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Johnston MJ, Lee JJY, Hu B, Nikolic A, Hasheminasabgorji E, Baguette A, Paik S, Chen H, Kumar S, Chen CCL, Jessa S, Balin P, Fong V, Zwaig M, Michealraj KA, Chen X, Zhang Y, Varadharajan S, Billon P, Juretic N, Daniels C, Rao AN, Giannini C, Thompson EM, Garami M, Hauser P, Pocza T, Ra YS, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska W, Perek-Polnik M, Agnihotri S, Mack S, Ellezam B, Weil A, Rich J, Bourque G, Chan JA, Yong VW, Lupien M, Ragoussis J, Kleinman C, Majewski J, Blanchette M, Jabado N, Taylor MD, Gallo M. TULIPs decorate the three-dimensional genome of PFA ependymoma. Cell 2024; 187:4926-4945.e22. [PMID: 38986619 DOI: 10.1016/j.cell.2024.06.023] [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: 08/27/2021] [Revised: 05/26/2022] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
Posterior fossa group A (PFA) ependymoma is a lethal brain cancer diagnosed in infants and young children. The lack of driver events in the PFA linear genome led us to search its 3D genome for characteristic features. Here, we reconstructed 3D genomes from diverse childhood tumor types and uncovered a global topology in PFA that is highly reminiscent of stem and progenitor cells in a variety of human tissues. A remarkable feature exclusively present in PFA are type B ultra long-range interactions in PFAs (TULIPs), regions separated by great distances along the linear genome that interact with each other in the 3D nuclear space with surprising strength. TULIPs occur in all PFA samples and recur at predictable genomic coordinates, and their formation is induced by expression of EZHIP. The universality of TULIPs across PFA samples suggests a conservation of molecular principles that could be exploited therapeutically.
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Affiliation(s)
- Michael J Johnston
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ana Nikolic
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Elham Hasheminasabgorji
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Audrey Baguette
- Quantitative Life Sciences, McGill University, Montreal, QC H3A 1B9, Canada
| | - Seungil Paik
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Haifen Chen
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada
| | - Sachin Kumar
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada
| | - Selin Jessa
- Quantitative Life Sciences, McGill University, Montreal, QC H3A 1B9, Canada
| | - Polina Balin
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Vernon Fong
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Melissa Zwaig
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada
| | | | - Xun Chen
- Department of Anatomy and Cell Biology, Kyoto University, Kyoto 606-8501, Japan
| | - Yanlin Zhang
- School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada
| | - Srinidhi Varadharajan
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pierre Billon
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Nikoleta Juretic
- Department of Pediatrics, McGill University and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Craig Daniels
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Caterina Giannini
- Pediatric Hematology-Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric M Thompson
- Department of Neurosurgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Miklos Garami
- Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - Peter Hauser
- Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - Timea Pocza
- Department of Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
| | - Young Shin Ra
- Department of Neurosurgery, University of Ulsan, Asan Medical Center, Seoul 05505, South Korea
| | - Byung-Kyu Cho
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 30322, South Korea
| | - Seung-Ki Kim
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 30322, South Korea
| | - Kyu-Chang Wang
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 30322, South Korea
| | - Ji Yeoun Lee
- Department of Neurosurgery, Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 30322, South Korea
| | - Wieslawa Grajkowska
- Department of Pathology, The Children's Memorial Health Institute, University of Warsaw, 04-730 Warsaw, Poland
| | - Marta Perek-Polnik
- Department of Oncology, The Children's Memorial Health Institute, University of Warsaw, 04-730 Warsaw, Poland
| | - Sameer Agnihotri
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, United States of America
| | - Stephen Mack
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Alex Weil
- Department of Pediatric Neurosurgery, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Jeremy Rich
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA 15213, USA; Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Jennifer A Chan
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - V Wee Yong
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Claudia Kleinman
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada
| | - Mathieu Blanchette
- Quantitative Life Sciences, McGill University, Montreal, QC H3A 1B9, Canada; School of Computer Science, McGill University, Montreal, QC H3A 2A7, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H2A 1B1, Canada; Department of Pediatrics, McGill University and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC H3A 3J1, Canada.
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Cancer and Hematology Center, Texas Children's Hospital, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Marco Gallo
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Cancer and Hematology Center, Texas Children's Hospital, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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2
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Wang B, Yan M, Han B, Liu X, Liu P. Impact of Molecular Subgroups on Prognosis and Survival Outcomes in Posterior Fossa Ependymomas: A Retrospective Study of 412 Cases. Neurosurgery 2024; 95:651-659. [PMID: 38529997 DOI: 10.1227/neu.0000000000002923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/25/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Posterior fossa ependymomas (PFEs) are rare brain tumors classified as PF-EPN-A (PFA) and PF-EPN-B (PFB) subgroups. The study aimed to evaluate the prognosis and survival outcomes in PFEs, with a focus on the impact of molecular subgroups. METHODS A retrospective study was conducted on 412 patients with PFEs. Kaplan-Meier survival analyses were conducted to evaluate the overall survival (OS) and progression-free survival. Cox regression analyses were conducted to assess the prognostic factors. A nomogram was developed to predict the OS rates of PFEs. RESULTS The study revealed significant differences between PFA and PFB in patient and tumor characteristics. PFAs were associated with poorer OS (hazard ratios [HR] 3.252, 95% CI 1.777-5.950, P < .001) and progression-free survival (HR 4.144, 95% CI 2.869-5.985, P < .001). World Health Organization grade 3 was associated with poorer OS (HR 2.389, 95% CI 1.236-4.617, P = .010). As for treatment patterns, gross total resection followed by radiotherapy or the combination of radiotherapy and chemotherapy yielded the most favorable OS for PFA ( P = .025 for both), whereas gross total resection followed by radiotherapy rather than observation showed improved OS for PFB ( P = .046). The nomogram demonstrated a high degree of accuracy and discrimination capacity for the prediction of OS rates for up to 10 years. In addition, 6 cases of PFA (3.51%) with H3K27M mutations were identified. CONCLUSION PFAs demonstrate worse prognosis and survival outcomes compared with PFBs. Both PFAs and PFBs necessitate maximal resection followed by intensive adjuvant therapies in long-term effects.
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Affiliation(s)
- Bo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing , China
| | - Minjun Yan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing , China
| | - Bo Han
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing , China
| | - Xing Liu
- Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing , China
| | - Pinan Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing , China
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Barresi V, Poliani PL. When do I ask for a DNA methylation array for primary brain tumor diagnosis? Curr Opin Oncol 2024:00001622-990000000-00204. [PMID: 39246157 DOI: 10.1097/cco.0000000000001089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
PURPOSE OF REVIEW Despite remarkable advances in molecular characterization, the diagnosis of brain tumors remains challenging, particularly in cases with ambiguous histology or contradictory molecular features. In this context, DNA methylation profiling plays an important role in improving diagnostic and prognostic accuracy. This review aims to provide diagnostic guidance regarding when DNA methylation arrays represent a useful tool for the diagnosis of primary brain tumors. RECENT FINDINGS Large-scale profiling has revealed that DNA methylation profiles of brain tumors are highly reproducible and stable. Therefore, DNA methylation profiling has been successfully used to classify brain tumors and identify new entities. This approach seems to be particularly promising for heterogeneous groups of tumors, such as IDH-wildtype gliomas, and glioneuronal and embryonal tumors, which include a variety of entities that are still under characterization. SUMMARY As underlined in the fifth edition of the WHO classification of central nervous system tumors, the diagnosis of brain tumors requires the integration of histological, molecular, clinical, and radiological features. Although advanced imaging and histological examination remain the standard diagnostic tools, DNA methylation analysis can significantly improve diagnostic accuracy, with a substantial impact on patient management.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, University of Verona, Verona
| | - Pietro Luigi Poliani
- Pathology Unit, San Raffaele Hospital Scientific Institute
- Vita-Salute San Raffaele University, Milan, Italy
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Tanaka Y, Natsumeda M, Ohashi M, Saito R, Higa N, Akahane T, Hashidate H, Ito J, Fujii S, Sasaki A, Tanimoto A, Hanaya R, Watanabe K, Oishi M, Kawashima H, Kakita A. Primary spinal cord gliomas: Pathologic features associated with prognosis. J Neuropathol Exp Neurol 2024:nlae084. [PMID: 39074166 DOI: 10.1093/jnen/nlae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024] Open
Abstract
Primary spinal cord gliomas are rare and are associated with high mortality. Unlike brain tumors, the clinicopathological features of spinal cord gliomas are not well defined. We analyzed clinical, histopathology, and immunohistochemical features and overall survival (OS) of 25 patients with primary spinal cord gliomas treated between 1994 and 2023 at 4 institutions. IDH1 R132H, H3K27M, and p53 were assessed by immunohistochemistry (IHC). Four (16%), 5 (20%), 2 (8%), and 13 (52%) patients were diagnosed as having grades 1, 2, 3, and 4 gliomas according to the World Health Organization (WHO) 2021 classification, respectively. One case (4%), with a circumscribed diffuse midline glioma, H3K27-altered, had a rare molecular profile and could not be graded. IHC demonstrated H3K27M positivity, indicative of H3F3A K27M or HIST1H3B K27M mutation, in 9 (36%) patients. H3K27me3-loss was evident in 13 (52%) patients. In one patient with a grade 1 tumor that showed negative staining for H3K27M and H3K27me3 loss, numbers of EZHIP-positive cells were increased, suggesting diffuse midline glioma, H3K27-altered (WHO grade 4). H3K27me3 loss, frequency of p53 positive cells (≥10%), MIB-1 index (≥10%), and high histopathological grades significantly correlated with poor OS. These results indicate the pathological and immunohistochemical characteristics of primary spinal cord gliomas that impact prognosis.
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Affiliation(s)
- Yuki Tanaka
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
- Division of Orthopedic Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Manabu Natsumeda
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masayuki Ohashi
- Division of Orthopedic Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Rie Saito
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Nayuta Higa
- Department of Neurosurgery, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Hideki Hashidate
- Department of Pathology, Niigata City General Hospital, Niigata, Japan
| | - Junko Ito
- Department of Pathology, Yokohama City University Hospital, Yokohama, Japan
| | - Satoshi Fujii
- Department of Pathology, Yokohama City University Hospital, Yokohama, Japan
- Department of Molecular Pathology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Sasaki
- Department of Pathology, Saitama Medical University, Saitama, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Ryosuke Hanaya
- Department of Neurosurgery, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kei Watanabe
- Division of Orthopedic Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Makoto Oishi
- Department of Neurosurgery, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroyuki Kawashima
- Division of Orthopedic Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024; 24:382-398. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Shi TH, Sugishita H, Gotoh Y. Crosstalk within and beyond the Polycomb repressive system. J Cell Biol 2024; 223:e202311021. [PMID: 38506728 PMCID: PMC10955045 DOI: 10.1083/jcb.202311021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
The development of multicellular organisms depends on spatiotemporally controlled differentiation of numerous cell types and their maintenance. To generate such diversity based on the invariant genetic information stored in DNA, epigenetic mechanisms, which are heritable changes in gene function that do not involve alterations to the underlying DNA sequence, are required to establish and maintain unique gene expression programs. Polycomb repressive complexes represent a paradigm of epigenetic regulation of developmentally regulated genes, and the roles of these complexes as well as the epigenetic marks they deposit, namely H3K27me3 and H2AK119ub, have been extensively studied. However, an emerging theme from recent studies is that not only the autonomous functions of the Polycomb repressive system, but also crosstalks of Polycomb with other epigenetic modifications, are important for gene regulation. In this review, we summarize how these crosstalk mechanisms have improved our understanding of Polycomb biology and how such knowledge could help with the design of cancer treatments that target the dysregulated epigenome.
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Affiliation(s)
- Tianyi Hideyuki Shi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroki Sugishita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
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7
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Kardian AS, Mack S. The Intersection of Epigenetic Alterations and Developmental State in Pediatric Ependymomas. Dev Neurosci 2024:000537694. [PMID: 38527429 DOI: 10.1159/000537694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/03/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Ependymomas are the third most common brain cancer in children and have no targeted therapies. They are divided into at least 9 major subtypes based on molecular characteristics and major drivers and have few genetic mutations compared to the adult form of this disease, leading to investigation of other mechanisms. SUMMARY Epigenetic alterations such as transcriptional programs activated by oncofusion proteins and alterations in histone modifications play an important role in development of this disease. Evidence suggests these alterations interact with the developmental epigenetic programs in the cell of origin to initiate neoplastic transformation and later disease progression, perhaps by keeping a portion of tumor cells in a developmental, proliferative state. KEY MESSAGES To better understand this disease, research on its developmental origins and associated epigenetic states needs to be further pursued. This could lead to better treatments, which are currently lacking due to the difficult-to-drug nature of known drivers such as fusion proteins. Epigenetic and developmental states characteristic of these tumors may not just be potential therapeutic targets, but used as a tool to find new avenues of treatment.
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8
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Miranda-Lloret P, Plaza-Ramírez E, Simal-Julián JA, Pancucci G, Cañete A, Montoya-Filardi A, Llavador G. Lateral-type posterior fossa ependymomas in pediatric population. NEUROCIRUGIA (ENGLISH EDITION) 2024; 35:87-94. [PMID: 38244924 DOI: 10.1016/j.neucie.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/03/2023] [Indexed: 01/22/2024]
Abstract
BACKGROUND Lateral-type posterior fossa ependymomas are a well-defined subtype of tumours both clinically and pathologically, with a poor prognosis. Their incidence is low and surgical management is challenging. The objective of the present work is to review our series of lateral-tye posterior fossa ependymomas and compare our results with those of previous series. METHODS Among 30 cases of ependymoma operated in our paediatric department in the last ten years, we identified seven cases of lateral-type posterior fossa ependymomas. We then performed a retrospective, descriptive study. RESULTS Mean age of our patients was 3.75 years. 6 cases presented with hydrocephalus. Mean tumour volume at diagnosis was 61 cc. A complete resection was achieved in six cases and a near-total resection in one patient. 5 patients transiently required a gastrostomy and a tracheostomy. Mean follow-up was 58 months. One case progressed along this period and eventually died. 4 cases of hydrocephalus required a ventriculoperitoneal CSF shunt and two were managed with a third ventriculostomy. At last follow-up 4 patients carried a normal life and two displayed a mild restriction according to Lansky´s scale. CONCLUSIONS The aim of surgical treatment in lateral-type posterior fossa ependymomas is complete resection. Neurological deficits associated to lower cranial nerve dysfunction are common but transient. Deeper genetic characterization of these tumours may identify risk factors that guide stratification of adjuvant therapies.
