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Abe E, Suzuki M, Ichimura K, Arakawa A, Satomi K, Ogino I, Hara T, Iwamuro H, Ohara Y, Kondo A. Implications of DNA Methylation Classification in Diagnosing Ependymoma. World Neurosurg 2024; 185:e1019-e1029. [PMID: 38479644 DOI: 10.1016/j.wneu.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Ependymoma is a central nervous system (CNS) tumor that arises from the ependymal cells of the brain's ventricles and spinal cord. The histopathology of ependymomas is indistinguishable regardless of the site of origin, and the prognosis varies. Recent studies have revealed that the development site and prognosis reflect the genetic background. In this study, we used genome-wide DNA methylation array analysis to investigate the epigenetic background of ependymomas from different locations treated at our hospital. METHODS Four cases of posterior fossa ependymomas and 11 cases of spinal ependymomas were analyzed. RESULTS DNA methylation profiling using the DKFZ methylation classifier showed that the methylation diagnoses of the 2 cases differed from the histopathological diagnoses, and 2 cases could not be classified. Tumor that spread from the brain to the spinal cord was molecularly distinguishable from other primary spinal tumors. CONCLUSIONS Although adding DNA methylation classification to conventional diagnostic methods may be helpful, the diagnosis in some cases remains undetermined. This may affect decision-making regarding treatment strategies and follow-up. Further investigations are required to improve the diagnostic accuracy of these tumors.
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Affiliation(s)
- Eiji Abe
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Mario Suzuki
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Koichi Ichimura
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan; Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Atsushi Arakawa
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kaishi Satomi
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Ikuko Ogino
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takeshi Hara
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hirokazu Iwamuro
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yukoh Ohara
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Akihide Kondo
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Kerdivel G, Amrouche F, Calmejane MA, Carallis F, Hamroune J, Hantel C, Bertherat J, Assié G, Boeva V. DNA hypermethylation driven by DNMT1 and DNMT3A favors tumor immune escape contributing to the aggressiveness of adrenocortical carcinoma. Clin Epigenetics 2023; 15:121. [PMID: 37528470 PMCID: PMC10394822 DOI: 10.1186/s13148-023-01534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 07/16/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Adrenocortical carcinoma is rare and aggressive endocrine cancer of the adrenal gland. Within adrenocortical carcinoma, a recently described subtype characterized by a CpG island methylator phenotype (CIMP) has been associated with an especially poor prognosis. However, the drivers of CIMP remain unknown. Furthermore, the functional relation between CIMP and poor clinical outcomes of patients with adrenocortical carcinoma stays elusive. RESULTS Here, we show that CIMP in adrenocortical carcinoma is linked to the increased expression of DNA methyltransferases DNMT1 and DNMT3A driven by a gain of gene copy number and cell hyperproliferation. Importantly, we demonstrate that CIMP contributes to tumor aggressiveness by favoring tumor immune escape. This effect could be at least partially reversed by treatment with the demethylating agent 5-azacytidine. CONCLUSIONS In sum, our findings suggest that co-treatment with demethylating agents might enhance the efficacy of immunotherapy and could represent a novel therapeutic approach for patients with high CIMP adrenocortical carcinoma.
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Affiliation(s)
- Gwenneg Kerdivel
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Floriane Amrouche
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Marie-Ange Calmejane
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | | | - Juliette Hamroune
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Constanze Hantel
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland
- Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Jérôme Bertherat
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Guillaume Assié
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Valentina Boeva
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France.
- Department of Computer Science, Institute for Machine Learning, ETH Zurich, Universitätstrasse 6, 8092, Zurich, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Zurich, Switzerland.
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Early ependymal tumor with MN1-BEND2 fusion: a mostly cerebral tumor of female children with a good prognosis that is distinct from classical astroblastoma. J Neurooncol 2023; 161:425-439. [PMID: 36604386 PMCID: PMC9992034 DOI: 10.1007/s11060-022-04222-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Review of the clinicopathologic and genetic features of early ependymal tumor with MN1-BEND2 fusion (EET MN1-BEND2), classical astroblastomas, and recently described related pediatric CNS tumors. I also briefly review general mechanisms of gene expression silencing by DNA methylation and chromatin remodeling, and genomic DNA methylation profiling as a powerful new tool for CNS tumor classification. METHODS Literature review and illustration of tumor histopathologic features and prenatal gene expression timelines. RESULTS Astroblastoma, originally descried by Bailey and Cushing in 1926, has been an enigmatic tumor. Whether they are of ependymal or astrocytic derivation was argued for decades. Recent genetic evidence supports existence of both ependymal and astrocytic astroblastoma-like tumors. Studies have shown that tumors exhibiting astroblastoma-like histology can be classified into discrete entities based on their genomic DNA methylation profiles, gene expression, and in some cases, the presence of unique gene fusions. One such tumor, EET MN1-BEND2 occurs mostly in female children, and has an overall very good prognosis with surgical management. It contains a gene fusion comprised of portions of the MN1 gene at chromosomal location 22q12.1 and the BEND2 gene at Xp22.13. Other emerging pediatric CNS tumor entities demonstrating ependymal or astroblastoma-like histological features also harbor gene fusions involving chromosome X, 11q22 and 22q12 breakpoint regions. CONCLUSIONS Genomic DNA profiling has facilitated discovery of several new CNS tumor entities, however, traditional methods, such as immunohistochemistry, DNA or RNA sequencing, and cytogenetic studies, including fluorescence in situ hybridization, remain necessary for their accurate biological classification and diagnosis.
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Lagou MK, Anastasiadou DP, Karagiannis GS. A Proposed Link Between Acute Thymic Involution and Late Adverse Effects of Chemotherapy. Front Immunol 2022; 13:933547. [PMID: 35844592 PMCID: PMC9283860 DOI: 10.3389/fimmu.2022.933547] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Epidemiologic data suggest that cancer survivors tend to develop a protuberant number of adverse late effects, including second primary malignancies (SPM), as a result of cytotoxic chemotherapy. Besides the genotoxic potential of these drugs that directly inflict mutational burden on genomic DNA, the precise mechanisms contributing to SPM development are poorly understood. Cancer is nowadays perceived as a complex process that goes beyond the concept of genetic disease and includes tumor cell interactions with complex stromal and immune cell microenvironments. The cancer immunoediting theory offers an explanation for the development of nascent neoplastic cells. Briefly, the theory suggests that newly emerging tumor cells are mostly eliminated by an effective tissue immunosurveillance, but certain tumor variants may occasionally escape innate and adaptive mechanisms of immunological destruction, entering an equilibrium phase, where immunologic tumor cell death "equals" new tumor cell birth. Subsequent microenvironmental pressures and accumulation of helpful mutations in certain variants may lead to escape from the equilibrium phase, and eventually cause an overt neoplasm. Cancer immunoediting functions as a dedicated sentinel under the auspice of a highly competent immune system. This perspective offers the fresh insight that chemotherapy-induced thymic involution, which is characterized by the extensive obliteration of the sensitive thymic epithelial cell (TEC) compartment, can cause long-term defects in thymopoiesis and in establishment of diverse T cell receptor repertoires and peripheral T cell pools of cancer survivors. Such delayed recovery of T cell adaptive immunity may result in prolonged hijacking of the cancer immunoediting mechanisms, and lead to development of persistent and mortal infections, inflammatory disorders, organ-specific autoimmunity lesions, and SPMs. Acknowledging that chemotherapy-induced thymic involution is a potential risk factor for the emergence of SPM demarcates new avenues for the rationalized development of pharmacologic interventions to promote thymic regeneration in patients receiving cytoreductive chemotherapies.
