 10.1007/s00381-020-04627-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/16/2020] [Indexed: 12/11/2022]
Abstract
Ependymomas, affecting both children and adults, are neuroepithelial tumors occurring throughout all compartments of the central nervous system. Pediatric ependymomas arise almost exclusively intracranially and are associated with a poor 10-year overall survival of around 60%. During the last years, the application of multi-omics technologies on the study and understanding of neuro-cancer diseases has become a standard; in this regard, application of these approaches on ependymomas has gained noticeable momentum. The objective of this review article was to summarize all knowledge generated by the application of modern omics approaches with regard to pediatric ependymal tumors, aiming at elucidating molecular mechanisms of oncogenesis as well as identification of pathway strategies that will help in therapeutic intervention.
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Affiliation(s)
- George Th Tsangaris
- Department of Proteomics, Division of Biotechnology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Maria C Anastasoviti
- Department of Proteomics, Division of Biotechnology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Athanasios K Anagnostopoulos
- Department of Proteomics, Division of Biotechnology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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4
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Montero AS, Tran S, Amelot A, Berriat F, Lot G, Gaillard S, Villa C, Polivka M, Adam C, Idbaih A, Feuvret L, Carpentier A, Parker F, Bielle F, Mathon B. Clinical characteristics and long-term surgical outcome of spinal myxopapillary ependymoma: a French cohort of 101 patients. J Neurooncol 2021; 152:491-499. [PMID: 33624261 DOI: 10.1007/s11060-021-03717-7] [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] [Received: 12/21/2020] [Accepted: 02/12/2021] [Indexed: 10/22/2022]
Abstract
PURPOSE Myxopapillary ependymoma (MPE) is the most frequent tumor affecting the medullary conus. The surgical therapeutic management is still debated and only few studies have focused on the postoperative clinical outcome of patients. This study aimed to demonstrate long-term postoperative outcome and to assess the predictive factors of recurrence as well as the clinical evolution of these patients. METHODS From 1984 to 2019, in four French centers, 101 adult patients diagnosed with MPE were retrospectively included. RESULTS Median age at surgery was 39 years. Median tumor size was 50 mm and lesions were multifocal in 13% of patients. All patients benefited from surgery and one patient received postoperative radiotherapy. Gross total resection was obtained in 75% of cases. Sixteen percent of patients presented recurrence after a median follow-up of 70 months. Progression free survival at 5 and 10 years were respectively estimated at 83% and 79%. After multivariable analysis, sacral localization, and subtotal resection were shown to be independently associated with tumor recurrence. 85% of the patients had a favorable evolution concerning pain. 12% of the patients presented a postoperative deterioration of sphincter function and 4% of motor function. CONCLUSION Surgery alone is an acceptable option for MPE patients. Patients with sacral location or incomplete resection are at high risk of recurrence and should be carefully monitored.
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Affiliation(s)
- Anne-Sophie Montero
- Department of Neurosurgery, Sorbonne University, AP-HP, La Pitié-Salpêtrière Hospital, 47-83, boulevard de L'Hôpital, 75651, Paris Cedex 13, France
| | - Suzanne Tran
- Department of Neuropathology, Sorbonne University, AP-HP, La Pitié-Salpêtrière Hospital, Paris, France
| | - Aymeric Amelot
- Department of Neurosurgery, Sorbonne University, AP-HP, La Pitié-Salpêtrière Hospital, 47-83, boulevard de L'Hôpital, 75651, Paris Cedex 13, France
| | - Félix Berriat
- Inserm U 1127, CNRS UMR 7225, UMR S 1127, Paris Brain Institute, ICM, Sorbonne Université, 75013, Paris, France
| | - Guillaume Lot
- Department of Neurosurgery, Fondation Ophtalmologique Rothschild, Paris, France
| | | | - Chiara Villa
- INSERM U 1016, Institut Cochin, 75014, Paris, France.,NCRS UMR 8104, 75014, Paris, France.,Université Paris Descartes-Université de Paris, 75006, Paris, France.,Department of Pathological Cytology and Anatomy, Foch Hospital, 92151, Suresnes, France
| | - Marc Polivka
- Department of Pathological Cytology and Anatomy, Lariboisière Hospital, APHP, 75010, Paris, France
| | - Clovis Adam
- Department of Neuropathology, GHU Paris-Sud-Hôpital Bicêtre, le Kremlin-Bicêtre, France
| | - Ahmed Idbaih
- Inserm, CNRS, UMR S 1127, Institut du Cerveau Et de La Moelle Épinière, ICM, Sorbonne Université, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, 75013, Paris, France
| | - Loïc Feuvret
- Department of Radiotherapy, Sorbonne University, AP-HP, La Pitié-Salpêtrière Hospital, Paris, France
| | - Alexandre Carpentier
- Department of Neurosurgery, Sorbonne University, AP-HP, La Pitié-Salpêtrière Hospital, 47-83, boulevard de L'Hôpital, 75651, Paris Cedex 13, France
| | - Fabrice Parker
- Department of Neurosurgery, Hôpitaux Universitaires Paris-Sud, AP-HP, Centre Hospitalier Universitaire Bicêtre, Paris, France
| | - Franck Bielle
- Department of Neuropathology, Sorbonne University, AP-HP, La Pitié-Salpêtrière Hospital, Paris, France.,Inserm U 1127, CNRS UMR 7225, UMR S 1127, Paris Brain Institute, ICM, Sorbonne Université, 75013, Paris, France
| | - Bertrand Mathon
- Department of Neurosurgery, Sorbonne University, AP-HP, La Pitié-Salpêtrière Hospital, 47-83, boulevard de L'Hôpital, 75651, Paris Cedex 13, France. .,Inserm U 1127, CNRS UMR 7225, UMR S 1127, Paris Brain Institute, ICM, Sorbonne Université, 75013, Paris, France.
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5
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Chan JL, Kashanian A, Bannykh SI, Majlessipour F, Breunig JJ, Danielpour M. RELA Fusion-Positive Ependymoma in a Child with Down Syndrome: A Case Report. Pediatr Neurosurg 2021; 56:146-151. [PMID: 33690230 DOI: 10.1159/000511673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 09/12/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Down syndrome (DS) is the most common multiple malformation syndrome in humans and is associated with an increased risk of childhood malignancy, particularly leukemia. Incidence of brain tumors in patients with DS is limited to sporadic cases. We report the first case of a RELA fusion-positive ependymoma in a 3-year-old boy with DS. CASE PRESENTATION Imaging prompted by new left-sided hemiparesis demonstrated an 8-cm hemorrhagic right temporal-parietal mass. Subsequent image-complete resection confirmed a RELA fusion-positive anaplastic ependymoma with 90% OLIG2 staining. Postoperatively, the patient, unfortunately, experienced fatal recurrence and drop metastases with leptomeningeal involvement. CONCLUSION To our knowledge, this is the first reported case of a confirmed RELA fusion-positive ependymoma in a child with DS. We discuss this finding in the context of intracranial tumors in children with DS, as well as the finding of 90% positive OLIG2 expression and its potential as a prognostic marker.
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Affiliation(s)
- Julie L Chan
- Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Alon Kashanian
- Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Serguei I Bannykh
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Fataneh Majlessipour
- Department of Pediatric Hematology and Oncology, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Moise Danielpour
- Maxine Dunitz Neurosurgical Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA,
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6
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Persistent Ependymal Tumor Arising from an Immature Ovarian Teratoma: A Rare Case. JOURNAL OF MOLECULAR PATHOLOGY 2020. [DOI: 10.3390/jmp1010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Primary ovarian ependymoma is a rare neuroectodermal neoplasm that can arise from immature ovarian teratoma. Due to the paucity of this entity, a complete molecular analysis of these tumors has not been done, thus creating a challenge for finding an effective and safe therapeutic treatment. In the limited literature, patients with primary ovarian ependymoma showed various responses to an array of individualized therapies, ranging from surgeries to chemotherapies. Here, we present a 38-year-old female with persistent ovarian ependymoma, with a molecular profile similar to traditional central nervous system ependymoma that is irresponsive to multiple cytoreduction and clinical experimental therapies. Therefore, a prompt recognition and reporting of this entity can greatly aid in expanding the understanding and standardization of therapies for this neoplasm.
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Kotecha R, Mehta MP, Chang EL, Brown PD, Suh JH, Lo SS, Das S, Samawi HH, Keith J, Perry J, Sahgal A. Updates in the management of intradural spinal cord tumors: a radiation oncology focus. Neuro Oncol 2020; 21:707-718. [PMID: 30977511 DOI: 10.1093/neuonc/noz014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Primary spinal cord tumors represent a hetereogeneous group of central nervous system malignancies whose management is complex given the relatively uncommon nature of the disease and variety of tumor subtypes, functional neurologic deficits from the tumor, and potential morbidities associated with definitive treatment. Advances in neuroimaging; integration of diagnostic, prognostic, and predictive molecular testing into tumor classification; and developments in neurosurgical techniques have refined the current role of radiotherapy in the multimodal management of patients with primary spinal cord tumors, and corroborated the need for prospective, multidisciplinary discussion and treatment decision making. Radiotherapeutic technological advances have dramatically improved the entire continuum from treatment planning to treatment delivery, and the development of stereotactic radiosurgery and proton radiotherapy provides new radiotherapy options for patients treated in the definitive, adjuvant, or salvage setting. The objective of this comprehensive review is to provide a contemporary overview of the management of primary intradural spinal cord tumors, with a focus on radiotherapy.
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Affiliation(s)
- Rupesh Kotecha
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Miami, Florida, USA.,Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
| | - Minesh P Mehta
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Miami, Florida, USA.,Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
| | - Eric L Chang
- Department of Radiation Oncology, University of Southern California, Los Angeles, California, USA
| | - Paul D Brown
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - John H Suh
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Taussig Cancer Institute, Cleveland, Ohio, USA.,Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Simon S Lo
- Department of Radiation Oncology, University of Washington, Seattle, Washington, USA
| | - Sunit Das
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Haider H Samawi
- Division of Hematology/Oncology, St Michael's Hospital, Toronto, Ontario, Canada
| | - Julia Keith
- Department of Anatomical Pathology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - James Perry
- Department of Neurology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Arjun Sahgal
- Department of Radiation Oncology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
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8
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Rauschenbach L. Spinal Cord Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1226:97-109. [PMID: 32030679 DOI: 10.1007/978-3-030-36214-0_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intramedullary spinal cord tumors (IMSCT) are rare entities for which there currently exist no standardized treatment paradigms. Consequently, patients usually receive treatment modalities that were established for intracerebral tumors; these approaches, however, typically result in functional impairment, recurrent tumor growth, and short overall survival. There is a distinct lack of promising research efforts in this field, which raises questions about whether spinal cord tumor microenvironment (TME) might promote the development, progression, and treatment resistance of IMSCT. In this review, we aim to examine spinal cord biology, compare spinal cord and brain microenvironments, and discuss mutual interactions between IMSCT and TME. Manipulating these pathways may provide new treatment approaches for future patient groups.
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Affiliation(s)
- Laurèl Rauschenbach
- Department of Neurosurgery, University Hospital Essen, Essen, Germany. .,DKFZ Division of Translational Neuro-Oncology at the West German Cancer Center (WTZ), German Cancer Consortium (DKTK) Partner Site, University Hospital Essen, Essen, Germany.