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Affiliation(s)
- Pablo Miranda-Lloret
- Servicios de Neurocirugía, Oncología Pediátrica, Radiología Pediátrica y Anatomía Patológica, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
| | - Estela Plaza-Ramírez
- Servicios de Neurocirugía, Oncología Pediátrica, Radiología Pediátrica y Anatomía Patológica, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Juan Antonio Simal-Julián
- Servicios de Neurocirugía, Oncología Pediátrica, Radiología Pediátrica y Anatomía Patológica, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Giovanni Pancucci
- Servicios de Neurocirugía, Oncología Pediátrica, Radiología Pediátrica y Anatomía Patológica, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Adela Cañete
- Servicios de Neurocirugía, Oncología Pediátrica, Radiología Pediátrica y Anatomía Patológica, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Alejandro Montoya-Filardi
- Servicios de Neurocirugía, Oncología Pediátrica, Radiología Pediátrica y Anatomía Patológica, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Gemma Llavador
- Servicios de Neurocirugía, Oncología Pediátrica, Radiología Pediátrica y Anatomía Patológica, Hospital Universitario y Politécnico La Fe, Valencia, Spain
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Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.27.23299068. [PMID: 38076942 PMCID: PMC10705664 DOI: 10.1101/2023.11.27.23299068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., MYCN for neuroblastoma, CDKN2A and PAX5 for B-/T-ALL, and SMARCB1 for AT/RT), and 7,590 polymorphism sites for interrogating tumors with aneuploidy, such as hyperdiploid and hypodiploid B-ALL or 17q gain neuroblastoma. We used driver alterations reported from an established real-time clinical genomics cohort (n=253) to validate this gene panel. Among the 485 pathogenic variants reported, our panel covered 417 variants (86%). For 90 rearrangements responsible for oncogenic fusions, our panel covered 74 events (82%). We re-sequenced 113 previously characterized clinical specimens at an average depth of 2,500X using SJPedPanel and recovered 354 (91%) of the 389 reported pathogenic variants. We then investigated the power of this panel in detecting mutations from specimens with low tumor purity (as low as 0.1%) using cell line-based dilution experiments and discovered that this gene panel enabled us to detect ∼80% variants with allele fraction of 0.2%, while the detection rate decreases to ∼50% when the allele fraction is 0.1%. We finally demonstrate its utility in disease monitoring on clinical specimens collected from AML patients in morphologic remission. Conclusions SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
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10
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Wagner MW, Jabehdar Maralani P, Bennett J, Nobre L, Lim-Fat MJ, Dirks P, Laughlin S, Tabori U, Ramaswamy V, Hawkins C, Ertl-Wagner BB. Brain Tumor Imaging in Adolescents and Young Adults: 2021 WHO Updates for Molecular-based Tumor Types. Radiology 2024; 310:e230777. [PMID: 38349246 DOI: 10.1148/radiol.230777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Published in 2021, the fifth edition of the World Health Organization (WHO) classification of tumors of the central nervous system (CNS) introduced new molecular criteria for tumor types that commonly occur in either pediatric or adult age groups. Adolescents and young adults (AYAs) are at the intersection of adult and pediatric care, and both pediatric-type and adult-type CNS tumors occur at that age. Mortality rates for AYAs with CNS tumors have increased by 0.6% per year for males and 1% per year for females from 2007 to 2016. To best serve patients, it is crucial that both pediatric and adult radiologists who interpret neuroimages are familiar with the various pediatric- and adult-type brain tumors and their typical imaging morphologic characteristics. Gliomas account for approximately 80% of all malignant CNS tumors in the AYA age group, with the most common types observed being diffuse astrocytic and glioneuronal tumors. Ependymomas and medulloblastomas also occur in the AYA population but are seen less frequently. Importantly, biologic behavior and progression of distinct molecular subgroups of brain tumors differ across ages. This review discusses newly added or revised gliomas in the fifth edition of the CNS WHO classification, as well as other CNS tumor types common in the AYA population.
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Affiliation(s)
- Matthias W Wagner
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Pejman Jabehdar Maralani
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Julie Bennett
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Liana Nobre
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Mary Jane Lim-Fat
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Peter Dirks
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Suzanne Laughlin
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Uri Tabori
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Vijay Ramaswamy
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Cynthia Hawkins
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
| | - Birgit B Ertl-Wagner
- From the Division of Neuroradiology, Department of Diagnostic Imaging (M.W.W., S.L., B.B.E.W.), Division of Hematology/Oncology (J.B., L.N., U.T., V.R.), Department of Paediatric Laboratory Medicine, Division of Pathology (C.H.), Division of Neurosurgery (P.D.), and Division of Pediatric Neuroradiology (M.W.W.), The Hospital for Sick Children, 555 University Ave, Toronto, ON, Canada M5G 1X8; Neurosciences & Mental Health Research Program, SickKids Research Institute, Toronto, Canada (M.W.W., B.B.E.W.); Department of Medical Imaging, University of Toronto, Toronto, Canada (M.W.W., P.J.M., B.B.E.W.); Department of Diagnostic and Interventional Neuroradiology, University Hospital Augsburg, Augsburg, Germany (M.W.W.); Divisions of Neuroradiology (P.J.M.) and Neurooncology (M.J.L.F.), Sunnybrook Health Science Centre, Toronto, Canada; and Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada (J.B.)
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11
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Miranda-Lloret P, Plaza-Ramírez E, López-Guerrero A, López-Bermeo D, García-Campos T, Vázquez-Sufuentes S, Munárriz PM, López-García E, Londoño-Quiroz A, Ferreras-García C, García-Conde M, Saceda-Gutiérrez J, Giménez-Pando J, Pancucci G, Iglesias-Moroño S. Lateral-type posterior fossa ependymomas in pediatric patients: a national collaborative study. Childs Nerv Syst 2024; 40:407-416. [PMID: 37889277 DOI: 10.1007/s00381-023-06194-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023]
Abstract
PURPOSE To review a multicentric series of lateral-type posterior fossa ependymomas operated in the last ten years and to analyze the factors related to clinical evolution and tumor survival. METHODS Descriptive, retrospective study. Active members of the Spanish Society of Pediatric Neurosurgery were invited to participate in this multicentric study. Clinical and radiological data were incorporated to an open database. The role of histologic grade, grade of resection, postoperative morbidities, and clinical follow-up was evaluated through bivariate associations (chi-square), Kaplan-Meier's curves (log-rank test), and multivariate analysis (binary logistic regression). RESULTS Fourteen centers entered the study, and 25 cases with a minimum follow-up of 6 months were included. There were 13 boys and 12 girls with a mean age close to 3 years. Mean tumor volume at diagnosis was over 60 cc. A complete resection was achieved in 8 patients and a near-total resection in 5 cases. Fifteen tumors were diagnosed as ependymoma grade 2 and ten as ependymoma grade 3. Major morbidity occurred postoperatively in 14 patients but was resolved in twelve within 6 months. There were six cases of death and 11 cases of tumor progression along the observation period. Mean follow-up was 44.8 months. Major morbidity was significantly associated with histologic grade but not with the degree of resection. Overall and progression-free survival were significantly associated with complete surgical resection. At the last follow-up, 16 patients carried a normal life, and three displayed a mild restriction according to Lansky's scale. CONCLUSIONS Lateral-type posterior fossa ependymomas constitute a specific pathologic and clinical tumor subtype with bad prognosis. Gross total resection is the goal of surgical treatment, for it significantly improves prognosis with no additional morbidity. Neurological deficits associated to lower cranial nerve dysfunction are common, but most are transient. Deeper genetic characterization of these tumors may identify risk factors that guide new treatments and stratification of adjuvant therapies.
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Affiliation(s)
- Pablo Miranda-Lloret
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain.
| | - Estela Plaza-Ramírez
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Antonio López-Guerrero
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Diego López-Bermeo
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Teresa García-Campos
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Silvia Vázquez-Sufuentes
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Pablo M Munárriz
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Elena López-García
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Alejandra Londoño-Quiroz
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Cristina Ferreras-García
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Mario García-Conde
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Javier Saceda-Gutiérrez
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Jorge Giménez-Pando
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Giovanni Pancucci
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Sara Iglesias-Moroño
- Unidad de Neurocirugía Pediátrica, Hospital Universitario y Politécnico La Fe, Avda Fernando Abril Martorell, 106, 46026, Valencia, Spain
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12
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Bertero L, Mangherini L, Ricci AA, Cassoni P, Sahm F. Molecular neuropathology: an essential and evolving toolbox for the diagnosis and clinical management of central nervous system tumors. Virchows Arch 2024; 484:181-194. [PMID: 37658995 PMCID: PMC10948579 DOI: 10.1007/s00428-023-03632-4] [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: 06/15/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
Molecular profiling has transformed the diagnostic workflow of CNS tumors during the last years. The latest WHO classification of CNS tumors (5th edition), published in 2021, pushed forward the integration between histopathological features and molecular hallmarks to achieve reproducible and clinically relevant diagnoses. To address these demands, pathologists have to appropriately deal with multiple molecular assays mainly including DNA methylation profiling and DNA/RNA next generation sequencing. Tumor classification by DNA methylation profiling is now a critical tool for many diagnostic tasks in neuropathology including the assessment of complex cases, to evaluate novel tumor types and to perform tumor subgrouping in hetereogenous entities like medulloblastoma or ependymoma. DNA/RNA NGS allow the detection of multiple molecular alterations including single nucleotide variations, small insertions/deletions (InDel), and gene fusions. These molecular markers can provide key insights for diagnosis, for example, if a tumor-specific mutation is detected, but also for treatment since targeted therapies are progressively entering the clinical practice. In the present review, a brief, but comprehensive overview of these tools will be provided, discussing their technical specifications, diagnostic value, and potential limitations. Moreover, the importance of molecular profiling will be shown in a representative series of CNS neoplasms including both the most frequent tumor types and other selected entities for which molecular characterization plays a critical role.
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Affiliation(s)
- Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin and Città Della Salute E Della Scienza University Hospital, Via Santena 7, 10126, Turin, Italy
| | - Luca Mangherini
- Pathology Unit, Department of Medical Sciences, University of Turin and Città Della Salute E Della Scienza University Hospital, Via Santena 7, 10126, Turin, Italy
| | - Alessia Andrea Ricci
- Pathology Unit, Department of Medical Sciences, University of Turin and Città Della Salute E Della Scienza University Hospital, Via Santena 7, 10126, Turin, Italy
| | - Paola Cassoni
- Pathology Unit, Department of Medical Sciences, University of Turin and Città Della Salute E Della Scienza University Hospital, Via Santena 7, 10126, Turin, Italy
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Im Neuenheimer Feld 672, 69120, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
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13
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Gödicke S, Kresbach C, Ehlert M, Obrecht D, Altendorf L, Hack K, von Hoff K, Carén H, Melcher V, Kerl K, Englinger B, Filbin M, Pajtler KW, Gojo J, Pietsch T, Rutkowski S, Schüller U. Clinically relevant molecular hallmarks of PFA ependymomas display intratumoral heterogeneity and correlate with tumor morphology. Acta Neuropathol 2024; 147:23. [PMID: 38265527 PMCID: PMC10808473 DOI: 10.1007/s00401-023-02682-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/05/2023] [Accepted: 12/30/2023] [Indexed: 01/25/2024]
Abstract
Posterior fossa type A (PF-EPN-A, PFA) ependymoma are aggressive tumors that mainly affect children and have a poor prognosis. Histopathology shows significant intratumoral heterogeneity, ranging from loose tissue to often sharply demarcated, extremely cell-dense tumor areas. To determine molecular differences in morphologically different areas and to understand their clinical significance, we analyzed 113 PF-EPN-A samples, including 40 corresponding relapse samples. Cell-dense areas ranged from 0 to 100% of the tumor area and displayed a higher proportion of proliferating tumor cells (p < 0.01). Clinically, cell density was associated with poor progression-free and overall survival (pPFS = 0.0026, pOS < 0.01). Molecularly, tumor areas with low and high cell density showed diverging DNA methylation profiles regarding their similarity to distinct previously discovered PF-EPN-A subtypes in 9/21 cases. Prognostically relevant chromosomal changes at 1q and 6q showed spatial heterogeneity within single tumors and were significantly enriched in cell-dense tumor areas as shown by single-cell RNA (scRNA)-sequencing as well as copy number profiling and fluorescence in situ hybridization (FISH) analyses of different tumor areas. Finally, spatial transcriptomics revealed cell-dense areas of different tumors to be more similar than various different areas of the same tumor. High-density areas distinctly overexpressed genes encoding histone proteins, WNT5A, TGFB1, or IGF2. Relapsing tumors displayed a higher proportion of cell-dense areas (p = 0.036), a change in PF-EPN-A methylation subtypes (13/32 patients), and novel chromosome 1q gains and 6q losses (12/32 cases) compared to corresponding primary tumors. Our data suggest that PF-EPN-A ependymomas habor a previously unrecognized intratumoral heterogeneity with clinical implications, which has to be accounted for when selecting diagnostic material, inter alia, by histological evaluation of the proportion of cell-dense areas.
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Affiliation(s)
- Swenja Gödicke
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Catena Kresbach
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Max Ehlert
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Denise Obrecht
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lea Altendorf
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Karoline Hack
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Helena Carén
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Viktoria Melcher
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149, Münster, Germany
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
- Center for Cancer Research and Comprehensive Cancer Center, Medical University Vienna, 1090, Vienna, Austria
| | - Mariella Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematolgoy and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center, Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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14
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Neyazi S, Yamazawa E, Hack K, Tanaka S, Nagae G, Kresbach C, Umeda T, Eckhardt A, Tatsuno K, Pohl L, Hana T, Bockmayr M, Kim P, Dorostkar MM, Takami T, Obrecht D, Takai K, Suwala AK, Komori T, Godbole S, Wefers AK, Otani R, Neumann JE, Higuchi F, Schweizer L, Nakanishi Y, Monoranu CM, Takami H, Engertsberger L, Yamada K, Ruf V, Nomura M, Mohme T, Mukasa A, Herms J, Takayanagi S, Mynarek M, Matsuura R, Lamszus K, Ishii K, Kluwe L, Imai H, von Deimling A, Koike T, Benesch M, Kushihara Y, Snuderl M, Nambu S, Frank S, Omura T, Hagel C, Kugasawa K, Mautner VF, Ichimura K, Rutkowski S, Aburatani H, Saito N, Schüller U. Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation. Acta Neuropathol 2024; 147:22. [PMID: 38265489 PMCID: PMC10808175 DOI: 10.1007/s00401-023-02668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024]
Abstract
Ependymomas encompass multiple clinically relevant tumor types based on localization and molecular profiles. Tumors of the methylation class "spinal ependymoma" (SP-EPN) represent the most common intramedullary neoplasms in children and adults. However, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical relevance have been described in a large, epigenetically defined series. Transcriptomic (n = 72), epigenetic (n = 225), genetic (n = 134), and clinical data (n = 112) were integrated for a detailed molecular overview on SP-EPN. Additionally, we mapped SP-EPN transcriptomes to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. The integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord revealed that SP-EPN display the highest similarities to mature adult ependymal cells. Unsupervised hierarchical clustering of transcriptomic data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype A tumors primarily carried previously known germline or sporadic NF2 mutations together with 22q loss (bi-allelic NF2 loss), resulting in decreased NF2 expression. Furthermore, they more often presented as multilocular disease and demonstrated a significantly reduced progression-free survival as compared to SP-EP subtype B. In contrast, subtype B predominantly contained samples without NF2 mutation detected in sequencing together with 22q loss (monoallelic NF2 loss). These tumors showed regular NF2 expression but more extensive global copy number alterations. Based on integrated molecular profiling of a large multi-center cohort, we identified two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.
