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Campos Mármol MC, Aguado M, Ramón Y Cajal T, Gallardo A, Catasús L, Gonzalez A, Méndez JE, Lasa A, Arumi M, Gallego Rubio O, Serra JB, Muñoz Hernandez F, von Deimling A, Kommoss FKF, Espinosa I. Non-C19MC-altered embryonal tumor with multilayered rosettes in a young woman with DICER1 syndrome: case report and review of the literature. Pathologica 2024; 116:170-175. [PMID: 38979591 DOI: 10.32074/1591-951x-970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/19/2024] [Indexed: 07/10/2024] Open
Abstract
Embryonal tumors with multilayered rosettes (ETMR) are highly aggressive and therapy-resistant pediatric central nervous system (CNS) tumors that have three histological patters: embryonal tumor with abundant neuropil and true rosettes, ependymoblastoma, and medulloepithelioma. We present a case of ETMR in an 18-year-old woman with DICER1 syndrome. This report confirms the important role of DNA-methylation analysis in the classification of CNS embryonal tumors and the importance of investigating somatic and germline DICER1 mutations in all CNS embryonal tumors.
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Affiliation(s)
| | - María Aguado
- Department of Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Teresa Ramón Y Cajal
- Genetic Counselling Unit, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Alberto Gallardo
- Department of Pathology, Hospital de la Santa Creu i Sant Pau, Institute of Biomedical Research (IIB Sant Pau), Autonomous University of Barcelona, Barcelona, Spain
| | - Luis Catasús
- Department of Pathology, Hospital de la Santa Creu i Sant Pau, Institute of Biomedical Research (IIB Sant Pau), Autonomous University of Barcelona, Barcelona, Spain
| | - Allan Gonzalez
- Department of Pathology, Hospital de la Santa Creu i Sant Pau, Institute of Biomedical Research (IIB Sant Pau), Autonomous University of Barcelona, Barcelona, Spain
| | | | - Adriana Lasa
- Department of Genetics, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Montse Arumi
- Department of Pathology, Hospital del Mar, Barcelona, Spain
| | - Oscar Gallego Rubio
- Department of Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Josep Balart Serra
- Department of Radiotherapeutic Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | | | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix K F Kommoss
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Iñigo Espinosa
- Department of Pathology, Hospital de la Santa Creu i Sant Pau, Institute of Biomedical Research (IIB Sant Pau), Autonomous University of Barcelona, Barcelona, Spain
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Schmid K, Sehring J, Németh A, Harter PN, Weber KJ, Vengadeswaran A, Storf H, Seidemann C, Karki K, Fischer P, Dohmen H, Selignow C, von Deimling A, Grau S, Schröder U, Plate KH, Stein M, Uhl E, Acker T, Amsel D. DistSNE: Distributed computing and online visualization of DNA methylation-based central nervous system tumor classification. Brain Pathol 2024; 34:e13228. [PMID: 38012085 PMCID: PMC11007060 DOI: 10.1111/bpa.13228] [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: 10/29/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023] Open
Abstract
The current state-of-the-art analysis of central nervous system (CNS) tumors through DNA methylation profiling relies on the tumor classifier developed by Capper and colleagues, which centrally harnesses DNA methylation data provided by users. Here, we present a distributed-computing-based approach for CNS tumor classification that achieves a comparable performance to centralized systems while safeguarding privacy. We utilize the t-distributed neighborhood embedding (t-SNE) model for dimensionality reduction and visualization of tumor classification results in two-dimensional graphs in a distributed approach across multiple sites (DistSNE). DistSNE provides an intuitive web interface (https://gin-tsne.med.uni-giessen.de) for user-friendly local data management and federated methylome-based tumor classification calculations for multiple collaborators in a DataSHIELD environment. The freely accessible web interface supports convenient data upload, result review, and summary report generation. Importantly, increasing sample size as achieved through distributed access to additional datasets allows DistSNE to improve cluster analysis and enhance predictive power. Collectively, DistSNE enables a simple and fast classification of CNS tumors using large-scale methylation data from distributed sources, while maintaining the privacy and allowing easy and flexible network expansion to other institutes. This approach holds great potential for advancing human brain tumor classification and fostering collaborative precision medicine in neuro-oncology.
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Affiliation(s)
- Kai Schmid
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Jannik Sehring
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Attila Németh
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Patrick N. Harter
- Neurological Institute (Edinger Institute)University Hospital FrankfurtFrankfurtGermany
- Present address:
Center for Neuropathology and Prion ResearchUniversity Hospital of MunichMunichGermany
| | - Katharina J. Weber
- Neurological Institute (Edinger Institute)University Hospital FrankfurtFrankfurtGermany
- German Cancer Consortium (DKTK)HeidelbergGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
- Frankfurt Cancer Institute (FCI)FrankfurtGermany
- University Cancer Center (UCT) FrankfurtFrankfurtGermany
| | - Abishaa Vengadeswaran
- Medical Informatics Group (MIG), Goethe University FrankfurtUniversity Hospital FrankfurtFrankfurt am MainGermany
| | - Holger Storf
- Medical Informatics Group (MIG), Goethe University FrankfurtUniversity Hospital FrankfurtFrankfurt am MainGermany
| | | | - Kapil Karki
- DIZ MarburgPhillips University MarburgMarburgGermany
| | - Patrick Fischer
- Institute for Medical InformaticsJustus‐Liebig UniversityGiessenGermany
- Department of Neuropathology, German Cancer Research Center (DKFZ)Universitätsklinikum Heidelberg, and CCU NeuropathologyHeidelbergGermany
| | - Hildegard Dohmen
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Carmen Selignow
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | | | - Stefan Grau
- Department of NeurosurgeryHospital FuldaFuldaGermany
| | - Uwe Schröder
- Department of NeurosurgeryMVZ Frankfurt/OderFrankfurtGermany
| | - Karl H. Plate
- Neurological Institute (Edinger Institute)University Hospital FrankfurtFrankfurtGermany
| | - Marco Stein
- Department of NeurosurgeryUniversity Hospital Giessen und Marburg Location GiessenGiessenGermany
| | - Eberhard Uhl
- Department of NeurosurgeryUniversity Hospital Giessen und Marburg Location GiessenGiessenGermany
| | - Till Acker
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Daniel Amsel
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
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3
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Tam OCH, Ho RSL, Chan S, Li KKW, Lam TL, Cheung ETY, Cheung OY, Ho WWS, Cheng KKF, Shing MMK, Ku DTL, Chung BHY, Yang W, Chan GCF, Ng HK, Liu APY. Genome-Wide DNA Methylation Profiling as Frontline Diagnostics for Central Nervous System Embryonal Tumors in Hong Kong. Cancers (Basel) 2023; 15:4880. [PMID: 37835574 PMCID: PMC10571663 DOI: 10.3390/cancers15194880] [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: 09/19/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
This paper examines the link between CNS tumor biology and heterogeneity and the use of genome-wide DNA methylation profiling as a clinical diagnostic platform. CNS tumors are the most common solid tumors in children, and their prognosis remains poor. This study retrospectively analyzed pediatric patients with CNS embryonal tumors in Hong Kong between 1999 and 2017, using data from the territory-wide registry and available formalin-fixed paraffin-embedded tumor tissue. After processing archival tumor tissue via DNA extraction, quantification, and methylation profiling, the data were analyzed by using the web-based DKFZ classifier (Molecular Neuropathology (MNP) 2.0 v11b4) and t-SNE analysis. Methylation profiles were deemed informative in 85 samples. Epigenetic data allowed molecular subgrouping and confirmed diagnosis in 65 samples, verified histologic diagnosis in 8, and suggested an alternative diagnosis in 12. This study demonstrates the potential of DNA methylation profiling in characterizing pediatric CNS embryonal tumors in a large cohort from Hong Kong, which should enable regional and international collaboration in future pediatric neuro-oncology research.
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Affiliation(s)
- Otto C. H. Tam
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (O.C.H.T.)
| | - Ronnie S. L. Ho
- Department of Pathology, Gleneagles Hospital, Wong Chuk Hang, Hong Kong
| | - Shing Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (O.C.H.T.)
| | - Kay K. W. Li
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Tit-Leung Lam
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | | | - Oi-Yee Cheung
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Wilson W. S. Ho
- Department of Neurosurgery, Queen Mary Hospital, Pok Fu Lam, Hong Kong
- Department of Neurosurgery, Hong Kong Children’s Hospital, Kowloon, Hong Kong
| | - Kevin K. F. Cheng
- Department of Neurosurgery, Queen Mary Hospital, Pok Fu Lam, Hong Kong
- Department of Neurosurgery, Hong Kong Children’s Hospital, Kowloon, Hong Kong
| | - Matthew M. K. Shing
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children’s Hospital, Kowloon, Hong Kong
| | - Dennis T. L. Ku
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children’s Hospital, Kowloon, Hong Kong
| | - Brian H. Y. Chung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (O.C.H.T.)
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (O.C.H.T.)
| | - Godfrey C. F. Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (O.C.H.T.)
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children’s Hospital, Kowloon, Hong Kong
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Anthony P. Y. Liu
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong; (O.C.H.T.)
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children’s Hospital, Kowloon, Hong Kong
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Tran QT, Upadhyaya SA, Billups CA, Onar-Thomas A, Alom MZ, Carey SS, Robinson GW, Ellison DW, Gajjar A, Orr BA. DNA-methylation subgroups carry no prognostic significance in ATRT-SHH patients in clinical trial cohorts. Acta Neuropathol 2023; 146:543-545. [PMID: 37522896 PMCID: PMC10412479 DOI: 10.1007/s00401-023-02614-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023]
Affiliation(s)
- Quynh T Tran
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 250, Memphis, TN, 38105, USA
| | - Santhosh A Upadhyaya
- Department of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Catherine A Billups
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Arzu Onar-Thomas
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Md Zahangir Alom
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 250, Memphis, TN, 38105, USA
| | - Steven S Carey
- Department of Hospitalist Medicine, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Giles W Robinson
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 250, Memphis, TN, 38105, USA
| | - Amar Gajjar
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 250, Memphis, TN, 38105, USA.
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Grahn P, Remes T, Kivisaari R, Suo-Palosaari MH, Arikoski PM, Koskenkorva PKT, Lähteenmäki PM, Lönnqvist TRI, Ojaniemi MK, Sirkiä KH, Sutela AK, Toiviainen-Salo SM, Rantala HMJ, Harila AH, Niinimäki J, Karppinen J, Ahonen M. Early disc degeneration in radiotherapy-treated childhood brain tumor survivors. BMC Musculoskelet Disord 2023; 24:441. [PMID: 37259117 DOI: 10.1186/s12891-023-06509-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Childhood brain tumor (BT) survivors have an increased risk of treatment-related late effects, which can reduce health-related quality of life and increase morbidity. This study aimed to investigate lumbar disc degeneration in magnetic resonance imaging (MRI) in adult survivors of radiotherapy-treated childhood BT compared to age and sex-matched population controls. METHODS In this cross-sectional comparative study, 127 survivors were identified from hospital registries. After a mean follow-up of 20.7 years (range 5-33.1), 67 survivors (mean age 28.4, range 16.2-43.5) were investigated with MRI and compared to 75 sex-matched population-based controls. Evaluated MRI phenotypes included Pfirrmann grading, , intervertebral disc protrusions, extrusions, and high-intensity-zone-lesions (HIZ). Groups were also compared for known risk factors of lumbar intervertebral disc (IVD) degeneration. RESULTS Childhood BT survivors had higher Pfirrmann grades than controls at all lumbar levels (all p < 0.001). Lumbar disc protrusions at L4-5 (p = 0.02) and extrusions at L3-4 (p = 0.04), L4-5 (p = 0.004), and L5-S1 (p = 0.01) were significantly more common in the BT group compared to the control. The survivor cohort also had significantly more HIZ-lesons than the controls (n=13 and n=1, p=0.003). Age at diagnosis was associated with lower degree of IVD degeneration (p < 0.01). Blood pressure correlated with IVD degeneration (P < 0.05). CONCLUSIONS Signs of early disc degeneration related to tumor treatment can be seen in the IVDs of survivors. Disc degeneration was more severe in children treated in adolescence.