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9
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Zhang M, Iyer RR, Azad TD, Wang Q, Garzon-Muvdi T, Wang J, Liu A, Burger P, Eberhart C, Rodriguez FJ, Sciubba DM, Wolinsky JP, Gokaslan Z, Groves ML, Jallo GI, Bettegowda C. Genomic Landscape of Intramedullary Spinal Cord Gliomas. Sci Rep 2019; 9:18722. [PMID: 31822682 PMCID: PMC6904446 DOI: 10.1038/s41598-019-54286-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/28/2019] [Indexed: 12/28/2022] Open
Abstract
Intramedullary spinal cord tumors (IMSCTs) are rare neoplasms that have limited treatment options and are associated with high rates of morbidity and mortality. To better understand the genetic basis of these tumors we performed whole exome sequencing on 45 tumors and matched germline DNA, including twenty-nine spinal cord ependymomas and sixteen astrocytomas. Though recurrent somatic mutations in IMSCTs were rare, we identified NF2 mutations in 15.7% of tumors (ependymoma, N = 7; astrocytoma, N = 1), RP1 mutations in 5.9% of tumors (ependymoma, N = 3), and ESX1 mutations in 5.9% of tumors (ependymoma, N = 3). We further identified copy number amplifications in CTU1 in 25% of myxopapillary ependymomas. Given the paucity of somatic driver mutations, we further performed whole-genome sequencing of 12 tumors (ependymoma, N = 9; astrocytoma, N = 3). Overall, we observed that IMSCTs with intracranial histologic counterparts (e.g. glioblastoma) did not harbor the canonical mutations associated with their intracranial counterparts. Our findings suggest that the origin of IMSCTs may be distinct from tumors arising within other compartments of the central nervous system and provides the framework to begin more biologically based therapeutic strategies.
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Affiliation(s)
- Ming Zhang
- Ludwig Center for Cancer Genetics, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Rajiv R Iyer
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Tej D Azad
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.,Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Qing Wang
- Ludwig Center for Cancer Genetics, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Tomas Garzon-Muvdi
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.,Department of Neurological Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joanna Wang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Ann Liu
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Peter Burger
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Charles Eberhart
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Fausto J Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Daniel M Sciubba
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Jean-Paul Wolinsky
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.,Department of Neurosurgery, Northwestern University School of Medicine, Chicago, IL, USA
| | - Ziya Gokaslan
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.,Department of Neurosurgery, Brown University School of Medicine, Providence, RI, USA
| | - Mari L Groves
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - George I Jallo
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA. .,Department of Neurosurgery, Johns Hopkins All Children's Hospital, Saint Petersburg, FL, USA.
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA. .,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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10
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Ependymoma of the Spinal Cord in Children: A Retrospective French Study. World Neurosurg 2019; 126:e1035-e1041. [DOI: 10.1016/j.wneu.2019.03.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 11/23/2022]
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11
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Butt E, Alyami S, Nageeti T, Saeed M, AlQuthami K, Bouazzaoui A, Athar M, Abduljaleel Z, Al-Allaf F, Taher M. Mutation profiling of anaplastic ependymoma grade III by Ion Proton next generation DNA sequencing. F1000Res 2019; 8:613. [PMID: 32612806 PMCID: PMC7317822 DOI: 10.12688/f1000research.18721.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/15/2020] [Indexed: 12/31/2022] Open
Abstract
Background: Ependymomas are glial tumors derived from differentiated ependymal cells. In contrast to other types of brain tumors, histological grading is not a good prognostic marker for these tumors. In order to determine genomic changes in an anaplastic ependymoma, we analyzed its mutation patterns by next generation sequencing (NGS). Methods: Tumor DNA was sequenced using an Ion PI v3 chip on Ion Proton instrument and the data were analyzed by Ion Reporter 5.6. Results: NGS analysis identified 19 variants, of which four were previously reported missense variants; c.395G>A in IDH1, c.1173A>G in PIK3CA, c.1416A>T in KDR and c.215C>G in TP53. The frequencies of the three missense mutations ( PIK3CA c.1173A>G, KDR c.1416A>T, TP53, c.215C>G) were high, suggesting that these are germline variants, whereas the IDH1 variant frequency was low (4.81%). However, based on its FATHMM score of 0.94, only the IDH1 variant is pathogenic; other variants TP53, PIK3CA and KDR had FATHMM scores of 0.22, 0.56 and 0.07, respectively. Eight synonymous mutations were found in FGFR3, PDGFRA, EGFR, RET, HRAS, FLT3, APC and SMAD4 genes. The mutation in FLT3 p.(Val592Val) was the only novel variant found. Additionally, two known intronic variants in KDR were found and intronic variants were also found in ERBB4 and PIK3CA. A known splice site mutation at an acceptor site in FLT3, a 3'-UTR variant in the CSF1R gene and a 5'_UTR variant in the SMARCB1 gene were also identified. The p-values were below 0.00001 for all variants and the average coverage for all variants was around 2000x. Conclusions: In this grade III ependymoma, one novel synonymous mutation and one deleterious missense mutation is reported. Many of the variants reported here have not been detected in ependymal tumors by NGS analysis previously and we therefore report these variants in brain tissue for the first time.
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Affiliation(s)
- Ejaz Butt
- Histopathology Division, Al-Noor Specialty Hospital, Makkah, Makkah, Saudi Arabia
- Histopathology Department, Amna Inayat Medical College, Sheikhupura, Punjab, Pakistan
| | - Sabra Alyami
- Department of Medical Genetics, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Tahani Nageeti
- Department of Radiation Oncology, King Abdullah Medical City, Makkah, Makkah, Saudi Arabia
| | - Muhammad Saeed
- Faculty of Medicine, Umm-Al-Qura University and Al-Noor Specialty Hospital, Makkah, Makkah, Saudi Arabia
| | - Khalid AlQuthami
- Department of Laboratory Medicine and Blood Bank, Al-Noor Specialty Hospital, Makkah, Makkah, Saudi Arabia
| | - Abdellatif Bouazzaoui
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Mohammad Athar
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Zainularifeen Abduljaleel
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Faisal Al-Allaf
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Mohiuddin Taher
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
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12
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Butt E, Alyami S, Nageeti T, Saeed M, AlQuthami K, Bouazzaoui A, Athar M, Abduljaleel Z, Al-Allaf F, Taher M. Mutation profiling of anaplastic ependymoma grade III by Ion Proton next generation DNA sequencing. F1000Res 2019; 8:613. [PMID: 32612806 PMCID: PMC7317822 DOI: 10.12688/f1000research.18721.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/26/2019] [Indexed: 03/30/2024] Open
Abstract
Background: Ependymomas are glial tumors derived from differentiated ependymal cells. In contrast to other types of brain tumors, histological grading is not a good prognostic marker for these tumors. In order to determine genomic changes in an anaplastic ependymoma, we analyzed its mutation patterns by next generation sequencing (NGS). Methods: Tumor DNA was sequenced using an Ion PI v3 chip on Ion Proton instrument and the data were analyzed by Ion Reporter 5.6. Results: NGS analysis identified 19 variants, of which four were previously reported missense variants; c.395G>A in IDH1, c.1173A>G in PIK3CA, c.1416A>T in KDR and c.215C>G in TP53. The frequencies of the three missense mutations ( PIK3CA c.1173A>G, KDR c.1416A>T, TP53, c.215C>G) were high, suggesting that these are germline variants, whereas the IDH1 variant frequency was low (4.81%). However, based on its FATHMM score of 0.94, only the IDH1 variant is pathogenic; other variants TP53, PIK3CA and KDR had FATHMM scores of 0.22, 0.56 and 0.07, respectively. Eight synonymous mutations were found in FGFR3, PDGFRA, EGFR, RET, HRAS, FLT3, APC and SMAD4 genes. The mutation in FLT3 p.(Val592Val) was the only novel variant found. Additionally, two known intronic variants in KDR were found and intronic variants were also found in ERBB4 and PIK3CA. A known splice site mutation at an acceptor site in FLT3, a 3'-UTR variant in the CSF1R gene and a 5'_UTR variant in the SMARCB1 gene were also identified. The p-values were below 0.00001 for all variants and the average coverage for all variants was around 2000x. Conclusions: In this grade III ependymoma, one novel synonymous mutation and one deleterious missense mutation is reported. Many of the variants reported here have not been detected in ependymal tumors by NGS analysis previously and we therefore report these variants in brain tissue for the first time.
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Affiliation(s)
- Ejaz Butt
- Histopathology Division, Al-Noor Specialty Hospital, Makkah, Makkah, Saudi Arabia
- Histopathology Department, Amna Inayat Medical College, Sheikhupura, Punjab, Pakistan
| | - Sabra Alyami
- Department of Medical Genetics, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Tahani Nageeti
- Department of Radiation Oncology, King Abdullah Medical City, Makkah, Makkah, Saudi Arabia
| | - Muhammad Saeed
- Faculty of Medicine, Umm-Al-Qura University and Al-Noor Specialty Hospital, Makkah, Makkah, Saudi Arabia
| | - Khalid AlQuthami
- Department of Laboratory Medicine and Blood Bank, Al-Noor Specialty Hospital, Makkah, Makkah, Saudi Arabia
| | - Abdellatif Bouazzaoui
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Mohammad Athar
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Zainularifeen Abduljaleel
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Faisal Al-Allaf
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
| | - Mohiuddin Taher
- Department of Medical Genetics and Science and Technology Unit, Umm-Al-Qura University, Makkah, Makkah, Saudi Arabia
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Azad TD, Jiang B, Bettegowda C. Molecular foundations of primary spinal tumors-implications for surgical management. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:222. [PMID: 31297387 DOI: 10.21037/atm.2019.04.46] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Primary spinal tumors are rare lesions that require careful clinical management due to their intimate relationship with critical neurovascular structures and the significant associated risk of morbidity. While the advent of molecular and genomic profiling is beginning to impact the management of the cranial counterparts, translation for spinal tumors has lagged behind. Maximal safe surgical resection remains the mainstay of patients with primary spinal tumors, with extent of resection and histology the only consistently identified independent predictors of survival. Adjuvant therapy has had limited impact. To develop targeted neoadjuvant and adjuvant therapies, improve prognostication, and enhance patient selection in spinal oncology, a thorough understanding of the current molecular and genomic landscape of spinal tumors is required. In this review, we detail the epidemiology, current standard-of-care, and molecular features of the most commonly encountered intramedullary spinal cord tumors (IMSCT), intradural extramedullary (IDEM) tumors, and primary spinal column malignancies (PSCM). We further discuss current efforts and future opportunities for integrating molecular advances in spinal oncology with clinical management.