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Affiliation(s)
- Sina Neyazi
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Erika Yamazawa
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Karoline Hack
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Genta Nagae
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Catena Kresbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Takayoshi Umeda
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Alicia Eckhardt
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Radiotherapy and Radiation Oncology, Hubertus Wald Tumor Center, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kenji Tatsuno
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Lara Pohl
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Taijun Hana
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Phyo Kim
- Utsunomiya Neurospine Center, Symphony Clinic, Utsunomiya, Japan
| | - Mario M Dorostkar
- Center for Neuropathology and Prion Research, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Toshihiro Takami
- Department of Neurosurgery, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Denise Obrecht
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Keisuke Takai
- Department of Neurosurgery, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Takashi Komori
- Department of Laboratory Medicine and Pathology, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Shweta Godbole
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ryohei Otani
- Department of Neurosurgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Julia E Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fumi Higuchi
- Department of Neurosurgery, University of Teikyo Hospital, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt Am Main, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt Am Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt Am Main, Germany
| | - Yuta Nakanishi
- Department of Neurosurgery, Osaka Metropolitan City University Graduate School of Medicine, Osaka, Japan
| | - Camelia-Maria Monoranu
- Department of Neuropathology, Institute of Pathology, University of Würzburg, Würzburg, Germany
| | - Hirokazu Takami
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lara Engertsberger
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Keisuke Yamada
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Viktoria Ruf
- Center for Neuropathology and Prion Research, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Masashi Nomura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Theresa Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Akitake Mukasa
- Department of Neurosurgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jochen Herms
- Center for Neuropathology and Prion Research, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reiko Matsuura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kazuhiko Ishii
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lan Kluwe
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hideaki Imai
- Department of Neurosurgery, Japan Community Health Care Organization Tokyo Shinjuku Medical Center, Tokyo, Japan
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Tsukasa Koike
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Martin Benesch
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Yoshihiro Kushihara
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, New York City, USA
| | - Shohei Nambu
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Stephan Frank
- Division of Neuropathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Takaki Omura
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Christian Hagel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kazuha Kugasawa
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Viktor F Mautner
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo, Japan
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hiroyuki Aburatani
- Genome Science and Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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15
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Pohl LC, Leitheiser M, Obrecht D, Schweizer L, Wefers AK, Eckhardt A, Raffeld M, Sturm D, Pajtler KW, Rutkowski S, Fukuoka K, Ichimura K, Bockmayr M, Schüller U. Molecular characteristics and improved survival prediction in a cohort of 2023 ependymomas. Acta Neuropathol 2024; 147:24. [PMID: 38265522 PMCID: PMC10808151 DOI: 10.1007/s00401-023-02674-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/04/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024]
Abstract
The diagnosis of ependymoma has moved from a purely histopathological review with limited prognostic value to an integrated diagnosis, relying heavily on molecular information. However, as the integrated approach is still novel and some molecular ependymoma subtypes are quite rare, few studies have correlated integrated pathology and clinical outcome, often focusing on small series of single molecular types. We collected data from 2023 ependymomas as classified by DNA methylation profiling, consisting of 1736 previously published and 287 unpublished methylation profiles. Methylation data and clinical information were correlated, and an integrated model was developed to predict progression-free survival. Patients with EPN-PFA, EPN-ZFTA, and EPN-MYCN tumors showed the worst outcome with 10-year overall survival rates of 56%, 62%, and 32%, respectively. EPN-PFA harbored chromosome 1q gains and/or 6q losses as markers for worse survival. In supratentorial EPN-ZFTA, a combined loss of CDKN2A and B indicated worse survival, whereas a single loss did not. Twelve out of 200 EPN-ZFTA (6%) were located in the posterior fossa, and these tumors relapsed or progressed even earlier than supratentorial tumors with a combined loss of CDKN2A/B. Patients with MPE and PF-SE, generally regarded as non-aggressive tumors, only had a 10-year progression-free survival of 59% and 65%, respectively. For the prediction of the 5-year progression-free survival, Kaplan-Meier estimators based on the molecular subtype, a Support Vector Machine based on methylation, and an integrated model based on clinical factors, CNV data, and predicted methylation scores achieved balanced accuracies of 66%, 68%, and 73%, respectively. Excluding samples with low prediction scores resulted in balanced accuracies of over 80%. In sum, our large-scale analysis of ependymomas provides robust information about molecular features and their clinical meaning. Our data are particularly relevant for rare and hardly explored tumor subtypes and seemingly benign variants that display higher recurrence rates than previously believed.
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Affiliation(s)
- Lara C Pohl
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Maximilian Leitheiser
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Denise Obrecht
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alicia Eckhardt
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Radiotherapy and Radiation Oncology, Hubertus Wald Tumor Center-University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark Raffeld
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit, Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kohei Fukuoka
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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16
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Cheng D, Zhuo Z, Du J, Weng J, Zhang C, Duan Y, Sun T, Wu M, Guo M, Hua T, Jin Y, Peng B, Li Z, Zhu M, Imami M, Bettegowda C, Sair H, Bai HX, Barkhof F, Liu X, Liu Y. A Fully Automated Deep-Learning Model for Predicting the Molecular Subtypes of Posterior Fossa Ependymomas Using T2-Weighted Images. Clin Cancer Res 2024; 30:150-158. [PMID: 37916978 DOI: 10.1158/1078-0432.ccr-23-1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/11/2023] [Accepted: 10/31/2023] [Indexed: 11/03/2023]
Abstract
PURPOSE We aimed to develop and validate a deep learning (DL) model to automatically segment posterior fossa ependymoma (PF-EPN) and predict its molecular subtypes [Group A (PFA) and Group B (PFB)] from preoperative MR images. EXPERIMENTAL DESIGN We retrospectively identified 227 PF-EPNs (development and internal test sets) with available preoperative T2-weighted (T2w) MR images and molecular status to develop and test a 3D nnU-Net (referred to as T2-nnU-Net) for tumor segmentation and molecular subtype prediction. The network was externally tested using an external independent set [n = 40; subset-1 (n = 31) and subset-2 (n =9)] and prospectively enrolled cases [prospective validation set (n = 27)]. The Dice similarity coefficient was used to evaluate the segmentation performance. Receiver operating characteristic analysis for molecular subtype prediction was performed. RESULTS For tumor segmentation, the T2-nnU-Net achieved a Dice score of 0.94 ± 0.02 in the internal test set. For molecular subtype prediction, the T2-nnU-Net achieved an AUC of 0.93 and accuracy of 0.89 in the internal test set, an AUC of 0.99 and accuracy of 0.93 in the external test set. In the prospective validation set, the model achieved an AUC of 0.93 and an accuracy of 0.89. The predictive performance of T2-nnU-Net was superior or comparable to that of demographic and multiple radiologic features (AUCs ranging from 0.87 to 0.95). CONCLUSIONS A fully automated DL model was developed and validated to accurately segment PF-EPNs and predict molecular subtypes using only T2w MR images, which could help in clinical decision-making.
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Affiliation(s)
- Dan Cheng
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
| | - Zhizheng Zhuo
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
| | - Jiang Du
- Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jinyuan Weng
- Department of Medical Imaging Product, Neusoft, Group Ltd., Shenyang, P.R. China
| | - Chengzhou Zhang
- Department of Radiology, Yantai Yuhuangding Hospital, Yantai, Shandong, P.R. China
| | - Yunyun Duan
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
| | - Ting Sun
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
| | - Minghao Wu
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
| | - Min Guo
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
| | - Tiantian Hua
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
| | - Ying Jin
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
| | - Boyang Peng
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
| | | | - Mingwang Zhu
- Department of Radiology, Sanbo Brain Hospital, Capital Medical University, Beijing, P.R. China
| | - Maliha Imami
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Haris Sair
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harrison X Bai
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Frederik Barkhof
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, United Kingdom
- Department of Radiology & Nuclear Medicine, Amsterdam UMC, Vrije Universiteit, the Netherlands
| | - Xing Liu
- Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yaou Liu
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, P.R. China
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17
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Jünger ST, Zschernack V, Messing-Jünger M, Timmermann B, Pietsch T. Ependymoma from Benign to Highly Aggressive Diseases: A Review. Adv Tech Stand Neurosurg 2024; 50:31-62. [PMID: 38592527 DOI: 10.1007/978-3-031-53578-9_2] [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] [Indexed: 04/10/2024]
Abstract
Ependymomas comprise biologically distinct tumor types with respect to age distribution, (epi)genetics, localization, and prognosis. Multimodal risk-stratification, including histopathological and molecular features, is essential in these biologically defined tumor types. Gross total resection (GTR), achieved with intraoperative monitoring and neuronavigation, and if necessary, second-look surgery, is the most effective treatment. Adjuvant radiation therapy is mandatory in high-risk tumors and in case of residual tumor. There is yet growing evidence that some ependymal tumors may be cured by surgery alone. To date, the role of chemotherapy is unclear and subject of current studies.Even though standard therapy can achieve reasonable survival rates for the majority of ependymoma patients, long-term follow-up still reveals a high probability of relapse in certain biological entities.With increasing knowledge of biologically distinct tumor types, risk-adapted adjuvant therapy gains importance. Beyond initial tumor control, and avoidance of therapy-induced morbidity for low-risk patients, intensified treatment for high-risk patients comprises another challenge. With identification of specific risk features regarding molecular alterations, targeted therapy may represent an option for individualized treatment modalities in the future.
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Affiliation(s)
- Stephanie T Jünger
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany.
- Center for Neurosurgery, Department of General Neurosurgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
| | - Valentina Zschernack
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
| | | | - Beate Timmermann
- Department of Particle Therapy, University Hospital Essen, West German Proton Therapy Center Essen (WPE), West German Cancer Center (WTZ), Germany, German Cancer Consortium, Essen, Germany
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn Medical Center, Bonn, Germany
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18
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Ghalibafian M, Mirzaei S, Girinsky T, Sadeghi Y, Saffar A, Ghodsinezhad N, Elmi S, Bouffet E. Challenges in Treating Childhood Infratentorial Ependymoma: A Low- and Middle-Income Country Experience. Int J Radiat Oncol Biol Phys 2023; 117:1181-1190. [PMID: 37454918 DOI: 10.1016/j.ijrobp.2023.06.2294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 05/30/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
PURPOSE Patients and physicians in low- and middle-income countries (LMICs) face challenges owing to limited expertise and suboptimal access to appropriate diagnostic and treatment modalities. We report our experience in treating posterior fossa ependymoma (PFE) at MAHAK, a charity organization in Iran whose radiation oncology department is the only one exclusively dedicated to childhood cancer in the whole country. METHODS AND MATERIALS Pediatric patients with PFE referred to MAHAK between November 2008 and January 2016 were identified. Details on investigations and management done before referral were collected. Management at MAHAK and patient outcomes were analyzed. RESULTS Of 80 patients diagnosed as having ependymoma, 54 with PFE were identified. Forty-three patients received adjuvant radiation therapy, and 11 were irradiated initially after recurrence. At a median follow-up of 5.1 years (range, 0.3-9.7 years), the latter group had the worst outcome, with a 5-year overall survival (OS) rate of 27% (95% CI, 7%-54%). Patients who started radiation therapy within 77 days after initial surgery had a better outcome compared with those who started later (5-year OS: 74% vs 32%; P = .05). Compliance with follow-up recommendations was poor. Only 22% of the patients had at least 2 IQ test assessments, and 50% showed some decline over time. Three cases of growth hormone deficiency were detected, but none of the patients received replacement therapy. CONCLUSIONS Access to pediatric neurosurgery, anesthesia, and timely radiation therapy are among the most challenging obstacles to be overcome in LMICs. Our series confirmed that chemotherapy is not an appropriate option for delaying radiation therapy, especially in young children. The importance of long-term follow-up should be acknowledged by the parents and medical team.
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Affiliation(s)
- Mithra Ghalibafian
- Department of Radiation Oncology, MAHAK Pediatric Cancer Treatment and Research Center, Tehran, Iran.
| | - Sajad Mirzaei
- Department of Radiation Physics, MAHAK Pediatric Cancer Treatment and Research Center, Tehran, Iran
| | | | - Yasaman Sadeghi
- MAHAK Hematology Oncology Research Center (MAHAK-HORC), MAHAK Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azam Saffar
- Department of Biostatistics, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Ghodsinezhad
- Department of Psychology, MAHAK Pediatric Cancer Treatment and Research Center, Tehran, Iran
| | - Sara Elmi
- Department of Audiology, MAHAK Pediatric Cancer Treatment and Research Center, Tehran, Iran
| | - Eric Bouffet
- Division of Hematology/Oncology, Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
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19
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Pratt D, Penas-Prado M, Gilbert MR. Clinical impact of molecular profiling in rare brain tumors. Curr Opin Neurol 2023; 36:579-586. [PMID: 37973025 DOI: 10.1097/wco.0000000000001211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to describe the commonly used molecular diagnostics and illustrate the prognostic importance to the more accurate diagnosis that also may uncover therapeutic targets. RECENT FINDINGS The most recent WHO Classification of Central Nervous System Tumours (2021) lists over 100 distinct tumor types. While traditional histology continues to be an important component, molecular testing is increasingly being incorporated as requisite diagnostic criteria. Specific molecular findings such as co-deletion of the short arm of chromosome 1 (1p) and long arm of chromosome 19 (19q) now define IDH-mutant gliomas as oligodendroglioma. In recent years, DNA methylation profiling has emerged as a dynamic tool with high diagnostic accuracy. The integration of specific genetic (mutations, fusions) and epigenetic (CpG methylation) alterations has led to diagnostic refinement and the discovery of rare brain tumor types with distinct clinical outcomes. Molecular profiling is anticipated to play an increasing role in routine surgical neuropathology, although costs, access, and logistical concerns remain challenging. SUMMARY This review summarizes the current state of molecular testing in neuro-oncology highlighting commonly used and developing technologies, while also providing examples of new tumor types/subtypes that have emerged as a result of improved diagnostic precision.