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Affiliation(s)
- Maria K. Lagou
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Tumor Microenvironment and Metastasis Program, Albert Einstein Cancer Center, Bronx, NY, United States
| | - Dimitra P. Anastasiadou
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Tumor Microenvironment and Metastasis Program, Albert Einstein Cancer Center, Bronx, NY, United States
| | - George S. Karagiannis
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Tumor Microenvironment and Metastasis Program, Albert Einstein Cancer Center, Bronx, NY, United States
- Cancer Dormancy and Tumor Microenvironment Institute, Albert Einstein Cancer Center, Bronx, NY, United States
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, United States
- Integrated Imaging Program, Albert Einstein College of Medicine, Bronx, NY, United States
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Zahnreich S, Schmidberger H. Childhood Cancer: Occurrence, Treatment and Risk of Second Primary Malignancies. Cancers (Basel) 2021; 13:cancers13112607. [PMID: 34073340 PMCID: PMC8198981 DOI: 10.3390/cancers13112607] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer represents the leading cause of disease-related death and treatment-associated morbidity in children with an increasing trend in recent decades worldwide. Nevertheless, the 5-year survival of childhood cancer patients has been raised impressively to more than 80% during the past decades, primarily attributed to improved diagnostic technologies and multiagent cytotoxic regimens. This strong benefit of more efficient tumor control and prolonged survival is compromised by an increased risk of adverse and fatal late sequelae. Long-term survivors of pediatric tumors are at the utmost risk for non-carcinogenic late effects such as cardiomyopathies, neurotoxicity, or pneumopathies, as well as the development of secondary primary malignancies as the most detrimental consequence of genotoxic chemo- and radiotherapy. Promising approaches to reducing the risk of adverse late effects in childhood cancer survivors include high precision irradiation techniques like proton radiotherapy or non-genotoxic targeted therapies and immune-based treatments. However, to date, these therapies are rarely used to treat pediatric cancer patients and survival rates, as well as incidences of late effects, have changed little over the past two decades in this population. Here we provide an overview of the epidemiology and etiology of childhood cancers, current developments for their treatment, and therapy-related adverse late health consequences with a special focus on second primary malignancies.
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Cho HJ, Park HY, Kim K, Chae H, Paek SH, Kim SK, Park CK, Choi SH, Park SH. Methylation and molecular profiles of ependymoma: Influence of patient age and tumor anatomic location. Mol Clin Oncol 2021; 14:88. [PMID: 33767857 DOI: 10.3892/mco.2021.2250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/05/2021] [Indexed: 12/30/2022] Open
Abstract
Ependymomas are tumors of the central nervous system that can occur in patients of all ages. Guidelines from the World Health Organization (WHO) for the grading of ependymomas consider patient age, tumor resection range, tumor location and histopathological grade. However, recent studies have suggested that a greater focus on both tumor location and patient age in terms of transcriptomic, genetic, and epigenetic analyses may provide a more accurate assessment of clinical prognosis than the grading system proposed by WHO guidelines. The current study identified the differences and similarities in ependymoma characteristics using three different molecular analyses and methylation arrays. Primary intracranial ependymoma tissues were obtained from 13 Korean patients (9 adults and 4 children), after which whole-exome sequencing (WES), ion-proton comprehensive cancer panel (CCP) analysis, RNA sequencing, and Infinium HumanMethylation450 BeadChip array analysis was performed. Somatic mutations, copy number variations, and fusion genes were identified. It was observed that the methylation status and differentially expressed genes were significantly different according to tumor location and patient age. Several novel gene fusions and somatic mutations were identified, including a yes-associated protein 1 fusion mutation in a child with a good prognosis. Moreover, the methylation microarray revealed that genes associated with neurogenesis and neuron differentiation were hypermethylated in the adult group, whereas genes in the homeobox gene family were hypermethylated in the supratentorial (ST) group. The results confirmed the existence of significantly differentially expressed tumor-specific genes based on tumor location and patient age. These results provided valuable insight into the epigenetic and genetic profiles of intracranial ependymomas and uncovered potential strategies for the identification of location- and age-based ependymoma-related prognostic factors.
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Affiliation(s)
- Hwa Jin Cho
- Department of Pathology, Inje University Busan Paik Hospital, Busan 47392, Republic of Korea
| | - Ha Young Park
- Department of Pathology, Inje University Busan Paik Hospital, Busan 47392, Republic of Korea
| | - Kwangsoo Kim
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Heejoon Chae
- Division of Computer Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sun Ha Paek
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Seung-Ki Kim
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Seung-Hong Choi
- Department of Radiology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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Lester McCully C, Rodgers LT, Cruz R, Thomas ML, Peer CJ, Figg WD, Warren KE. Plasma and cerebrospinal fluid pharmacokinetics of the DNA methyltransferase inhibitor, 5-azacytidine, alone and with inulin, in nonhuman primate models. Neurooncol Adv 2020; 2:vdaa005. [PMID: 32309806 PMCID: PMC7146732 DOI: 10.1093/noajnl/vdaa005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Epigenetic modifiers are being investigated for a number of CNS malignancies as tumor-associated mutations such as isocitrate dehydrogenase mutations (IDH1/IDH2) and H3K27M mutations, which result in aberrant signaling, are identified. We evaluated the CNS exposure of the DNA methyltransferase inhibitor, 5-azacytidine (5-AZA), in preclinical nonhuman primate (NHP) models to inform its clinical development for CNS tumors. METHODS 5-AZA and 5-AZA+Inulin pharmacokinetics (PK) were evaluated in NHPs (n = 10) following systemic (intravenous [IV]) and intrathecal (intraventricular [IT-V], intralumbar [IT-L], and cisternal [IT-C]) administration. Plasma, cerebrospinal fluid (CSF), cortical extracellular fluid (ECF), and tissues were collected. 5-AZA levels were quantified via ultra-high-performance liquid chromatography with tandem mass spectrometric detection assay and inulin via ELISA. PK parameters were calculated using noncompartmental methods. RESULTS After IV administration, minimal plasma exposure (area under the curve [AUC] range: 2.4-3.2 h*µM) and negligible CSF exposure were noted. CSF exposure was notably higher after IT-V administration (AUCINF 1234.6-5368.4 h*µM) compared to IT-L administration (AUCINF 7.5-19.3 h*µM). CSF clearance after IT administration exceeded the mean inulin CSF flow rate of 0.018 ± 0.003 ml/min as determined by inulin IT-V administration. 5-AZA IT-V administration with inulin increased the 5-AZA CSF duration of exposure by 2.2-fold. IT-C administration yielded no quantifiable 5-AZA ECF concentrations but resulted in quantifiable tissue levels. CONCLUSIONS IT administration of 5-AZA is necessary to achieve adequate CNS exposure. IT administration results in pronounced and prolonged 5-AZA CSF exposure above the reported IC50 range for IDH-mutated glioma cell lines. Inulin administered with 5-AZA increased the duration of exposure for 5-AZA.