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Affiliation(s)
- Tej D Azad
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Bowen Jiang
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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14
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Narasimhaiah D, Legrand C, Damotte D, Remark R, Munda M, De Potter P, Coulie PG, Vikkula M, Godfraind C. DNA alteration-based classification of uveal melanoma gives better prognostic stratification than immune infiltration, which has a neutral effect in high-risk group. Cancer Med 2019; 8:3036-3046. [PMID: 31025552 PMCID: PMC6558590 DOI: 10.1002/cam4.2122] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/12/2018] [Accepted: 12/27/2018] [Indexed: 01/21/2023] Open
Abstract
Background In uveal melanomas, immune infiltration is a marker of poor prognosis. This work intended to decipher the biological characteristics of intra‐tumor immune population, compare it to other established biomarkers and to patients' outcome. Methods Primary, untreated, and mainly large uveal melanomas with retinal detachment were analyzed using: transcriptomic profiling (n = 15), RT‐qPCR (n = 36), immunohistochemistry (n = 89), Multiplex Ligation‐dependent Probe Amplification (MLPA) for copy number alterations (CNA) analysis (n = 89), array‐CGH (n = 17), and survival statistics (n = 86). Results Gene expression analysis divided uveal melanomas into two groups, according to the IFNγ/STAT1‐IRF1 pathway activation. Tumors with IFNγ‐signature had poorer prognosis and showed increased infiltration of CD8+ T lymphocytes and macrophages. Cox multivariate analyses of immune cell infiltration with MLPA data delineated better prognostic value for three prognostic groups (three‐tier stratification) than two (two‐tier stratification). CNA‐based model comprising monosomy 3, 8q amplification, and LZTS1and NBL1 deletions emerged as the best predictor for disease‐free survival. It outperformed immune cell infiltration in receiver operating characteristic curves. The model that combined CNA and immune infiltration defined risk‐groups according to the number of DNA alterations. Immune cell infiltration was increased in the high‐risk group (73.7%), where it did not correlate with patient survival, while it was associated with poorer outcome in the intermediate risk‐group. Conclusions High degree of immune cell infiltration occurs in a subset of uveal melanomas, is interferon‐gamma‐related, and associated with poor survival. It allows for two‐tier stratification, which is prognostically less efficient than a three‐tier one. The best prognostic stratification is by CNA model with three risk‐groups where immune cell infiltration impacts only some subgroups.
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Affiliation(s)
- Deepti Narasimhaiah
- Human Molecular Genetics, de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Catherine Legrand
- Institute of Statistics, Biostatistics and Actuarial Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Diane Damotte
- Team "Cancer, Immune control, and Escape", Centre de Recherche des Cordeliers, INSERM U1138, Paris, France
| | - Romain Remark
- Team "Cancer, Immune control, and Escape", Centre de Recherche des Cordeliers, INSERM U1138, Paris, France
| | - Marco Munda
- Institute of Statistics, Biostatistics and Actuarial Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Patrick De Potter
- Department of Ophthalmology, Université catholique de Louvain, Brussels, Belgium
| | - Pierre G Coulie
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Catherine Godfraind
- Human Molecular Genetics, de Duve Institute, Université catholique de Louvain, Brussels, Belgium.,Department of Pathology, CHU Gabriel Montpied, Clermont-Ferrand, France
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15
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Abd-El-Barr MM, Huang KT, Moses ZB, Iorgulescu JB, Chi JH. Recent advances in intradural spinal tumors. Neuro Oncol 2019; 20:729-742. [PMID: 29216380 DOI: 10.1093/neuonc/nox230] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Intradural spinal tumors are rare tumors of the central nervous system. Due to the eloquence of the spinal cord and its tracts, the compact architecture of the cord and nerves, and the infiltrative nature of some of these tumors, surgical resection is difficult to achieve without causing neurological deficits. Likewise, chemotherapy and radiotherapy are utilized more cautiously in the treatment of intradural spinal tumors than their cranial counterparts. Targeted therapies aimed at the genetic alterations and molecular biology tailored to these tumors would be helpful but are lacking.Here, we review the major types of intradural spinal tumors, with an emphasis on genetic alterations, molecular biology, and experimental therapies for these difficult to treat neoplasms.
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Affiliation(s)
- Muhammad M Abd-El-Barr
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kevin T Huang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ziev B Moses
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - J Bryan Iorgulescu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - John H Chi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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16
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Fuller C. A little piece of mind: best practices for brain tumor intraoperative consultation. Mod Pathol 2019; 32:44-57. [PMID: 30600316 DOI: 10.1038/s41379-018-0147-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 07/31/2018] [Indexed: 01/01/2023]
Abstract
The workup of the vast majority of brain tumors is initiated at intraoperative consultation. These fresh tumor samples are often quite small and given the nature of the "prime real estate" being sampled, there is never a guarantee that additional tissue will be provided to the responsible pathologist upon request. The 2016 World Health Organization (WHO) Classification of Central Nervous System (CNS) Tumors introduced the concept of "integrative diagnoses," many diagnostic entities now requiring molecular testing in addition to the more routine pathologic workup. Molecular testing relative to targeted therapeutics may also be requested in many circumstances. That said, appropriate preparation for and handling of any potential brain tumor sample at intraoperative consultation is crucial to (1) provide diagnostic information to the operating neurosurgeon that can influence the course of the procedure, and (2) best allow for any necessary ancillary studies purposed for diagnosis and patient care. This review highlights best practices in handling brain tumor intraoperative consultations in this era of expanding required molecular testing. Included is a high-yield overview of ancillary/molecular testing commonly utilized in the workup of infiltrative gliomas, CNS embryonal tumors, and ependymomas, as well as molecular testing to aid in determination of targeted therapeutic options.
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Affiliation(s)
- Christine Fuller
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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17
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Malgulwar PB, Sharma V, Tomar AS, Verma C, Nambirajan A, Singh M, Suri V, Sarkar C, Sharma MC. Transcriptional co-expression regulatory network analysis for Snail and Slug identifies IL1R1, an inflammatory cytokine receptor, to be preferentially expressed in ST-EPN- RELA and PF-EPN-A molecular subgroups of intracranial ependymomas. Oncotarget 2018; 9:35480-35492. [PMID: 30464804 PMCID: PMC6231457 DOI: 10.18632/oncotarget.26211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/08/2018] [Indexed: 12/14/2022] Open
Abstract
Recent molecular subgrouping of ependymomas (EPN) by DNA methylation profiling has identified ST-EPN-RELA and PF-EPN-A subgroups to be associated with poor outcome. Snail/Slug are cardinal epithelial-to-mesenchymal transcription factors (EMT-TFs) and are overexpressed in several CNS tumors, including EPNs. A systematic analysis of gene-sets/modules co-expressed with Snail and Slug genes using published expression microarray dataset (GSE27279)identified 634 genes for Snail with enriched TGF-β, PPAR and PI3K signaling pathways, and 757 genes for Slug with enriched focal adhesion, ECM-receptor interaction and regulation of actin cytoskeleton related pathways. Of 37 genes commonly expressed with both Snail and Slug, IL1R1, a cytokine receptor of interleukin-1 receptor family, was positively correlated with Snail (r=0.43) and Slug (r=0.51), preferentially expressed in ST-EPN-RELA and PF-EPN-A molecular groups, and enriched for pathways related to inflammation, angiogenesis and glycolysis. IL1R1 expression was fairly specific to EPNs among various CNS tumors analyzed. It also showed significant positive correlation with EMT, stemness and MDSC (myeloid derived suppressor cell) markers. Our study reports IL1R1 as a poor prognostic marker associated with EMT-like phenotype and stemness in EPNs. Our findings emphasize the need to further examine and validate IL1R1 as a novel therapeutic target in aggressive subsets of intracranial EPNs.
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Affiliation(s)
- Prit Benny Malgulwar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Vikas Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Ashutosh Singh Tomar
- Center for Cellular and Molecular Biology-Council of Scientific and Industrial Research (CCMB-CSIR), Hyderabad, Telangana-500007, India
| | - Chaitenya Verma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Manmohan Singh
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi-110029, India
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18
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Testa U, Castelli G, Pelosi E. Genetic Abnormalities, Clonal Evolution, and Cancer Stem Cells of Brain Tumors. Med Sci (Basel) 2018; 6:E85. [PMID: 30279357 PMCID: PMC6313628 DOI: 10.3390/medsci6040085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023] Open
Abstract
Brain tumors are highly heterogeneous and have been classified by the World Health Organization in various histological and molecular subtypes. Gliomas have been classified as ranging from low-grade astrocytomas and oligodendrogliomas to high-grade astrocytomas or glioblastomas. These tumors are characterized by a peculiar pattern of genetic alterations. Pediatric high-grade gliomas are histologically indistinguishable from adult glioblastomas, but they are considered distinct from adult glioblastomas because they possess a different spectrum of driver mutations (genes encoding histones H3.3 and H3.1). Medulloblastomas, the most frequent pediatric brain tumors, are considered to be of embryonic derivation and are currently subdivided into distinct subgroups depending on histological features and genetic profiling. There is emerging evidence that brain tumors are maintained by a special neural or glial stem cell-like population that self-renews and gives rise to differentiated progeny. In many instances, the prognosis of the majority of brain tumors remains negative and there is hope that the new acquisition of information on the molecular and cellular bases of these tumors will be translated in the development of new, more active treatments.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
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Is NF2 a Key Player of the Differentially Expressed Gene Between Spinal Cord Ependymoma and Intracranial Ependymoma? World Neurosurg 2018; 118:e906-e917. [PMID: 30031196 DOI: 10.1016/j.wneu.2018.07.096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Although intracranial and spinal ependymomas are histopathologically similar, the molecular landscape is heterogeneous. An urgent need exists to identify differences in the genomic profiles to tailor treatment strategies. In the present study, we delineated differential gene expression patterns between intracranial and spinal ependymomas. METHODS We searched the Gene Expression Omnibus database using the term "ependymoma" and analyzed the raw gene expression profiles of 292 ependymomas (31 spinal and 261 intracranial). The gene expression data were analyzed to find differentially expressed genes (DEGs) between 2 regions. The fold change (FC) and false discovery rate (FDR) were used to assess DEGs after gene integration (|log2FC|>2; FDR P < 0.01). Enrichment and pathway analysis was also performed. RESULTS A total of 201 genes (105 upregulated and 96 downregulated) were significant DEGs in the data sets. The underexpression of NF2 in spinal ependymomas was statistically significant (FDR P = 7.91 × 10-9). However, the FC of NF2 did not exceed the cutoff value (log2FC, -1.2). The top 5 ranked upregulated genes were ARX, HOXC6, HOXA9, HOXA5, and HOXA3, which indicated that spinal ependymomas frequently demonstrate overexpression of HOX family genes, which play fundamental roles in specifying anterior/posterior body patterning. Moreover, the gene ontology enrichment analysis specified "anterior/posterior pattern specification" and "neuron migration" in spinal and intracranial ependymomas, respectively. CONCLUSIONS The most substantial magnitude of DEGs in ependymoma might be HOX genes. However, whether the differential expression of these genes is the cause or consequence of the disease remains to be elucidated in a larger prospective study.