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Affiliation(s)
| | - Marta Penas-Prado
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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20
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Kihara A, Amano Y, Fukushima N, Fujiwara H, Niki T. H3K27me3 deficiency in dedifferentiated carcinoma and carcinosarcoma of the endometrium. Virchows Arch 2023; 483:885-890. [PMID: 37770766 DOI: 10.1007/s00428-023-03665-9] [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: 08/07/2023] [Revised: 09/05/2023] [Accepted: 09/21/2023] [Indexed: 09/30/2023]
Abstract
The present study immunohistochemically investigated trimethylation of lysine 27 of histone 3 (H3K27me3) expression in 769 endometrial carcinomas and 196 uterine mesenchymal tumors. One dedifferentiated endometrial carcinoma (DEC) and one carcinosarcoma showed H3K27me3 deficiency that was limited to undifferentiated and sarcomatous components, respectively. Switch/sucrose nonfermenting (SWI/SNF) complex subunits (SMARCA4, SMARCB1, and ARID1A/1B) and mismatch repair proteins were proficient in both tumors. The dimethylation of H3K27 (H3K27me2) was deficient in the undifferentiated component, whereas the sarcomatous component had scattered H3K27me2-positive cells. CXorf67, which inhibits PRC2 function, was diffusely expressed in the sarcomatous component. CXorf67 was negative in the undifferentiated component, which was submitted to a genetic analysis and showed no alterations in PRC2 core subunits or H3K27. The present results suggest H3K27 methylation dysregulation as a cause of SWI/SNF-proficient DEC and carcinosarcoma and imply differences in their level of and the mechanisms underlying H3K27 methylation dysregulation.
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Affiliation(s)
- Atsushi Kihara
- Department of Pathology, Jichi Medical University, 3311-1, Yakushiji, Shimotsuke city, Tochigi, 329-0498, Japan.
| | - Yusuke Amano
- Department of Pathology, Jichi Medical University, 3311-1, Yakushiji, Shimotsuke city, Tochigi, 329-0498, Japan
| | - Noriyoshi Fukushima
- Department of Pathology, Jichi Medical University, 3311-1, Yakushiji, Shimotsuke city, Tochigi, 329-0498, Japan
| | - Hiroyuki Fujiwara
- Department of Obstetrics and Gynaecology, Jichi Medical University, Tochigi, 329-0498, Japan
| | - Toshiro Niki
- Department of Pathology, Jichi Medical University, 3311-1, Yakushiji, Shimotsuke city, Tochigi, 329-0498, Japan
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21
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Jin Y, Cheng D, Duan Y, Zhuo Z, Weng J, Zhang C, Zhu M, Liu X, Du J, Hua T, Li H, Haller S, Barkhof F, Liu Y. "Soap bubble" sign as an imaging marker for posterior fossa ependymoma Group B. Neuroradiology 2023; 65:1707-1714. [PMID: 37837480 DOI: 10.1007/s00234-023-03231-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
PURPOSE To investigate the predictive value of the "soap bubble" sign on molecular subtypes (Group A [PFA] and Group B [PFB]) of posterior fossa ependymomas (PF-EPNs). METHODS MRI scans of 227 PF-EPNs (internal retrospective discovery set) were evaluated by two independent neuroradiologists to assess the "soap bubble" sign, which was defined as clusters of cysts of various sizes that look like "soap bubbles" on T2-weighted images. Two independent cohorts (external validation set [n = 31] and prospective validation set [n = 27]) were collected to validate the "soap bubble" sign. RESULTS Across three datasets, the "soap bubble" sign was observed in 21 PFB cases (7.4% [21/285] of PF-EPNs and 12.9% [21/163] of PFB); none in PFA. Analysis of the internal retrospective discovery set demonstrated substantial interrater agreement (1st Rating: κ = 0.71 [0.53-0.90], 2nd Rating: κ = 0.83 [0.68-0.98]) and intrarater agreement (Rater 1: κ = 0.73 [0.55-0.91], Rater 2: κ = 0.74 [0.55-0.92]) for the "soap bubble" sign; all 13 cases positive for the "soap bubble" sign were PFB (p = 0.002; positive predictive value [PPV] = 100%, negative predictive value [NPV] = 44%, sensitivity = 10%, specificity = 100%). The findings from the external validation set and the prospective validation set were similar, all cases positive for the "soap bubble" sign were PFB (p < 0.001; PPV = 100%). CONCLUSION The "soap bubble" sign represents a highly specific imaging marker for the PFB molecular subtype of PF-EPNs.
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Affiliation(s)
- Ying Jin
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Dan Cheng
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Yunyun Duan
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zhizheng Zhuo
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jinyuan Weng
- Department of Medical Imaging Product, Neusoft, Group Ltd., Shenyang, 110179, China
| | - Chengzhou Zhang
- Department of Radiology, Yantai Yuhuangding Hospital, Yantai, 264000, Shandong, China
| | - Mingwang Zhu
- Department of Radiology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100070, China
| | - Xing Liu
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jiang Du
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Tiantian Hua
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Hongfang Li
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Sven Haller
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- CIMC-Centre d'Imagerie Médicale de Cornavin, Geneva, Switzerland
- Department of Surgical Sciences, Radiology, Uppsala University, Uppsala, Sweden
- Faculty of Medicine of the University of Geneva, Geneva, Switzerland
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
- Queen Square Institute of Neurology and Center for Medical Image Computing, University College London, London, UK
| | - Yaou Liu
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
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22
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Park JW, Lee K, Kim EE, Kim SI, Park SH. Brain Tumor Classification by Methylation Profile. J Korean Med Sci 2023; 38:e356. [PMID: 37935168 PMCID: PMC10627723 DOI: 10.3346/jkms.2023.38.e356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/12/2023] [Indexed: 11/09/2023] Open
Abstract
The goal of the methylation classifier in brain tumor classification is to accurately classify tumors based on their methylation profiles. Accurate brain tumor diagnosis is the first step for healthcare professionals to predict tumor prognosis and establish personalized treatment plans for patients. The methylation classifier can be used to perform classification on tumor samples with diagnostic difficulties due to ambiguous histology or mismatch between histopathology and molecular signatures, i.e., not otherwise specified (NOS) cases or not elsewhere classified (NEC) cases, aiding in pathological decision-making. Here, the authors elucidate upon the application of a methylation classifier as a tool to mitigate the inherent complexities associated with the pathological evaluation of brain tumors, even when pathologists are experts in histopathological diagnosis and have access to enough molecular genetic information. Also, it should be emphasized that methylome cannot classify all types of brain tumors, and it often produces erroneous matches even with high matching scores, so, excessive trust is prohibited. The primary issue is the considerable difficulty in obtaining reference data regarding the methylation profile of each type of brain tumor. This challenge is further amplified when dealing with recently identified novel types or subtypes of brain tumors, as such data are not readily accessible through open databases or authors of publications. An additional obstacle arises from the fact that methylation classifiers are primarily research-based, leading to the unavailability of charging patients. It is important to note that the application of methylation classifiers may require specialized laboratory techniques and expertise in DNA methylation analysis.
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Affiliation(s)
- Jin Woo Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Kwanghoon Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Eric Eunshik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Seong-Ik Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Institute of Neuroscience, Seoul National University College of Medicine, Seoul, Korea.
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23
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Serdyukova K, Swearingen AR, Coradin M, Nevo M, Tran H, Bajric E, Brumbaugh J. Leveraging dominant-negative histone H3 K-to-M mutations to study chromatin during differentiation and development. Development 2023; 150:dev202169. [PMID: 38771302 PMCID: PMC10617616 DOI: 10.1242/dev.202169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Histone modifications are associated with regulation of gene expression that controls a vast array of biological processes. Often, these associations are drawn by correlating the genomic location of a particular histone modification with gene expression or phenotype; however, establishing a causal relationship between histone marks and biological processes remains challenging. Consequently, there is a strong need for experimental approaches to directly manipulate histone modifications. A class of mutations on the N-terminal tail of histone H3, lysine-to-methionine (K-to-M) mutations, was identified as dominant-negative inhibitors of histone methylation at their respective and specific residues. The dominant-negative nature of K-to-M mutants makes them a valuable tool for studying the function of specific methylation marks on histone H3. Here, we review recent applications of K-to-M mutations to understand the role of histone methylation during development and homeostasis. We highlight important advantages and limitations that require consideration when using K-to-M mutants, particularly in a developmental context.
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Affiliation(s)
- Ksenia Serdyukova
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Alison R. Swearingen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mariel Coradin
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mika Nevo
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Huong Tran
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emir Bajric
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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24
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Donson AM, Bertrand KC, Riemondy KA, Gao D, Zhuang Y, Sanford B, Norris GA, Chapman RJ, Fu R, Willard N, Griesinger AM, Ribeiro de Sousa G, Amani V, Grimaldo E, Hankinson TC, Booker F, Sill M, Grundy RG, Pajtler KW, Ellison DW, Foreman NK, Ritzmann TA. Significant increase of high-risk chromosome 1q gain and 6q loss at recurrence in posterior fossa group A ependymoma: A multicenter study. Neuro Oncol 2023; 25:1854-1867. [PMID: 37246777 PMCID: PMC10547517 DOI: 10.1093/neuonc/noad096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Ependymoma (EPN) posterior fossa group A (PFA) has the highest rate of recurrence and the worst prognosis of all EPN molecular groups. At relapse, it is typically incurable even with re-resection and re-irradiation. The biology of recurrent PFA remains largely unknown; however, the increasing use of surgery at first recurrence has now provided access to clinical samples to facilitate a better understanding of this. METHODS In this large longitudinal international multicenter study, we examined matched samples of primary and recurrent disease from PFA patients to investigate the biology of recurrence. RESULTS DNA methylome derived copy number variants (CNVs) revealed large-scale chromosome gains and losses at recurrence in PFA. CNV changes were dominated by chromosome 1q gain and/or 6q loss, both previously identified as high-risk factors in PFA, which were present in 23% at presentation but increased to 61% at first recurrence. Multivariate survival analyses of this cohort showed that cases with 1q gain or 6q loss at first recurrence were significantly more likely to recur again. Predisposition to 1q+/6q- CNV changes at recurrence correlated with hypomethylation of heterochromatin-associated DNA at presentation. Cellular and molecular analyses revealed that 1q+/6q- PFA had significantly higher proportions of proliferative neuroepithelial undifferentiated progenitors and decreased differentiated neoplastic subpopulations. CONCLUSIONS This study provides clinically and preclinically actionable insights into the biology of PFA recurrence. The hypomethylation predisposition signature in PFA is a potential risk-classifier for trial stratification. We show that the cellular heterogeneity of PFAs evolves largely because of genetic evolution of neoplastic cells.
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Affiliation(s)
- Andrew M Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | | | - Kent A Riemondy
- RNA Biosciences Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dexiang Gao
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- University of Colorado Cancer Center Biostatistics and Bioinformatics Shared Resource, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Yonghua Zhuang
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- University of Colorado Cancer Center Biostatistics and Bioinformatics Shared Resource, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Bridget Sanford
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Gregory A Norris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Rebecca J Chapman
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Rui Fu
- Computational Biology, New York Genome Center, New York, New York, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Denver, Aurora, Colorado, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Graziella Ribeiro de Sousa
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Vladimir Amani
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Enrique Grimaldo
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Todd C Hankinson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, Colorado, USA
| | - Ffyona Booker
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Martin Sill
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Richard G Grundy
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
| | - Kristian W Pajtler
- Hopp-Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Timothy A Ritzmann
- Children’s Brain Tumor Research Centre, University of Nottingham, Nottingham, UK
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25
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Chapman RJ, Ghasemi DR, Andreiuolo F, Zschernack V, Espariat AT, Buttarelli FR, Giangaspero F, Grill J, Haberler C, Paine SML, Scott I, Jacques TS, Sill M, Pfister S, Kilday JP, Leblond P, Massimino M, Witt H, Modena P, Varlet P, Pietsch T, Grundy RG, Pajtler KW, Ritzmann TA. Optimizing biomarkers for accurate ependymoma diagnosis, prognostication, and stratification within International Clinical Trials: A BIOMECA study. Neuro Oncol 2023; 25:1871-1882. [PMID: 36916248 PMCID: PMC10547510 DOI: 10.1093/neuonc/noad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Accurate identification of brain tumor molecular subgroups is increasingly important. We aimed to establish the most accurate and reproducible ependymoma subgroup biomarker detection techniques, across 147 cases from International Society of Pediatric Oncology (SIOP) Ependymoma II trial participants, enrolled in the pan-European "Biomarkers of Ependymoma in Children and Adolescents (BIOMECA)" study. METHODS Across 6 European BIOMECA laboratories, we evaluated epigenetic profiling (DNA methylation array); immunohistochemistry (IHC) for nuclear p65-RELA, H3K27me3, and Tenascin-C; copy number analysis via fluorescent in situ hybridization (FISH) and MLPA (1q, CDKN2A), and MIP and DNA methylation array (genome-wide copy number evaluation); analysis of ZFTA- and YAP1-fusions by RT-PCR and sequencing, Nanostring and break-apart FISH. RESULTS DNA Methylation profiling classified 65.3% (n = 96/147) of cases as EPN-PFA and 15% (n = 22/147) as ST-ZFTA fusion-positive. Immunohistochemical loss of H3K27me3 was a reproducible and accurate surrogate marker for EPN-PFA (sensitivity 99%-100% across 3 centers). IHC for p65-RELA, FISH, and RNA-based analyses effectively identified ZFTA- and YAP-fused supratentorial ependymomas. Detection of 1q gain using FISH exhibited only 57% inter-center concordance and low sensitivity and specificity while MIP, MLPA, and DNA methylation-based approaches demonstrated greater accuracy. CONCLUSIONS We confirm, in a prospective trial cohort, that H3K27me3 immunohistochemistry is a robust EPN-PFA biomarker. Tenascin-C should be abandoned as a PFA marker. DNA methylation and MIP arrays are effective tools for copy number analysis of 1q gain, 6q, and CDKN2A loss while FISH is inadequate. Fusion detection was successful, but rare novel fusions need more extensive technologies. Finally, we propose test sets to guide future diagnostic approaches.
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Affiliation(s)
- Rebecca J Chapman
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - David R Ghasemi
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felipe Andreiuolo
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
- Instituto Estadual do Cerebro Paulo Niemeyer, Rio de Janerio, Brazil
- IDOR Institute, Rio de Janeiro, Brazil
| | - Valentina Zschernack
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Arnault Tauziede Espariat
- Departement de Neuropathologie, Hopital Sainte-Anne, Paris, France
- INSERM Unit 981 and Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Francesca R Buttarelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Jacques Grill
- INSERM Unit 981 and Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Simon M L Paine
- Department of Neuropathology, Nottingham University Hospital, Nottingham, UK
| | - Ian Scott
- Department of Neuropathology, Nottingham University Hospital, Nottingham, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK
- Department of Histopathology, Great Ormond Street Hospital for Children, London, UK
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Stefan Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - John-Paul Kilday
- Children’s Brain Tumour Research Network (CBTRN), Royal Manchester Children’s Hospital, Manchester, UK
- The Centre for Paediatric, Teenage and Young Adult Cancer, Institute of Cancer Sciences, University of Manchester, Manchester, UK
| | - Pierre Leblond
- Institute of Hematology and Pediatric Oncology (IHOPe), Leon Berard Comprehensive Cancer Center, Lyon, France
| | - Maura Massimino
- Paediatric Unit, Fondazione Istituto Di Ricovero e Cura a Carattere Scientifico, Istituto Nazionale dei Tumori, Milano, Italy
| | - Hendrik Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Pascale Varlet
- Departement de Neuropathologie, Hopital Sainte-Anne, Paris, France
- INSERM Unit 981 and Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Richard G Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Kristian W Pajtler
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Timothy A Ritzmann
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
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26
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Boop SH, Shimony N, Boop FA. Review and update on pediatric ependymoma. Childs Nerv Syst 2023; 39:2667-2673. [PMID: 37493720 DOI: 10.1007/s00381-023-06091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/27/2023]
Abstract
Since our last Special Annual Issue dedicated to the topic of ependymoma in 2009, critical advancements have been made in the understanding of this disease which is largely confined to childhood. In the era of molecular profiling, the prior classification of ependymoma based on histology has become largely irrelevant, with multiple new subtypes of this disease now being described in the newest 2021 WHO CNS Tumor Classification System. Despite our advancements in understanding the underlying biology of these tumors, the mainstays of treatment-gross total surgical resection followed by confocal radiation therapy-have continued to yield the best treatment results across multiple studies and centers. Here, we provide an update on our understanding of the advancements made in tumor biology, surgical, and oncologic management of this disease. As we move into an era of more personalized medicine, it is critical to reflect on our historical understanding of different disease entities, to better understand the future directions of our treatments.