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Affiliation(s)
- Petra Grahn
- Department of Pediatric Orthopedics and Traumatology, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 9, PL 281, 00029, Helsinki, Finland.
| | - Tiina Remes
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, and Research Unit of Clinical Medicine, University of Oulu, Helsinki, Finland
- Department of Child Neurology, New Children's Hospital, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Reetta Kivisaari
- Department of Radiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maria H Suo-Palosaari
- Department of Diagnostic Radiology, Oulu University Hospital and Research Unit of Medical Imaging, Physics, and Technology Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Pekka M Arikoski
- Kuopio Pediatric Research Unit, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Päivi K T Koskenkorva
- Department of Clinical Radiology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Päivi M Lähteenmäki
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, Turku University, Turku, Finland
| | - Tuula R I Lönnqvist
- Department of Child Neurology, New Children's Hospital, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Marja K Ojaniemi
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, and Research Unit of Clinical Medicine, University of Oulu, Helsinki, Finland
| | - Kirsti H Sirkiä
- Department of Pediatrics and Adolescence, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anna K Sutela
- Department of Clinical Radiology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Heikki M J Rantala
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, and Research Unit of Clinical Medicine, University of Oulu, Helsinki, Finland
| | - Arja H Harila
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Jaakko Niinimäki
- Department of Diagnostic Radiology, Oulu University Hospital and Research Unit of Medical Imaging, Physics, and Technology Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Jaro Karppinen
- Medical Research Center Oulu, Department of Physical and Rehabilitation Medicine, University of Oulu and Oulu University Hospital, Oulu, Finland
- Finnish Institute of Occupational Health, Oulu, Finland
- Rehabilitation Services of South Karelia Social and Health Care District, Lappeenranta, Finland
| | - Matti Ahonen
- Department of Pediatric Orthopedics and Traumatology, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 9, PL 281, 00029, Helsinki, Finland
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Fernández-García P, Malet-Engra G, Torres M, Hanson D, Rosselló CA, Román R, Lladó V, Escribá PV. Evolving Diagnostic and Treatment Strategies for Pediatric CNS Tumors: The Impact of Lipid Metabolism. Biomedicines 2023; 11:biomedicines11051365. [PMID: 37239036 DOI: 10.3390/biomedicines11051365] [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: 03/10/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Pediatric neurological tumors are a heterogeneous group of cancers, many of which carry a poor prognosis and lack a "standard of care" therapy. While they have similar anatomic locations, pediatric neurological tumors harbor specific molecular signatures that distinguish them from adult brain and other neurological cancers. Recent advances through the application of genetics and imaging tools have reshaped the molecular classification and treatment of pediatric neurological tumors, specifically considering the molecular alterations involved. A multidisciplinary effort is ongoing to develop new therapeutic strategies for these tumors, employing innovative and established approaches. Strikingly, there is increasing evidence that lipid metabolism is altered during the development of these types of tumors. Thus, in addition to targeted therapies focusing on classical oncogenes, new treatments are being developed based on a broad spectrum of strategies, ranging from vaccines to viral vectors, and melitherapy. This work reviews the current therapeutic landscape for pediatric brain tumors, considering new emerging treatments and ongoing clinical trials. In addition, the role of lipid metabolism in these neoplasms and its relevance for the development of novel therapies are discussed.
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Affiliation(s)
- Paula Fernández-García
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- Laminar Pharmaceuticals, Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Gema Malet-Engra
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- Laminar Pharmaceuticals, Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Manuel Torres
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Derek Hanson
- Hackensack Meridian Health, 343 Thornall Street, Edison, NJ 08837, USA
| | - Catalina A Rosselló
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- Laminar Pharmaceuticals, Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Ramón Román
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- Laminar Pharmaceuticals, Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Victoria Lladó
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- Laminar Pharmaceuticals, Isaac Newton, 07121 Palma de Mallorca, Spain
| | - Pablo V Escribá
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
- Laminar Pharmaceuticals, Isaac Newton, 07121 Palma de Mallorca, Spain
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7
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Saenz A, Basilotta Y, Dalton EA, Argañaraz R, Mantese B. Giant Supratentorial Brain Tumors in Children: Functional Outcome and Progression-Free Survival Analysis. Pediatr Neurosurg 2023; 58:117-127. [PMID: 37037189 DOI: 10.1159/000530592] [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: 11/29/2022] [Accepted: 03/16/2023] [Indexed: 04/12/2023]
Abstract
INTRODUCTION This study aimed to identify factors affecting progression-free survival (PFS) in pediatric patients with giant supratentorial brain tumors (GSBTs) treated with surgical excision. The secondary aim was to analyze how these same factors affected the functional outcome in the long term. METHODS We performed a retrospective, analytical, single-center cohort study. We included all pediatric patients with GSBT between January 2014 and June 2018. Patients were followed for a minimum of 24 months for the PFS and overall survival (OS) analysis. Functional status score (FSS) was used to assess the functional outcome. RESULTS We included 27 patients with GSBT, the median age was six (range 2-12), and eleven patients had a grade IV tumor. The 24-month PFS and OS were 51.85% and 74.04%, respectively. A PFS-ending event or treatment failure occurred in 13 patients. We found that patients with postoperative FFS >16 have a worse PFS than patients with a postoperative FSS <15 (HR 4.51; p = 0.03). Patients with more than three surgeries had worse PFS than patients with one or two procedures (HR 11.39; p = 0.004). High-grade tumors were associated with worse PFS than low-grade tumors (HR 1.55; p = 0.04). Finally, patients with CNS infections had worse PFS than patients without that complication (HR 2.70; p = 0.04). CONCLUSIONS GSBTs in pediatric patients are complex lesions that require multidisciplinary management. Surgical management and quality of life should be considered when choosing the best treatment. Factors influencing long-term PFS were high-grade histopathology, the need for three or more surgeries, postoperative FSS >16, and CNS infections.
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Affiliation(s)
- Amparo Saenz
- Pediatric Neurosurgery Department, Pediatric Hospital Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Yamila Basilotta
- Pediatric Neurosurgery Department, Pediatric Hospital Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Emma A Dalton
- Neurosurgery Department, The National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Romina Argañaraz
- Pediatric Neurosurgery Department, Pediatric Hospital Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Beatriz Mantese
- Pediatric Neurosurgery Department, Pediatric Hospital Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
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8
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Parisi R, Patel RR, Rood G, Bowden A, Turco G, Korones DN, Andolina JR, Comito M, Barth M, Weintraub L. Multi-institution analysis of tumor mutational burden and outcomes in pediatric central nervous system tumor patients. Pediatr Blood Cancer 2023; 70:e30139. [PMID: 36573296 DOI: 10.1002/pbc.30139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Pediatric central nervous system (CNS) tumors are the leading cause of pediatric cancer mortality. Research addressing genomic biomarkers and clinical outcomes is needed to inform therapeutic decision-making. METHODS We conducted a retrospective analysis of pediatric patients (age <21) diagnosed with a primary CNS tumor at four upstate New York hospitals from 2008 to 2021. Clinical and histopathologic data were identified from each patient, including genomic analysis of somatic mutations and tumor mutational burden (TMB) where available. These variables were each compared with overall survival using Cox regression analyses. Multivariable analysis was conducted to identify patient characteristics that may independently predict survival. RESULTS We identified 119 patients. Common tumor types included low-grade glioma (N = 51), high-grade glioma (N = 29), and medulloblastoma (N = 11). Common driver mutations included TP53 inactivation (N = 16), BRAF-KIAA1549 fusion (N = 16), FGFR1 amplification (N = 12), BRAF V600E mutation (N = 12), NF1 loss (N = 12), and H3F3A K28M mutation (N = 6). Median TMB was one mutation/megabase (mut/Mb, range = 0-132). Overall survival was 79.9%. Variables associated with poorer survival on univariable analysis were higher TMB (p = .002, HR 4.97), high-grade tumors (p = .009, HR 84.3), and high-grade glioma histology (p = .021, HR 3.14). Multivariable analyses further identified TMB (p = .011, HR 4.46) and high-grade histology (p = .015, HR 5.28) as independently predictive of worse survival. Tumor progression was more common in high-TMB (N = 15, 44%) than in low-TMB tumors (N = 19, 35%). CONCLUSIONS High TMB is correlated with higher rates of progression and death as compared to low-TMB tumors. These findings may help identify patients who may benefit from alternative treatments, such as immunotherapies.
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Affiliation(s)
- Rose Parisi
- Albany Medical College, Albany, New York, USA
| | - Roshal R Patel
- Albany Medical College, Albany, New York, USA.,Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gavrielle Rood
- Upstate Medical University College of Medicine, Syracuse, New York, USA
| | - Acacia Bowden
- University of Rochester School of Medicine, Rochester, New York, USA
| | - George Turco
- Pediatric Hematology/Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - David N Korones
- Pediatric Hematology/Oncology, University of Rochester Medical Center, Rochester, New York, USA
| | - Jeffrey R Andolina
- Pediatric Hematology/Oncology, University of Rochester Medical Center, Rochester, New York, USA
| | - Melanie Comito
- Pediatric Hematology/Oncology, Upstate University Hospital, Syracuse, New York, USA
| | - Matthew Barth
- Pediatric Hematology/Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Lauren Weintraub
- Pediatric Hematology/Oncology, Albany Medical Center, Albany, New York, USA
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9
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O’Donohue T, Sait SF, Bender JG. Progress in precision therapy in pediatric oncology. Curr Opin Pediatr 2023; 35:41-47. [PMID: 36377257 PMCID: PMC9812924 DOI: 10.1097/mop.0000000000001198] [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] [Indexed: 11/17/2022]
Abstract
PURPOSE OF REVIEW The fields of precision medicine and cancer genomics in pediatric oncology are rapidly evolving. Novel diagnostic tools are critical in refining cancer diagnoses, stratifying patient risk, and informing treatment decisions. This review is timely and relevant as it discusses advantages and drawbacks of common molecular profiling techniques and highlights novel platforms, which may address select limitations. We discuss recent publications demonstrating utility of large-scale molecular profiling and feasibility and logistics of matching targeted therapies to patients. RECENT FINDINGS We describe the increased accessibility of next-generation sequencing, complementary profiling methods, and strategies to guide treatment decisions. We describe curation and sharing of large genomic datasets and novel mechanisms to obtain matched targeted therapies. Importantly, we discuss relevant publications in distinct disease domains that support indications for evidence-based precision therapy. Lastly, we introduce the incremental analyses that can be obtained via whole-genome and transcriptome sequencing. SUMMARY Here we highlight high-yield clinical scenarios of precision medicine approaches and identify the ongoing challenges including universally defining clinical actionability, optimizing trial design to account for molecular heterogeneity while acknowledging limitations in patient accrual, expanding access to molecularly targeted therapies, and validating new tools and technology to aid in precision medicine therapeutic approaches.
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Affiliation(s)
- Tara O’Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sameer Farouk Sait
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Julia Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
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10
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The spectrum of morphological findings in pediatric central nervous system MN1-fusion-positive neuroepithelial tumors. Childs Nerv Syst 2023; 39:379-386. [PMID: 36534132 DOI: 10.1007/s00381-022-05741-y] [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: 01/26/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022]
Abstract
PURPOSE Central nervous system high-grade neuroepithelial tumor with MN1 alteration (CNS-HGNET-MN1) is a rare entity defined by its DNA methylation pattern and pathologically considered to be high-grade with mixed patterns, stromal hyalinization, and with astrocytic differentiation. Our aim was to present six pediatric cases to contribute to the characterization of this group of tumors. MATERIAL AND METHODS Six female patients aged 4 to 12 years with CNS tumors with MN1 alteration identified using genome-wide methylation arrays and/or RT-PCR were included. Clinicopathological, morphological, immunohistochemical, and molecular findings were analyzed. RESULTS Tumor location was the parietal lobe in four and the intramedullary spinal cord in two. Two were morphologically diagnosed as ependymomas, one as gliofibroma, one as a HGNET-MN1 altered and the other two were difficult to classify. All were well-defined tumors, with a cystic component in three. Only two tumors had extensive stromal hyalinization, three had pseudopapillary formations, and four had other patterns. Multinucleated, clear, and rhabdoid cells were present. Necrosis and histiocyte clusters were also observed. Proliferative index was >10 in four. GFAP, EMA, CK, and SYN were variable, while Olig2 staining was mostly positive. Four of six patients with supratentorial tumors and complete resections were alive and tumor free after 2 to 10 years of follow-up. The two cases with medullary involvement and incomplete resections were alive and undergoing treatment 2 years after surgery. CONCLUSION Neuroepithelial-MN1 tumors are challenging and suspicion requires molecular confirmation. Our pediatric data contribute to the knowledge for accurate diagnosis. Although further studies with a larger number of cases should be conducted in order to draw more robust conclusions regarding clinico-pathological features, here we present valuable pediatric data to increase the knowledge that may lead to the accurate management of this group of tumors.