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Abstract
In the adult mouse spinal cord, the ependymal cell population that surrounds the central canal is thought to be a promising source of quiescent stem cells to treat spinal cord injury. Relatively little is known about the cellular origin of ependymal cells during spinal cord development, or the molecular mechanisms that regulate ependymal cells during adult homeostasis. Using genetic lineage tracing based on the Wnt target gene Axin2, we have characterized Wnt-responsive cells during spinal cord development. Our results revealed that Wnt-responsive progenitor cells are restricted to the dorsal midline throughout spinal cord development, which gives rise to dorsal ependymal cells in a spatially restricted pattern. This is contrary to previous reports that suggested an exclusively ventral origin of ependymal cells, suggesting that ependymal cells may retain positional identities in relation to their neural progenitors. Our results further demonstrated that in the postnatal and adult spinal cord, all ependymal cells express the Wnt/β-catenin signaling target gene Axin2, as well as Wnt ligands. Genetic elimination of β-catenin or inhibition of Wnt secretion in Axin2-expressing ependymal cells in vivo both resulted in impaired proliferation, indicating that Wnt/β-catenin signaling promotes ependymal cell proliferation. These results demonstrate the continued importance of Wnt/β-catenin signaling for both ependymal cell formation and regulation. By uncovering the molecular signals underlying the formation and regulation of spinal cord ependymal cells, our findings thus enable further targeting and manipulation of this promising source of quiescent stem cells for therapeutic interventions.
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21
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Cossu G, Lacroix C, Adams C, Daniel R, Parker F, Messerer M. Neuroglial intramedullary tumors: The collaboration between neurosurgeons and neuropathologists. Neurochirurgie 2017; 63:413-418. [DOI: 10.1016/j.neuchi.2016.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/19/2016] [Accepted: 06/12/2016] [Indexed: 01/03/2023]
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22
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Campello C, Parker F, Slimani S, Le Floch A, Herbrecht A, Aghakhani N, Lacroix C, Loiseau H, Lejeune J, Perrin G, Honnorat J, Dufour H, Chinot O, Figarella D, Bauchet L, Duffau H, Lonjon M, Labauge P, Messerer M, Daures J, Fabbro P, Ducot B. Tumeurs gliales intramédullaires de l’adulte : la série du rapport. Neurochirurgie 2017; 63:381-390. [DOI: 10.1016/j.neuchi.2016.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 09/18/2016] [Accepted: 10/23/2016] [Indexed: 10/19/2022]
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Fuller CE, Jones DTW, Kieran MW. New Classification for Central Nervous System Tumors: Implications for Diagnosis and Therapy. Am Soc Clin Oncol Educ Book 2017; 37:753-763. [PMID: 28561665 DOI: 10.1200/edbk_175088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The 2016 World Health Organization Classification of Tumors of the Central Nervous System (WHO 2016) represents a noteworthy divergence from prior classification schemas. This new classification introduced the concept of "integrated diagnoses" based on a marriage of both phenotypic (microscopic) and genotypic parameters, with the intended goals of improving diagnostic accuracy and patient management. The result is a major restructuring in many of the brain tumor categories, with the codification of multiple new tumor entities and subgroups. It is therefore imperative that pathologists, clinicians, and neuro-oncology researchers alike rapidly become familiar with this new classification schema. Many of the diagnostic updates set forth in the WHO 2016 have impacted brain tumor types that commonly arise in the pediatric age group, particularly within the diffuse glioma, ependymoma, and embryonal tumor categories. This review gives a brief overview of (1) the WHO 2016 as it relates to pediatric central nervous system (CNS) tumors, with an emphasis on molecular diagnostic tools used in the clinical arena, (2) ongoing and developing approaches to the molecular and genomic classification of pediatric CNS tumors, and (3) the impact of this new classification schema on clinical trials in pediatric neuro-oncology.
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Affiliation(s)
- Christine E Fuller
- From the Cincinnati Children's Hospital Medical Center, Cincinnati, OH; German Cancer Research Center, Heidelberg, Germany; Dana-Farber Cancer Institute, Boston, MA
| | - David T W Jones
- From the Cincinnati Children's Hospital Medical Center, Cincinnati, OH; German Cancer Research Center, Heidelberg, Germany; Dana-Farber Cancer Institute, Boston, MA
| | - Mark W Kieran
- From the Cincinnati Children's Hospital Medical Center, Cincinnati, OH; German Cancer Research Center, Heidelberg, Germany; Dana-Farber Cancer Institute, Boston, MA
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Central nervous system gliomas. Crit Rev Oncol Hematol 2017; 113:213-234. [DOI: 10.1016/j.critrevonc.2017.03.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/22/2022] Open
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25
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Virág J, Haberler C, Baksa G, Piurkó V, Hegedüs Z, Reiniger L, Bálint K, Chocholous M, Kiss A, Lotz G, Glasz T, Schaff Z, Garami M, Hegedűs B. Region Specific Differences of Claudin-5 Expression in Pediatric Intracranial Ependymomas: Potential Prognostic Role in Supratentorial Cases. Pathol Oncol Res 2017; 23:245-252. [PMID: 27395057 PMCID: PMC5371650 DOI: 10.1007/s12253-016-0084-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/28/2016] [Indexed: 10/26/2022]
Abstract
Ependymomas are common pediatric brain tumors that originate from the ependyma and characterized by poor prognosis due to frequent recurrence. However, the current WHO grading system fails to accurately predict outcome. In a retrospective study, we analyzed 54 intracranial pediatric ependymomas and found a significantly higher overall survival in supratentorial cases when compared to infratentorial tumors. Next we performed region-specific immunohistochemical analysis of the ependyma in neonatal and adult ependyma from the central canal of spinal cord to the choroid plexus of lateral ventricles for components of cell-cell junctions including cadherins, claudins and occludin. We found robust claudin-5 expression in the choroid plexus epithelia but not in other compartments of the ependyma. Ultrastructural studies demonstrated distinct regional differences in cell-cell junction organization. Surprisingly, we found that 9 out of 20 supratentorial but not infratentorial ependymomas expressed high levels of the brain endothelial tight junction component claudin-5 in tumor cells. Importantly, we observed an increased overall survival in claudin-5 expressing supratentorial ependymoma. Our data indicates that claudin-5 expressing ependymomas may follow a distinct course of disease. The assessment of claudin-5 expression in ependymoma has the potential to become a useful prognostic marker in this pediatric malignancy.
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Affiliation(s)
- József Virág
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Christine Haberler
- Institute of Neuropathology, Medical University of Vienna, Vienna, Austria
| | - Gábor Baksa
- 1st Department of Anatomy, Semmelweis University, Budapest, Hungary
| | - Violetta Piurkó
- 2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, H-1091, Hungary
| | - Zita Hegedüs
- 2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, H-1091, Hungary
| | - Lilla Reiniger
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences - Semmelweis University, Budapest, Hungary
| | - Katalin Bálint
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Monika Chocholous
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - András Kiss
- 2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, H-1091, Hungary
| | - Gábor Lotz
- 2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, H-1091, Hungary
| | - Tibor Glasz
- 2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, H-1091, Hungary
| | - Zsuzsa Schaff
- 2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, H-1091, Hungary
| | - Miklós Garami
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Balázs Hegedűs
- 2nd Department of Pathology, Semmelweis University, Üllői út 93, Budapest, H-1091, Hungary.
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.
- Molecular Oncology Research Group, Hungarian Academy of Sciences - Semmelweis University, Budapest, Hungary.
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Tsangaris GT, Papathanasiou C, Adamopoulos PG, Scorilas A, Vorgias CE, Prodromou N, Stathopoulou FT, Stravopodis DJ, Anagnostopoulos AK. Pediatric Ependymoma: A Proteomics Perspective. Cancer Genomics Proteomics 2017; 14:127-136. [PMID: 28387652 PMCID: PMC5369312 DOI: 10.21873/cgp.20025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/25/2017] [Accepted: 02/28/2017] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND/AIM Proteomics based on high-resolution mass spectrometry (MS) is the tool of choice for the analysis of protein presence, modifications and interactions, with increasing emphasis on the examination of tumor tissues. Application of MS-based proteomics offers a detailed picture of tumor tissue characteristics, facilitating the appreciation of different tumor entities, whilst providing reliable and fast results for therapeutic marker targeting and prognostic factor assessment. Through use of the high analytical resolution of nano-high-pressure liquid chromatography (nanoHPLC) and the high resolution of an Orbitrap Elite mass spectrometer, the present study aimed to provide knowledge on the proteome of the generally unknown entity of pediatric ependymal tumors. MATERIALS AND METHODS Ten resected specimens of childhood ependymoma were analyzed through a one-dimensional (1D) nanoLC-MS/MS approach. Method optimization steps were undertaken for both the sample preparation/protein extraction procedure and LC parameters, aiming to achieve the highest possible identification rates. RESULTS Following method optimization, each nanoLC-MS/MS run resulted in identification of more than 5,000 proteins and more than 25,000 peptides for every analyzed sample, thus detailing the greater part of the ependymoma proteome. Identified proteins were found to spread throughout all known tumor categories regarding their molecular function and subcellular localization. CONCLUSION Through the proposed nanoLC-MS/MS method herein we report, for the firs time, the ependymoma proteome database. A large number of similarities regarding proteome content are revealed compared to other two pediatric brain tumor entities; astrocytomas and medulloblastomas. Furthermore, through our approach, the majority of currently proposed markers for ependymoma (e.g. nucleolin, nestin, Ki67 and laminin subunit A2) as well as all major key players of the phosphoinositide 3-kinase pathway (seemingly implicated in ependymoma), were definitely detected.
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Affiliation(s)
- George Th Tsangaris
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Chrissa Papathanasiou
- Hematology/Oncology Unit, First Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens, Greece
| | | | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Constantinos E Vorgias
- Department of Biochemistry and Molecular Biology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Neofytos Prodromou
- Department of Neurosurgery, Aghia Sophia Children's Hospital, Athens, Greece
| | - Foteini Tzortzatou Stathopoulou
- Hematology/Oncology Unit, First Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens, Greece
| | - Dimitrios J Stravopodis
- Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
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[Intramedullary ependymomas: A French retrospective multicenter study of 221 cases]. Neurochirurgie 2017; 63:391-397. [PMID: 28162253 DOI: 10.1016/j.neuchi.2016.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/21/2016] [Accepted: 07/17/2016] [Indexed: 11/23/2022]
Abstract
AIM Intramedullary ependymomas (IE) are the most frequent intramedullary tumors in the adult population. The gold standard treatment is to obtain gross total removal without any new postoperative neurological deficit. The authors report the results of a multicenter series with a long-term follow-up and the analysis of clinical, radiological, surgical data as well as the complementary treatments. MATERIALS AND METHODS A retrospective analysis of adult patients with IE operated on between January 1984 and December 2011 at 7 French centers (Bordeaux, Kremlin-Bicêtre, Lille, Lyon, Marseille, Montpellier, Nice, and Nîmes) was performed. The minimal follow-up was 12 months. The clinical evaluation was based on the McCormick classification in the pre and postoperative period at 3 months, 1 and 5 years. RESULTS Data of 221 adult patients with a pathologically confirmed diagnosis of IE were considered: 134 patients were treated at the Neurosurgical Department of Kremlin-Bicêtre Hospital, 26 were treated at Lille and 61 were treated in the southern region of France (Marseille, Bordeaux, Montpellier, and Lyon). The epidemiological analysis was performed on the entire cohort of patients, while follow-up considerations were made solely on the 134 patients managed at Kremlin-Bicêtre Hospital to obtain homogeneous data. A slight male prevalence was observed (59 % of cases), with an average age of 41.8 years at diagnosis. The mean age at first clinical manifestations was 39.6 years, thus the average duration of symptoms before the diagnosis was 29 months. Neuropathic pain and neurological deficit were the most revealing symptoms in 64 % and 32 % of cases respectively. The localization of the IE was basically cervical in 35.7 %, primarily thoracic in 25.8 % and cervico-thoracic in 22.2 %. The mean tumor length in the sagittal plan was 20.4mm (range 1 to 99mm). A cystic cavity was present in 76.5 % of cases while an intratumoral hemorrhage was detected in 30.3 % of cases. The rate of complete removal was performed in 79.2 % of cases when considering the whole cohort and in 91 % of cases treated at Bicêtre Hospital. In 95 % of cases a WHO grade I or II ependymoma was isolated and in 5 % of cases a WHO grade III. The McCormick scale (MCs) (Lou et al., 2012) [1] was used to rate the degree of preoperative functional impairment in 4 grades. In the immediate postoperative period a worsening of functional capacity was observed. Only 28.8 % of patients had MCs 1 in the immediate postoperative period; 34.8 % had MCs 2; 20.4 % had MCs 3 and 16 % had MCs 4. At 5 years of follow-up (101 patients) the frequencies of grades 1 and 2 were increased: 59 % of patients had MCs 1, 20.8 % had MCs 2, 10,9 % had MCs 3 and 9.3 % had MCs 4. The extension of the lesion on the sagittal plan calculated on the preoperative MRI, was the only predictive factor associated with the immediate postoperative outcome and the short-term follow-up (P=0.04), whereas the preoperative neurological status is the only predictive factor for long-term follow-up (P=0.005). CONCLUSION Gross total removal remains the mainstay treatment for IE. Early surgery is indicated if the patient is symptomatic or the tumor increases in size. A postoperative regular follow-up is mandatory for at least 10 years due to the risk of recurrence. If a growing residue is detected, a second intervention is recommended without any adjuvant treatment if a WHO grade I lesion is confirmed by the pathological analysis. Complementary treatment should be reserved for high-grade ependymomas or in case of unresectable and progressive residue.