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Affiliation(s)
- Cynthia Lester McCully
- Pediatric Neuro-Oncology Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Louis T Rodgers
- Pediatric Neuro-Oncology Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Clinical Pharmacology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rafael Cruz
- Pediatric Neuro-Oncology Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Laboratory Animal Science Program and Leidos Biomedical Research, Inc., National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marvin L Thomas
- Office of Research Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Cody J Peer
- Clinical Pharmacology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - William D Figg
- Clinical Pharmacology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Katherine E Warren
- Pediatric Neuro-Oncology Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Pérez-Ramírez M, García-Méndez A, Siordia-Reyes AG, Chavarría A, Gómez C, García-Hernández N. Pediatric ependymoma: GNAO1, ASAH1, IMMT and IPO7 protein expression and 5-year prognosis correlation. Clin Neurol Neurosurg 2019; 186:105488. [PMID: 31505435 DOI: 10.1016/j.clineuro.2019.105488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/18/2019] [Accepted: 08/11/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The aim of this work was to evaluate a pediatric ependymoma protein expression that may be useful as a molecular biomarker candidate for prognosis, correlated with clinical features such as age, gender, histopathological grade, ependymal tumor recurrence and patient survival. PATIENTS AND METHODS Immunohistochemistry assays were performed for GNAO1, ASAH1, IMMT, IPO7, Cyclin D1, P53 and Ki-67 proteins. Kaplan-Meier and Cox analysis were performed for age, gender, histopathological grade, relapse and survival correlation. RESULTS We found that three proteins correlate with histopathological grade and relapse; two proteins correlate with survival; one protein does not correlate with any clinical feature. CONCLUSION Our results suggest that, out of the proteins analyzed, five may be considered suitable prognostic biomarkers and one may be considered a predictive biomarker for response to treatment of pediatric ependymoma.
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Affiliation(s)
- Monserrat Pérez-Ramírez
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freud", Centro Médico Nacional Siglo XXI, IMSS. Av. Cuauhtémoc 330, Col. Doctores, Del. Cuauhtémoc, 06720, Mexico
| | - Antonio García-Méndez
- Servicio de Neurocirugía Pediátrica, Hospital General "Dr. Gaudencio González Garza", Centro Médico Nacional "La Raza", IMSS, Calzada Vallejo y Jacarandas S/N, Col. La Raza, Del. Azcapotzalco, 02980, Ciudad de México, Mexico
| | - Alicia Georgina Siordia-Reyes
- Servicio de Patología, Hospital de Pediatría "Dr. Silvestre Frenk Freud", Centro Médico Nacional Siglo XXI, IMSS. Av. Cuauhtémoc 330, Col. Doctores, Del. Cuauhtémoc, 06720, Ciudad de México, Mexico
| | - Anahí Chavarría
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico
| | - Celedonio Gómez
- Facultad de Química, Universidad Nacional Autónoma de México, Avenida Ciudad Universitaria 3000, Coyoacán, 04360, Ciudad de México, Mexico
| | - Normand García-Hernández
- Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría "Dr. Silvestre Frenk Freud", Centro Médico Nacional Siglo XXI, IMSS. Av. Cuauhtémoc 330, Col. Doctores, Del. Cuauhtémoc, 06720, Mexico.
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Rogers HA, Chapman R, Kings H, Allard J, Barron-Hastings J, Pajtler KW, Sill M, Pfister S, Grundy RG. Limitations of current in vitro models for testing the clinical potential of epigenetic inhibitors for treatment of pediatric ependymoma. Oncotarget 2018; 9:36530-36541. [PMID: 30559935 PMCID: PMC6284855 DOI: 10.18632/oncotarget.26370] [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: 05/16/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022] Open
Abstract
Background Epigenetic modifications have been shown to play an important role in the classification and pathogenesis of the pediatric brain tumor ependymoma, suggesting they are a potential therapeutic target. Results Agents targeting epigenetic modifications inhibited the growth and induced the death of ependymoma cells with variable efficiency. However, this was often not at clinically achievable doses. Additionally, DNA methylation profiling revealed a lack of similarity to primary ependymomas suggesting alterations were induced during culture. Toxicity to fetal neural stem cells was also seen at similar drug concentrations Conclusions Agents targeting epigenetic modifications were able to inhibit the growth and induced the death of ependymoma cells grown in vitro. However, many agents were only active at high doses, outside clinical ranges, and also resulted in toxicity to normal brain cells. The lack of similarity in DNA methylation profiles between cultured cells and primary ependymomas questions the validity of using in vitro cultured cells for pre-clinical analysis of agents targeting epigenetic mechanisms and suggests further investigation using models that are more appropriate should be undertaken before agents are taken forward for clinical testing. Materials and Methods The effects of agents targeting epigenetic modifications on the growth and death of a panel of ependymoma cell lines was investigated, as well as toxicity to normal fetal neural stem cells. The ependymoma cell lines were characterized using DNA methylation profiling.