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11
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Alom Z, Tran QT, Bag AK, Lucas JT, Orr BA. Predicting methylation class from diffusely infiltrating adult gliomas using multimodality MRI data. Neurooncol Adv 2023; 5:vdad045. [PMID: 37215955 PMCID: PMC10195196 DOI: 10.1093/noajnl/vdad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Background Radiogenomic studies of adult-type diffuse gliomas have used magnetic resonance imaging (MRI) data to infer tumor attributes, including abnormalities such as IDH-mutation status and 1p19q deletion. This approach is effective but does not generalize to tumor types that lack highly recurrent alterations. Tumors have intrinsic DNA methylation patterns and can be grouped into stable methylation classes even when lacking recurrent mutations or copy number changes. The purpose of this study was to prove the principle that a tumor's DNA-methylation class could be used as a predictive feature for radiogenomic modeling. Methods Using a custom DNA methylation-based classification model, molecular classes were assigned to diffuse gliomas in The Cancer Genome Atlas (TCGA) dataset. We then constructed and validated machine learning models to predict a tumor's methylation family or subclass from matched multisequence MRI data using either extracted radiomic features or directly from MRI images. Results For models using extracted radiomic features, we demonstrated top accuracies above 90% for predicting IDH-glioma and GBM-IDHwt methylation families, IDH-mutant tumor methylation subclasses, or GBM-IDHwt molecular subclasses. Classification models utilizing MRI images directly demonstrated average accuracies of 80.6% for predicting methylation families, compared to 87.2% and 89.0% for differentiating IDH-mutated astrocytomas from oligodendrogliomas and glioblastoma molecular subclasses, respectively. Conclusions These findings demonstrate that MRI-based machine learning models can effectively predict the methylation class of brain tumors. Given appropriate datasets, this approach could generalize to most brain tumor types, expanding the number and types of tumors that could be used to develop radiomic or radiogenomic models.
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Affiliation(s)
- Zahangir Alom
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Quynh T Tran
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Asim K Bag
- Department of Diagnostic Imaging, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - John T Lucas
- Department of Radiation Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Brent A Orr
- Corresponding Author: Brent A. Orr MD, PhD, Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS 250, Memphis, TN 38-105-3678, USA ()
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12
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Smith HL, Wadhwani N, Horbinski C. Major Features of the 2021 WHO Classification of CNS Tumors. Neurotherapeutics 2022; 19:1691-1704. [PMID: 35578106 PMCID: PMC9723092 DOI: 10.1007/s13311-022-01249-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
Advances in the understanding of the molecular biology of central nervous system (CNS) tumors prompted a new World Health Organization (WHO) classification scheme in 2021, only 5 years after the prior iteration. The 2016 version was the first to include specific molecular alterations in the diagnoses of a few tumors, but the 2021 system greatly expanded this approach, with over 40 tumor types and subtypes now being defined by their key molecular features. Many tumors have also been reconceptualized into new "supercategories," including adult-type diffuse gliomas, pediatric-type diffuse low- and high-grade gliomas, and circumscribed astrocytic gliomas. Some entirely new tumors are in this scheme, particularly pediatric tumors. Naturally, these changes will impact how CNS tumor patients are diagnosed and treated, including clinical trial enrollment. This review addresses the most clinically relevant changes in the 2021 WHO book, including diffuse and circumscribed gliomas, ependymomas, embryonal tumors, and meningiomas.
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Affiliation(s)
- Heather L Smith
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Nitin Wadhwani
- Department of Pathology, Lurie Children's Hospital, Chicago, IL, USA
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Feinberg School of Medicine, Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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13
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Zhou S, Li M, Ostrow D, Ruble D, Mascarenhas L, Pawel B, Buckley JD, Triche TJ. Potential methylation-regulated genes and pathways in hepatocellular neoplasm, not otherwise specified. Front Oncol 2022; 12:952325. [PMID: 36212481 PMCID: PMC9532972 DOI: 10.3389/fonc.2022.952325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background and Aims The molecular basis of hepatocellular neoplasm, not otherwise specified (HCN-NOS) is unknown. We aimed to identify gene expression patterns, potential methylation-regulated genes and pathways that characterize the tumor, and its possible relationship to hepatoblastoma and hepatocellular carcinoma (HCC). Approach & Results Parallel genome-wide profiling of gene expression (RNAseq) and DNA methylation (EPIC850) was performed on 4 pairs of pre-treatment HCN-NOS tumors and adjacent non-tumor controls. 2530 significantly differentially expressed genes (DEGs) were identified between tumors and controls. Many of these DEGs were associated with hepatoblastoma and/or HCC. Analysis Match in Ingenuity Pathway Analysis determined that the gene expression profile of HCN-NOS was unique but significantly similar to that of both hepatoblastoma and HCC. A total of 27,195 CpG sites (CpGs) were significantly differentially methylated (DM) between tumors and controls, with a global hypomethylation pattern and predominant CpG island hypermethylation in promotor regions. Aberrant DNA methylation predominated in Developmental Process and Molecular Function Regulator pathways. Embryonic stem cell pathways were significantly enriched. In total, 1055 aberrantly methylated (at CpGs) and differentially expressed genes were identified, including 25 upstream regulators and sixty-one potential CpG island methylation-regulated genes. Eight methylation-regulated genes (TCF3, MYBL2, SRC, HMGA2, PPARGC1A, SLC22A1, COL2A1 and MYCN) had highly consistent gene expression patterns and prognostic value in patients with HCC, based on comparison to publicly available datasets. Conclusions HCN-NOS has a unique, stem-cell like gene expression and DNA methylation profile related to both hepatoblastoma and HCC but distinct therefrom. Further, 8 methylation-regulated genes associated with prognosis in HCC were identified.
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Affiliation(s)
- Shengmei Zhou
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- *Correspondence: Shengmei Zhou,
| | - Meng Li
- USC Libraries Bioinformatics Services, University of Southern California, Los Angeles, CA, United States
| | - Dejerianne Ostrow
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - David Ruble
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Leo Mascarenhas
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Cancer and Blood Disease Institute, Division of Hematology/Oncology, Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Bruce Pawel
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jonathan David Buckley
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Timothy J. Triche
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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14
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Utility of Targeted Next-Generation Sequencing Assay to Detect 1p/19q Co-Deletion in Formalin-fixed Paraffin-embedded Glioma Specimens. Hum Pathol 2022; 126:63-76. [PMID: 35561840 DOI: 10.1016/j.humpath.2022.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Molecular classification of brain neoplasms is important for diagnosis, prognosis, and treatment outcome of histologically similar tumors. Oligodendroglioma is a glioma subtype characterized by 1p/19q co-deletion and IDH1/IDH2 mutations, which predicts a good prognosis, responsiveness to therapy and an improved overall survival compared to other adult gliomas. In a routine clinical setting, 1p/19q co-deletion is detected by interphase-FISH and SNP microarray, and somatic mutations are detected by targeted next generation sequencing (NGS). The aim of this proof-of-principle study was to investigate the feasibility of using targeted NGS to simultaneously detect both 1p/19q co-deletion and somatic mutations. Among two hundred forty-seven consecutive patients with formalin-fixed paraffin-embedded brain tumors with various subtypes, NGS revealed 1p/19q co-deletion in twenty-six oligodendrogliomas and an IDH-wildtype astrocytoma, and partial loss across chromosomes 1p and 19q/whole-arm loss of 1p or 19q/copy neutral loss of heterozygosity in eleven non-oligodendrogliomas. For this 247 brain-tumor cohort, the overall sensitivity, specificity, and accuracy of detecting 1p/19q co-deletion by NGS in oligodendrogliomas were 96.2%, 99.6%, and 99.2%, respectively. The oligodendroglioma cohort had more mutations in IDH1/IDH2, CIC, FUBP1, and TERT, and fewer mutations in ATRX and TP53 than the non-oligodendroglioma cohort. This proof-of-concept study demonstrated that targeted NGS can simultaneously detect both 1p/19q co-deletion and somatic mutations, which can provide a more comprehensive genetic profiling for patients with gliomas using a single assay in a clinical setting.
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15
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Lutz K, Jünger ST, Messing-Jünger M. Essential Management of Pediatric Brain Tumors. CHILDREN 2022; 9:children9040498. [PMID: 35455542 PMCID: PMC9031600 DOI: 10.3390/children9040498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 02/02/2023]
Abstract
Brain tumors are the most common solid tumors in children and are associated with high mortality. The most common childhood brain tumors are grouped as low-grade gliomas (LGG), high grade gliomas (HGG), ependymomas, and embryonal tumors, according to the World Health Organization (WHO). Advances in molecular genetics have led to a shift from pure histopathological diagnosis to integrated diagnosis. For the first time, these new criteria were included in the WHO classification published in 2016 and has been further updated in the 2021 edition. Integrated diagnosis is based on molecular genomic similarities of the tumor subclasses, and it can better explain the differences in clinical courses of previously histopathologically identical entities. Important advances have also been made in pediatric neuro-oncology. A growing understanding of the molecular-genetic background of tumorigenesis has improved the diagnostic accuracy. Re-stratification of treatment protocols and the development of targeted therapies will significantly affect overall survival and quality of life. For some pediatric tumors, these advances have significantly improved therapeutic management and prognosis in certain tumor subgroups. Some therapeutic approaches also have serious long-term consequences. Therefore, optimized treatments are greatly needed. Here, we discuss the importance of multidisciplinary collaboration and the role of (pediatric) neurosurgery by briefly describing the most common childhood brain tumors and their currently recognized molecular subgroups.
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Affiliation(s)
- Katharina Lutz
- Neurosurgery Department, Inselspital, 3010 Bern, Switzerland
- Pediatric Neurosurgery, Asklepios Children’s Hospital, 53757 Sankt Augustin, Germany;
- Correspondence:
| | - Stephanie T. Jünger
- Center for Neurosurgery, Department of General Neurosurgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany;
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16
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Shi ZF, Li KKW, Huang QJQ, Wang WW, Kwan JSH, Chen H, Liu XZ, Li WC, Chan DTM, Zhang ZY, Mao Y, Ng HK. Molecular landscape of IDH-wildtype, H3-wildtype glioblastomas of adolescents and young adults (AYA). Neuropathol Appl Neurobiol 2022; 48:e12802. [PMID: 35191072 DOI: 10.1111/nan.12802] [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: 02/26/2021] [Revised: 01/17/2022] [Accepted: 02/05/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE We aimed to characterise glioblastomas of adolescents and young adults (AYA) that were IDH wildtype (wt) and H3 wildtype (wt). MATERIALS AND METHODS Fifty such patients (aged 16-32) were studied by methylation profiling, targeted sequencing and targeted RNA-seq. RESULTS Tumours predominantly clustered into three methylation classes according to the terminology of Capper et al. (2018): (anaplastic) PXA (21 cases), GBM_midline (15 cases) and glioblastoma RTK/mesenchymal (7 cases). Two cases clustered with ANA_PA, 4 cases with LGG classes and 1 with GBM_MYCN. Only fifteen cases reached a calibrated score >0.84 when the cases were uploaded to DKFZ Classifier. GBM_midline-clustered tumours had a poorer overall survival (OS) compared to the PXA-clustered tumours (p=0.030). LGG-clustered cases had a significantly better survival than GBM_midline-clustered tumours and glioblastoma RTK/mesenchymal-clustered tumours. Only 13/21 (62%) of PXA-clustered cases were BRAF V600E mutated. Most GBM_midline-clustered cases were not located in the midline. GBM_midline-clustered cases were characterized by PDGFRA amplification/mutation (73.3%), mutations of mismatch repair genes (40.0%), and all showed H3K27me3 and EZH1P loss, and an unmethylated MGMT promoter. Across the whole cohort, MGMT promoter methylation and wildtype TERT promoter were favourable prognosticators. Mismatch repair gene mutations were poor prognosticators and together with methylation class and MGMT methylation, maintained their significance in multi-variate analyses. BRAF mutation was a good prognosticator in the PXA-clustered tumours. CONCLUSION Methylation profiling is a useful tool in the diagnosis and prognostication of AYA glioblastomas and the methylation classes have distinct molecular characteristics. The usual molecular diagnostic criteria for adult IDHwt glioblastoma should be applied with caution within the AYA age group.