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Affiliation(s)
- Scott H Boop
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Nir Shimony
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Le Bonheur Neuroscience Institute, LeBonheur Children's Hospital, Memphis, TN, USA
- Department of Neurological Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
- Semmes Murphey Clinic, Memphis, TN, USA
| | - Frederick A Boop
- Department of Neurological Surgery, University of Tennessee Health Science Center, Memphis, TN, USA.
- Global Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Durand MA, Drouin A, Mouchard A, Durand L, Esnault C, Berthon P, Tallet A, Le Corre Y, Hainaut-Wierzbicka E, Blom A, Saiag P, Beneton N, Bens G, Nardin C, Aubin F, Dinulescu M, Collin C, Fromont-Hankard G, Cribier B, Laurent-Roussel S, Cokelaere K, Houben R, Schrama D, Peixoto P, Hervouet E, Bachiri K, Kantar D, Coyaud E, Guyétant S, Samimi M, Touzé A, Kervarrec T. Distinct Regulation of EZH2 and its Repressive H3K27me3 Mark in Polyomavirus-Positive and -Negative Merkel Cell Carcinoma. J Invest Dermatol 2023; 143:1937-1946.e7. [PMID: 37037414 DOI: 10.1016/j.jid.2023.02.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 04/12/2023]
Abstract
Merkel cell carcinoma (MCC) is an aggressive skin cancer for which Merkel cell polyomavirus integration and expression of viral oncogenes small T and Large T have been identified as major oncogenic determinants. Recently, a component of the PRC2 complex, the histone methyltransferase enhancer of zeste homolog 2 (EZH2) that induces H3K27 trimethylation as a repressive mark has been proposed as a potential therapeutic target in MCC. Because divergent results have been reported for the levels of EZH2 and trimethylation of lysine 27 on histone 3, we analyzed these factors in a large MCC cohort to identify the molecular determinants of EZH2 activity in MCC and to establish MCC cell lines' sensitivity to EZH2 inhibitors. Immunohistochemical expression of EZH2 was observed in 92% of MCC tumors (156 of 170), with higher expression levels in virus-positive than virus-negative tumors (P = 0.026). For the latter, we showed overexpression of EZHIP, a negative regulator of the PRC2 complex. In vitro, ectopic expression of the large T antigen in fibroblasts led to the induction of EZH2 expression, whereas the knockdown of T antigens in MCC cell lines resulted in decreased EZH2 expression. EZH2 inhibition led to selective cytotoxicity on virus-positive MCC cell lines. This study highlights the distinct mechanisms of EZH2 induction between virus-negative and -positive MCC.
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Affiliation(s)
- Marie-Alice Durand
- Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France
| | - Aurélie Drouin
- Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France
| | - Alice Mouchard
- Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France; Department of Dermatology, CHRU of Tours, University of Tours, Chambray-lès-Tours, France
| | - Laurine Durand
- Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France
| | - Clara Esnault
- Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France
| | - Patricia Berthon
- Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France
| | - Anne Tallet
- Platform of Somatic Tumor Molecular Genetics, CHU of Tours, University of Tours, Tours, France
| | - Yannick Le Corre
- Dermatology Department, CHU of Angers, LUNAM University, Angers, France
| | | | - Astrid Blom
- Department of General and Oncologic Dermatology, Ambroise-Paré Hospital, CARADERM Network, Boulogne-Billancourt, France; Research unit EA 4340, University of Versailles-Saint-Quentin-en-Yvelines, Paris-Saclay University, Boulogne-Billancourt, France
| | - Philippe Saiag
- Department of General and Oncologic Dermatology, Ambroise-Paré Hospital, CARADERM Network, Boulogne-Billancourt, France; Research unit EA 4340, University of Versailles-Saint-Quentin-en-Yvelines, Paris-Saclay University, Boulogne-Billancourt, France
| | - Nathalie Beneton
- Dermatology Department, CHU of Le Mans, University of Le Mans, Le Mans, France
| | - Guido Bens
- Dermatology department, CHR Orleans, Orleans, France
| | - Charlee Nardin
- Dermatology, CHU Besançon, Besançon, France; INSERM 1098, Université Bourgogne Franche-Comté, Besançon, France
| | - François Aubin
- Dermatology, CHU Besançon, Besançon, France; INSERM 1098, Université Bourgogne Franche-Comté, Besançon, France
| | - Monica Dinulescu
- Dermatology department, CHU Rennes, Institut Dermatologique du Grand Ouest (IDGO), Rennes, France
| | - Christine Collin
- Platform of Somatic Tumor Molecular Genetics, CHU of Tours, University of Tours, Tours, France
| | | | - Bernard Cribier
- Dermatology Department, CHU of Strasbourg, University of Strasbourg, Strasbourg, France
| | | | | | - Roland Houben
- Department of Dermatology, Venerology and Allergology, University Hospital of Würzburg, Würzburg, Germany
| | - David Schrama
- Department of Dermatology, Venerology and Allergology, University Hospital of Würzburg, Würzburg, Germany
| | - Paul Peixoto
- INSERM, EFS-BFC, UMR 1098 RIGHT, University Bourgogne-Franche-Comté, Besançon, France; EPIgenetics and GENe Expression Technical Platform (EPIGENExp), University Bourgogne Franche-Comté, Besançon, France
| | - Eric Hervouet
- INSERM, EFS-BFC, UMR 1098 RIGHT, University Bourgogne-Franche-Comté, Besançon, France; EPIgenetics and GENe Expression Technical Platform (EPIGENExp), University Bourgogne Franche-Comté, Besançon, France
| | - Kamel Bachiri
- Department of Biology, Inserm U1192, Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, CHU Lille, Université de Lille, Lille, France
| | - Diala Kantar
- Department of Biology, Inserm U1192, Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, CHU Lille, Université de Lille, Lille, France
| | - Etienne Coyaud
- Department of Biology, Inserm U1192, Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, CHU Lille, Université de Lille, Lille, France
| | - Serge Guyétant
- Pathology Department, CHU of Tours, University of Tours, Tours, France; Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France
| | - Mahtab Samimi
- Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France; Department of Dermatology, CHRU of Tours, University of Tours, Chambray-lès-Tours, France
| | - Antoine Touzé
- Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France
| | - Thibault Kervarrec
- Team "Biologie des Infections à Polyomavirus", ISP UMR 1282, INRAE, University of Tours, Tours, France; Pathology Department, CHU of Tours, University of Tours, Tours, France.
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Griesinger AM, Riemondy K, Eswaran N, Donson AM, Willard N, Prince EW, Paine SM, Bowes G, Rheaume J, Chapman RJ, Ramage J, Jackson A, Grundy RG, Foreman NK, Ritzmann TA. Multi-omic approach identifies hypoxic tumor-associated myeloid cells that drive immunobiology of high-risk pediatric ependymoma. iScience 2023; 26:107585. [PMID: 37694144 PMCID: PMC10484966 DOI: 10.1016/j.isci.2023.107585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/01/2023] [Accepted: 08/04/2023] [Indexed: 09/12/2023] Open
Abstract
Ependymoma (EPN) is a devastating childhood brain tumor. Single-cell analyses have illustrated the cellular heterogeneity of EPN tumors, identifying multiple neoplastic cell states including a mesenchymal-differentiated subpopulation which characterizes the PFA1 subtype. Here, we characterize the EPN immune environment, in the context of both tumor subtypes and tumor cell subpopulations using single-cell sequencing (scRNAseq, n = 27), deconvolution of bulk tumor gene expression (n = 299), spatial proteomics (n = 54), and single-cell cytokine release assays (n = 12). We identify eight distinct myeloid-derived subpopulations from which a group of cells, termed hypoxia myeloid cells, demonstrate features of myeloid-derived suppressor cells, including IL6/STAT3 pathway activation and wound healing ontologies. In PFA tumors, hypoxia myeloid cells colocalize with mesenchymal-differentiated cells in necrotic and perivascular niches and secrete IL-8, which we hypothesize amplifies the EPN immunosuppressive microenvironment. This myeloid cell-driven immunosuppression will need to be targeted for immunotherapy to be effective in this difficult-to-cure childhood brain tumor.
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Affiliation(s)
- Andrea M. Griesinger
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
- Colorado Clinical and Translational Sciences Institute, University of Colorado Denver, Aurora, CO 80045, USA
| | - Kent Riemondy
- RNA Bioscience Initiative, University of Colorado Denver, Aurora, CO 80045, USA
| | - Nithyashri Eswaran
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Andrew M. Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Denver, Aurora, CO 80045, USA
| | - Eric W. Prince
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, CO 80045, USA
| | - Simon M.L. Paine
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Queen’s Medical Centre, Derby Road, Nottingham NG7 2UH, UK
| | - Georgia Bowes
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | | | - Rebecca J. Chapman
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Judith Ramage
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Andrew Jackson
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Richard G. Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Queen’s Medical Centre, Derby Road, Nottingham NG7 2UH, UK
| | - Nicholas K. Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
- Colorado Clinical and Translational Sciences Institute, University of Colorado Denver, Aurora, CO 80045, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, CO 80045, USA
| | - Timothy A. Ritzmann
- Children’s Brain Tumour Research Centre, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Queen’s Medical Centre, Derby Road, Nottingham NG7 2UH, UK
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Cohen-Gogo S, Denburg AE, Villani A, Thacker N, Egan G, Simao Rafael M, Malkin D, Morgenstern DA. Precision oncology for children: A primer for paediatricians. Paediatr Child Health 2023; 28:278-284. [PMID: 37484033 PMCID: PMC10362955 DOI: 10.1093/pch/pxac123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/09/2022] [Indexed: 07/25/2023] Open
Abstract
Cancer is the leading cause of disease-related death in children, adolescents, and young adults beyond the newborn period in North America. Improving survival rates for patients with hard-to-cure cancer remains a challenge. One approach that has gained particular traction is 'precision oncology', whereby next-generation sequencing is used to identify genomic or transcriptomic changes that can help clarify the diagnosis, refine prognosis, define an underlying genetic cause, or identify a unique treatment target for a patient's cancer. In this primer, we provide a brief overview of the evolution of precision paediatric oncology, its current application to clinical oncology practice, and its future potential as a foundational approach to paediatric oncology care in Canada and around the world. We also address the many challenges and limitations inherent to the implementation of precision oncology as the standard of care, including ethical and economic considerations.
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Affiliation(s)
- Sarah Cohen-Gogo
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Avram E Denburg
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Anita Villani
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Nirav Thacker
- Division of Hematology/Oncology, Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Grace Egan
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margarida Simao Rafael
- Department of Oncology, Solid Tumor Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - David Malkin
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel A Morgenstern
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
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30
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Yamaguchi J, Ohka F, Motomura K, Saito R. Latest classification of ependymoma in the molecular era and advances in its treatment: a review. Jpn J Clin Oncol 2023; 53:653-663. [PMID: 37288489 DOI: 10.1093/jjco/hyad056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
Ependymoma is a rare central nervous system (CNS) tumour occurring in all age groups and is one of the most common paediatric malignant brain tumours. Unlike other malignant brain tumours, ependymomas have few identified point mutations and genetic and epigenetic features. With advances in molecular understanding, the latest 2021 World Health Organization (WHO) classification of CNS tumours divided ependymomas into 10 diagnostic categories based on the histology, molecular information and location; this accurately reflected the prognosis and biology of this tumour. Although maximal surgical resection followed by radiotherapy is considered the standard treatment method, and chemotherapy is considered ineffective, the validation of the role of these treatment modalities continues. Although the rarity and long-term clinical course of ependymoma make designing and conducting prospective clinical trials challenging, knowledge is steadily accumulating and progress is being made. Much of the clinical knowledge obtained from clinical trials to date was based on the previous histology-based WHO classifications, and the addition of new molecular information may lead to more complex treatment strategies. Therefore, this review presents the latest findings on the molecular classification of ependymomas and advances in its treatment.
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Affiliation(s)
- Junya Yamaguchi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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31
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Träger M, Schweizer L, Pérez E, Schmid S, Hain EG, Dittmayer C, Onken J, Fukuoka K, Ichimura K, Schüller U, Dührsen L, Müther M, Paulus W, Thomas C, Gutt-Will M, Schucht P, Maragkou T, Schittenhelm J, Eckert F, Niyazi M, Fleischmann DF, Dorostkar MM, Feyer P, May SA, Moskopp D, Badakhshi H, Radke C, Walter J, Ehret F, Capper D, Kaul D. Adult intracranial ependymoma-relevance of DNA methylation profiling for diagnosis, prognosis, and treatment. Neuro Oncol 2023; 25:1286-1298. [PMID: 36734226 PMCID: PMC10326475 DOI: 10.1093/neuonc/noad030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND A methylation-based classification of ependymoma has recently found broad application. However, the diagnostic advantage and implications for treatment decisions remain unclear. Here, we retrospectively evaluate the impact of surgery and radiotherapy on outcome after molecular reclassification of adult intracranial ependymomas. METHODS Tumors diagnosed as intracranial ependymomas from 170 adult patients collected from 8 diagnostic institutions were subjected to DNA methylation profiling. Molecular classes, patient characteristics, and treatment were correlated with progression-free survival (PFS). RESULTS The classifier indicated an ependymal tumor in 73.5%, a different tumor entity in 10.6%, and non-classifiable tumors in 15.9% of cases, respectively. The most prevalent molecular classes were posterior fossa ependymoma group B (EPN-PFB, 32.9%), posterior fossa subependymoma (PF-SE, 25.9%), and supratentorial ZFTA fusion-positive ependymoma (EPN-ZFTA, 11.2%). With a median follow-up of 60.0 months, the 5- and 10-year-PFS rates were 64.5% and 41.8% for EPN-PFB, 67.4% and 45.2% for PF-SE, and 60.3% and 60.3% for EPN-ZFTA. In EPN-PFB, but not in other molecular classes, gross total resection (GTR) (P = .009) and postoperative radiotherapy (P = .007) were significantly associated with improved PFS in multivariable analysis. Histological tumor grading (WHO 2 vs. 3) was not a predictor of the prognosis within molecularly defined ependymoma classes. CONCLUSIONS DNA methylation profiling improves diagnostic accuracy and risk stratification in adult intracranial ependymoma. The molecular class of PF-SE is unexpectedly prevalent among adult tumors with ependymoma histology and relapsed as frequently as EPN-PFB, despite the supposed benign nature. GTR and radiotherapy may represent key factors in determining the outcome of EPN-PFB patients.