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Gonzalez-Fernandez C, Arevalo-Martin A, Paniagua-Torija B, Ferrer I, Rodriguez FJ, Garcia-Ovejero D. Wnts Are Expressed in the Ependymal Region of the Adult Spinal Cord. Mol Neurobiol 2016; 54:6342-6355. [PMID: 27722925 DOI: 10.1007/s12035-016-0132-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/14/2016] [Indexed: 12/21/2022]
Abstract
The Wnt family of proteins plays key roles during central nervous system development and in several physiological processes during adulthood. Recently, experimental evidence has linked Wnt-related genes to regulation and maintenance of stem cells in the adult neurogenic niches. In the spinal cord, the ependymal cells surrounding the central canal form one of those niches, but little is known about their Wnt expression patterns. Using microdissection followed by TaqMan® low-density arrays, we show here that the ependymal regions of young, mature rats and adult humans express several Wnt-related genes, including ligands, conventional and non-conventional receptors, co-receptors, and soluble inhibitors. We found 13 genes shared between rats and humans, 4 exclusively expressed in rats and 9 expressed only in humans. Also, we observed a reduction with age on spontaneous proliferation of ependymal cells in rats paralleled by a decrease in the expression of Fzd1, Fzd8, and Fzd9. Our results suggest a role for Wnts in the regulation of the adult spinal cord neurogenic niche and provide new data on the specific differences in this region between humans and rodents.
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Affiliation(s)
- Carlos Gonzalez-Fernandez
- Laboratory of Molecular Neurology, Hospital Nacional de Paraplejicos (SESCAM), Finca La Peraleda s/n, 45071, Toledo, Spain
| | - Angel Arevalo-Martin
- Laboratory of Neuroinflammation, Hospital Nacional de Paraplejicos (SESCAM), Finca La Peraleda s/n, 45071, Toledo, Spain
| | - Beatriz Paniagua-Torija
- Laboratory of Neuroinflammation, Hospital Nacional de Paraplejicos (SESCAM), Finca La Peraleda s/n, 45071, Toledo, Spain
| | - Isidro Ferrer
- Institut de Neuropatologia, Serveid'AnatomiaPatològica, IDIBELL-Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Spain
| | - Francisco J Rodriguez
- Laboratory of Molecular Neurology, Hospital Nacional de Paraplejicos (SESCAM), Finca La Peraleda s/n, 45071, Toledo, Spain.
| | - Daniel Garcia-Ovejero
- Laboratory of Neuroinflammation, Hospital Nacional de Paraplejicos (SESCAM), Finca La Peraleda s/n, 45071, Toledo, Spain.
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Abstract
Over the past 150 years since Virchow's initial characterization of ependymoma, incredible efforts have been made in the classification of these tumors and in the care of pediatric patients with this disease. While the advent of modern neurosurgery and the optimization of radiation have provided significant gains, a more complex but incomplete picture of pediatric ependymomas has begun to form through a combination of international collaborations and detailed genetic and histologic characterizations. This review includes and synthesizes the clinical understanding of pediatric ependymoma and their developing molecular insight into what is truly a family of malignancies in which distinct members require different surgical approaches, radiation plans, and targeted therapies.
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Affiliation(s)
- Nicholas A Vitanza
- Division of Child Neurology, Department of Neurology, Lucile Packard Children's Hospital at Stanford, Stanford University, Palo Alto, CA, USA
| | - Sonia Partap
- Division of Child Neurology, Department of Neurology, Lucile Packard Children's Hospital at Stanford, Stanford University, Palo Alto, CA, USA
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Expression alterations define unique molecular characteristics of spinal ependymomas. Oncotarget 2016; 6:19780-91. [PMID: 25909290 PMCID: PMC4637320 DOI: 10.18632/oncotarget.3715] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 03/11/2015] [Indexed: 12/18/2022] Open
Abstract
Ependymomas are glial tumors that originate in either intracranial or spinal regions. Although tumors from different regions are histologically similar, they are biologically distinct. We therefore sought to identify molecular characteristics of spinal ependymomas (SEPN) in order to better understand the disease biology of these tumors. Using gene expression profiles of 256 tumor samples, we identified increased expression of 1,866 genes in SEPN when compared to intracranial ependymomas. These genes are mainly related to anterior/posterior pattern specification, response to oxidative stress, glial cell differentiation, DNA repair, and PPAR signalling, and also significantly enriched with cellular senescence genes (P = 5.5 × 10-03). In addition, a high number of significantly down-regulated genes in SEPN are localized to chromosome 22 (81 genes from chr22: 43,325,255 - 135,720,974; FDR = 1.77 × 10-23 and 22 genes from chr22: 324,739 - 32,822,302; FDR = 2.07 × 10-09) including BRD1, EP300, HDAC10, HIRA, HIC2, MKL1, and NF2. Evaluation of NF2 co-expressed genes further confirms the enrichment of chromosome 22 regions. Finally, systematic integration of chromosome 22 genes with interactome and NF2 co-expression data identifies key candidate genes. Our results reveal unique molecular characteristics of SEPN such as altered expression of cellular senescence and chromosome 22 genes.
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Connolly ID, Ali R, Li Y, Gephart MH. Genetic and molecular distinctions in spinal ependymomas: A review. Clin Neurol Neurosurg 2015; 139:210-5. [DOI: 10.1016/j.clineuro.2015.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 12/17/2022]
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Singh N, Sahu DK, Chowdhry R, Mishra A, Goel MM, Faheem M, Srivastava C, Ojha BK, Gupta DK, Kant R. IsoSeq analysis and functional annotation of the infratentorial ependymoma tumor tissue on PacBio RSII platform. Meta Gene 2015; 7:70-5. [PMID: 26862483 PMCID: PMC4707247 DOI: 10.1016/j.mgene.2015.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/10/2015] [Accepted: 11/16/2015] [Indexed: 12/07/2022] Open
Abstract
Here, we sequenced and functionally annotated the long reads (1–2 kb) cDNAs library of an infratentorial ependymoma tumor tissue on PacBio RSII by Iso-Seq protocol using SMRT technology. 577 MB, data was generated from the brain tissues of ependymoma tumor patient, producing 1,19,313 high-quality reads assembled into 19,878 contigs using Celera assembler followed by Quiver pipelines, which produced 2952 unique protein accessions in the nr protein database and 307 KEGG pathways. Additionally, when we compared GO terms of second and third level with alternative splicing data obtained through HTA Array2.0. We identified four and twelve transcript cluster IDs in Level-2 and Level-3 scores respectively with alternative splicing index predicting mainly the major pathways of hallmarks of cancer. Out of these transcript cluster IDs only transcript cluster IDs of gene PNMT, SNN and LAMB1 showed Reads Per Kilobase of exon model per Million mapped reads (RPKM) values at gene-level expression (GE) and transcript-level (TE) track. Most importantly, brain-specific genes–—PNMT, SNN and LAMB1 show their involvement in Ependymoma. Produced 2952 unique protein accessions in the nr protein database Identified 307 KEGG-pathways with 442 enzyme-codes for 1172 unique-sequences Identified transcript cluster-IDs in Level-2 and -3 GO-terms with alternative splicing index Involvement of PNMT, SNN and LAMB1-brain specific genes in Ependymoma
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Affiliation(s)
- Neetu Singh
- Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow 226003, India
| | - Dinesh Kumar Sahu
- Imperial Life Sciences, 463 Phase City 2nd, Sector 37, Gurgaon, Haryana 122001, India
| | - Rebecca Chowdhry
- Department of Periodontics, King George's Medical University, Lucknow 226003, India
| | - Archana Mishra
- Department of Biochemistry, King George's Medical University, Lucknow 226003, India
| | - Madhu Mati Goel
- Department of Pathology, King George's Medical University, Lucknow 226003, India
| | - Mohd Faheem
- Department of Neuro Surgery, King George's Medical University, Lucknow, Uttar Pradesh 226003, India
| | - Chhitij Srivastava
- Department of Neuro Surgery, King George's Medical University, Lucknow, Uttar Pradesh 226003, India
| | - Bal Krishna Ojha
- Department of Neuro Surgery, King George's Medical University, Lucknow, Uttar Pradesh 226003, India
| | - Devendra Kumar Gupta
- Department of Pediatric Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ravi Kant
- Department of Surgical Oncology, King George's Medical University, Lucknow, Uttar Pradesh 226003, India
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Singh N, Sahu DK, Mishra A, Agarwal P, Goel MM, Chandra A, Singh SK, Srivastava C, Ojha BK, Gupta DK, Kant R. Multiomics approach showing genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric brain tumors. Gene 2015; 576:734-42. [PMID: 26456192 DOI: 10.1016/j.gene.2015.09.078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 12/07/2022]
Abstract
PURPOSE Based on copy number alterations and transcriptional profiles, the posterior fossa tumors (medulloblastoma (MB), ependymoma and pilocytic astrocytoma) have been classified into various subgroups. The study design was aimed to identify and catalog genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric posterior fossa tumors and matched control tissue through Molecular Inversion Probe (MIP) Based and Human Transcriptome Array. EXPERIMENTAL DESIGN MIP based OncoScan Array and Human Transcriptome Array 2.0 were used to molecularly-categorize histopathologically and immunohistochemically proven tumor samples on the basis of copy number variations and altered gene expression patterns and/or alternative splicing events. RESULTS Based on molecular, histopathological/immunohistochemical and age-dependent factors MB was subgrouped into group-3 MB, Wnt and SHH; ependymoma into balanced, numerical and structural/anaplastic; and pilocytic astrocytoma was stratified age-dependently. Compared with the vermis tissue of MB, the vermis tissue of ependymoma showed higher levels of gain and losses compared with their counter tumor parts implicating metastasis within the confined region. Group-3 MB and anaplastic ependymoma represented highest differentially expressed genes both at gene and exon levels in the CN altered regions compared with other subgroups of MB and ependymoma respectively. CONCLUSION This multiomics approach based molecular characterization of posterior fossa tumors together with clinical and histopathological factors may help us in the area of personalized medicine.