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Affiliation(s)
- Hazel Anne Rogers
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Rebecca Chapman
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Holly Kings
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Julie Allard
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Jodie Barron-Hastings
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Kristian W Pajtler
- Hopp Children's Cancer Centre at the NCT (KiTZ), Heidelberg, Germany.,German Cancer Research Centre (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Haematology and Oncology, University Hospital, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Centre at the NCT (KiTZ), Heidelberg, Germany.,German Cancer Research Centre (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan Pfister
- Hopp Children's Cancer Centre at the NCT (KiTZ), Heidelberg, Germany.,German Cancer Research Centre (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Haematology and Oncology, University Hospital, Heidelberg, Germany
| | - Richard Guy Grundy
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
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Alexiou GA, Voulgaris S. Letter to the Editor. Second cancer risk in patients with spinal ependymomas. J Neurosurg Spine 2018; 29:612-613. [DOI: 10.3171/2018.6.spine18719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Ependymoma is a locally aggressive tumor with metastatic potential that arises in diverse locations throughout the brain and spine in children. Tumor and treatment may result in significant morbidity. Cure remains elusive for many patients owing to diverse biology and resistance to conventional therapy. The implementation of systematic postoperative irradiation in clinical trials during the past 20 years has increased the proportion of patients achieving durable disease control with excellent results, as measured by objective functional outcome measures. Clinical, pathologic, and molecular risk stratification should be used to refine treatment regimens for children with ependymoma to reduce the risk of complications associated with therapy and increase the rate of disease control in the setting of combined modality or more intensive therapy. This review covers standards of care and current clinical trials for children with ependymoma, emphasizing the history and evolution of treatment regimens during the past 20 years and the clinical questions they hoped to address.
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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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13
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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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14
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Lee CH, Chung CK, Ohn JH, Kim CH. The Similarities and Differences between Intracranial and Spinal Ependymomas : A Review from a Genetic Research Perspective. J Korean Neurosurg Soc 2016; 59:83-90. [PMID: 26962412 PMCID: PMC4783489 DOI: 10.3340/jkns.2016.59.2.83] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 11/20/2015] [Accepted: 01/01/2016] [Indexed: 11/27/2022] Open
Abstract
Ependymomas occur in both the brain and spine. The prognosis of these tumors sometimes differs for different locations. The genetic landscape of ependymoma is very heterogeneous despite the similarity of histopathologic findings. In this review, we describe the genetic differences between spinal ependymomas and their intracranial counterparts to better understand their prognosis. From the literature review, many studies have reported that spinal cord ependymoma might be associated with NF2 mutation, NEFL overexpression, Merlin loss, and 9q gain. In myxopapillary ependymoma, NEFL and HOXB13 overexpression were reported to be associated. Prior studies have identified HIC-1 methylation, 4.1B deletion, and 4.1R loss as common features in intracranial ependymoma. Supratentorial ependymoma is usually characterized by NOTCH-1 mutation and p75 expression. TNC mutation, no hypermethylation of RASSF1A, and GFAP/NeuN expression may be diagnostic clues of posterior fossa ependymoma. Although MEN1, TP53, and PTEN mutations are rarely reported in ependymoma, they may be related to a poor prognosis, such as recurrence or metastasis. Spinal ependymoma has been found to be quite different from intracranial ependymoma in genetic studies, and the favorable prognosis in spinal ependymoma may be the result of the genetic differences. A more detailed understanding of these various genetic aberrations may enable the identification of more specific prognostic markers as well as the development of customized targeted therapies.
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Affiliation(s)
- Chang-Hyun Lee
- Department of Neurosurgery, Ilsan Paik Hospital, Inje University College of Medicine, Goyang, Korea
| | - Chun Kee Chung
- Department of Neurosurgery, Seoul National University Hospital, Seoul, Korea.; Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea.; Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul, Korea.; Clinical Research Institute, Seoul National University Hospital, Seoul, Korea.; Department of Brain and Cognitive Sciences, Seoul National University College of Natural Sciences, Seoul, Korea
| | - Jung Hun Ohn
- Bioinformatics, Samsung Gene Institute, Samsung Medical Center, Seoul, Korea
| | - Chi Heon Kim
- Department of Neurosurgery, Seoul National University Hospital, Seoul, Korea.; Department of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea.; Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul, Korea.; Clinical Research Institute, Seoul National University Hospital, Seoul, Korea
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15
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Abstract
PURPOSE OF REVIEW Central nervous system tumors represent the most common solid tumors in children and are a leading cause of cancer-related fatalities in this age group. Here, we provide an update on insights gained through molecular profiling of the most common malignant childhood brain tumors. RECENT FINDINGS Genomic profiling studies of medulloblastoma, ependymoma, and diffuse intrinsic pontine glioma (diffuse midline glioma, with H3-K27M mutation), have refined, if not redefined, the diagnostic classification and therapeutic stratification of patients with these tumors. They detail the substantial genetic heterogeneity across each disease type and, importantly, link genotypic information to clinical course. The most aggressive, treatment-resistant (and also treatment-sensitive) forms within each disease entity are identified, and their potentially actionable targets. SUMMARY Molecularly based classification of pediatric brain tumors provides a critical framework for the more precise stratification and treatment of children with brain tumors.
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16
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Morfouace M, Nimmervoll B, Boulos N, Patel YT, Shelat A, Freeman BB, Robinson GW, Wright K, Gajjar A, Stewart CF, Gilbertson RJ, Roussel MF. Preclinical studies of 5-fluoro-2'-deoxycytidine and tetrahydrouridine in pediatric brain tumors. J Neurooncol 2016; 126:225-34. [PMID: 26518542 PMCID: PMC4718940 DOI: 10.1007/s11060-015-1965-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/19/2015] [Indexed: 12/15/2022]
Abstract
Chemotherapies active in preclinical studies frequently fail in the clinic due to lack of efficacy, which limits progress for rare cancers since only small numbers of patients are available for clinical trials. Thus, a preclinical drug development pipeline was developed to prioritize potentially active regimens for pediatric brain tumors spanning from in vitro drug screening, through intracranial and intra-tumoral pharmacokinetics to in vivo efficacy studies. Here, as an example of the pipeline, data are presented for the combination of 5-fluoro-2'-deoxycytidine and tetrahydrouridine in three pediatric brain tumor models. The in vitro activity of nine novel therapies was tested against tumor spheres derived from faithful mouse models of Group 3 medulloblastoma, ependymoma, and choroid plexus carcinoma. Agents with the greatest in vitro potency were then subjected to a comprehensive series of in vivo pharmacokinetic (PK) and pharmacodynamic (PD) studies culminating in preclinical efficacy trials in mice harboring brain tumors. The nucleoside analog 5-fluoro-2'-deoxycytidine (FdCyd) markedly reduced the proliferation in vitro of all three brain tumor cell types at nanomolar concentrations. Detailed intracranial PK studies confirmed that systemically administered FdCyd exceeded concentrations in brain tumors necessary to inhibit tumor cell proliferation, but no tumor displayed a significant in vivo therapeutic response. Despite promising in vitro activity and in vivo PK properties, FdCyd is unlikely to be an effective treatment of pediatric brain tumors, and therefore was deprioritized for the clinic. Our comprehensive and integrated preclinical drug development pipeline should reduce the attrition of drugs in clinical trials.