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Affiliation(s)
- Zhi-Feng Shi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Hong Kong and Shanghai Brain Consortium (HSBC)
| | - Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Shatin, Hong Kong, China.,Hong Kong and Shanghai Brain Consortium (HSBC)
| | - Queenie Jun-Qi Huang
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Wei-Wei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Johnny Sheung-Him Kwan
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiang-Zhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wen-Cai Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Danny Tat-Ming Chan
- Division of Neurosurgery, Department of Surgery, Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Zhen-Yu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Shatin, Hong Kong, China.,Hong Kong and Shanghai Brain Consortium (HSBC)
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17
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Liu APY, Northcott PA, Robinson GW, Gajjar A. Circulating tumor DNA profiling for childhood brain tumors: Technical challenges and evidence for utility. J Transl Med 2022; 102:134-142. [PMID: 34934181 DOI: 10.1038/s41374-021-00719-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 11/09/2022] Open
Abstract
Cell-free DNA (cfDNA) profiling as liquid biopsy has proven value in adult-onset malignancies, serving as a patient-specific surrogate for residual disease and providing a non-invasive tool for serial interrogation of tumor genomics. However, its application in neoplasms of the central nervous system (CNS) has not been as extensively studied. Unique considerations and methodological challenges exist, which need to be addressed before cfDNA studies can be incorporated as a clinical assay for primary CNS diseases. Here, we review the current status of applying cfDNA analysis in patients with CNS tumors, with special attention to diagnosis in pediatric patients. Technical concerns, evidence for utility, and potential developments are discussed.
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Affiliation(s)
- Anthony Pak-Yin Liu
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong, SAR, China.
| | - Paul A Northcott
- Division of Brain Tumor Research, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Giles W Robinson
- Division of Neuro-Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Amar Gajjar
- Division of Neuro-Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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18
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Cole BL. Neuropathology of Pediatric Brain Tumors: A Concise Review. Neurosurgery 2022; 90:7-15. [PMID: 34114043 DOI: 10.1093/neuros/nyab182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/31/2021] [Indexed: 01/07/2023] Open
Abstract
Pediatric brain tumors are an incredibly diverse group of neoplasms and neuropathological tumor classification is an essential part of patient care. Classification of pediatric brain tumors has changed considerably in recent years as molecular diagnostics have become incorporated with routine histopathology in the diagnostic process. This article will focus on the fundamental major histologic, immunohistochemical, and molecular features that neuropathologists use to make an integrated diagnosis of pediatric brain tumors. This concise review will focus on tumors that are integral to the central nervous system in pediatric patients including: embryonal tumors, low and high grade gliomas, glioneuronal tumors, ependymomas, and choroid plexus tumors.
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Affiliation(s)
- Bonnie L Cole
- Department of Laboratories, Seattle Children's Hospital , Seattle , Washington , USA.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine , Seattle , Washington , USA
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19
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Hill RM, Plasschaert SLA, Timmermann B, Dufour C, Aquilina K, Avula S, Donovan L, Lequin M, Pietsch T, Thomale U, Tippelt S, Wesseling P, Rutkowski S, Clifford SC, Pfister SM, Bailey S, Fleischhack G. Relapsed Medulloblastoma in Pre-Irradiated Patients: Current Practice for Diagnostics and Treatment. Cancers (Basel) 2021; 14:126. [PMID: 35008290 PMCID: PMC8750207 DOI: 10.3390/cancers14010126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 02/07/2023] Open
Abstract
Relapsed medulloblastoma (rMB) accounts for a considerable, and disproportionate amount of childhood cancer deaths. Recent advances have gone someway to characterising disease biology at relapse including second malignancies that often cannot be distinguished from relapse on imaging alone. Furthermore, there are now multiple international early-phase trials exploring drug-target matches across a range of high-risk/relapsed paediatric tumours. Despite these advances, treatment at relapse in pre-irradiated patients is typically non-curative and focuses on providing life-prolonging and symptom-modifying care that is tailored to the needs and wishes of the individual and their family. Here, we describe the current understanding of prognostic factors at disease relapse such as principal molecular group, adverse molecular biology, and timing of relapse. We provide an overview of the clinical diagnostic process including signs and symptoms, staging investigations, and molecular pathology, followed by a summary of treatment modalities and considerations. Finally, we summarise future directions to progress understanding of treatment resistance and the biological mechanisms underpinning early therapy-refractory and relapsed disease. These initiatives include development of comprehensive and collaborative molecular profiling approaches at relapse, liquid biopsies such as cerebrospinal fluid (CSF) as a biomarker of minimal residual disease (MRD), modelling strategies, and the use of primary tumour material for real-time drug screening approaches.
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Affiliation(s)
- Rebecca M. Hill
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne NE1 7RU, UK; (S.C.C.); (S.B.)
| | - Sabine L. A. Plasschaert
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (S.L.A.P.); (M.L.); (P.W.)
| | - Beate Timmermann
- Department of Particle Therapy, West German Proton Therapy Centre Essen (WPE), West German Cancer Center (WTZ), University Hospital Essen, 45147 Essen, Germany;
| | - Christelle Dufour
- Department of Pediatric and Adolescent Oncology, Gustave Roussy, 94800 Villejuif, France;
| | - Kristian Aquilina
- Department of Neurosurgery, Great Ormond Street Hospital, London WC1N 3JH, UK;
| | - Shivaram Avula
- Department of Radiology, Alder Hey Children’s NHS Foundation Trust, Liverpool L12 2AP, UK;
| | - Laura Donovan
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK;
| | - Maarten Lequin
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (S.L.A.P.); (M.L.); (P.W.)
| | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, 53127 Bonn, Germany;
| | - Ulrich Thomale
- Department of Neurosurgery, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany;
| | - Stephan Tippelt
- Department of Pediatrics III, Center for Translational Neuro- and Behavioral Sciences (CTNBS), University Hospital of Essen, 45147 Essen, Germany;
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (S.L.A.P.); (M.L.); (P.W.)
- Department of Pathology, Amsterdam University Medical Centers/VUmc, 1081 HV Amsterdam, The Netherlands
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Steven C. Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne NE1 7RU, UK; (S.C.C.); (S.B.)
| | - Stefan M. Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany;
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Pediatric Oncology and Hematology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne NE1 7RU, UK; (S.C.C.); (S.B.)
| | - Gudrun Fleischhack
- Department of Pediatrics III, Center for Translational Neuro- and Behavioral Sciences (CTNBS), University Hospital of Essen, 45147 Essen, Germany;
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20
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Enayet A. Brain tumors in the first two years of life. EGYPTIAN JOURNAL OF NEUROSURGERY 2021. [DOI: 10.1186/s41984-021-00130-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Brain tumors in the first years of life are frequently encountered recently with the advancement in neuroimaging, neurosurgery and neuroanethesia where early diagnosis of these lesions became available even before birth. Their management is challenging where the surgery is technically demanding, radiotherapy is omitted in this age because of its late sequelae and chemotherapy role may be beneficial, but it is limited also by its side effects and neurotoxicity. The aim of this article is to review the current literature about the brain tumors in the first two years of life, their diagnosis and treatment.
Main body
Brain tumors in the first two years of life encompass mainly fetal/congenital tumors and infantile tumors. They account for 1.4–18% of cases of pediatric brain tumor, and most of them are diagnosed in the first year of life. The main histopathologies diagnosed are glial tumors, choroid plexus tumors, medulloblastoma and other embryonal tumors, teratoma and ependymoma. They are mainly supratentorial. Large head and bulging fontanelles are the main presenting symptoms and signs secondary to increased intracranial pressure secondary to large tumors or associated hydrocephalus. Prenatal and postnatal ultrasonography represents the initial imaging step in the diagnosis that should be complemented by MRI and CT brain. The main and first line of treatment of infantile brain tumors is surgical excision as the prognosis is directly related to the extent of resection besides surgery offers specimens for histopathological diagnosis and adjuvant chemotherapy is given for residual irresectable cases and malignant tumors with the main aim to delay radiotherapy beyond the age of three years.
Conclusion
Brain tumors in the first two years of life are a challenging group of different histopathological entities with underlying specific molecular characterization and genetic predispositions. They have aggressive behavior and general poor prognosis with limited options of management. Individualized multidisciplinary management for each case is needed, and future studies for therapeutic medications targeting underlying molecular biology may improve their outcome.
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21
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Yang J, Wang J, Tian S, Wang Q, Zhao Y, Wang B, Cao L, Liang Z, Zhao H, Lian H, Ma J. An Integrated Analysis of Tumor Purity of Common Central Nervous System Tumors in Children Based on Machine Learning Methods. Front Genet 2021; 12:707802. [PMID: 34925437 PMCID: PMC8678112 DOI: 10.3389/fgene.2021.707802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/10/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Tumor purity is defined as the proportion of cancer cells in the tumor tissue, and its effects on molecular genetics, the immune microenvironment, and the prognosis of children’s central nervous system (CNS) tumors are under-researched. Methods: We applied random forest machine learning, the InfiniumPurify algorithm, and the ESTIMATE algorithm to estimate the tumor purity of every child’s CNS tumor sample in several published pediatric CNS tumor sample datasets from Gene Expression Omnibus (GEO), aiming to perform an integrated analysis on the tumor purity of children’s CNS tumors. Results: Only the purity of CNS tumors in children based on the random forest (RF) machine learning method was normally distributed. In addition, the children’s CNS tumor purity was associated with primary clinical pathological and molecular indicators. Enrichment analysis of biological pathways related to the purity of medulloblastoma (MB) revealed some classical signaling pathways associated with MB biology and development-related pathways. According to the correlation analysis between MB purity and the immune microenvironment, three immune-related genes, namely, CD8A, CXCR2, and TNFRSF14, were negatively related to MB purity. In contrast, no significant correlation was detected between immunotherapy-associated markers, such as PD-1, PD-L1, and CTLA4; most infiltrating immune cells; and MB purity. In the tumor purity–related survival analysis of MB, ependymoma (EPN), and children’s high-grade glioma, we discovered a minor effect of tumor purity on the survival of the aforementioned pediatric patients with CNS tumors. Conclusion: Our purity pediatric pan-CNS tumor analysis provides a deeper understanding and helps with the clinical management of pediatric CNS tumors.
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Affiliation(s)
- Jian Yang
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiajia Wang
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuaiwei Tian
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qinhua Wang
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Zhao
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baocheng Wang
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liangliang Cao
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhuangzhuang Liang
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Heng Zhao
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Lian
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Ma
- Department of Pediatric Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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22
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Chen S, Deng X, Sheng H, Rong Y, Zheng Y, Zhang Y, Lin J. Noncoding RNAs in pediatric brain tumors: Molecular functions and pathological implications. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:417-431. [PMID: 34552822 PMCID: PMC8426460 DOI: 10.1016/j.omtn.2021.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Brain tumors are common solid pediatric malignancies and the main reason for cancer-related death in the pediatric setting. Recently, evidence has revealed that noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), play a critical role in brain tumor development and progression. Therefore, in this review article, we describe the functions and molecular mechanisms of ncRNAs in multiple types of cancer, including medulloblastoma, pilocytic astrocytoma, ependymoma, atypical teratoid/rhabdoid tumor, glioblastoma, diffuse intrinsic pontine glioma, and craniopharyngioma. We also mention the limitations of using ncRNAs as therapeutic targets because of the nonspecificity of ncRNA targets and the delivery methods of ncRNAs. Due to the critical role of ncRNAs in brain oncogenesis, targeting aberrantly expressed ncRNAs might be an effective strategy to improve the outcomes of pediatric patients with brain tumors.
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Affiliation(s)
- Shaohuai Chen
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Deng
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hansong Sheng
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuxi Rong
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanhao Zheng
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yusong Zhang
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jian Lin
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
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23
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Dandapath I, Chakraborty R, Kaur K, Mahajan S, Singh J, Sharma MC, Sarkar C, Suri V. Molecular alterations of low-grade gliomas in young patients: Strategies and platforms for routine evaluation. Neurooncol Pract 2021; 8:652-661. [PMID: 34777834 PMCID: PMC8579091 DOI: 10.1093/nop/npab053] [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: 11/12/2022] Open
Abstract
In recent years, it has been established that molecular biology of pediatric low-grade gliomas (PLGGs) is entirely distinct from adults. The majority of the circumscribed pediatric gliomas are driven by mitogen-activated protein kinase (MAPK) pathway, which has yielded important diagnostic, prognostic, and therapeutic biomarkers. Further, the Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT) Steering Committee in their fourth meeting, suggested including a panel of molecular markers for integrated diagnosis in "pediatric-type" diffuse gliomas. However, a designated set of platforms for the evaluation of these alterations has yet not been mentioned for easier implementation in routine molecular diagnostics. Herein, we have reviewed the relevance of analyzing these markers and discussed the strategies and platforms best apposite for clinical laboratories.