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Affiliation(s)
- Neetu Singh
- Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow 226 003, India.
| | - Dinesh Kumar Sahu
- Imperial Life Sciences, 463 Phase City 2nd, Sector 37, Gurgaon, Haryana 122001, India
| | - Archana Mishra
- Department of Biochemistry, King George's Medical University, Lucknow 226 003, India
| | - Preeti Agarwal
- Department of Pathology, King George's Medical University, Lucknow 226 003, India
| | - Madhu Mati Goel
- Department of Pathology, King George's Medical University, Lucknow 226 003, India
| | - Anil Chandra
- Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Sunil Kumar Singh
- Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Chhitij Srivastava
- Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Bal Krishna Ojha
- Department of Neurosurgery, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
| | - Devendra Kumar Gupta
- Department of Pediatric Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ravi Kant
- Department of Surgical Oncology, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India
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Tenenhaus A, Philippe C, Frouin V. Kernel Generalized Canonical Correlation Analysis. Comput Stat Data Anal 2015. [DOI: 10.1016/j.csda.2015.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Nambirajan A, Sharma MC, Gupta RK, Suri V, Singh M, Sarkar C. Study of stem cell marker nestin and its correlation with vascular endothelial growth factor and microvascular density in ependymomas. Neuropathol Appl Neurobiol 2015; 40:714-25. [PMID: 24224478 DOI: 10.1111/nan.12097] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/08/2013] [Indexed: 12/21/2022]
Abstract
BACKGROUND Ependymomas are relatively rare glial tumours, whose pathogenesis is not well elucidated. They are enigmatic tumours that show site-specific differences in their biological behaviour. Recent studies have hypothesized that ependymoma cancer stem cells (CSCs) are derived from radial glia and express stem cell markers such as nestin, which is associated with a poor prognosis. CSCs reside in 'vascular niches', where endothelial cells and molecular signals like vascular endothelial growth factor (VEGF) play an important role in their survival. Studies analysing VEGF expression in ependymomas showed that ependymal vascular proliferation is less sensitive to induction by VEGF, questioning the possible beneficial effect of anti-VEGF therapy in ependymomas. We aimed to study nestin and VEGF immunoexpression in ependymomas, correlate them with clinicopathological parameters and reveal a role for VEGF in ependymomas that extends beyond the context of tumour angiogenesis. METHODS We analysed 126 cases of ependymomas of different grades and locations for nestin and VEGF immunoexpression. Endothelial cells were labelled with CD34. Vascular patterns and microvascular density was determined. RESULTS Nestin and VEGF expression in tumour cells were more frequent in supratentorial tumours [89% (33/37) and 65% (24/37) respectively], and were associated with a significantly poor progression-free survival (PFS). VEGF expression did not reveal any correlation with necrosis or bizarre vascular patterns. CONCLUSIONS Supratentorial location is an independent predictor of a poor PFS. Significant coexpression of nestin and VEGF suggests that latter possibly augments stem cell survival. Thus, anti-VEGF therapy may be a good option in future for nestin immunopositive ependymomas.
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Affiliation(s)
- Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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de Andrade FG, Marie SKN, Uno M, Matushita H, Taricco MA, Teixeira MJ, Rosemberg S, Oba-Shinjo SM. Immunohistochemical expression of cyclin D1 is higher in supratentorial ependymomas and predicts relapses in gross total resection cases. Neuropathology 2015; 35:312-23. [PMID: 25946121 DOI: 10.1111/neup.12195] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/21/2014] [Accepted: 12/22/2014] [Indexed: 12/29/2022]
Abstract
Ependymomas are tumors of the CNS. Although cyclin D1 overexpression has been related to several cancers, its prognostic value in ependymomas has not yet been fully established. We evaluated cyclin D1 expression by an immunohistochemistry analysis of 149 samples of ependymomas, including some relapses, corresponding to 121 patients. Eighty-one patients were adults, 60 were intracranial cases and 92 tumors were grade II. Gross total resection (GTR) was achieved in 62% of cases, and relapse was confirmed in 41.4% of cases. Cyclin D1 protein expression was analyzed by immunohistochemistry and scored with a labeling index (LI) calculated as the percentage of positively stained cells by intensity. We also analyzed expression of CCND1 and NOTCH1 in 33 samples of ependymoma by quantitative real-time PCR. A correlation between cyclin D1 LI score and anaplastic cases (P < 0.001), supratentorial location (P < 0.001) and age (P = 0.001) were observed. A stratified analysis demonstrated that cyclin D1 protein expression was strong in tumors with a supratentorial location, independent of the histological grade or age. Relapse was more frequent in cases with a higher cyclin D1 LI score (P = 0.046), and correlation with progression-free survival was observed in cases with GTR (P = 0.002). Only spinal canal tumor location and GTR were suggestive markers of PFS in multivarite analyses. Higher expression levels were observed in anaplastic cases for CCND1 (P = 0.002), in supratentorial cases for CCND1 (P = 0.008) and NOTCH1 (P = 0.011). There were correlations between the cyclin D1 mRNA and protein expression levels (P < 0.0001) and between CCND1 and NOTCH1 expression levels (P = 0.003). Higher cyclin D1 LI was predominant in supratentorial location and predict relapse in GTR cases. Cyclin D1 could be used as an immunohistochemical marker to guide follow-up and treatment in these cases.
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Affiliation(s)
- Fernanda Gonçalves de Andrade
- Laboratory of Cellular and Molecular Biology, Department of Neurology, University of Sao Paulo, Sao Paulo, Brazil.,Division of Neurosurgery, Department of Neurology, University of Sao Paulo, Sao Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- Laboratory of Cellular and Molecular Biology, Department of Neurology, University of Sao Paulo, Sao Paulo, Brazil
| | - Miyuki Uno
- Laboratory of Cellular and Molecular Biology, Department of Neurology, University of Sao Paulo, Sao Paulo, Brazil
| | - Hamilton Matushita
- Division of Neurosurgery, Department of Neurology, University of Sao Paulo, Sao Paulo, Brazil
| | - Mario Augusto Taricco
- Division of Neurosurgery, Department of Neurology, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Sergio Rosemberg
- Pathology, Hospital das Clinicas, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Sueli Mieko Oba-Shinjo
- Laboratory of Cellular and Molecular Biology, Department of Neurology, University of Sao Paulo, Sao Paulo, Brazil
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Garcia-Ovejero D, Arevalo-Martin A, Paniagua-Torija B, Florensa-Vila J, Ferrer I, Grassner L, Molina-Holgado E. The ependymal region of the adult human spinal cord differs from other species and shows ependymoma-like features. Brain 2015; 138:1583-97. [PMID: 25882650 DOI: 10.1093/brain/awv089] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/30/2015] [Indexed: 12/20/2022] Open
Abstract
Several laboratories have described the existence of undifferentiated precursor cells that may act like stem cells in the ependyma of the rodent spinal cord. However, there are reports showing that this region is occluded and disassembled in humans after the second decade of life, although this has been largely ignored or interpreted as a post-mortem artefact. To gain insight into the patency, actual structure, and molecular properties of the adult human spinal cord ependymal region, we followed three approaches: (i) with MRI, we estimated the central canal patency in 59 control subjects, 99 patients with traumatic spinal cord injury, and 26 patients with non-traumatic spinal cord injuries. We observed that the central canal is absent from the vast majority of individuals beyond the age of 18 years, gender-independently, throughout the entire length of the spinal cord, both in healthy controls and after injury; (ii) with histology and immunohistochemistry, we describe morphological properties of the non-lesioned ependymal region, which showed the presence of perivascular pseudorosettes, a common feature of ependymoma; and (iii) with laser capture microdissection, followed by TaqMan® low density arrays, we studied the gene expression profile of the ependymal region and found that it is mainly enriched in genes compatible with a low grade or quiescent ependymoma (53 genes); this region is enriched only in 14 genes related to neurogenic niches. In summary, we demonstrate here that the central canal is mainly absent in the adult human spinal cord and is replaced by a structure morphologically and molecularly different from that described for rodents and other primates. The presented data suggest that the ependymal region is more likely to be reminiscent of a low-grade ependymoma. Therefore, a direct translation to adult human patients of an eventual therapeutic potential of this region based on animal models should be approached with caution.
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Affiliation(s)
- Daniel Garcia-Ovejero
- 1 Laboratory of Neuroinflammation, Hospital Nacional de Paraplejicos (SESCAM), Toledo, Spain
| | - Angel Arevalo-Martin
- 1 Laboratory of Neuroinflammation, Hospital Nacional de Paraplejicos (SESCAM), Toledo, Spain
| | - Beatriz Paniagua-Torija
- 1 Laboratory of Neuroinflammation, Hospital Nacional de Paraplejicos (SESCAM), Toledo, Spain
| | - José Florensa-Vila
- 2 Radiology Unit, Hospital Nacional de Paraplejicos (SESCAM), Toledo, Spain
| | - Isidro Ferrer
- 3 Institut de Neuropatologia, Servei d'Anatomia Patolo`gica, IDIBELL-Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain
| | - Lukas Grassner
- 4 Center for Spinal Cord Injuries, Trauma Center Murnau, Germany 5 Institute of Molecular Regenerative Medicine, SCI-TReCS (Spinal Cord Injury and Tissue Regeneration Center Salzburg), Paracelsus Medical University, Salzburg, Austria
| | - Eduardo Molina-Holgado
- 1 Laboratory of Neuroinflammation, Hospital Nacional de Paraplejicos (SESCAM), Toledo, Spain
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Study of chromosome 9q gain, Notch pathway regulators and Tenascin-C in ependymomas. J Neurooncol 2013; 116:267-74. [PMID: 24178439 DOI: 10.1007/s11060-013-1287-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]
Abstract
Ependymomas are relatively uncommon tumours of the central nervous system which arise from the ependymal lining of the ventricles and spinal canal. The molecular changes leading to ependymal oncogenesis are not completely understood. We examined chromosome 9q33-34 locus for gain, potential oncogenes at this locus (Notch-1 and Tenascin-C) and Notch pathway target genes (Hes-1, Hey-2 & C-myc) in ependymomas by fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC), respectively, to assess if they have any correlation with clinical characteristics. We analyzed 50 cases of ependymomas by FISH for 9q gain and by IHC for Notch-1 and its target gene proteins (Hes-1, Hey-2 and C-myc) expression. We also performed IHC for Tenascin-C to rule out any correlation with aggressiveness/grade of tumour. FISH study revealed significant chromosome 9q gain in ependymomas of adult onset (age > 18 years) and spinal cord origin. Notch-1 showed significantly more frequent immunohistochemical expression in supratentorial and anaplastic ependymomas. Tenascin-C (TN-C) expression was significant in intracranial, childhood (age ≤ 18 years) and anaplastic ependymomas. Of the three Notch pathway target gene proteins (Hes-1, Hey-2 and C-myc), Hes-1 and C-myc expression showed significant correlation with anaplastic and adult onset ependymomas, respectively. Genetic alterations are independent prognostic markers in ependymomas. A clinicopathological correlation with various molecular signatures may be helpful in the development of new therapeutic targets.