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Affiliation(s)
- Marie Morfouace
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Birgit Nimmervoll
- CR UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 ORE, UK
| | - Nidal Boulos
- CR UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 ORE, UK
| | - Yogesh T Patel
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anang Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Burgess B Freeman
- Preclinical Pharmacokinetic Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Giles W Robinson
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Karen Wright
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Amar Gajjar
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Clinton F Stewart
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Richard J Gilbertson
- CR UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 ORE, UK.
| | - Martine F Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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17
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Gupta K, Salunke P. Understanding Ependymoma Oncogenesis: an Update on Recent Molecular Advances and Current Perspectives. Mol Neurobiol 2015; 54:15-21. [PMID: 26712502 DOI: 10.1007/s12035-015-9646-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 12/16/2015] [Indexed: 01/12/2023]
Abstract
Remarkable progress has been made in the last decade in understanding the biology and oncogenesis of this relatively rare childhood brain tumor-the ependymoma. Surgery and irradiation are the mainstays of therapeutic options; chemotherapy is yet to predictably affect outcome, and its role is currently being explored in several clinical trials. While WHO scores this tumor into three grades, grading of ependymoma into grade II and grade III is controversial because of its elusive histological criteria where no cut-offs have been defined for mitoses or percentage of tumor depicting increased cellularity. Grading remains unreliable in predicting outcome in several instances. There is a compelling need to integrate the molecular biomarkers highlighted in several studies over the past decade into patient risk stratification to help in better predicting the clinical outcome and to design effective tailored therapy. Genomic and transcriptomic studies lately have defined distinct molecular subgroups within ependymoma arising at three anatomic compartments-supratentorial, posterior fossa, and spinal cord. Review of pertinent literature on several seminal studies that have established a paradigm shift in understanding the oncogenesis of ependymoma has been carried out. The outcome, impact, and clinical relevance of these studies are also discussed. The review provides an update on progress and recent advances in understanding the biology and oncogenesis of ependymoma. The establishment of robust subgroups which are demographically, clinically, and molecularly distinct will provide new avenues for further refinement of therapeutic strategies.
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Affiliation(s)
- Kirti Gupta
- Neuropathology fellowship (St Jude, Memphis), Department of Histopathology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India.
| | - Pravin Salunke
- Department of Neurosurgery, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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18
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Meco D, Servidei T, Lamorte G, Binda E, Arena V, Riccardi R. Ependymoma stem cells are highly sensitive to temozolomide in vitro and in orthotopic models. Neuro Oncol 2014; 16:1067-77. [PMID: 24526307 DOI: 10.1093/neuonc/nou008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Ependymoma management remains challenging because of the inherent chemoresistance of this tumor. To determine whether ependymoma stem cells (SCs) might contribute to therapy resistance, we investigated the sensitivity of ependymoma SCs to temozolomide and etoposide. METHODS The efficacies of the two DNA damaging agents were explored in two ependymoma SC lines in vitro and in vivo models. RESULTS Ependymoma SC lines were highly sensitive to temozolomide and etoposide in vitro, but only temozolomide impaired tumor-initiation properties. Consistently, temozolomide but not etoposide showed significant antitumoral activity on ependymoma SC-driven subcutaneous and orthotopic xenografts by reducing the mitotic fraction. In vitro temozolomide at the EC50 (10 µM) induced accumulation of cells in the G2/M phase that was unexpectedly accompanied by downregulation of p27 and p21 without modulation of full-length p53 (FLp53). Differentiation-committed ependymoma SCs acquired resistance to temozolomide. Inhibition of proliferation was partly due to apoptosis, that occurred earlier in differentiated cells as compared to neurospheres. The activation of apoptosis correlated with an increase in p53β/γ isoforms without modulation of FLp53 under both serum-free and differentiation-promoting media. Incubation of cells in both conditions with temozolomide resulted in increased glioneuronal differentiation exhibiting elevated glial fibrillary acidic protein, galactosylceramidase, and βIII-tubulin expression compared to untreated controls. O(6)-methylguanine DNA methyltransferase (MGMT) transcript levels were very low in SCs, and were increased by treatment and, epigenetically, by differentiation through MGMT promoter unmethylation. CONCLUSION Ependymoma growth might be impaired by temozolomide through preferential depletion of a less differentiated, more tumorigenic, MGMT-negative cell population with stem-like properties.
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Affiliation(s)
- Daniela Meco
- Department of Pediatric Oncology, Catholic University, Rome, Italy (D.M., T.S., R.R.); Istituto CSS - Mendel Laboratory, Rome, Italy (G.L.); Department of Biotechnology and Biosciences, Building U3, University of Milan Bicocca, Milan, Italy (E.B.); Institute of Pathology, Catholic University, Rome, Italy (V.A.)
| | - Tiziana Servidei
- Department of Pediatric Oncology, Catholic University, Rome, Italy (D.M., T.S., R.R.); Istituto CSS - Mendel Laboratory, Rome, Italy (G.L.); Department of Biotechnology and Biosciences, Building U3, University of Milan Bicocca, Milan, Italy (E.B.); Institute of Pathology, Catholic University, Rome, Italy (V.A.)
| | - Giuseppe Lamorte
- Department of Pediatric Oncology, Catholic University, Rome, Italy (D.M., T.S., R.R.); Istituto CSS - Mendel Laboratory, Rome, Italy (G.L.); Department of Biotechnology and Biosciences, Building U3, University of Milan Bicocca, Milan, Italy (E.B.); Institute of Pathology, Catholic University, Rome, Italy (V.A.)
| | - Elena Binda
- Department of Pediatric Oncology, Catholic University, Rome, Italy (D.M., T.S., R.R.); Istituto CSS - Mendel Laboratory, Rome, Italy (G.L.); Department of Biotechnology and Biosciences, Building U3, University of Milan Bicocca, Milan, Italy (E.B.); Institute of Pathology, Catholic University, Rome, Italy (V.A.)
| | - Vincenzo Arena
- Department of Pediatric Oncology, Catholic University, Rome, Italy (D.M., T.S., R.R.); Istituto CSS - Mendel Laboratory, Rome, Italy (G.L.); Department of Biotechnology and Biosciences, Building U3, University of Milan Bicocca, Milan, Italy (E.B.); Institute of Pathology, Catholic University, Rome, Italy (V.A.)
| | - Riccardo Riccardi
- Department of Pediatric Oncology, Catholic University, Rome, Italy (D.M., T.S., R.R.); Istituto CSS - Mendel Laboratory, Rome, Italy (G.L.); Department of Biotechnology and Biosciences, Building U3, University of Milan Bicocca, Milan, Italy (E.B.); Institute of Pathology, Catholic University, Rome, Italy (V.A.)