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Affiliation(s)
- Iman Dandapath
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Kavneet Kaur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Swati Mahajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Jyotsna Singh
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar C Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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24
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Helligsoe ASL, Kenborg L, Henriksen LT, Udupi A, Hasle H, Winther JF. Incidence and survival of childhood central nervous system tumors in Denmark, 1997-2019. Cancer Med 2021; 11:245-256. [PMID: 34800006 PMCID: PMC8704152 DOI: 10.1002/cam4.4429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/01/2021] [Accepted: 11/04/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Incidence rates in Denmark of central nervous system (CNS) tumors remain among the highest in the world. Survival rates, however, have improved in the past decades in high-income countries. METHODS We analyzed incidence and survival of childhood CNS tumors in Denmark diagnosed from 1997 to 2019 based on data from the Danish Childhood Cancer Registry and information on histological types, tumor localization, and treatment from medical records. RESULTS From 1997 to 2019, 949 children<15 years were diagnosed with a CNS tumor. Age-standardized incidence was 42.1 (95% CI, 39.4-44.6) per million person-years and stable during this period. Age-specific incidence for children aged 0-4 years was 47.7 per million. More than one-third (n = 374, 39.4%) were treated with surgery alone. Overall survival rates 5 and 10 years after diagnosis were 77.6% (95% CI, 74.7-80.2) and 74.7% (95% CI, 71.7-77.5). Five-year overall survival improved from 73.0% (95% CI, 68.9-76.7) in 1997-2008 to 83.2% (95% CI, 79.2-86.4) in 2009-2019 (p-value < 0.0001) in children aged 0-4 years (p = 0.0006). CONCLUSION Incidence rates are stable but remain among the highest in the world. Despite improved survival rates in recent years in younger children, some subtypes still have a poor prognosis.
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Affiliation(s)
- Anne Sophie Lind Helligsoe
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Line Kenborg
- Childhood Cancer Research Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Louise Tram Henriksen
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Aparna Udupi
- Biostatistical Advisory Service (BIAS), Faculty of Health, Aarhus University, Denmark
| | - Henrik Hasle
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jeanette Falck Winther
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark.,Childhood Cancer Research Group, Danish Cancer Society Research Center, Copenhagen, Denmark
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25
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Ak M, Toll SA, Hein KZ, Colen RR, Khatua S. Evolving Role and Translation of Radiomics and Radiogenomics in Adult and Pediatric Neuro-Oncology. AJNR Am J Neuroradiol 2021; 43:792-801. [PMID: 34649914 DOI: 10.3174/ajnr.a7297] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022]
Abstract
Exponential technologic advancements in imaging, high-performance computing, and artificial intelligence, in addition to increasing access to vast amounts of diverse data, have revolutionized the role of imaging in medicine. Radiomics is defined as a high-throughput feature-extraction method that unlocks microscale quantitative data hidden within standard-of-care medical imaging. Radiogenomics is defined as the linkage between imaging and genomics information. Multiple radiomics and radiogenomics studies performed on conventional and advanced neuro-oncology image modalities show that they have the potential to differentiate pseudoprogression from true progression, classify tumor subgroups, and predict recurrence, survival, and mutation status with high accuracy. In this article, we outline the technical steps involved in radiomics and radiogenomics analyses with the use of artificial intelligence methods and review current applications in adult and pediatric neuro-oncology.
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Affiliation(s)
- M Ak
- From the Department of Radiology (M.A., R.R.C.), University of Pittsburgh, Pittsburgh, Pennsylvania.,Hillman Cancer Center (M.A., R.R.C.), University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - S A Toll
- Department of Hematology-Oncology (S.A.T.), Children's Hospital of Michigan, Detroit, Michigan
| | - K Z Hein
- Department of Leukemia (K.Z.H.), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - R R Colen
- From the Department of Radiology (M.A., R.R.C.), University of Pittsburgh, Pittsburgh, Pennsylvania.,Hillman Cancer Center (M.A., R.R.C.), University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - S Khatua
- Department of Pediatric Hematology-Oncology (S.K.), Mayo Clinic, Rochester, Minnesota.
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26
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Lebrun L, Bizet M, Melendez B, Alexiou B, Absil L, Van Campenhout C, D'Haene N, Rorive S, Fuks F, Decaestecker C, Salmon I. Analyses of DNA Methylation Profiling in the Diagnosis of Intramedullary Astrocytomas. J Neuropathol Exp Neurol 2021; 80:663-673. [PMID: 34363673 PMCID: PMC8357340 DOI: 10.1093/jnen/nlab052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Intramedullary astrocytomas (IMAs) consist of a heterogeneous group of rare central nervous system (CNS) tumors associated with variable outcomes. A DNA methylation-based classification approach has recently emerged as a powerful tool to further classify CNS tumors. However, no DNA methylation-related studies specifically addressing to IMAs have been performed yet. In the present study, we analyzed 16 IMA samples subjected to morphological and molecular analyses, including DNA methylation profiling. Among the 16 samples, only 3 cases were classified in a reference methylation class (MC) with the recommended calibrated score (≥0.9). The remaining cases were either considered “no-match” cases (calibrated score <0.3, n = 7) or were classified with low calibrated scores (ranging from 0.32 to 0.53, n = 6), including inconsistent classification. To obtain a more comprehensive tool for pathologists, we used different unsupervised analyses of DNA methylation profiles, including our data and those from the Heidelberg reference cohort. Even though our cohort included only 16 cases, hypotheses regarding IMA-specific classification were underlined; a potential specific MC of PA_SPINE was identified and high-grade IMAs, probably consisting of H3K27M wild-type IMAs, were mainly associated with ANA_PA MC. These hypotheses strongly suggest that a specific classification for IMAs has to be investigated.
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Affiliation(s)
- Laetitia Lebrun
- From the Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Barbara Melendez
- Molecular Pathology Research Unit, Department of Pathology, Virgen de la Salud Hospital, Toledo, Spain
| | - Barbara Alexiou
- From the Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Lara Absil
- From the Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Claude Van Campenhout
- From the Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Nicky D'Haene
- From the Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sandrine Rorive
- From the Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Centre Universitaire inter Régional d'expertise en Anatomie Pathologique Hospitalière (CurePath, CHIREC, CHU Tivoli, ULB), Jumet, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Christine Decaestecker
- DIAPath, Center for Microscopy and Molecular Imaging, ULB, Gosselies, Belgium.,Laboratory of Image Synthesis and Analysis, Brussels School of Engineering/École Polytechnique de Brussels, ULB, Brussels, Belgium
| | - Isabelle Salmon
- From the Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium.,DIAPath, Center for Microscopy and Molecular Imaging, ULB, Gosselies, Belgium.,Laboratory of Image Synthesis and Analysis, Brussels School of Engineering/École Polytechnique de Brussels, ULB, Brussels, Belgium
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27
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Leary SES, Packer RJ, Li Y, Billups CA, Smith KS, Jaju A, Heier L, Burger P, Walsh K, Han Y, Embry L, Hadley J, Kumar R, Michalski J, Hwang E, Gajjar A, Pollack IF, Fouladi M, Northcott PA, Olson JM. Efficacy of Carboplatin and Isotretinoin in Children With High-risk Medulloblastoma: A Randomized Clinical Trial From the Children's Oncology Group. JAMA Oncol 2021; 7:1313-1321. [PMID: 34292305 DOI: 10.1001/jamaoncol.2021.2224] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Brain tumors are the leading cause of disease-related death in children. Medulloblastoma is the most common malignant embryonal brain tumor, and strategies to increase survival are needed. Objective To evaluate therapy intensification with carboplatin as a radiosensitizer and isotretinoin as a proapoptotic agent in children with high-risk medulloblastoma in a randomized clinical trial and, with a correlative biology study, facilitate planned subgroup analysis according to World Health Organization consensus molecular subgroups of medulloblastoma. Design, Setting, and Participants A randomized clinical phase 3 trial was conducted from March 2007 to September 2018. Analysis was completed in September 2020. Patients aged 3 to 21 years with newly diagnosed high-risk medulloblastoma from Children's Oncology Group institutions within the US, Canada, Australia, and New Zealand were included. High-risk features included metastasis, residual disease, or diffuse anaplasia. Interventions Patients were randomized to receive 36-Gy craniospinal radiation therapy and weekly vincristine with or without daily carboplatin followed by 6 cycles of maintenance chemotherapy with cisplatin, cyclophosphamide, and vincristine with or without 12 cycles of isotretinoin during and following maintenance. Main Outcomes and Measures The primary clinical trial end point was event-free survival, using the log-rank test to compare arms. The primary biology study end point was molecular subgroup classification by DNA methylation array. Results Of 294 patients with medulloblastoma, 261 were evaluable after central radiologic and pathologic review; median age, 8.6 years (range, 3.3-21.2); 183 (70%) male; 189 (72%) with metastatic disease; 58 (22%) with diffuse anaplasia; and 14 (5%) with greater than 1.5-cm2 residual disease. For all participants, the 5-year event-free survival was 62.9% (95% CI, 55.6%-70.2%) and overall survival was 73.4% (95% CI, 66.7%-80.1%). Isotretinoin randomization was closed early owing to futility. Five-year event-free survival was 66.4% (95% CI, 56.4%-76.4%) with carboplatin vs 59.2% (95% CI, 48.8%-69.6%) without carboplatin (P = .11), with the effect exclusively observed in group 3 subgroup patients: 73.2% (95% CI, 56.9%-89.5%) with carboplatin vs 53.7% (95% CI, 35.3%-72.1%) without (P = .047). Five-year overall survival differed by molecular subgroup (P = .006): WNT pathway activated, 100% (95% CI, 100%-100%); SHH pathway activated, 53.6% (95% CI, 33.0%-74.2%); group 3, 73.7% (95% CI, 61.9%-85.5%); and group 4, 76.9% (95% CI, 67.3%-86.5%). Conclusions and Relevance In this randomized clinical trial, therapy intensification with carboplatin improved event-free survival by 19% at 5 years for children with high-risk group 3 medulloblastoma. These findings further support the value of an integrated clinical and molecular risk stratification for medulloblastoma. Trial Registration ClinicalTrials.gov Identifier: NCT00392327.
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Affiliation(s)
- Sarah E S Leary
- Cancer and Blood Disorders Center, Seattle Children's, Seattle, Washington.,Department of Pediatrics, University of Washington School of Medicine, Seattle.,Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Roger J Packer
- Center for Neuroscience and Behavioral Health, Children's National Hospital, Washington, DC
| | - Yimei Li
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Catherine A Billups
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Kyle S Smith
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Alok Jaju
- Department of Radiology, Ann and Robert H. Lurie Children's Hospital, Chicago, Illinois
| | - Linda Heier
- Department of Radiology, NYP/Weill Cornell Medical Center, New York, New York
| | - Peter Burger
- Sidney Kimmel Cancer Center, Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Karin Walsh
- Division of Neuropsychology, Children's National Hospital, Washington, DC
| | - Yuanyuan Han
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Leanne Embry
- Pediatric Hematology/Oncology, UT Health San Antonio, San Antonio, Texas
| | - Jennifer Hadley
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Rahul Kumar
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeff Michalski
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Eugene Hwang
- Center for Cancer and Blood Disorders, Children's National Hospital, Washington, DC
| | - Amar Gajjar
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Ian F Pollack
- Department of Neurosurgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Maryam Fouladi
- Pediatric Hematology & Oncology, Nationwide Children's Hospital, Columbus, Ohio
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - James M Olson
- Cancer and Blood Disorders Center, Seattle Children's, Seattle, Washington.,Department of Pediatrics, University of Washington School of Medicine, Seattle.,Fred Hutchinson Cancer Research Center, Seattle, Washington
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28
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Abstract
Central nervous system (CNS) tumors are the most common solid tumor in pediatrics and represent the largest cause of childhood cancer-related mortality. With advances in molecular characterization of tumors, considerable developments have occurred impacting diagnosis and management, and refined prognostication. Advances in management have led to better survival, but mortality remains high and significant morbidity persists. Novel therapeutic approaches targeting the biology of these tumors are being investigated to improve overall survival and decrease treatment-related morbidity. Further molecular understanding of pediatric CNS tumors will lead to continued refinement of tumor classification, management, and prognostication.