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Ebrahimi A, Schittenhelm J, Honegger J, Schluesener H. Prognostic relevance of global histone 3 lysine 9 acetylation in ependymal tumors. J Neurosurg 2013; 119:1424-31. [PMID: 24116725 DOI: 10.3171/2013.9.jns13511] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECT Ependymal tumors are highly variable in clinical and molecular behavior and affect both children and adults. Regarding the paucity of appropriate experimental models, the underlying molecular mechanisms of their behavioral variability are poorly understood. Considering the increasing evidence of epigenetic changes in various tumors, in addition to the preclinical success of epigenetic-based therapeutics in tumors of the CNS, epigenetic study of ependymal tumors is warranted. METHODS Using immunohistochemistry, the authors investigated the patterns of global acetylation of lysine position 9 of histone 3 (H3K9Ac), an epigenetic marker of active gene transcription, in 85 ependymal tumors with various WHO grades and clinicopathological characteristics. RESULTS Most of the nuclei in all ependymal tumors were H3K9Ac negative (mean ± SD 65.9% ± 26.5 vs 34.1% ± 26.5% positive, p < 0.0001). Subependymomas had more H3K9Ac-positive nuclei (67.2% ± 10.2%) than myxopapillary ependymomas, ependymomas, and anaplastic ependymomas (p < 0.05). Additionally, intracranial parenchymal tumors had significantly fewer H3K9Ac-positive nuclei (13.1% ± 21.9%) than tumors of other CNS localizations (p < 0.001), and supratentorial ventricular tumors had the highest number of H3K9Ac-positive nuclei (66.4% ± 11.8%) among CNS ependymal tumors (p < 0.0001). The H3K9Ac pattern in ependymal tumors also revealed prognostic significance such that tumors with less than 20% acetylated nuclei had a higher probability of recurrence than tumors with 20% or more acetylated nuclei (p = 0.0327), and recurrent tumors had significantly fewer H3K9Ac-positive nuclei than primary ones (16% ± 22.5% vs. 38% ± 25.8%; p < 0.0001). However, the effect of tumor location on survival of patients was nonsignificant in a multivariate survival analysis, and H3K9 acetylation levels of tumors contributed independently to the survival of patients. In addition, ependymal tumors with more than or equal to 20% H3K9 acetylated cells had lower MIB-1 expression than those with less than 20% H3K9 acetylated cells (p < 0.01). CONCLUSIONS Global H3K9Ac contributes independently to the prognosis of patients with ependymal tumors such that tumors with lower H3K9Ac values have a higher probability of recurrence and are more proliferative. Additionally, subependymomas have a higher H3K9Ac profile than other ependymal tumor subclasses, underlining their benign clinical behavior.
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Andreiuolo F, Ferreira C, Puget S, Grill J. Current and evolving knowledge of prognostic factors for pediatric ependymomas. Future Oncol 2013; 9:183-91. [PMID: 23414469 DOI: 10.2217/fon.12.174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ependymomas are one of the most common pediatric malignant brain tumors. Prognosis, especially in young children, remains poor due to their inherent chemo- and radio-resistance and effective treatment remains one of the more difficult tasks in pediatric oncology: up to half of the patients may die from the disease. The only reproducible prognostic factor is the extent of surgery; neither histological grading nor other biomarkers can be used to reliably make treatment decisions in clinical practice. None of the studies identifying new biomarkers have been conducted prospectively, only few have been undertaken within the context of a clinical trial and most have been conducted with limited samples (often including adults and childhood samples). International collaboration is needed to improve ependymoma prognostication.
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Affiliation(s)
- Felipe Andreiuolo
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 8203 Vectorology & Anticancer Therapeutics, Gustave Roussy Cancer Institute, Paris-Sud University, Villejuif, France
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Kim JH, Huang Y, Griffin AS, Rajappa P, Greenfield JP. Ependymoma in children: molecular considerations and therapeutic insights. Clin Transl Oncol 2013; 15:759-65. [PMID: 23615979 DOI: 10.1007/s12094-013-1041-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/02/2013] [Indexed: 01/22/2023]
Abstract
A multi-modality approach that encompasses maximal surgical resection in combination with adjuvant therapy is critical for achieving optimal disease control in children with ependymoma. In view of its complex biology and variable response to therapy, ependymoma remains a challenge for clinicians involved in the care of these patients. Meanwhile, translation of molecular findings can characterize unique features of childhood ependymoma and their natural history. Furthermore, understanding the biology of pediatric ependymoma serves as a platform for development of future targeted therapies. In line with these goals, we review the molecular basis of pediatric ependymoma and its prognostic implications, as well as novel therapeutic advances in the management of ependymoma in children.
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Affiliation(s)
- J-H Kim
- Department of Neurological Surgery, Weill Cornell Medical College, 525 East 68th Street, Box 99, New York, NY, 10065, USA,
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Abstract
Tumours of the spinal cord, although rare, are associated with high morbidity. Surgical resection remains the primary treatment for patients with this disease, and offers the best chance for cure. Such surgical procedures, however, carry substantial risks such as worsening of neurological deficit, paralysis and death. New therapeutic avenues for spinal cord tumours are needed, but genetic studies of the molecular mechanisms governing tumourigenesis in the spinal cord are limited by the scarcity of high-quality human tumour samples. Many spinal cord tumours have intracranial counterparts that have been extensively studied, but emerging data show that the tumours are genetically and biologically distinct. The differences between brain and spine tumours make extrapolation of data from one to the other difficult. In this Review, we describe the demographics, genetics and current treatment approaches for the most commonly encountered spinal cord tumours--namely, ependymomas, astrocytomas, haemangioblastomas and meningiomas. We highlight advances in understanding of the biological basis of these lesions, and explain how the latest progress in genetics and beyond are being translated to improve patient care.
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Hagel C, Treszl A, Fehlert J, Harder J, von Haxthausen F, Kern M, von Bueren AO, Kordes U. Supra- and infratentorial pediatric ependymomas differ significantly in NeuN, p75 and GFAP expression. J Neurooncol 2013; 112:191-7. [PMID: 23371454 DOI: 10.1007/s11060-013-1062-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 01/22/2013] [Indexed: 12/13/2022]
Abstract
Ependymomas comprise 8 % of all intracranial tumors in children <15 years. Recent studies revealed that some supratentorial ependymomas express neuronal antigens and that high expression of neurofilament protein light polypeptide (NEFL) correlates with better clinical outcome. We retrospectively analyzed an expanded panel of proteins in 6 supratentorial, 15 posterior fossa and 4 spinal pediatric ependymomas by immunohistochemistry. Expression of high and low affinity neurotrophin receptors TrkA (NTRK1) and p75 (NGFR), pan-neuronal markers NeuN (RBFOX3) and synaptophysin, radial glial marker SOX9, adhesion molecules CD56 (NCAM) and CD44, junctional protein connexin 43 (GJA1), glial fibrillary acidic protein (GFAP), epithelial membrane antigen and proliferation associated antigen Ki-67 were evaluated in a semi-quantitative or quantitative (Ki-67 and NeuN-index) fashion. We found p75 and NeuN to be expressed at significantly higher levels in supratentorial versus infratentorial tumors and GFAP to be expressed at significantly higher levels in infratentorial lesions. In conclusion, immunohistochemical expression of p75, NeuN and GFAP differed in ependymomas depending on tumor topography supporting the view of divergent cells of origin. However, because of the small sample size the results are of preliminary nature and replication in a larger cohort would be desirable.
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Affiliation(s)
- Christian Hagel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany.
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Abstract
Brain tumors are the leading cause of cancer death in children, with ependymoma being the third most common and posing a significant clinical burden. Its mechanism of pathogenesis, reliable prognostic indicators, and effective treatments other than surgical resection have all remained elusive. Until recently, ependymoma research was hindered by the small number of tumors available for study, low resolution of cytogenetic techniques, and lack of cell lines and animal models. Ependymoma heterogeneity, which manifests as variations in tumor location, patient age, histological grade, and clinical behavior, together with the observation of a balanced genomic profile in up to 50% of cases, presents additional challenges in understanding the development and progression of this disease. Despite these difficulties, we have made significant headway in the past decade in identifying the genetic alterations and pathways involved in ependymoma tumorigenesis through collaborative efforts and the application of microarray-based genetic (copy number) and transcriptome profiling platforms. Genetic characterization of ependymoma unraveled distinct mRNA-defined subclasses and led to the identification of radial glial cells as its cell type of origin. This review summarizes our current knowledge in the molecular genetics of ependymoma and proposes future research directions necessary to further advance this field.
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Affiliation(s)
- Yuan Yao
- Hospital for Sick Children, Toronto, Ontario, Canada
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Nagasawa DT, Trang A, Choy W, Spasic M, Yew A, Zarinkhou G, Garcia HM, Yang I. Genetic expression profiles of adult and pediatric ependymomas: molecular pathways, prognostic indicators, and therapeutic targets. Clin Neurol Neurosurg 2013; 115:388-99. [PMID: 23374238 DOI: 10.1016/j.clineuro.2012.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 11/06/2012] [Accepted: 12/02/2012] [Indexed: 12/21/2022]
Abstract
Ependymomas are tumors that can present within either the intracranial or spinal regions. While 90% of all pediatric ependymomas are intracranial, spinal cord ependymomas are more commonly found in patients 20-40 years old. Treatment for spinal lesions has achieved local control rates up to 100% following gross total resection, while pediatric intracranial tumors have 40-60% mortality. Given the inability to effectively treat ependymomas with current standard practices, researchers have focused their efforts on evaluating chromosomal alterations, genetic expression profiles, epigenetic events, and molecular pathways. While these studies have provided critical insight into the potential mechanisms underlying ependymoma pathogenesis, understanding of the intricate interplay between the various pathways involved in tumor initiation, development, and progression will require deeper investigation. However, several potential prognostic markers and therapeutic targets have been identified, providing key areas of focus for future research. The utilization of unique genetic expression profiles based upon patient age, tumor location, tumor grade, and subtype has revealed a multitude of findings warranting further study. Inspection of various molecular pathways associated with ependymomas may establish the foundation for developing novel therapies capable of achieving significant clinical improvements with individualized regimens specifically designed for personalized treatment strategies.