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Affiliation(s)
- Malte Träger
- Department of Radiation Oncology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leonille Schweizer
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Edinger Institute, Institute of Neurology, University of Frankfurt am Main, Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Eilís Pérez
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Simone Schmid
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisabeth G Hain
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carsten Dittmayer
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia Onken
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurosurgery, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kohei Fukuoka
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Müther
- Department of Neurosurgery, University Hospital Münster, Münster, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Marielena Gutt-Will
- Department of Neurosurgery, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Philippe Schucht
- Department of Neurosurgery, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Theoni Maragkou
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Jens Schittenhelm
- Department of Neuropathology, Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Franziska Eckert
- Department of Radiation Oncology, University of Tübingen, Tübingen, Germany
- Department of Radiation Oncology, Medical University Vienna, AKH, Comprehensive Cancer Center, Vienna, Austria
| | - Maximilian Niyazi
- Department of Radiation Oncology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
- German Cancer Consortium (DKTK) partner site Munich, Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Daniel F Fleischmann
- Department of Radiation Oncology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
- German Cancer Consortium (DKTK) partner site Munich, Munich, Germany
| | - Mario M Dorostkar
- Center for Neuropathology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Petra Feyer
- Department of Radiation Oncology, Vivantes Hospital Neukölln, Berlin, Germany
| | - Sven-Axel May
- Department of Neurosurgery, Klinikum Chemnitz, Chemnitz, Germany
| | - Dag Moskopp
- Department of Neurosurgery, Vivantes Klinikum Im Friedrichshain, Berlin, Germany
| | - Harun Badakhshi
- Department of Clinical Radiation Oncology, Ernst Von Bergmann Medical Center Potsdam, Potsdam, Germany
| | - Cornelia Radke
- Department of Pathology, Ernst Von Bergmann Medical Center Potsdam, Potsdam, Germany
| | - Jan Walter
- Department of Neurosurgery, Jena University Hospital, Jena, Germany
- Department of Neurosurgery, Medical Center Saarbrücken, Saarbrücken, Germany
| | - Felix Ehret
- Department of Radiation Oncology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Kaul
- Department of Radiation Oncology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Ocasio JK, Budd KM, Roach JT, Andrews JM, Baker SJ. Oncohistones and disrupted development in pediatric-type diffuse high-grade glioma. Cancer Metastasis Rev 2023; 42:367-388. [PMID: 37119408 PMCID: PMC10441521 DOI: 10.1007/s10555-023-10105-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
Recurrent, clonal somatic mutations in histone H3 are molecular hallmarks that distinguish the genetic mechanisms underlying pediatric and adult high-grade glioma (HGG), define biological subgroups of diffuse glioma, and highlight connections between cancer, development, and epigenetics. These oncogenic mutations in histones, now termed "oncohistones", were discovered through genome-wide sequencing of pediatric diffuse high-grade glioma. Up to 80% of diffuse midline glioma (DMG), including diffuse intrinsic pontine glioma (DIPG) and diffuse glioma arising in other midline structures including thalamus or spinal cord, contain histone H3 lysine 27 to methionine (K27M) mutations or, rarely, other alterations that result in a depletion of H3K27me3 similar to that induced by H3 K27M. This subgroup of glioma is now defined as diffuse midline glioma, H3K27-altered. In contrast, histone H3 Gly34Arg/Val (G34R/V) mutations are found in approximately 30% of diffuse glioma arising in the cerebral hemispheres of older adolescents and young adults, now classified as diffuse hemispheric glioma, H3G34-mutant. Here, we review how oncohistones modulate the epigenome and discuss the mutational landscape and invasive properties of histone mutant HGGs of childhood. The distinct mechanisms through which oncohistones and other mutations rewrite the epigenetic landscape provide novel insights into development and tumorigenesis and may present unique vulnerabilities for pHGGs. Lessons learned from these rare incurable brain tumors of childhood may have broader implications for cancer, as additional high- and low-frequency oncohistone mutations have been identified in other tumor types.
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Affiliation(s)
- Jennifer K Ocasio
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kaitlin M Budd
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, USA
| | - Jordan T Roach
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, USA
- College of Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Jared M Andrews
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, USA.
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33
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Bertrand KC, Klimo P. Recent Advancements in Ependymoma: Challenges and Therapeutic Opportunities. Pediatr Neurosurg 2023; 58:307-312. [PMID: 37231859 DOI: 10.1159/000530868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/14/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Ependymoma is one of the most common malignant pediatric brain tumors and can be difficult to treat. Over the last decade, much progress has been made in the understanding of the underlying molecular drivers within this group of tumors, but clinical outcomes remain unchanged. SUMMARY Here, we review the most recent molecular advances in pediatric ependymoma, evaluate results of recent clinical trials and discuss the ongoing challenges in the field and questions that remain. KEY MESSAGES The field of ependymoma has vastly changed over the last several decades with ten distinct molecular subgroups now described, but much progress needs to be made in developing new therapeutic strategies and targets.
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Affiliation(s)
- Kelsey C Bertrand
- Division of Neuro-oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA,
| | - Paul Klimo
- Department of Surgery, St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Neurosurgery, University of Tennessee Health and Science Center, Memphis, Tennessee, USA
- Le Bonheur Neuroscience Institute, Le Bonheur Children's Hospital, Memphis, Tennessee, USA
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34
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Andrade AF, Chen CCL, Jabado N. Oncohistones in brain tumors: the soil and seed. Trends Cancer 2023; 9:444-455. [PMID: 36933956 PMCID: PMC11075889 DOI: 10.1016/j.trecan.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 03/18/2023]
Abstract
Recurrent somatic mutations in histone 3 (H3) variants (termed 'oncohistones') have been identified in high-grade gliomas (HGGs) in children and young adults and induce tumorigenesis through disruption of chromatin states. Oncohistones occur with exquisite neuroanatomical specificity and are associated with specific age distribution and epigenome landscapes. Here, we review the known intrinsic ('seed') and the extrinsic ('soil') factors needed for their optimal oncogenic effect and highlight the many unresolved questions regarding their effects on development and crosstalk with the tumor microenvironment. The 'seed and soil' analogy, used to explain tumor metastatic niches, also applies to oncohistones, which mainly thrive and flourish in specific chromatin states during very narrow windows of development, creating exquisite vulnerabilities, which could provide effective therapies for these deadly cancers.
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Affiliation(s)
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada; Department of Pediatrics, McGill University, Montreal, QC, H3A 0C7, Canada; The Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada.
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35
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Dang DD, Rosenblum JS, Shah AH, Zhuang Z, Doucet-O’Hare TT. Epigenetic Regulation in Primary CNS Tumors: An Opportunity to Bridge Old and New WHO Classifications. Cancers (Basel) 2023; 15:2511. [PMID: 37173979 PMCID: PMC10177493 DOI: 10.3390/cancers15092511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Originally approved in 1979, a specific grading classification for central nervous system (CNS) tumors was devised by the World Health Organization (WHO) in an effort to guide cancer treatment and better understand prognosis. These "blue books" have since undergone several iterations based on tumor location, advancements in histopathology, and most recently, diagnostic molecular pathology in its fifth edition. As new research methods have evolved to elucidate complex molecular mechanisms of tumorigenesis, a need to update and integrate these findings into the WHO grading scheme has become apparent. Epigenetic tools represent an area of burgeoning interest that encompasses all non-Mendelian inherited genetic features affecting gene expression, including but not limited to chromatin remodeling complexes, DNA methylation, and histone regulating enzymes. The SWItch/Sucrose non-fermenting (SWI/SNF) chromatin remodeling complex is the largest mammalian family of chromatin remodeling proteins and is estimated to be altered in 20-25% of all human malignancies; however, the ways in which it contributes to tumorigenesis are not fully understood. We recently discovered that CNS tumors with SWI/SNF mutations have revealed an oncogenic role for endogenous retroviruses (ERVs), remnants of exogenous retroviruses that integrated into the germline and are inherited like Mendelian genes, several of which retain open reading frames for proteins whose expression putatively contributes to tumor formation. Herein, we analyzed the latest WHO classification scheme for all CNS tumors with documented SWI/SNF mutations and/or aberrant ERV expression, and we summarize this information to highlight potential research opportunities that could be integrated into the grading scheme to better delineate diagnostic criteria and therapeutic targets.
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Affiliation(s)
- Danielle D. Dang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared S. Rosenblum
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ashish H. Shah
- Section of Virology and Immunotherapy, Department of Neurosurgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Zhengping Zhuang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tara T. Doucet-O’Hare
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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36
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Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nat Commun 2023; 14:2300. [PMID: 37085539 PMCID: PMC10121654 DOI: 10.1038/s41467-023-38044-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/13/2023] [Indexed: 04/23/2023] Open
Abstract
Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aylin Camgöz
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Owen Chapman
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sameena Wani
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Donglim Esther Park
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
| | - Jens-Martin Hübner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Abhijit Chakraborty
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Meghana Pagadala
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Rosalind Bump
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sahaana Chandran
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Rocio Acuna-Hidalgo
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Derek Reid
- Arima Genomics, Inc, San Diego, CA, 92121, USA
| | | | - Monika Mauermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Edwin F Juarez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Anne Jenseit
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - James T Robinson
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Petra Fiesel
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- CCU Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ling Morgan
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sunita Sridhar
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Nicole G Coufal
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Michael Levy
- Neurosurgery, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Denise Malicki
- Pathology, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Stephen Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, NYU Grossman School of Medicine, 550 First Ave, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - John Crawford
- Department of Neurosciences, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Robert J Wechsler-Reya
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tom Belle Davidson
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Jennifer Cotter
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - George Michaiel
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Gudrun Fleischhack
- German Cancer Consortium (DKTK), West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Hannah Carter
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kulandaimanuvel Antony Michealraj
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Sachin A Kumar
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Jeremy Rich
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Frank Buchholz
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, Dresden, Germany
| | - Jill P Mesirov
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ferhat Ay
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Jesse R Dixon
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Lukas Chavez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA.
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA.
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37
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Rigsby RK, Brahmbhatt P, Desai AB, Bathla G, Ebner BA, Gupta V, Vibhute P, Agarwal AK. Newly Recognized CNS Tumors in the 2021 World Health Organization Classification: Imaging Overview with Histopathologic and Genetic Correlation. AJNR Am J Neuroradiol 2023; 44:367-380. [PMID: 36997287 PMCID: PMC10084895 DOI: 10.3174/ajnr.a7827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/14/2022] [Indexed: 04/01/2023]
Abstract
In 2021, the World Health Organization released an updated classification of CNS tumors. This update reflects the growing understanding of the importance of genetic alterations related to tumor pathogenesis, prognosis, and potential targeted treatments and introduces 22 newly recognized tumor types. Herein, we review these 22 newly recognized entities and emphasize their imaging appearance with correlation to histologic and genetic features.
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Affiliation(s)
- R K Rigsby
- From the Department of Radiology (R.K.R., P.B., A.B.D., V.G., P.V., A.K.A.), Mayo Clinic, Jacksonville, Florida
| | - P Brahmbhatt
- From the Department of Radiology (R.K.R., P.B., A.B.D., V.G., P.V., A.K.A.), Mayo Clinic, Jacksonville, Florida
| | - A B Desai
- From the Department of Radiology (R.K.R., P.B., A.B.D., V.G., P.V., A.K.A.), Mayo Clinic, Jacksonville, Florida
| | - G Bathla
- Department of Radiology (G.B.), Mayo Clinic, Rochester, Minnesota
| | - B A Ebner
- Department of Laboratory Medicine and Pathology (B.A.E.), Mayo Clinic, Rochester, Minnesota
| | - V Gupta
- From the Department of Radiology (R.K.R., P.B., A.B.D., V.G., P.V., A.K.A.), Mayo Clinic, Jacksonville, Florida
| | - P Vibhute
- From the Department of Radiology (R.K.R., P.B., A.B.D., V.G., P.V., A.K.A.), Mayo Clinic, Jacksonville, Florida
| | - A K Agarwal
- From the Department of Radiology (R.K.R., P.B., A.B.D., V.G., P.V., A.K.A.), Mayo Clinic, Jacksonville, Florida
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38
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Hwang EI, Hanson D, Filbin MG, Mack SC. Why haven't we solved intracranial pediatric ependymoma? Current questions and barriers to treatment advances. Neoplasia 2023; 39:100895. [PMID: 36944298 PMCID: PMC10036929 DOI: 10.1016/j.neo.2023.100895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/22/2023]
Abstract
Pediatric intracranial ependymoma has seen a recent exponential expansion of biological findings, rapidly dividing the diagnosis into several subgroups, each with specific molecular and clinical characteristics. While such subdivision may complicate clinical conclusions from historical trials, this knowledge also provides an opportunity for interrogating the major clinical and biological questions preventing near-term translation into effective therapy for children with ependymoma. In this article, we briefly review some of the most critical clinical questions facing both patient management and the construct of future trials in childhood ependymoma, as well as explore some of the current barriers to efficient translation of preclinical discovery to the clinic.
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39
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Ajuyah P, Mayoh C, Lau LMS, Barahona P, Wong M, Chambers H, Valdes-Mora F, Senapati A, Gifford AJ, D'Arcy C, Hansford JR, Manoharan N, Nicholls W, Williams MM, Wood PJ, Cowley MJ, Tyrrell V, Haber M, Ekert PG, Ziegler DS, Khuong-Quang DA. Histone H3-wild type diffuse midline gliomas with H3K27me3 loss are a distinct entity with exclusive EGFR or ACVR1 mutation and differential methylation of homeobox genes. Sci Rep 2023; 13:3775. [PMID: 36882456 PMCID: PMC9992705 DOI: 10.1038/s41598-023-30395-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
Diffuse midline gliomas (DMG) harbouring H3K27M mutation are paediatric tumours with a dismal outcome. Recently, a new subtype of midline gliomas has been described with similar features to DMG, including loss of H3K27 trimethylation, but lacking the canonical H3K27M mutation (H3-WT). Here, we report a cohort of five H3-WT tumours profiled by whole-genome sequencing, RNA sequencing and DNA methylation profiling and combine their analysis with previously published cases. We show that these tumours have recurrent and mutually exclusive mutations in either ACVR1 or EGFR and are characterised by high expression of EZHIP associated to its promoter hypomethylation. Affected patients share a similar poor prognosis as patients with H3K27M DMG. Global molecular analysis of H3-WT and H3K27M DMG reveal distinct transcriptome and methylome profiles including differential methylation of homeobox genes involved in development and cellular differentiation. Patients have distinct clinical features, with a trend demonstrating ACVR1 mutations occurring in H3-WT tumours at an older age. This in-depth exploration of H3-WT tumours further characterises this novel DMG, H3K27-altered sub-group, characterised by a specific immunohistochemistry profile with H3K27me3 loss, wild-type H3K27M and positive EZHIP. It also gives new insights into the possible mechanism and pathway regulation in these tumours, potentially opening new therapeutic avenues for these tumours which have no known effective treatment. This study has been retrospectively registered on clinicaltrial.gov on 8 November 2017 under the registration number NCT03336931 ( https://clinicaltrials.gov/ct2/show/NCT03336931 ).