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19
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Karakoula K, Jacques TS, Phipps KP, Harkness W, Thompson D, Harding BN, Darling JL, Warr TJ. Epigenetic genome-wide analysis identifies BEX1 as a candidate tumour suppressor gene in paediatric intracranial ependymoma. Cancer Lett 2013; 346:34-44. [PMID: 24333734 DOI: 10.1016/j.canlet.2013.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/02/2013] [Accepted: 12/04/2013] [Indexed: 12/13/2022]
Abstract
Promoter hypermethylation and transcriptional silencing is a common epigenetic mechanism of gene inactivation in cancer. To identify targets of epigenetic silencing in paediatric intracranial ependymoma, we used a pharmacological unmasking approach through treatment of 3 ependymoma short-term cell cultures with the demethylating agent 5-Aza-2'-deoxycytidine followed by global expression microarray analysis. We identified 55 candidate epigenetically silenced genes, which are involved in the regulation of apoptosis, Wnt signalling, p53 and cell differentiation. The methylation status of 26 of these genes was further determined by combined bisulfite restriction analysis (COBRA) and genomic sequencing in a cohort of 40 ependymoma samples. The most frequently methylated genes were BEX1 (27/40 cases), BAI2 (20/40), CCND2 (18/40), and CDKN2A (14/40). A high correlation between promoter hypermethylation and decreased gene expression levels was established by real-time quantitative PCR, suggesting the involvement of these genes in ependymoma tumourigenesis. Furthermore, ectopic expression of brain-expressed X-linked 1 (BEX1) in paediatric ependymoma short-term cell cultures significantly suppressed cell proliferation and colony formation. These data suggest that promoter hypermethylation contributes to silencing of target genes in paediatric intracranial ependymoma. Epigenetic inactivation of BEX1 supports its role as a candidate tumour suppressor gene in intracranial ependymoma, and a potential target for novel therapies for ependymoma in children.
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Affiliation(s)
- Katherine Karakoula
- Brain Tumour Research Centre, School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, UK.
| | - Thomas S Jacques
- Neural Development Unit, Birth Defects Research Centre, UCL Institute of Child Health, University College London, London WC1E 6BT, UK; Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Kim P Phipps
- Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - William Harkness
- Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Dominic Thompson
- Department of Neurosurgery, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Brian N Harding
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104-4399, USA
| | - John L Darling
- Brain Tumour Research Centre, School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, UK
| | - Tracy J Warr
- Brain Tumour Research Centre, School of Applied Sciences, University of Wolverhampton, Wolverhampton WV1 1LY, UK
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20
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Schwalbe EC, Hayden JT, Rogers HA, Miller S, Lindsey JC, Hill RM, Nicholson SL, Kilday JP, Adamowicz-Brice M, Storer L, Jacques TS, Robson K, Lowe J, Williamson D, Grundy RG, Bailey S, Clifford SC. Histologically defined central nervous system primitive neuro-ectodermal tumours (CNS-PNETs) display heterogeneous DNA methylation profiles and show relationships to other paediatric brain tumour types. Acta Neuropathol 2013; 126:943-6. [PMID: 24212602 DOI: 10.1007/s00401-013-1206-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 11/01/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Ed C Schwalbe
- Northern Institute for Cancer Research, Newcastle University, Sir James Spence Institute Level 5, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
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21
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Rogers HA, Mayne C, Chapman RJ, Kilday JP, Coyle B, Grundy RG. PI3K pathway activation provides a novel therapeutic target for pediatric ependymoma and is an independent marker of progression-free survival. Clin Cancer Res 2013; 19:6450-60. [PMID: 24077346 DOI: 10.1158/1078-0432.ccr-13-0222] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Currently, there are few effective adjuvant therapies for pediatric ependymoma outside confocal radiation, and prognosis remains poor. The phosphoinositide 3-kinase (PI3K) pathway is one of the most commonly activated pathways in cancer. PI3Ks transduce signals from growth factors and cytokines, resulting in the phosphorylation and activation of AKT, which in turn induces changes in cell growth, proliferation, and apoptosis. EXPERIMENTAL DESIGN PI3K pathway status was analyzed in ependymoma using gene expression data and immunohistochemical analysis of phosphorylated AKT (P-AKT). The effect of the PI3K pathway on cell proliferation was investigated by immunohistochemical analysis of cyclin D1 and Ki67, plus in vitro functional analysis. To identify a potential mechanism of PI3K pathway activation, PTEN protein expression and the mutation status of PI3K catalytic subunit α-isoform gene (PIK3CA) was investigated. RESULTS Genes in the pathway displayed significantly higher expression in supratentorial than in posterior fossa and spinal ependymomas. P-AKT protein expression, indicating pathway activation, was seen in 72% of tumors (n = 169) and P-AKT expression was found to be an independent marker of a poorer progression-free survival. A significant association between PI3K pathway activation and cell proliferation was identified, suggesting that pathway activation was influencing this process. PTEN protein loss was not associated with P-AKT staining and no mutations were identified in PIK3CA. CONCLUSIONS Our results suggest that the PI3K pathway could act as a biomarker, not only identifying patients with a worse prognosis but also those that could be treated with therapies targeted against the pathway, a strategy potentially effective in a high percentage of ependymoma patients.
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Affiliation(s)
- Hazel A Rogers
- Authors' Affiliation: Children's Brain Tumour Research Centre, D Floor Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
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22
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He H, Mao L, Xu P, Xi Y, Xu N, Xue M, Yu J, Ye X. Ossification of the posterior longitudinal ligament related genes identification using microarray gene expression profiling and bioinformatics analysis. Gene 2013; 533:515-9. [PMID: 24055420 DOI: 10.1016/j.gene.2013.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 12/13/2022]
Abstract
Ossification of the posterior longitudinal ligament (OPLL) is a kind of disease with physical barriers and neurological disorders. The objective of this study was to explore the differentially expressed genes (DEGs) in OPLL patient ligament cells and identify the target sites for the prevention and treatment of OPLL in clinic. Gene expression data GSE5464 was downloaded from Gene Expression Omnibus; then DEGs were screened by limma package in R language, and changed functions and pathways of OPLL cells compared to normal cells were identified by DAVID (The Database for Annotation, Visualization and Integrated Discovery); finally, an interaction network of DEGs was constructed by string. A total of 1536 DEGs were screened, with 31 down-regulated and 1505 up-regulated genes. Response to wounding function and Toll-like receptor signaling pathway may involve in the development of OPLL. Genes, such as PDGFB, PRDX2 may involve in OPLL through response to wounding function. Toll-like receptor signaling pathway enriched genes such as TLR1, TLR5, and TLR7 may involve in spine cord injury in OPLL. PIK3R1 was the hub gene in the network of DEGs with the highest degree; INSR was one of the most closely related genes of it. OPLL related genes screened by microarray gene expression profiling and bioinformatics analysis may be helpful for elucidating the mechanism of OPLL.