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Affiliation(s)
- Fatema Malbari
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Texas Children's Hospital, Baylor College of Medicine, 6701 Fannin Street, Suite 1250, Houston, TX 77030, USA.
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29
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Fangusaro J, Cefalo MG, Garré ML, Marshall LV, Massimino M, Benettaib B, Biserna N, Poon J, Quan J, Conlin E, Lewandowski J, Simcock M, Jeste N, Hargrave DR, Doz F, Warren KE. Phase 2 Study of Pomalidomide (CC-4047) Monotherapy for Children and Young Adults With Recurrent or Progressive Primary Brain Tumors. Front Oncol 2021; 11:660892. [PMID: 34168987 PMCID: PMC8218626 DOI: 10.3389/fonc.2021.660892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction Treatment of recurrent primary pediatric brain tumors remains a major challenge, with most children succumbing to their disease. We conducted a prospective phase 2 study investigating the safety and efficacy of pomalidomide (POM) in children and young adults with recurrent and progressive primary brain tumors. Methods Patients with recurrent and progressive high-grade glioma (HGG), diffuse intrinsic pontine glioma (DIPG), ependymoma, or medulloblastoma received POM 2.6 mg/m2/day (the recommended phase 2 dose [RP2D]) on days 1-21 of a 28-day cycle. A Simon's Optimal 2-stage design was used to determine efficacy. Primary endpoints included objective response (OR) and long-term stable disease (LTSD) rates. Secondary endpoints included duration of response, progression-free survival (PFS), overall survival (OS), and safety. Results 46 patients were evaluable for response (HGG, n = 19; DIPG, ependymoma, and medulloblastoma, n = 9 each). Two patients with HGG achieved OR or LTSD (10.5% [95% CI, 1.3%-33.1%]; 1 partial response and 1 LTSD) and 1 patient with ependymoma had LTSD (11.1% [95% CI, 0.3%-48.2%]). There were no ORs or LTSD in the DIPG or medulloblastoma cohorts. The median PFS for patients with HGG, DIPG, ependymoma, and medulloblastoma was 7.86, 11.29, 8.43, and 8.43 weeks, respectively. Median OS was 5.06, 3.78, 12.02, and 11.60 months, respectively. Neutropenia was the most common grade 3/4 adverse event. Conclusions Treatment with POM monotherapy did not meet the primary measure of success in any cohort. Future studies are needed to evaluate if POM would show efficacy in tumors with specific molecular signatures or in combination with other anticancer agents. Clinical Trial Registration ClinicalTrials.gov, identifier NCT03257631; EudraCT, identifier 2016-002903-25.
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Affiliation(s)
- Jason Fangusaro
- Department of Pediatrics, Children's Healthcare of Atlanta and Aflac Cancer Center at Emory University Medical School, Atlanta, GA, United States
| | - Maria Giuseppina Cefalo
- Department of Hematology/Oncology and Stem Cell Transplantation, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Lynley V Marshall
- Children and Young People's Unit, The Royal Marsden Hospital and The Institute of Cancer Research, London, United Kingdom
| | - Maura Massimino
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Noha Biserna
- Bristol Myers Squibb, Princeton, NJ, United States
| | | | - Jackie Quan
- Bristol Myers Squibb, Princeton, NJ, United States
| | - Erin Conlin
- Bristol Myers Squibb, Princeton, NJ, United States
| | | | | | - Neelum Jeste
- Bristol Myers Squibb, Princeton, NJ, United States
| | - Darren R Hargrave
- Pediatric Oncology Unit, UCL Great Ormond Street Hospital for Children, London, United Kingdom
| | - François Doz
- Department of Pediatric Oncology, Institut Curie and University of Paris, Paris, France
| | - Katherine E Warren
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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30
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Yuan M, White D, Resar L, Bar E, Groves M, Cohen A, Jackson E, Bynum J, Rubens J, Mumm J, Chen L, Jiang L, Raabe E, Rodriguez FJ, Eberhart CG. Conditional reprogramming culture conditions facilitate growth of lower-grade glioma models. Neuro Oncol 2021; 23:770-782. [PMID: 33258947 DOI: 10.1093/neuonc/noaa263] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The conditional reprogramming cell culture method was developed to facilitate growth of senescence-prone normal and neoplastic epithelial cells, and involves co-culture with irradiated fibroblasts and the addition of a small molecule Rho kinase (ROCK) inhibitor. The aim of this study was to determine whether this approach would facilitate the culture of compact low-grade gliomas. METHODS We attempted to culture 4 pilocytic astrocytomas, 2 gangliogliomas, 2 myxopapillary ependymomas, 2 anaplastic gliomas, 2 difficult-to-classify low-grade neuroepithelial tumors, a desmoplastic infantile ganglioglioma, and an anaplastic pleomorphic xanthoastrocytoma using a modified conditional reprogramming cell culture approach. RESULTS Conditional reprogramming resulted in robust increases in growth for a majority of these tumors, with fibroblast conditioned media and ROCK inhibition both required. Switching cultures to standard serum containing media, or serum-free neurosphere conditions, with or without ROCK inhibition, resulted in decreased proliferation and induction of senescence markers. Rho kinase inhibition and conditioned media both promoted Akt and Erk1/2 activation. Several cultures, including one derived from a NF1-associated pilocytic astrocytoma (JHH-NF1-PA1) and one from a BRAF p.V600E mutant anaplastic pleomorphic xanthoastrocytoma (JHH-PXA1), exhibited growth sufficient for preclinical testing in vitro. In addition, JHH-NF1-PA1 cells survived and migrated in larval zebrafish orthotopic xenografts, while JHH-PXA1 formed orthotopic xenografts in mice histopathologically similar to the tumor from which it was derived. CONCLUSIONS These studies highlight the potential for the conditional reprogramming cell culture method to promote the growth of glial and glioneuronal tumors in vitro, in some cases enabling the establishment of long-term culture and in vivo models.
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Affiliation(s)
- Ming Yuan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David White
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Linda Resar
- Division of Pediatric Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eli Bar
- Department of Pathology, University of Maryland, Baltimore, Maryland, USA
| | - Mari Groves
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alan Cohen
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eric Jackson
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer Bynum
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey Rubens
- Division of Pediatric Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeff Mumm
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Liam Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Liqun Jiang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eric Raabe
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fausto J Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Charles G Eberhart
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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31
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Abedalthagafi M, Mobark N, Al-Rashed M, AlHarbi M. Epigenomics and immunotherapeutic advances in pediatric brain tumors. NPJ Precis Oncol 2021; 5:34. [PMID: 33931704 PMCID: PMC8087701 DOI: 10.1038/s41698-021-00173-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Brain tumors are the leading cause of childhood cancer-related deaths. Similar to adult brain tumors, pediatric brain tumors are classified based on histopathological evaluations. However, pediatric brain tumors are often histologically inconsistent with adult brain tumors. Recent research findings from molecular genetic analyses have revealed molecular and genetic changes in pediatric tumors that are necessary for appropriate classification to avoid misdiagnosis, the development of treatment modalities, and the clinical management of tumors. As many of the molecular-based therapies developed from clinical trials on adults are not always effective against pediatric brain tumors, recent advances have improved our understanding of the molecular profiles of pediatric brain tumors and have led to novel epigenetic and immunotherapeutic treatment approaches currently being evaluated in clinical trials. In this review, we focus on primary malignant brain tumors in children and genetic, epigenetic, and molecular characteristics that differentiate them from brain tumors in adults. The comparison of pediatric and adult brain tumors highlights the need for treatments designed specifically for pediatric brain tumors. We also discuss the advancements in novel molecularly targeted drugs and how they are being integrated with standard therapy to improve the classification and outcomes of pediatric brain tumors in the future.
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Affiliation(s)
- Malak Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Kingdom of Saudi Arabia.
| | - Nahla Mobark
- Department of Paediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - May Al-Rashed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Chair of Medical and Molecular Genetics Research, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Musa AlHarbi
- Department of Paediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
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32
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DNA Methylation Profiling Discriminates between Malignant Pleural Mesothelioma and Neoplastic or Reactive Histologic Mimics. J Mol Diagn 2021; 23:834-846. [PMID: 33887463 DOI: 10.1016/j.jmoldx.2021.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/20/2021] [Accepted: 04/01/2021] [Indexed: 11/23/2022] Open
Abstract
The diagnosis of malignant pleural mesothelioma (MPM) is challenging because of its potential overlap with other neoplasms or even with reactive conditions. DNA methylation analysis is effective in diagnosing tumors. In the present study, this approach was tested for use in MPM diagnosis. The DNA methylation patterns of a discovery cohort and an independent-validation cohort of MPMs were compared to those of 202 cases representing malignant and benign diagnostic mimics (angiosarcoma, desmoid-type fibromatosis, epithelioid sarcoma, leiomyosarcoma, lung adenocarcinoma, lung squamous cell carcinoma, melanoma, nodular fasciitis, reactive mesothelial hyperplasia, sclerosing fibrous pleuritis, solitary fibrous tumor, and synovial sarcoma). By both unsupervised hierarchical clustering and t-distributed stochastic neighbor embedding analysis, MPM samples in the discovery cohort exhibited a DNA methylation profile different from those of other neoplastic and reactive mimics. These results were confirmed in the independent validation cohort and by in silico analysis of the MPM-The Cancer Genome Atlas data set. Copy number variation profiles were also inferred to identify molecular hallmarks of MPM, including CDKN2A and NF2 deletions. Methylation profiling was effective in the diagnosis of MPM, although caution is advised in samples with low tumor cell content.
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Simone V, Rizzo D, Cocciolo A, Caroleo AM, Carai A, Mastronuzzi A, Tornesello A. Infantile Brain Tumors: A Review of Literature and Future Perspectives. Diagnostics (Basel) 2021; 11:diagnostics11040670. [PMID: 33917833 PMCID: PMC8068230 DOI: 10.3390/diagnostics11040670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 01/08/2023] Open
Abstract
Brain tumors in infants including those diagnosed in fetal age, newborns and under a year old represent less than 10% of pediatric nervous system tumors and present differently when compared with older children in terms of clinical traits, location and histology. The most frequent clinical finding is a macrocephaly but non-specific symptoms can also be associated. The prognosis is usually poor and depends on several factors. Surgery continues to be the main option in terms of therapeutic strategies whereas the role of chemotherapy is not yet well defined and radiotherapy is exceptionally undertaken. In view of this situation, a molecular characterization could assist in providing therapeutic options for these tumors. This review highlights the recent advances in the diagnosis and treatment of brain tumors in infants with a particular focus on the molecular landscape and future clinical applications.
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Affiliation(s)
- Valeria Simone
- Pediatric Oncology Unit, Ospedale Vito Fazzi, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (D.R.); (A.C.)
- Correspondence: (V.S.); (A.T.)
| | - Daniela Rizzo
- Pediatric Oncology Unit, Ospedale Vito Fazzi, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (D.R.); (A.C.)
| | - Alessandro Cocciolo
- Pediatric Oncology Unit, Ospedale Vito Fazzi, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (D.R.); (A.C.)
| | - Anna Maria Caroleo
- Department of Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital (IRCCS), Piazza Sant’Onofrio 4, 00146 Rome, Italy; (A.M.C.); (A.M.)
| | - Andrea Carai
- Neurosurgery Unit, Department of Neurological and Psychiatric Sciences, Bambino Gesù Children’s Hospital (IRCCS), Piazza Sant’Onofrio 4, 00146 Rome, Italy;
| | - Angela Mastronuzzi
- Department of Onco-Hematology and Cell and Gene Therapy, Bambino Gesù Children’s Hospital (IRCCS), Piazza Sant’Onofrio 4, 00146 Rome, Italy; (A.M.C.); (A.M.)
| | - Assunta Tornesello
- Pediatric Oncology Unit, Ospedale Vito Fazzi, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (D.R.); (A.C.)
- Correspondence: (V.S.); (A.T.)