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Affiliation(s)
- Pamela Ajuyah
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia
| | - Chelsea Mayoh
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Loretta M S Lau
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Paulette Barahona
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia
| | - Marie Wong
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Hazel Chambers
- Department of Anatomical Pathology, Royal Children's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Fatima Valdes-Mora
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Akanksha Senapati
- Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Andrew J Gifford
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,Anatomical Pathology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Colleen D'Arcy
- Department of Anatomical Pathology, Royal Children's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.,Michael Rice Cancer Centre, Women's and Children's Hospital, Adelaide, SA, Australia.,South Australia Health and Medical Research Institute, Adelaide, SA, Australia.,South Australia Immunogenomics Cancer Institute, Adelaide, SA, Australia.,University of Adelaide, Adelaide, SA, Australia
| | - Neevika Manoharan
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia
| | - Wayne Nicholls
- Oncology Service, Children's Health Queensland Hospital & Health Service, Brisbane, QLD, Australia
| | - Molly M Williams
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Paul J Wood
- Department of Paediatrics, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Mark J Cowley
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Vanessa Tyrrell
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Michelle Haber
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia
| | - Paul G Ekert
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia.,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - David S Ziegler
- Lowy Cancer Research Centre, Children's Cancer Institute, UNSW Sydney, Kensington, NSW, Australia. .,School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia. .,University of New South Wales Centre for Childhood Cancer Research, UNSW, Kensington, NSW, Australia. .,Kids Cancer Centre, Sydney Children's Hospital, High Street, Randwick, NSW, 2031, Australia.
| | - Dong-Anh Khuong-Quang
- Children's Cancer Centre, Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia. .,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
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40
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Whitehouse JP, Hii H, Mayoh C, Wong M, Ajuyah P, Barahona P, Cui L, Dholaria H, White CL, Buntine MK, Byrne J, Rodrigues da Silva K, Howlett M, Girard EJ, Tsoli M, Ziegler DS, Dyke JM, Lee S, Ekert PG, Cowley MJ, Gottardo NG, Endersby R. In vivo loss of tumorigenicity in a patient-derived orthotopic xenograft mouse model of ependymoma. Front Oncol 2023; 13:1123492. [PMID: 36937401 PMCID: PMC10020925 DOI: 10.3389/fonc.2023.1123492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/09/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Ependymomas (EPN) are the third most common malignant brain cancer in children. Treatment strategies for pediatric EPN have remained unchanged over recent decades, with 10-year survival rates stagnating at just 67% for children aged 0-14 years. Moreover, a proportion of patients who survive treatment often suffer long-term neurological side effects as a result of therapy. It is evident that there is a need for safer, more effective treatments for pediatric EPN patients. There are ten distinct subgroups of EPN, each with their own molecular and prognostic features. To identify and facilitate the testing of new treatments for EPN, in vivo laboratory models representative of the diverse molecular subtypes are required. Here, we describe the establishment of a patient-derived orthotopic xenograft (PDOX) model of posterior fossa A (PFA) EPN, derived from a metastatic cranial lesion. Methods Patient and PDOX tumors were analyzed using immunohistochemistry, DNA methylation profiling, whole genome sequencing (WGS) and RNA sequencing. Results Both patient and PDOX tumors classified as PFA EPN by methylation profiling, and shared similar histological features consistent with this molecular subgroup. RNA sequencing revealed that gene expression patterns were maintained across the primary and metastatic tumors, as well as the PDOX. Copy number profiling revealed gains of chromosomes 7, 8 and 19, and loss of chromosomes 2q and 6q in the PDOX and matched patient tumor. No clinically significant single nucleotide variants were identified, consistent with the low mutation rates observed in PFA EPN. Overexpression of EZHIP RNA and protein, a common feature of PFA EPN, was also observed. Despite the aggressive nature of the tumor in the patient, this PDOX was unable to be maintained past two passages in vivo. Discussion Others who have successfully developed PDOX models report some of the lowest success rates for EPN compared to other pediatric brain cancer types attempted, with loss of tumorigenicity not uncommon, highlighting the challenges of propagating these tumors in the laboratory. Here, we discuss our collective experiences with PFA EPN PDOX model generation and propose potential approaches to improve future success in establishing preclinical EPN models.
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Affiliation(s)
- Jacqueline P. Whitehouse
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
- Centre for Child Health Research, University of Western Australia, Nedlands, WA, Australia
| | - Hilary Hii
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
| | - Chelsea Mayoh
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
| | - Marie Wong
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
| | - Pamela Ajuyah
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Paulette Barahona
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Louise Cui
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
| | - Hetal Dholaria
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children’s Hospital, Nedlands, WA, Australia
- Division of Paediatrics, University of Western Australia Medical School, Nedlands, WA, Australia
| | - Christine L. White
- Genetics and Molecular Pathology Laboratory, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
- Division of Genetics and Genomics, Victorian Clinical Genetics Services, Parkville, VIC, Australia
| | - Molly K. Buntine
- Genetics and Molecular Pathology Laboratory, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Jacob Byrne
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
| | - Keteryne Rodrigues da Silva
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
- Medical School of Rbeirão Preto (FMRP-USP), University of São Paulo, São Paulo, Brazil
| | - Meegan Howlett
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
- Centre for Child Health Research, University of Western Australia, Nedlands, WA, Australia
| | - Emily J. Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Maria Tsoli
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
| | - David S. Ziegler
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Jason M. Dyke
- Department of Neuropathology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, WA, Australia
- Pathology and Laboratory Medicine, University of Western Australia, Nedlands, WA, Australia
| | - Sharon Lee
- Department of Neurosurgery, Perth Children’s Hospital, Nedlands, WA, Australia
| | - Paul G. Ekert
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Mark J. Cowley
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
| | - Nicholas G. Gottardo
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
- Centre for Child Health Research, University of Western Australia, Nedlands, WA, Australia
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children’s Hospital, Nedlands, WA, Australia
| | - Raelene Endersby
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
- Centre for Child Health Research, University of Western Australia, Nedlands, WA, Australia
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Changes to pediatric brain tumors in 2021 World Health Organization classification of tumors of the central nervous system. Pediatr Radiol 2023; 53:523-543. [PMID: 36348014 DOI: 10.1007/s00247-022-05546-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/12/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022]
Abstract
New tumor types are continuously being described with advances in molecular testing and genomic analysis resulting in better prognostics, new targeted therapy options and improved patient outcomes. As a result of these advances, pathological classification of tumors is periodically updated with new editions of the World Health Organization (WHO) Classification of Tumors books. In 2021, WHO Classification of Tumors of the Central Nervous System, 5th edition (CNS5), was published with major changes in pediatric brain tumors officially recognized including pediatric gliomas being separated from adult gliomas, ependymomas being categorized based on anatomical compartment and many new tumor types, most of them seen in children. Additional general changes, such as tumor grading now being done within tumor types rather than across entities and changes in definition of glioblastoma, are also relevant to pediatric neuro-oncology practice. The purpose of this manuscript is to highlight the major changes in pediatric brain tumors in CNS5 most relevant to radiologists. Additionally, brief descriptions of newly recognized entities will be presented with a focus on imaging findings.
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Pun M, Pratt D, Nano PR, Joshi PK, Jiang L, Englinger B, Rao A, Cieslik M, Chinnaiyan AM, Aldape K, Pfister S, Filbin MG, Bhaduri A, Venneti S. Common molecular features of H3K27M DMGs and PFA ependymomas map to hindbrain developmental pathways. Acta Neuropathol Commun 2023; 11:25. [PMID: 36759899 PMCID: PMC9912509 DOI: 10.1186/s40478-023-01514-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
Globally decreased histone 3, lysine 27 tri-methylation (H3K27me3) is a hallmark of H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs). H3K27-altered DMGs are largely characterized by lysine-to-methionine mutations in histone 3 at position 27 (H3K27M). Most PFAs overexpress EZH inhibitory protein (EZHIP), which possesses a region of similarity to the mutant H3K27M. Both H3K27M and EZHIP inhibit the function of the polycomb repressive complex 2 (PRC2) responsible for H3K27me3 deposition. These tumors often arise in neighboring regions of the brainstem and posterior fossa. In rare cases PFAs harbor H3K27M mutations, and DMGs overexpress EZHIP. These findings together raise the possibility that certain cell populations in the developing hindbrain/posterior fossa are especially sensitive to modulation of H3K27me3 states. We identified shared molecular features by comparing genomic, bulk transcriptomic, chromatin-based profiles, and single-cell RNA-sequencing (scRNA-seq) data from the two tumor classes. Our approach demonstrated that 1q gain, a key biomarker in PFAs, is prognostic in H3.1K27M, but not H3.3K27M gliomas. Conversely, Activin A Receptor Type 1 (ACVR1), which is associated with mutations in H3.1K27M gliomas, is overexpressed in a subset of PFAs with poor outcome. Despite diffuse H3K27me3 reduction, previous work shows that both tumors maintain genomic H3K27me3 deposition at select sites. We demonstrate heterogeneity in shared patterns of residual H3K27me3 for both tumors that largely segregated with inferred anatomic tumor origins and progenitor populations of tumor cells. In contrast, analysis of genes linked to H3K27 acetylation (H3K27ac)-marked enhancers showed higher expression in astrocytic-like tumor cells. Finally, common H3K27me3-marked genes mapped closely to expression patterns in the human developing hindbrain. Overall, our data demonstrate developmentally relevant molecular similarities between PFAs and H3K27M DMGs and support the overall hypothesis that deregulated mechanisms of hindbrain development are central to the biology of both tumors.
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Affiliation(s)
- Matthew Pun
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, 3520E MSRB 1, 1150 W. Medical Center, Ann Arbor, MI, 41804, USA
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Patricia R Nano
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Piyush K Joshi
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
- Center for Cancer Research and Comprehensive Cancer Center, Medical University Vienna, 1090, Vienna, Austria
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Stefan Pfister
- Hopp Children's Cancer Center (KiTZ) Heidelberg, Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sriram Venneti
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan, 3520E MSRB 1, 1150 W. Medical Center, Ann Arbor, MI, 41804, USA.
- Chad Carr Pediatric Tumor Center, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA.
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Montgomery EY, Thirunavu V, Pagadala M, Shlobin NA, Plant-Fox AS, Lam S, DeCuypere M. Recurrent pediatric infratentorial ependymomas: a systematic review and meta-analysis on outcomes and molecular classification. J Neurosurg Pediatr 2023; 31:132-142. [PMID: 36433871 DOI: 10.3171/2022.10.peds22154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/07/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The aim of this study was to summarize the prognosis of recurrent infratentorial ependymomas based on treatment and molecular characterization. METHODS Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, the authors searched the PubMed, Scopus, Embase, and Ovid databases for studies on recurrent infratentorial ependymomas in patients younger than 25 years of age. Exclusion criteria included case series of fewer than 5 patients and studies that did not provide time-dependent survival data. RESULTS The authors' database search yielded 482 unique articles, of which 18 were included in the final analysis. There were 479 recurrent infratentorial pediatric ependymomas reported; 53.4% were WHO grade II and 46.6% were WHO grade III tumors. The overall mortality for recurrent infratentorial pediatric ependymomas was 49.1% (226/460). The pooled mean survival was 30.2 months after recurrence (95% CI 22.4-38.0 months). Gross-total resection (GTR) was achieved in 243 (59.0%) patients at initial presentation. The mean survival postrecurrence for those who received initial GTR was 42.3 months (95% CI 35.7-47.6 months) versus 26.0 months (95% CI 9.6-44.6 months) for those who received subtotal resection (STR) (p = 0.032). There was no difference in the mean survival between patients who received GTR (49.3 months, 95% CI 32.3-66.3 months) versus those who received STR (41.4 months, 95% CI 11.6-71.2 months) for their recurrent tumor (p = 0.610). In the studies that included molecular classification data, there were 169 (83.3%) posterior fossa group A (PFA) tumors and 34 (16.7%) posterior fossa group B (PFB) tumors, with 28 tumors harboring a 1q gain. PFA tumors demonstrated worse mean postprogression patient survival (24.7 months, 95% CI 15.3-34.0 months) compared with PFB tumors (48.0 months, 95% CI 32.8-63.2 months) (p = 0.0073). The average postrecurrence survival for patients with 1q+ tumors was 14.7 months. CONCLUSIONS The overall mortality rate for recurrent infratentorial ependymomas was found to be 49.1%, with a pooled mean survival of 30.2 months in the included sample population. More than 80% of recurrent infratentorial ependymomas were of the PFA molecular subtype, and both PFA tumors and those with 1q gain demonstrated worse prognosis after recurrence.
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Affiliation(s)
| | - Vineeth Thirunavu
- 2Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Illinois
| | - Manasa Pagadala
- 2Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Illinois
| | - Nathan A Shlobin
- 2Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Illinois
| | - Ashley S Plant-Fox
- 3Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Illinois; and
| | - Sandi Lam
- 2Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Illinois
- 4Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Michael DeCuypere
- 2Division of Pediatric Neurosurgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Illinois
- 4Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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Vallero SG, Bertero L, Morana G, Sciortino P, Bertin D, Mussano A, Ricci FS, Peretta P, Fagioli F. Pediatric diffuse midline glioma H3K27- altered: A complex clinical and biological landscape behind a neatly defined tumor type. Front Oncol 2023; 12:1082062. [PMID: 36727064 PMCID: PMC9885151 DOI: 10.3389/fonc.2022.1082062] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023] Open
Abstract
The 2021 World Health Organization Classification of Tumors of the Central Nervous System, Fifth Edition (WHO-CNS5), has strengthened the concept of tumor grade as a combination of histologic features and molecular alterations. The WHO-CNS5 tumor type "Diffuse midline glioma, H3K27-altered," classified within the family of "Pediatric-type diffuse high-grade gliomas," incarnates an ideally perfect integrated diagnosis in which location, histology, and genetics clearly define a specific tumor entity. It tries to evenly characterize a group of neoplasms that occur primarily in children and midline structures and that have a dismal prognosis. Such a well-defined pathological categorization has strongly influenced the pediatric oncology community, leading to the uniform treatment of most cases of H3K27-altered diffuse midline gliomas (DMG), based on the simplification that the mutation overrides the histological, radiological, and clinical characteristics of such tumors. Indeed, multiple studies have described pediatric H3K27-altered DMG as incurable tumors. However, in biology and clinical practice, exceptions are frequent and complexity is the rule. First of all, H3K27 mutations have also been found in non-diffuse gliomas. On the other hand, a minority of DMGs are H3K27 wild-type but have a similarly poor prognosis. Furthermore, adult-type tumors may rarely occur in children, and differences in prognosis have emerged between adult and pediatric H3K27-altered DMGs. As well, tumor location can determine differences in the outcome: patients with thalamic and spinal DMG have significantly better survival. Finally, other concomitant molecular alterations in H3K27 gliomas have been shown to influence prognosis. So, when such additional mutations are found, which one should we focus on in order to make the correct clinical decision? Our review of the current literature on pediatric diffuse midline H3K27-altered DMG tries to address such questions. Indeed, H3K27 status has become a fundamental supplement to the histological grading of pediatric gliomas; however, it might not be sufficient alone to exhaustively define the complex biological behavior of DMG in children and might not represent an indication for a unique treatment strategy across all patients, irrespective of age, additional molecular alterations, and tumor location.