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Affiliation(s)
- Daniel T Nagasawa
- UCLA Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, United States
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Yang I, Nagasawa DT, Kim W, Spasic M, Trang A, Lu DC, Martin NA. Chromosomal anomalies and prognostic markers for intracranial and spinal ependymomas. J Clin Neurosci 2012; 19:779-85. [PMID: 22516549 PMCID: PMC3615711 DOI: 10.1016/j.jocn.2011.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 11/03/2011] [Indexed: 10/28/2022]
Abstract
Ependymomas are neoplasms that can occur anywhere along the craniospinal axis. They are the third most common brain tumor in children, representing 10% of pediatric intracranial tumors, 4% of adult brain tumors, and 15% of all spinal cord tumors. As the heterogeneity of ependymomas has severely limited the prognostic value of the World Health Organization grading system, numerous studies have focused on genetic alterations as a potential basis for classification and prognosis. However, this endeavor has proven difficult due to variations of findings depending on tumor location, tumor grade, and patient age. While many have evaluated chromosomal abnormalities for ependymomas as a whole group, others have concentrated their efforts on specific subsets of populations. Here, we review modern findings of chromosomal analyses, their relationships with various genes, and their prognostic implications for intracranial and spinal cord ependymomas.
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Affiliation(s)
- Isaac Yang
- Department of Neurosurgery, University of California Los Angeles, UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
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Rogers HA, Kilday JP, Mayne C, Ward J, Adamowicz-Brice M, Schwalbe EC, Clifford SC, Coyle B, Grundy RG. Supratentorial and spinal pediatric ependymomas display a hypermethylated phenotype which includes the loss of tumor suppressor genes involved in the control of cell growth and death. Acta Neuropathol 2012; 123:711-25. [PMID: 22109108 PMCID: PMC3316934 DOI: 10.1007/s00401-011-0904-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 10/26/2011] [Accepted: 10/27/2011] [Indexed: 01/19/2023]
Abstract
Epigenetic alterations, including methylation, have been shown to be an important mechanism of gene silencing in cancer. Ependymoma has been well characterized at the DNA copy number and mRNA expression levels. However little is known about DNA methylation changes. To gain a more global view of the methylation profile of ependymoma we conducted an array-based analysis. Our data demonstrated tumors to segregate according to their location in the CNS, which was associated with a difference in the global level of methylation. Supratentorial and spinal tumors displayed significantly more hypermethylated genes than posterior fossa tumors, similar to the ‘CpG island methylator phenotype’ (CIMP) identified in glioma and colon carcinoma. This hypermethylated profile was associated with an increase in expression of genes encoding for proteins involved in methylating DNA, suggesting an underlying mechanism. An integrated analysis of methylation and mRNA expression array data allowed us to identify methylation-induced expression changes. Most notably genes involved in the control of cell growth and death and the immune system were identified, including members of the JNK pathway and PPARG. In conclusion, we have generated a global view of the methylation profile of ependymoma. The data suggests epigenetic silencing of tumor suppressor genes is an important mechanism in the pathogenesis of supratentorial and spinal, but not posterior fossa ependymomas. Hypermethylation correlated with a decrease in expression of a number of tumor suppressor genes and pathways that could be playing an important role in tumor pathogenesis.
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Affiliation(s)
- Hazel A. Rogers
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - John-Paul Kilday
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Cerys Mayne
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Jennifer Ward
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Martyna Adamowicz-Brice
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Ed C. Schwalbe
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Steven C. Clifford
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Beth Coyle
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Richard G. Grundy
- Children’s Brain Tumour Research Centre, D Floor Medical School, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
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Wani K, Armstrong TS, Vera-Bolanos E, Raghunathan A, Ellison D, Gilbertson R, Vaillant B, Goldman S, Packer RJ, Fouladi M, Pollack I, Mikkelsen T, Prados M, Omuro A, Soffietti R, Ledoux A, Wilson C, Long L, Gilbert MR, Aldape K. A prognostic gene expression signature in infratentorial ependymoma. Acta Neuropathol 2012; 123:727-38. [PMID: 22322993 DOI: 10.1007/s00401-012-0941-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 01/05/2012] [Indexed: 12/12/2022]
Abstract
Patients with ependymoma exhibit a wide range of clinical outcomes that are currently unexplained by clinical or histological factors. Little is known regarding molecular biomarkers that could predict clinical behavior. Since recent data suggest that these tumors display biological characteristics according to their location (cerebral vs. infratentorial vs. spinal cord), rather than explore a broad spectrum of ependymoma, we focused on molecular alterations in ependymomas arising in the infratentorial compartment. Unsupervised clustering of available gene expression microarray data revealed two major subgroups of infratentorial ependymoma. Group 1 tumors over expressed genes that were associated with mesenchyme, Group 2 tumors showed no distinct gene ontologies. To assess the prognostic significance of these gene expression subgroups, real-time reverse transcriptase polymerase chain reaction assays were performed on genes defining the subgroups in a training set. This resulted in a 10-gene prognostic signature. Multivariate analysis showed that the 10-gene signature was an independent predictor of recurrence-free survival after adjusting for clinical factors. Evaluation of an external dataset describing subgroups of infratentorial ependymomas showed concordance of subgroup definition, including validation of the mesenchymal subclass. Importantly, the 10-gene signature was validated as a predictor of recurrence-free survival in this dataset. Taken together, the results indicate a link between clinical outcome and biologically identified subsets of infratentorial ependymoma and offer the potential for prognostic testing to estimate clinical aggressiveness in these tumors.
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Affiliation(s)
- Khalida Wani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, 77030, USA
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Puget S, Philippe C, Bax DA, Job B, Varlet P, Junier MP, Andreiuolo F, Carvalho D, Reis R, Guerrini-Rousseau L, Roujeau T, Dessen P, Richon C, Lazar V, Le Teuff G, Sainte-Rose C, Geoerger B, Vassal G, Jones C, Grill J. Mesenchymal transition and PDGFRA amplification/mutation are key distinct oncogenic events in pediatric diffuse intrinsic pontine gliomas. PLoS One 2012; 7:e30313. [PMID: 22389665 PMCID: PMC3289615 DOI: 10.1371/journal.pone.0030313] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 12/15/2011] [Indexed: 12/17/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is one of the most frequent malignant pediatric brain tumor and its prognosis is universaly fatal. No significant improvement has been made in last thirty years over the standard treatment with radiotherapy. To address the paucity of understanding of DIPGs, we have carried out integrated molecular profiling of a large series of samples obtained with stereotactic biopsy at diagnosis. While chromosomal imbalances did not distinguish DIPG and supratentorial tumors on CGHarrays, gene expression profiling revealed clear differences between them, with brainstem gliomas resembling midline/thalamic tumours, indicating a closely-related origin. Two distinct subgroups of DIPG were identified. The first subgroup displayed mesenchymal and pro-angiogenic characteristics, with stem cell markers enrichment consistent with the possibility to grow tumor stem cells from these biopsies. The other subgroup displayed oligodendroglial features, and appeared largely driven by PDGFRA, in particular through amplification and/or novel missense mutations in the extracellular domain. Patients in this later group had a significantly worse outcome with an hazard ratio for early deaths, ie before 10 months, 8 fold greater that the ones in the other subgroup (p = 0.041, Cox regression model). The worse outcome of patients with the oligodendroglial type of tumors was confirmed on a series of 55 paraffin-embedded biopsy samples at diagnosis (median OS of 7.73 versus 12.37 months, p = 0.045, log-rank test). Two distinct transcriptional subclasses of DIPG with specific genomic alterations can be defined at diagnosis by oligodendroglial differentiation or mesenchymal transition, respectively. Classifying these tumors by signal transduction pathway activation and by mutation in pathway member genes may be particularily valuable for the development of targeted therapies.
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Affiliation(s)
- Stephanie Puget
- Department of Neurosurgery, Necker-Sick Children Hospital, University Paris V Descartes, Paris, France
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique «Vectorology and Anticancer Therapeutics», Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
| | - Cathy Philippe
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique «Vectorology and Anticancer Therapeutics», Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
| | - Dorine A. Bax
- Section of Pediatric Oncology, The Institute of Cancer Research/Royal Marsden Hospital, Sutton, Surrey, United Kingdom
| | - Bastien Job
- Formation de Recherche en Evolution 2939 du Centre National de la Recherche Scientifique, Integrated Research Cancer Institute in Villejuif, University Paris XI, Villejuif, France
| | - Pascale Varlet
- Team Glial Plasticity, Unite Mixte de Recherche 894 de l'Institut National de la Santé et de la Recherche Medicale and Department of Neuropathology, Sainte-Anne Hospital, University Paris V Descartes, Paris, France
| | - Marie-Pierre Junier
- Team Glial Plasticity, Unite Mixte de Recherche 894 de l'Institut National de la Santé et de la Recherche Medicale and Department of Neuropathology, Sainte-Anne Hospital, University Paris V Descartes, Paris, France
| | - Felipe Andreiuolo
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique «Vectorology and Anticancer Therapeutics», Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
| | - Dina Carvalho
- Section of Pediatric Oncology, The Institute of Cancer Research/Royal Marsden Hospital, Sutton, Surrey, United Kingdom
- Life and Health Sciences Research Institute, University Do Minho, Braga, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ricardo Reis
- Life and Health Sciences Research Institute, University Do Minho, Braga, Portugal
| | - Lea Guerrini-Rousseau
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique «Vectorology and Anticancer Therapeutics», Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
| | - Thomas Roujeau
- Department of Neurosurgery, Necker-Sick Children Hospital, University Paris V Descartes, Paris, France
| | - Philippe Dessen
- Formation de Recherche en Evolution 2939 du Centre National de la Recherche Scientifique, Integrated Research Cancer Institute in Villejuif, University Paris XI, Villejuif, France
| | - Catherine Richon
- Functional Genomics Unit, Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
| | - Vladimir Lazar
- Functional Genomics Unit, Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
| | - Gwenael Le Teuff
- Department of Biostatistics and Epidemiology, Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
| | - Christian Sainte-Rose
- Department of Neurosurgery, Necker-Sick Children Hospital, University Paris V Descartes, Paris, France
| | - Birgit Geoerger
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique «Vectorology and Anticancer Therapeutics», Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
| | - Gilles Vassal
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique «Vectorology and Anticancer Therapeutics», Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
| | - Chris Jones
- Section of Pediatric Oncology, The Institute of Cancer Research/Royal Marsden Hospital, Sutton, Surrey, United Kingdom
| | - Jacques Grill
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique «Vectorology and Anticancer Therapeutics», Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Institute, University Paris XI, Villejuif, France
- * E-mail:
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Abstract
PURPOSE OF REVIEW Ependymomas remain a therapeutic challenge in pediatric neuro-oncology. These tumors are chemoresistant and rather radioresistant and until recently little was known about their biology. RECENT FINDINGS Histopathological grading of ependymomas according to the WHO classification is neither reproducible, nor correlated with outcome, especially in young children. Characterization of molecular abnormalities in ependymomas offers now a better understanding of their initiation and progression; different biological subtypes of tumors have been described and would need further validation. The identification of new prognostic biomarkers, such as tenascin-C overexpression or chromosome 1q gain, will considerably help patient stratification in future trials. Finally, the recent discovery of specific pathways involved in ependymomas oncogenesis, such as Notch-1or EPHB2 offers new perspectives for the development of targeted therapies. SUMMARY A comprehensive biological work-out including CGHarray and immunohistochemistry for specific biomarkers should now be recommended for the current management of pediatric ependymoma, especially in young children if radiotherapy has to be omitted in the first line of treatment.
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