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Pediatric Glioma: An Update of Diagnosis, Biology, and Treatment. Cancers (Basel) 2021; 13:cancers13040758. [PMID: 33673070 PMCID: PMC7918156 DOI: 10.3390/cancers13040758] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 01/03/2023] Open
Abstract
Simple Summary Recent research has enhanced our understanding of the diverse biological processes that occur in pediatric gliomas; and molecular genetic analysis has become essential to diagnose and treat these conditions. Because targetable molecular aberrations can be detected in pediatric gliomas, identifying these aberrations is very important. This review provides an overview of pediatric gliomas, and describes recent developments made in strategies for their diagnosis and treatment. Additionally, it presents a current picture of pediatric gliomas in light of advances in molecular genetics, and describes the current scientific progress in gliomas’ treatment using information from recently completed and ongoing clinical trials. The era of incorporating molecular genetic analysis into clinical practice is emerging. Abstract Recent research has promoted elucidation of the diverse biological processes that occur in pediatric central nervous system (CNS) tumors. Molecular genetic analysis is essential not only for proper classification, but also for monitoring biological behavior and clinical management of tumors. Ever since the 2016 World Health Organization classification of CNS tumors, molecular profiling has become an indispensable step in the diagnosis, prediction of prognosis, and treatment of pediatric as well as adult CNS tumors. These molecular data are changing diagnosis, leading to new guidelines, and offering novel molecular targeted therapies. The Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT-NOW) makes practical recommendations using recent advances in CNS tumor classification, particularly in molecular discernment of these neoplasms as morphology-based classification of tumors is being replaced by molecular-based classification. In this article, we summarize recent knowledge to provide an overview of pediatric gliomas, which are major pediatric CNS tumors, and describe recent developments in strategies employed for their diagnosis and treatment.
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35
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SIMONIAN M. Proteogenomics for pediatric brain cancer. BIOCELL 2021; 45:1459-1463. [PMID: 35002040 PMCID: PMC8740781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pediatric central nervous system tumors are the most common tumors in children, it constitute 15%-20% of all malignancies in children and are the leading cause of cancer related deaths in children. Proteogenomics is an emerging field of biological research that utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of biomarkers for diagnosis and therapeutic purposes. Integrative proteogenomics analysis of pediatric tumors identified underlying biological processes and potential treatments as well as the functional effects of somatic mutations and copy number variation driving tumorigenesis.
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36
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Baroni LV, Rugilo C, Lubieniecki F, Sampor C, Freytes C, Nobre L, Hansford JR, Malalasekera VS, Zapotocky M, Dodgshun A, Martinez OC, La Madrid AM, Lavarino C, Suñol M, Rutkowski S, Schuller U, Bouffet E, Ramaswamy V, Alderete D. Treatment response of CNS high-grade neuroepithelial tumors with MN1 alteration. Pediatr Blood Cancer 2020; 67:e28627. [PMID: 32959992 DOI: 10.1002/pbc.28627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 01/02/2023]
Abstract
Central nervous system high-grade neuroepithelial tumor with MN1 alteration (CNS HGNET-MN1) is a rare recently described entity. Fourteen CNS HGNET-MN1 patients were identified using genome-wide methylation arrays/RT-PCR across seven institutions. All patients had surgery (gross total resection: 10; subtotal resection: four) as initial management followed by observation alone in three patients, followed by radiotherapy in eight patients (focal: five; craniospinal: two; CyberKnife: one) and systemic chemotherapy in three patients. Seven patients relapsed; five local and two metastatic, despite adjuvant radiotherapy, of which three died. Treatment of CNS HGNET-MN1 remains a major treatment challenge despite aggressive surgical resections and upfront radiotherapy, warranting new approaches to this rare malignancy.
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Affiliation(s)
- Lorena V Baroni
- Service of Hematology/Oncology, Hospital JP Garrahan, Buenos Aires, Argentina
| | - Carlos Rugilo
- Service of Diagnostic Imaging, Hospital JP Garrahan, Buenos Aires, Argentina
| | | | - Claudia Sampor
- Service of Hematology/Oncology, Hospital JP Garrahan, Buenos Aires, Argentina
| | - Candela Freytes
- Service of Hematology/Oncology, Hospital JP Garrahan, Buenos Aires, Argentina
| | - Liana Nobre
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, Melbourne, Victoria, Australia.,Division of Cancer, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Michal Zapotocky
- Department of Paediatric Haematology and Oncology, Second Medical School, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Andrew Dodgshun
- Children's Haematology/Oncology Centre, Christchurch Hospital, Christchurch, New Zealand
| | | | | | - Cinzia Lavarino
- Developmental Tumor Biology Laboratory, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schuller
- 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
| | - Eric Bouffet
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada.,Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniel Alderete
- Service of Hematology/Oncology, Hospital JP Garrahan, Buenos Aires, Argentina
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37
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Methylation profiling-based diagnosis of radiologically suspected congenital glioma. Brain Tumor Pathol 2020; 38:78-80. [PMID: 33063135 DOI: 10.1007/s10014-020-00384-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/05/2020] [Indexed: 10/23/2022]
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38
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The Epigenetic Progenitor Origin of Cancer Reassessed: DNA Methylation Brings Balance to the Stem Force. EPIGENOMES 2020; 4:epigenomes4020008. [PMID: 34968242 PMCID: PMC8594692 DOI: 10.3390/epigenomes4020008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 12/17/2022] Open
Abstract
Cancer initiation and progression toward malignant stages occur as the results of accumulating genetic alterations and epigenetic dysregulation. During the last decade, the development of next generation sequencing (NGS) technologies and the increasing pan-genomic knowledge have revolutionized how we consider the evolving epigenetic landscapes during homeostasis and tumor progression. DNA methylation represents the best studied mark and is considered as a common mechanism of epigenetic regulation in normal homeostasis and cancer. A remarkable amount of work has recently started clarifying the central role played by DNA methylation dynamics on the maintenance of cell identity and on cell fate decisions during the different steps of normal development and tumor evolution. Importantly, a growing number of studies show that DNA methylation is key in the maintenance of adult stemness and in orchestrating commitment in multiple ways. Perturbations of the normal DNA methylation patterns impair the homeostatic balance and can lead to tumor initiation. Therefore, DNA methylation represents an interesting therapeutic target to recover homeostasis in tumor stem cells.
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39
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Li G, Wang Y, Cai L, Zhou L. Screening for genes and subnetworks associated with atypical teratoid/rhabdoid tumors using bioinformatics analysis. Int J Neurosci 2020; 131:319-326. [PMID: 32202192 DOI: 10.1080/00207454.2020.1746306] [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: 02/08/2023]
Abstract
Objectives: Atypical teratoid/rhabdoid tumors (AT/RTs) are rare, fast-growing lesions of central nervous system and their prognosis is poor. Nowadays, multimodal managements, including surgery, chemotherapy and radiation therapy are advocated; however, low survival rate and severe neurocognitive toxicity of chemotherapy as well as the irreversible long-term sequelae of irradiation in infants and young children with AT/RTs are alarming. The aim of our study is to provide valid biological information for more tailored advance therapy for these lesions.Methods: Gene expression profile of GSE94349 was downloaded from GEO database and was analyzed using limma R package. Function and enrichment analyses of DEGs were performed based on DAVID database. PPI network construction, hub gene selection and module analysis were conducted in Cytoscape software.Results: In this study, 224 up-regulated genes and 572 down-regulated genes were selected as DEGs. The up-regulated genes were mainly enriched in molecular function and cell component, which mainly included protein binding and nucleus, respectively. The down-regulated DEGs were significantly involved in cell component such as plasma membrane and integral component of membrane. Cell cycle and retrograde endocannabinoid signaling were the main KEGG pathway of up and down DEGs, respectively. CDK1, CCNA2, CDC20, TOP2A were identified as hub genes and two significant network modules were also obtained.Conclusions: Our study may help to further understand the molecular characteristics and provide more tailored targets for future treatment of AT/RTs. Hub genes CDK1, CCNA2, CDC20, TOP2A as well as cell cycle signaling pathway may be new more tailored targets for future treatment of AT/RTs.
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Affiliation(s)
- Gaowei Li
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuelong Wang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Linjun Cai
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liangxue Zhou
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Miele E, De Vito R, Ciolfi A, Pedace L, Russo I, De Pasquale MD, Di Giannatale A, Crocoli A, Angelis BD, Tartaglia M, Alaggio R, Milano GM. DNA Methylation Profiling for Diagnosing Undifferentiated Sarcoma with Capicua Transcriptional Receptor ( CIC) Alterations. Int J Mol Sci 2020; 21:ijms21051818. [PMID: 32155762 PMCID: PMC7084764 DOI: 10.3390/ijms21051818] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/15/2020] [Accepted: 03/03/2020] [Indexed: 12/31/2022] Open
Abstract
Undifferentiated soft tissue sarcomas are a group of diagnostically challenging tumors in the pediatric population. Molecular techniques are instrumental for the categorization and differential diagnosis of these tumors. A subgroup of recently identified soft tissue sarcomas with undifferentiated round cell morphology was characterized by Capicua transcriptional receptor (CIC) rearrangements. Recently, an array-based DNA methylation analysis of undifferentiated tumors with small blue round cell histology was shown to provide a highly robust and reproducible approach for precisely classifying this diagnostically challenging group of tumors. We describe the case of an undifferentiated sarcoma of the abdominal wall in a 12-year-old girl. The patient presented with a voluminous mass of the abdominal wall, and multiple micro-nodules in the right lung. The tumor was unclassifiable with current immunohistochemical and molecular approaches. However, DNA methylation profiling allowed us to classify this neoplasia as small blue round cell tumor with CIC alterations. The patient was treated with neoadjuvant chemotherapy followed by complete surgical resection and adjuvant chemotherapy. After 22 months, the patient is disease-free and in good clinical condition. To put our experience in context, we conducted a literature review, analyzing current knowledge and state-of-the-art diagnosis, prognosis, and clinical management of CIC rearranged sarcomas. Our findings further support the use of DNA methylation profiling as an important tool to improve diagnosis of non-Ewing small round cell tumors.
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Affiliation(s)
- Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
- Correspondence:
| | - Rita De Vito
- Department of Laboratories, Pathology Unit, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (R.D.V.); (R.A.)
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.C.); (M.T.)
| | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Ida Russo
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Maria Debora De Pasquale
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Angela Di Giannatale
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Alessandro Crocoli
- Department of Surgery, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy;
| | - Biagio De Angelis
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital (IRCCS), 00165 Rome, Italy; (A.C.); (M.T.)
| | - Rita Alaggio
- Department of Laboratories, Pathology Unit, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (R.D.V.); (R.A.)
| | - Giuseppe Maria Milano
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, IRCCS Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (L.P.); (I.R.); (M.D.D.P.); (A.D.G.); (B.D.A.); (G.M.M.)
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Malbari F, Lindsay H. Genetics of Common Pediatric Brain Tumors. Pediatr Neurol 2020; 104:3-12. [PMID: 31948735 DOI: 10.1016/j.pediatrneurol.2019.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022]
Abstract
Central nervous system tumors are the most common solid tumors in pediatrics and represent the largest cause of childhood cancer-related mortality. Improvements have occurred in the management of these patients leading to better survival, but significant morbidity persists. With the era of next generation sequencing, considerable advances have occurred in the understanding of these tumors both biologically and clinically. This information has impacted diagnosis and management. Subgroups have been identified, improving risk stratification. Novel therapeutic approaches, specifically targeting the biology of these tumors, are being investigated to improve overall survival and decrease treatment-related morbidity. The intent of this review is to discuss the genetics of common pediatric brain tumors and the clinical implications. This review will include known genetic disorders associated with central nervous system tumors, neurofibromatosis, tuberous sclerosis, Li-Fraumeni syndrome, Gorlin syndrome, and Turcot syndrome, as well as somatic mutations of glioma, medulloblastoma, and ependymoma.