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Affiliation(s)
- Stefano Gabriele Vallero
- Pediatric Oncohematology Division, Regina Margherita Children’s Hospital, Azienda Ospedaliera Universitaria (AOU) Città della Salute e della Scienza, Turin, Italy,*Correspondence: Stefano Gabriele Vallero,
| | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Giovanni Morana
- Neuroradiology Unit, Department of Neuroscience, University of Turin, Turin, Italy
| | - Paola Sciortino
- Department of Neuroradiology, Azienda Ospedaliera Universitaria (AOU) Città della Salute e della Scienza, Turin, Italy
| | - Daniele Bertin
- Pediatric Oncohematology Division, Regina Margherita Children’s Hospital, Azienda Ospedaliera Universitaria (AOU) Città della Salute e della Scienza, Turin, Italy
| | - Anna Mussano
- Radiotherapy Unit, Regina Margherita Children’s Hospital, Azienda Ospedaliera Universitaria (AOU) Città della Salute e della Scienza, Turin, Italy
| | - Federica Silvia Ricci
- Child and Adolescent Neuropsychiatry Division, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Paola Peretta
- Pediatric Neurosurgery Division, Regina Margherita Children’s Hospital, Azienda Ospedaliera Universitaria (AOU) Città della Salute e della Scienza, Turin, Italy
| | - Franca Fagioli
- Pediatric Oncohematology Division, Regina Margherita Children’s Hospital, Azienda Ospedaliera Universitaria (AOU) Città della Salute e della Scienza, Turin, Italy,Department of Public Health and Pediatrics, University of Turin, Turin, Italy
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Ahmad Z, Rahim S, Abdul-Ghafar J, Chundriger Q, Ud Din N. Events in CNS Tumor Pathology Post-2016 WHO CNS: cIMPACT-NOW Updates and Other Advancements: A Comprehensive Review Plus a Summary of the Salient Features of 2021 WHO CNS 5. Int J Gen Med 2023; 16:107-127. [PMID: 36644568 PMCID: PMC9833325 DOI: 10.2147/ijgm.s394872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction The 2016 World Health Organization Classification (WHO) of Tumors of the Central Nervous System (CNS) represented a major change. It recommended an "integrated diagnosis" comprising histologic and molecular information facilitating a more precise diagnosis of specific CNS tumors. Its goal was to provide greater diagnostic precision and reproducibility resulting in more clinical relevance and predictive value, ultimately leading to better patient care. Advances in molecular classification, mostly resulting from DNA methylation array profiling of CNS tumors, were occurring at a very rapid pace and required more rapid integration into clinical practice. Methods cIMPACT-NOW updates and other recent papers plus salient features of 2021 WHO CNS5 in this comprehensive write-up were reviewed. Results CNS tumor classification needs to be updated at a rapid pace and mechanisms put into place to guide diagnosticians and clinicians in the interim period if major changes in the classification of tumor types came to light. Recognizing the need to integrate these into clinical practice more rapidly and without inordinate delay, the International Society of Neuropathology (ISN) 2016 sponsored an initiative called cIMPACT-NOW. Discussion and/or Conclusion Goal of cIMPACT-NOW was to provide clarification regarding contentious issues arising in the wake of the 2016 WHO CNS update as well as report new advancements in molecular classification of CNS tumors and new tumor entities emerging as a result of these advancements. cIMPACT-NOW updates: It thus laid the foundation for the 5th edition of the WHO Classification of CNS tumors (2021 WHO CNS 5). We have discussed cIMPACT updates in detail in this review. In addition, molecular diagnostics including DNA methylation-based classification of CNS tumors and the practical use of molecular classification in the prognostication and treatment of CNS tumors is discussed. Finally, the salient features of the new CNS tumor classification are summarized.
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Affiliation(s)
- Zubair Ahmad
- Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Shabina Rahim
- Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Jamshid Abdul-Ghafar
- Department of Pathology and Clinical Laboratory, French Medical Institute for Mothers and Children (FMIC), Kabul, Afghanistan,Correspondence: Jamshid Abdul-Ghafar, Department of Pathology and Clinical Laboratory, French Medical Institute for Mothers and Children (FMIC), Kabul, Afghanistan, Tel +93 792 827 287, Email
| | - Qurratulain Chundriger
- Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Nasir Ud Din
- Department of Pathology and Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
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Halfpenny AM, Wood MD. Review of the Recent Changes in the WHO Classification for Pediatric Brain and Spinal Cord Tumors. Pediatr Neurosurg 2023; 58:337-355. [PMID: 36617415 PMCID: PMC10664345 DOI: 10.1159/000528957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Periodic updates to the World Health Organization (WHO) classification system for central nervous system (CNS) tumors reflect advances in the pathological diagnosis, categorization, and molecular underpinnings of primary brain, spinal cord, and peripheral nerve tumors. The 5th edition of the WHO Classification of CNS Tumors was published in 2021. This review discusses the guiding principles of the revision, introduces the more common new diagnostic entities, and describes tumor classification and nomenclature changes that are relevant for pediatric neurological surgeons. SUMMARY Revisions to the WHO CNS tumor classification system introduced new diagnostic entities, restructured and renamed other entities with particular impact in the diffuse gliomas and CNS embryonal tumors, and expanded the requirements for incorporating both molecular and histological features of CNS tumors into a unified integrated diagnosis. Many of the new diagnostic entities occur at least occasionally in pediatric patients and will thus be encountered by pediatric neurosurgeons. New nomenclature impacts the terminology that is applied in communication between pathologists, surgeons, clinicians, and patients. Requirements for molecular information in tumor diagnosis are expected to refine diagnostic categories while also introducing practical considerations for intraoperative consultation, preliminary histological evaluation, and triaging of neurosurgical tissue samples for histology, molecular testing, and clinical trial requirements. KEY MESSAGES Pediatric brain tumor diagnosis and clinical management are a multidisciplinary effort that is rapidly advancing in the molecular era. Interdisciplinary collaboration is critical for providing the best care for pediatric CNS tumor patients. Pediatric neurosurgeons and their local neuropathologists and neuro-oncologists must work collaboratively to put the most current CNS tumor diagnostic guidelines into standard practice.
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Affiliation(s)
| | - Matthew D. Wood
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University, Portland, Oregon, USA
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de Almeida Magalhães T, Alencastro Veiga Cruzeiro G, Ribeiro de Sousa G, Englinger B, Fernando Peinado Nagano L, Ancliffe M, Rodrigues da Silva K, Jiang L, Gojo J, Cherry Liu Y, Carline B, Kuchibhotla M, Pinto Saggioro F, Kazue Nagahashi Marie S, Mieko Oba-Shinjo S, Andres Yunes J, Gomes de Paula Queiroz R, Alberto Scrideli C, Endersby R, Filbin MG, Silva Borges K, Salic A, Gonzaga Tone L, Valera ET. Activation of Hedgehog signaling by the oncogenic RELA fusion reveals a primary cilia-dependent vulnerability in supratentorial ependymoma. Neuro Oncol 2023; 25:185-198. [PMID: 35640920 PMCID: PMC9825332 DOI: 10.1093/neuonc/noac147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Supratentorial RELA fusion (ST-RELA) ependymomas (EPNs) are resistant tumors without an approved chemotherapeutic treatment. Unfortunately, the molecular mechanisms that lead to chemoresistance traits of ST-RELA remain elusive. The aim of this study was to assess RELA fusion-dependent signaling modules, specifically the role of the Hedgehog (Hh) pathway as a novel targetable vulnerability in ST-RELA. METHODS Gene expression was analyzed in EPN from patient cohorts, by microarray, RNA-seq, qRT-PCR, and scRNA-seq. Inhibitors against Smoothened (SMO) (Sonidegib) and Aurora kinase A (AURKA) (Alisertib) were evaluated. Protein expression, primary cilia formation, and drug effects were assessed by immunoblot, immunofluorescence, and immunohistochemistry. RESULTS Hh components were selectively overexpressed in EPNs induced by the RELA fusion. Single-cell analysis showed that the Hh signature was primarily confined to undifferentiated, stem-like cell subpopulations. Sonidegib exhibited potent growth-inhibitory effects on ST-RELA cells, suggesting a key role in active Hh signaling; importantly, the effect of Sonidegib was reversed by primary cilia loss. We, thus, tested the effect of AURKA inhibition by Alisertib, to induce cilia stabilization/reassembly. Strikingly, Alisertib rescued ciliogenesis and synergized with Sonidegib in killing ST-RELA cells. Using a xenograft model, we show that cilia loss is a mechanism for acquiring resistance to the inhibitory effect of Sonidegib. However, Alisertib fails to rescue cilia and highlights the need for other strategies to promote cilia reassembly, for treating ST-RELA tumors. CONCLUSION Our study reveals a crucial role for the Hh pathway in ST-RELA tumor growth, and suggests that rescue of primary cilia represents a vulnerability of the ST-RELA EPNs.
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Affiliation(s)
- Taciani de Almeida Magalhães
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gustavo Alencastro Veiga Cruzeiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Graziella Ribeiro de Sousa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Luis Fernando Peinado Nagano
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mathew Ancliffe
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Keteryne Rodrigues da Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Johannes Gojo
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Yulu Cherry Liu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Brooke Carline
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Mani Kuchibhotla
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Fabiano Pinto Saggioro
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- Cellular and Molecular Biology Laboratory, Department of Neurology, Faculdade de Medicina (FMUSP), University of São Paulo, São Paulo, Brazil
| | - Sueli Mieko Oba-Shinjo
- Cellular and Molecular Biology Laboratory, Department of Neurology, Faculdade de Medicina (FMUSP), University of São Paulo, São Paulo, Brazil
| | - José Andres Yunes
- Molecular Biology Laboratory, Boldrini Children’s Center, Campinas, São Paulo, Brazil
| | | | - Carlos Alberto Scrideli
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Raelene Endersby
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Kleiton Silva Borges
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Adrian Salic
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Luiz Gonzaga Tone
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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AlRayahi J, Alwalid O, Mubarak W, Maaz AUR, Mifsud W. Pediatric Brain Tumors in the Molecular Era: Updates for the Radiologist. Semin Roentgenol 2023; 58:47-66. [PMID: 36732011 DOI: 10.1053/j.ro.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/28/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jehan AlRayahi
- Department of Pediatric Radiology, Sidra Medicine, Doha, Qatar.
| | - Osamah Alwalid
- Department of Pediatric Radiology, Sidra Medicine, Doha, Qatar
| | - Walid Mubarak
- Department of Pediatric Radiology, Sidra Medicine, Doha, Qatar
| | - Ata Ur Rehman Maaz
- Department of Pediatric Hematology-Oncology, Sidra Medicine, Doha, Qatar
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Bertero L, Ricci AA, Tampieri C, Cassoni P, Modena P. Ependymomas. Pathologica 2022; 114:436-446. [PMID: 36534422 PMCID: PMC9763977 DOI: 10.32074/1591-951x-817] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2022] Open
Abstract
Ependymal neoplasms are a heterogenous group of neoplasms arising from the progenitors of the cells lining the ventricular system and the spinal central canal. During the last few years, significant novel data concerning oncogenesis, molecular characteristics and clinical correlations of these tumours have been collected, with a strong relevance for their pathological classification. The recently published 5th edition of WHO Classification of Central Nervous System Tumours integrates this novel knowledge and represents a substantial update compared to the previous edition. Concerning supratentorial ependymomas, the previous RELA fusion-positive ependymoma has been renamed into ZFTA fusion-positive and the novel YAP1 fusion-positive ependymoma subtype has been added. Posterior fossa ependymomas should now be allocated either to the Type A or Type B subtypes based on molecular profiling or using the H3 K27me3 immunohistochemical surrogate. Regarding spinal ependymomas, a novel subtype has been added based on a distinctive molecular trait, presence of MYCN amplification, and on the unfavourable outcome. Finally, myxopapillary ependymoma is now classified as a grade 2 tumour in accordance with its overall prognosis which mirrors that of conventional spinal ependymomas. The aim of this review is to present these changes and summarize the current diagnostic framework of ependymal tumours, according to the most recent updates.
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Affiliation(s)
- Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy,Correspondence Luca Bertero Pathology Unit, Dept. Medical Sciences, University of Turin, via Santena 7, 10126 Torino, Italy Tel.: +390116336181 E-mail:
| | - Alessia Andrea Ricci
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Cristian Tampieri
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paola Cassoni
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
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K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas. Nat Genet 2022; 54:1865-1880. [PMID: 36471070 PMCID: PMC9742294 DOI: 10.1038/s41588-022-01205-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/16/2022] [Indexed: 12/12/2022]
Abstract
Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations and molecular profiles. The contribution of the cell of origin to these differences has been challenging to uncouple from the oncogenic reprogramming induced by the mutation. Here, we perform an integrated analysis of 116 tumors, including single-cell transcriptome and chromatin accessibility, 3D chromatin architecture and epigenomic profiles, and show that K27M-mutant gliomas faithfully maintain chromatin configuration at developmental genes consistent with anatomically distinct oligodendrocyte precursor cells (OPCs). H3.3K27M thalamic gliomas map to prosomere 2-derived lineages. In turn, H3.1K27M ACVR1-mutant pontine gliomas uniformly mirror early ventral NKX6-1+/SHH-dependent brainstem OPCs, whereas H3.3K27M gliomas frequently resemble dorsal PAX3+/BMP-dependent progenitors. Our data suggest a context-specific vulnerability in H3.1K27M-mutant SHH-dependent ventral OPCs, which rely on acquisition of ACVR1 mutations to drive aberrant BMP signaling required for oncogenesis. The unifying action of K27M mutations is to restrict H3K27me3 at PRC2 landing sites, whereas other epigenetic changes are mainly contingent on the cell of origin chromatin state and cycling rate.
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