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Affiliation(s)
- Hailong He
- Department of Orthopaedics, Changzheng Hospital, The Second Military Medical University, No. 415, Fengyang Road, Huangpu District, Shanghai 200003, China.
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23
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Differential expression and methylation of brain developmental genes define location-specific subsets of pilocytic astrocytoma. Acta Neuropathol 2013; 126:291-301. [PMID: 23660940 DOI: 10.1007/s00401-013-1124-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/30/2013] [Accepted: 05/01/2013] [Indexed: 10/26/2022]
Abstract
Pilocytic astrocytomas (PAs) are the most common brain tumors in pediatric patients and can cause significant morbidity, including chronic neurological deficiencies. They are characterized by activating alterations in the mitogen-activated protein kinase pathway, but little else is known about their development. To map the global DNA methylation profiles of these tumors, we analyzed 62 PAs and 7 normal cerebellum samples using Illumina 450K microarrays. These data revealed two subgroups of PA that separate according to tumor location (infratentorial versus supratentorial), and identified key neural developmental genes that are differentially methylated between the two groups, including NR2E1 and EN2. Integration with transcriptome microarray data highlighted significant expression differences, which were unexpectedly associated with a strong positive correlation between methylation and expression. Differentially methylated probes were often identified within the gene body and/or regions up- or downstream of the gene, rather than at the transcription start site. We also identified a large number of differentially methylated genes between cerebellar PAs and normal cerebellum, which were again enriched for developmental genes. In addition, we found a significant association between differentially methylated genes and SUZ12 binding sites, indicating potential disruption of the polycomb repressor complex 2 (PRC2). Taken together, these data suggest that PA from different locations in the brain may arise from region-specific cells of origin, and highlight the potential disruption of key developmental regulators during tumorigenesis. These findings have implications for future basic research and clinical trials, as therapeutic targets and drug sensitivity may differ according to tumor location.
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24
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The role of the WNT/β-catenin pathway in central nervous system primitive neuroectodermal tumours (CNS PNETs). Br J Cancer 2013; 108:2130-41. [PMID: 23591193 PMCID: PMC3670474 DOI: 10.1038/bjc.2013.170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background: Central nervous system primitive neuroectodermal tumours (CNS PNETs) are embryonal tumours occurring predominantly in children. Current lack of knowledge regarding their underlying biology hinders development of more effective treatments. We previously identified WNT/β-catenin pathway activation in one-third of CNS PNETs, which was potentially linked to a better prognosis. In this study, we have extended our cohort, achieving a statistically significant correlation with prognosis. We additionally investigated the biological effects of WNT/β-catenin pathway activation in tumour pathogenesis. Methods: A total of 42 primary and 8 recurrent CNS PNETs were analysed for WNT/β-catenin pathway status using β-catenin immunohistochemistry. Genomic copy number and mRNA expression data were analysed to identify a molecular profile linked to WNT/β-catenin pathway activation. Results: Pathway activation was seen in 26% of CNS PNETs and was significantly associated with longer overall survival. Genes displaying a significant difference in expression levels, between tumours with and without WNT/β-catenin pathway activation, included several involved in normal CNS development suggesting aberrant pathway activation may be disrupting this process. Conclusion: We have identified WNT/β-catenin pathway status as a marker, which could potentially be used to stratify disease risk for patients with CNS PNET. Gene expression data suggest pathway activation is disrupting normal differentiation in the CNS.
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25
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Raghunathan A, Wani K, Armstrong TS, Vera-Bolanos E, Fouladi M, Gilbertson R, Gajjar A, Goldman S, Lehman NL, Metellus P, Mikkelsen T, Necesito-Reyes MJT, Omuro A, Packer RJ, Partap S, Pollack IF, Prados MD, Robins HI, Soffietti R, Wu J, Miller CR, Gilbert MR, Aldape KD. Histological predictors of outcome in ependymoma are dependent on anatomic site within the central nervous system. Brain Pathol 2013; 23:584-94. [PMID: 23452038 DOI: 10.1111/bpa.12050] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/22/2013] [Indexed: 12/11/2022] Open
Abstract
Ependymomas originate in posterior fossa (PF), supratentorial (ST) or spinal cord (SC) compartments. At present, grading schemes are applied independent of anatomic site. We performed detailed histological examination on 238 World Health Organization grade II and III ependymomas. Among PF ependymomas, the presence of hypercellular areas, necrosis, microvascular proliferation and elevated mitotic rate (all P < 0.01) were significantly associated with worse progression-free survival (PFS), while extensive ependymal canal formation was not (P = 0.89). Similar to the PF tumors, microvascular proliferation (P = 0.01) and elevated mitotic rate (P = 0.03) were significantly associated with worse PFS in the ST tumors. However, in contrast to PF tumors, extensive ependymal canals (P = 0.03) were associated with worse clinical outcome in ST ependymomas, but hypercellularity (P = 0.57) and necrosis (P = 0.47) were not. On multivariate Cox regression, after adjusting for relevant clinical variables, individual histological factors and a composite histological score remained significant among ST and PF ependymoma. In contrast to both PF and ST ependymoma, histological features were not found to be associated with PFS in SC tumors. Taken together, the clinical relevance of specific histological features in ependymoma appears to be related to the anatomic site of origin and suggests that site-specific grading criteria be considered in future classification systems.
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Mack SC, Witt H, Wang X, Milde T, Yao Y, Bertrand KC, Korshunov A, Pfister SM, Taylor MD. Emerging insights into the ependymoma epigenome. Brain Pathol 2013; 23:206-9. [PMID: 23432646 PMCID: PMC8028955 DOI: 10.1111/bpa.12020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/02/2013] [Indexed: 12/31/2022] Open
Abstract
Ependymoma is the third most common pediatric brain tumor, yet because of the paucity of effective therapeutic interventions, 45% of patients remain incurable. Recent transcriptional and copy number profiling of the disease has identified few driver genes and in fact points to a balanced genomic profile. Candidate gene approaches looking at hypermethylated promoters and genome-wide epigenetic arrays suggest that DNA methylation may be critical to ependymoma pathogenesis. This review attempts to highlight existing and emerging evidence implicating the ependymoma epigenome as a key player and that epigenetic modifiers may offer new targeted therapeutic avenues for patients.