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Affiliation(s)
- Fatema Malbari
- Division of Pediatric Neurology and Developmental Neurosciences, Department of Pediatrics, Texas Children's Hospital/Baylor College of Medicine, Houston, Texas.
| | - Holly Lindsay
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Texas Children's Hospital/Baylor College of Medicine, Houston, Texas
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42
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Danielsson A, Barreau K, Kling T, Tisell M, Carén H. Accumulation of DNA methylation alterations in paediatric glioma stem cells following fractionated dose irradiation. Clin Epigenetics 2020; 12:26. [PMID: 32046773 PMCID: PMC7014676 DOI: 10.1186/s13148-020-0817-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/27/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Radiation is an important therapeutic tool. However, radiotherapy has the potential to promote co-evolution of genetic and epigenetic changes that can drive tumour heterogeneity, formation of radioresistant cells and tumour relapse. There is a clinical need for a better understanding of DNA methylation alterations that may follow radiotherapy to be able to prevent the development of radiation-resistant cells. METHODS We examined radiation-induced changes in DNA methylation profiles of paediatric glioma stem cells (GSCs) in vitro. Five GSC cultures were irradiated in vitro with repeated doses of 2 or 4 Gy. Radiation was given in 3 or 15 fractions. DNA methylation profiling using Illumina DNA methylation arrays was performed at 14 days post-radiation. The cellular characteristics were studied in parallel. RESULTS Few fractions of radiation did not result in significant accumulation of DNA methylation alterations. However, extended dose fractionations changed DNA methylation profiles and induced thousands of differentially methylated positions, specifically in enhancer regions, sites involved in alternative splicing and in repetitive regions. Radiation induced dose-dependent morphological and proliferative alterations of the cells as a consequence of the radiation exposure. CONCLUSIONS DNA methylation alterations of sites with regulatory functions in proliferation and differentiation were identified, which may reflect cellular response to radiation stress through epigenetic reprogramming and differentiation cues.
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Affiliation(s)
- Anna Danielsson
- Sahlgrenska Cancer Center, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Kristell Barreau
- Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Tisell
- Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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Ramón Y Cajal S, Sesé M, Capdevila C, Aasen T, De Mattos-Arruda L, Diaz-Cano SJ, Hernández-Losa J, Castellví J. Clinical implications of intratumor heterogeneity: challenges and opportunities. J Mol Med (Berl) 2020; 98:161-177. [PMID: 31970428 PMCID: PMC7007907 DOI: 10.1007/s00109-020-01874-2] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 11/05/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
In this review, we highlight the role of intratumoral heterogeneity, focusing on the clinical and biological ramifications this phenomenon poses. Intratumoral heterogeneity arises through complex genetic, epigenetic, and protein modifications that drive phenotypic selection in response to environmental pressures. Functionally, heterogeneity provides tumors with significant adaptability. This ranges from mutual beneficial cooperation between cells, which nurture features such as growth and metastasis, to the narrow escape and survival of clonal cell populations that have adapted to thrive under specific conditions such as hypoxia or chemotherapy. These dynamic intercellular interplays are guided by a Darwinian selection landscape between clonal tumor cell populations and the tumor microenvironment. Understanding the involved drivers and functional consequences of such tumor heterogeneity is challenging but also promises to provide novel insight needed to confront the problem of therapeutic resistance in tumors.
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Affiliation(s)
- Santiago Ramón Y Cajal
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain. .,Pathology Department, Vall d'Hebron Hospital, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain. .,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain. .,Department of Pathology, Vall d'Hebron University Hospital, Autonomous University of Barcelona, Pg. Vall d'Hebron, 119-129, 08035, Barcelona, Spain.
| | - Marta Sesé
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Claudia Capdevila
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Department of Genetics and Development, Columbia University Medical Center, New York, NY, 10032, USA
| | - Trond Aasen
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Leticia De Mattos-Arruda
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, c/Natzaret, 115-117, 08035, Barcelona, Spain
| | - Salvador J Diaz-Cano
- Department of Histopathology, King's College Hospital and King's Health Partners, London, UK
| | - Javier Hernández-Losa
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Pathology Department, Vall d'Hebron Hospital, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Josep Castellví
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Pathology Department, Vall d'Hebron Hospital, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
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44
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Hermans E, Hulleman E. Patient-Derived Orthotopic Xenograft Models of Pediatric Brain Tumors: In a Mature Phase or Still in Its Infancy? Front Oncol 2020; 9:1418. [PMID: 31970083 PMCID: PMC6960099 DOI: 10.3389/fonc.2019.01418] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 11/28/2019] [Indexed: 12/19/2022] Open
Abstract
In recent years, molecular profiling has led to the discovery of an increasing number of brain tumor subtypes, and associated therapeutic targets. These molecular features have been incorporated in the 2016 new World Health Organization (WHO) Classification of Tumors of the Central Nervous System (CNS), which now distinguishes tumor subgroups not only histologically, but also based on molecular characteristics. Despite an improved diagnosis of (pediatric) tumors in the CNS however, the survival of children with malignant brain tumors still is far worse than for those suffering from other types of malignancies. Therefore, new treatments need to be developed, based on subgroup-specific genetic aberrations. Here, we provide an overview of the currently available orthotopic xenograft models for pediatric brain tumor subtypes as defined by the 2016 WHO classification, to facilitate the choice of appropriate animal models for the preclinical testing of novel treatment strategies, and to provide insight into the current gaps and challenges.
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Affiliation(s)
- Eva Hermans
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands.,Departments of Pediatric Oncology/Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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45
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Barsan V, Paul M, Gorsi H, Malicki D, Elster J, Kuo DJ, Crawford J. Clinical Impact of Next-generation Sequencing in Pediatric Neuro-Oncology Patients: A Single-institutional Experience. Cureus 2019; 11:e6281. [PMID: 31827999 PMCID: PMC6892579 DOI: 10.7759/cureus.6281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The implementation of next-generation sequencing (NGS) in pediatric neuro-oncology may impact diagnosis, prognosis, therapeutic strategies, clinical trial enrollment, and germline risk. We retrospectively analyzed 58 neuro-oncology patients (31 boys, 27 girls, average age 7.4 years) who underwent NGS tumor profiling using a single commercially available platform on paraffin-embedded tissue obtained at diagnosis (20 low-grade gliomas, 12 high-grade gliomas, 11 embryonal tumors, four ependymal tumors, three meningeal tumors, and eight other CNS tumors) from May 2014 to December 2016. NGS results were analyzed for actionable mutations, variants of unknown significance and clinical impact. Seventy-four percent of patients (43 of 57) had actionable mutations; 26% had only variants of uncertain significance (VUS). NGS findings impacted treatment decisions in 55% of patients; 24% were given a targeted treatment based on NGS findings. Seven of eight patients with low-grade tumors treated with targeted therapy (everolimus, trametinib, or vemurafenib) experienced partial response or stable disease. All high-grade tumors had progressive disease on targeted therapy. Forty percent of patients had a revision or refinement of their diagnosis, and nine percent of patients were diagnosed with a previously unconfirmed cancer predisposition syndrome. Turnaround time between sample shipment and report generation averaged 13.4 ± 6.4 days. One sample failed due to insufficient DNA quantity. Our experience highlights the feasibility and clinical utility of NGS in the management of pediatric neuro-oncology patients. Future prospective clinical trials using NGS are needed to establish efficacy.
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Affiliation(s)
- Valentin Barsan
- Pediatric Hematology/Oncology, Stanford University School of Medicine, Palo Alto, USA
| | - Megan Paul
- Pediatric Hematology/Oncology, University of California San Diego, La Jolla, USA
| | - Hamza Gorsi
- Pediatric Hematology/Oncology, Children's Hospital of Michigan, Michigan, USA
| | - Denise Malicki
- Pathology, University of California San Diego, La Jolla, USA
| | - Jennifer Elster
- Pediatric Hematology/Oncology, University of California San Diego, La Jolla, USA
| | - Dennis J Kuo
- Pediatric Hematology/Oncology, University of California San Diego, La Jolla, USA
| | - John Crawford
- Neurosciences and Pediatrics, University of California San Diego, La Jolla, USA
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46
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Specific glioblastoma multiforme prognostic-subtype distinctions based on DNA methylation patterns. Cancer Gene Ther 2019; 27:702-714. [PMID: 31619751 DOI: 10.1038/s41417-019-0142-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/01/2019] [Accepted: 10/04/2019] [Indexed: 12/14/2022]
Abstract
DNA methylation is an important regulator of gene expression, and plays a significant role in carcinogenesis in the brain. Here, we explored specific prognosis-subtypes based on DNA methylation status using 138 Glioblastoma Multiforme (GBM) samples from The Cancer Genome Atlas (TCGA) database. The methylation profiles of 11,637 CpG sites that significantly correlated with survival in the training set were employed for consensus clustering. We identified three GBM molecular subtypes, and their survival curves were distinct from each other. Furthermore, ten feature CpG sites were obtained on conducting a weighted gene co-expression network analysis (WGCNA) of the CpG sites. We were able to classify the samples into high- and low-methylation groups, and classified the prognosis information of the samples after cluster analysis of the training set samples using the hierarchical clustering algorithm. Similar results were obtained in the test set and clinical GBM specimens. Finally, we found that a positive relationship existed between methylation level and sensitivity to temozolomide (or radiotherapy) or anti-migration ability of GBM cells. Taken together, these results suggest that the model constructed in this study could help explain the heterogeneity of previous molecular subgroups in GBM and can provide guidance to clinicians regarding the prognosis of GBM.
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47
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Chai RC, Chang YZ, Wang QW, Zhang KN, Li JJ, Huang H, Wu F, Liu YQ, Wang YZ. A Novel DNA Methylation-Based Signature Can Predict the Responses of MGMT Promoter Unmethylated Glioblastomas to Temozolomide. Front Genet 2019; 10:910. [PMID: 31611911 PMCID: PMC6776832 DOI: 10.3389/fgene.2019.00910] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/28/2019] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant glioma, with a median overall survival (OS) of 14–16 months. Temozolomide (TMZ) is the first-line chemotherapy drug for glioma, but whether TMZ should be withheld from patients with GBMs that lack O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation is still under debate. DNA methylation profiling holds great promise for further stratifying the responses of MGMT promoter unmethylated GBMs to TMZ. In this study, we studied 147 TMZ-treated MGMT promoter unmethylated GBM, whose methylation information was obtained from the HumanMethylation27 (HM-27K) BeadChips (n = 107) and the HumanMethylation450 (HM-450K) BeadChips (n = 40) for training and validation, respectively. In the training set, we performed univariate Cox regression and identified that 3,565 CpGs were significantly associated with the OS of the TMZ-treated MGMT promoter unmethylated GBMs. Functional analysis indicated that the genes corresponding to these CpGs were enriched in the biological processes or pathways of mitochondrial translation, cell cycle, and DNA repair. Based on these CpGs, we developed a 31-CpGs methylation signature utilizing the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm. In both training and validation datasets, the signature identified the TMZ-sensitive GBMs in the MGMT promoter unmethylated GBMs, and only the patients in the low-risk group appear to benefit from the TMZ treatment. Furthermore, these identified TMZ-sensitive MGMT promoter unmethylated GBMs have a similar OS when compared with the MGMT promoter methylated GBMs after TMZ treatment in both two datasets. Multivariate Cox regression demonstrated the independent prognostic value of the signature in TMZ-treated MGMT promoter unmethylated GBMs. Moreover, we also noticed that the hallmark of epithelial–mesenchymal transition, ECM related biological processes and pathways were highly enriched in the MGMT unmethylated GBMs with the high-risk score, indicating that enhanced ECM activities could be involved in the TMZ-resistance of GBM. In conclusion, our findings promote our understanding of the roles of DNA methylation in MGMT umethylated GBMs and offer a very promising TMZ-sensitivity predictive signature for these GBMs that could be tested prospectively.
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Affiliation(s)
- Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu-Zhou Chang
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qiang-Wei Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jing-Jun Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hua Huang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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48
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Sweet-Cordero EA, Biegel JA. The genomic landscape of pediatric cancers: Implications for diagnosis and treatment. Science 2019; 363:1170-1175. [PMID: 30872516 PMCID: PMC7757338 DOI: 10.1126/science.aaw3535] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The past decade has witnessed a major increase in our understanding of the genetic underpinnings of childhood cancer. Genomic sequencing studies have highlighted key differences between pediatric and adult cancers. Whereas many adult cancers are characterized by a high number of somatic mutations, pediatric cancers typically have few somatic mutations but a higher prevalence of germline alterations in cancer predisposition genes. Also noteworthy is the remarkable heterogeneity in the types of genetic alterations that likely drive the growth of pediatric cancers, including copy number alterations, gene fusions, enhancer hijacking events, and chromoplexy. Because most studies have genetically profiled pediatric cancers only at diagnosis, the mechanisms underlying tumor progression, therapy resistance, and metastasis remain poorly understood. We discuss evidence that points to a need for more integrative approaches aimed at identifying driver events in pediatric cancers at both diagnosis and relapse. We also provide an overview of key aspects of germline predisposition for cancer in this age group.
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Affiliation(s)
- E Alejandro Sweet-Cordero
- Department of Pediatrics, Division of Hematology and Oncology, University of California, San Francisco, CA 94158, USA.
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, and Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.
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