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Affiliation(s)
- Stephen C. Mack
- Developmental and Stem Cell Biology ProgramThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Hendrik Witt
- Division of Pediatric NeurooncologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of Pediatric Hematology, Oncology and ImmunologyUniversity Hospital HeidelbergHeidelbergGermany
| | - Xin Wang
- Developmental and Stem Cell Biology ProgramThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Till Milde
- Department of Pediatric Hematology, Oncology and ImmunologyUniversity Hospital HeidelbergHeidelbergGermany
- Clinical Cooperation Unit Pediatric Oncology G340German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Yuan Yao
- Developmental and Stem Cell Biology ProgramThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Kelsey C. Bertrand
- Developmental and Stem Cell Biology ProgramThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Andrey Korshunov
- Clinical Cooperation Unit Pediatric Oncology G340German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuropathologyUniversity Hospital HeidelbergHeidelbergGermany
| | - Stefan M. Pfister
- Division of Pediatric NeurooncologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of Pediatric Hematology, Oncology and ImmunologyUniversity Hospital HeidelbergHeidelbergGermany
| | - Michael D. Taylor
- Developmental and Stem Cell Biology ProgramThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
- Department of SurgeryDivision of Neurosurgery and Labatt Brain Tumour Research CentreThe Hospital for Sick ChildrenTorontoOntarioCanada
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Landau E, Boop FA, Conklin HM, Wu S, Xiong X, Merchant TE. Supratentorial ependymoma: disease control, complications, and functional outcomes after irradiation. Int J Radiat Oncol Biol Phys 2012; 85:e193-9. [PMID: 23245280 DOI: 10.1016/j.ijrobp.2012.10.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 10/18/2012] [Accepted: 10/19/2012] [Indexed: 10/27/2022]
Abstract
PURPOSE Ependymoma is less commonly found in the supratentorial brain and has known clinical and molecular features that are unique. Our single-institution series provides valuable information about disease control for supratentorial ependymoma and the complications of supratentorial irradiation in children. METHODS AND MATERIALS A total of 50 children with newly diagnosed supratentorial ependymoma were treated with adjuvant radiation therapy (RT); conformal methods were used in 36 after 1996. The median age at RT was 6.5 years (range, 1-18.9 years). The entire group was characterized according to sex (girls 27), race (white 43), extent of resection (gross-total 46), and tumor grade (anaplastic 28). The conformal RT group was prospectively evaluated for neurologic, endocrine, and cognitive effects. RESULTS With a median follow-up time of 9.1 years from the start of RT for survivors (range, 0.2-23.2 years), the 10-year progression-free and overall survival were 73% + 7% and 76% + 6%, respectively. None of the evaluated factors was prognostic for disease control. Local and distant failures were evenly divided among the 16 patients who experienced progression. Eleven patients died of disease, and 1 of central nervous system necrosis. Seizure disorders were present in 17 patients, and 4 were considered to be clinically disabled. Clinically significant cognitive effects were limited to children with difficult-to-control seizures. The average values for intelligence quotient and academic achievement (reading, spelling, and math) were within the range of normal through 10 years of follow-up. Central hypothyroidism was the most commonly treated endocrinopathy. CONCLUSION RT may be administered with acceptable risks for complications in children with supratentorial ependymoma. These results suggest that outcomes for these children are improving and that complications may be limited by use of focal irradiation methods.
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Affiliation(s)
- Efrat Landau
- Department of Radiation Oncology, Sheba Medical Center, Ramat Gan, Israel
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29
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Tan C, Scotting PJ. Stem cell research points the way to the cell of origin for intracranial germ cell tumours. J Pathol 2012; 229:4-11. [DOI: 10.1002/path.4098] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 08/15/2012] [Accepted: 08/22/2012] [Indexed: 12/12/2022]
Affiliation(s)
- Chris Tan
- Children's Brain Tumour Research Centre, School of Biology; University of Nottingham, Queen's Medical Centre; Nottingham UK
| | - Paul J Scotting
- Children's Brain Tumour Research Centre, School of Biology; University of Nottingham, Queen's Medical Centre; Nottingham UK
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WNT/β-catenin pathway activation in Myc immortalised cerebellar progenitor cells inhibits neuronal differentiation and generates tumours resembling medulloblastoma. Br J Cancer 2012; 107:1144-52. [PMID: 22929883 PMCID: PMC3461168 DOI: 10.1038/bjc.2012.377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: Medulloblastoma is the most common malignant childhood brain tumour. Aberrant activation of the WNT/β-catenin pathway occurs in approximately 25% of medulloblastomas. However, its role in medulloblastoma pathogenesis is not understood. Methods: We have developed a model of WNT/β-catenin pathway-activated medulloblastoma. Pathway activation was induced in a Myc immortalised cerebellar progenitor cell line through stable expression of Wnt1. In vitro and in vivo analysis was undertaken to understand the effect of pathway activation and identify the potential cell of origin. Results: Tumours that histologically resembled classical medulloblastoma formed in vivo using cells overexpressing Wnt1, but not with the control cell line. Wnt1 overexpression inhibited neuronal differentiation in vitro, suggesting WNT/β-catenin pathway activation prevents cells terminally differentiating, maintaining them in a more ‘stem-like’ state. Analysis of cerebellar progenitor cell markers demonstrated the cell line resembled cells from the cerebellar ventricular zone. Conclusion: We have developed a cell line with the means of orthotopically modelling WNT/β-catenin pathway-activated medulloblastoma. We provide evidence of the role pathway activation is playing in tumour pathogenesis and suggest medulloblastomas can arise from cells other than granule cell progenitors. This cell line is a valuable resource to further understand the role of pathway activation in tumorigenesis and for investigation of targeted therapies.
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PPARG Epigenetic Deregulation and Its Role in Colorectal Tumorigenesis. PPAR Res 2012; 2012:687492. [PMID: 22848209 PMCID: PMC3405724 DOI: 10.1155/2012/687492] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 04/21/2012] [Indexed: 12/12/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) plays critical roles in lipid storage, glucose metabolism, energy homeostasis, adipocyte differentiation, inflammation, and cancer. Its function in colon carcinogenesis has largely been debated; accumulating evidence, however, supports a role as tumor suppressor through modulation of crucial pathways in cell differentiation, apoptosis, and metastatic dissemination. Epigenetics adds a further layer of complexity to gene regulation in several biological processes. In cancer, the relationship with epigenetic modifications has provided important insights into the underlying molecular mechanisms. These studies have highlighted how epigenetic modifications influence PPARG gene expression in colorectal tumorigenesis. In this paper, we take a comprehensive look at the current understanding of the relationship between PPARγ and cancer development. The role that epigenetic mechanisms play is also addressed disclosing novel crosstalks between PPARG signaling and the epigenetic machinery and suggesting how this dysregulation may contribute to colon cancer development.
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