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Carton RJ, Doyle MG, Kearney H, Steward CA, Lench NJ, Rogers A, Heinzen EL, McDonald S, Fay J, Lacey A, Beausang A, Cryan J, Brett F, El-Naggar H, Widdess-Walsh P, Costello D, Kilbride R, Doherty CP, Sweeney KJ, O'Brien DF, Henshall DC, Delanty N, Cavalleri GL, Benson KA. Somatic variants as a cause of drug-resistant epilepsy including mesial temporal lobe epilepsy with hippocampal sclerosis. Epilepsia 2024. [PMID: 38491957 DOI: 10.1111/epi.17943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
OBJECTIVE The contribution of somatic variants to epilepsy has recently been demonstrated, particularly in the etiology of malformations of cortical development. The aim of this study was to determine the diagnostic yield of somatic variants in genes that have been previously associated with a somatic or germline epilepsy model, ascertained from resected brain tissue from patients with multidrug-resistant focal epilepsy. METHODS Forty-two patients were recruited across three categories: (1) malformations of cortical development, (2) mesial temporal lobe epilepsy with hippocampal sclerosis, and (3) nonlesional focal epilepsy. Participants were subdivided based on histopathology of the resected brain. Paired blood- and brain-derived DNA samples were sequenced using high-coverage targeted next generation sequencing to high depth (585× and 1360×, respectively). Variants were identified using Genome Analysis ToolKit (GATK4) MuTect-2 and confirmed using high-coverage Amplicon-EZ sequencing. RESULTS Sequence data on 41 patients passed quality control. Four somatic variants were validated following amplicon sequencing: within CBL, ALG13, MTOR, and FLNA. The diagnostic yield across 41 patients was 10%, 9% in mesial temporal lobe epilepsy with hippocampal sclerosis and 20% in malformations of cortical development. SIGNIFICANCE This study provides novel insights into the etiology of mesial temporal lobe epilepsy with hippocampal sclerosis, highlighting a potential pathogenic role of somatic variants in CBL and ALG13. We also report candidate diagnostic somatic variants in FLNA in focal cortical dysplasia, while providing further insight into the importance of MTOR and related genes in focal cortical dysplasia. This work demonstrates the potential molecular diagnostic value of variants in both germline and somatic epilepsy genes.
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Affiliation(s)
- Robert J Carton
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Michael G Doyle
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
- Strategic Academic Recruitment Doctor of Medicine Programme, Royal College of Surgeons in Ireland in collaboration with Blackrock Clinic, Dublin, Ireland
| | - Hugh Kearney
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | | | | | - Anthony Rogers
- Congenica Limited, BioData Innovation Centre, Cambridge, UK
| | - Erin L Heinzen
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Seamus McDonald
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Joanna Fay
- Royal College of Surgeons in Ireland Biobanking Service, Dublin, Ireland
| | - Austin Lacey
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Hany El-Naggar
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Peter Widdess-Walsh
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Daniel Costello
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Neurology, Cork University Hospital, Cork, Ireland
| | - Ronan Kilbride
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Colin P Doherty
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Neurology, St. James's Hospital, Dublin, Ireland
| | - Kieron J Sweeney
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Donncha F O'Brien
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - David C Henshall
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Norman Delanty
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Gianpiero L Cavalleri
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Katherine A Benson
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
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2
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Leister H, Krause FF, Gil B, Prus R, Prus I, Hellhund-Zingel A, Mitra M, Da Rosa Gerbatin R, Delanty N, Beausang A, Brett FM, Farrell MA, Cryan J, O’Brien DF, Henshall DC, Helmprobst F, Pagenstecher A, Steinhoff U, Visekruna A, Engel T. Immunoproteasome deficiency results in age-dependent development of epilepsy. Brain Commun 2024; 6:fcae017. [PMID: 38317856 PMCID: PMC10839634 DOI: 10.1093/braincomms/fcae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/17/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024] Open
Abstract
The immunoproteasome is a central protease complex required for optimal antigen presentation. Immunoproteasome activity is also associated with facilitating the degradation of misfolded and oxidized proteins, which prevents cellular stress. While extensively studied during diseases with increasing evidence suggesting a role for the immunoproteasome during pathological conditions including neurodegenerative diseases, this enzyme complex is believed to be mainly not expressed in the healthy brain. In this study, we show an age-dependent increase in polyubiquitination in the brains of wild-type mice, accompanied by an induction of immunoproteasomes, which was most prominent in neurons and microglia. In contrast, mice completely lacking immunoproteasomes (triple-knockout mice), displayed a strong increase in polyubiquitinated proteins already in the young brain and developed spontaneous epileptic seizures, beginning at the age of 6 months. Injections of kainic acid led to high epilepsy-related mortality of aged triple-knockout mice, confirming increased pathological hyperexcitability states. Notably, the expression of the immunoproteasome was reduced in the brains of patients suffering from epilepsy. In addition, the aged triple-knockout mice showed increased anxiety, tau hyperphosphorylation and degeneration of Purkinje cell population with the resulting ataxic symptoms and locomotion alterations. Collectively, our study suggests a critical role for the immunoproteasome in the maintenance of a healthy brain during ageing.
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Affiliation(s)
- Hanna Leister
- Institute for Medical Microbiology and Hygiene, Philipps-University, 35043 Marburg, Germany
| | - Felix F Krause
- Institute for Medical Microbiology and Hygiene, Philipps-University, 35043 Marburg, Germany
| | - Beatriz Gil
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
| | - Ruslan Prus
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
| | - Inna Prus
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
| | - Anne Hellhund-Zingel
- Institute for Medical Microbiology and Hygiene, Philipps-University, 35043 Marburg, Germany
| | - Meghma Mitra
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
| | - Rogerio Da Rosa Gerbatin
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
| | - Norman Delanty
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
- Department of Neurology, Beaumont Hospital, D09V2N0 Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, D09V2N0 Dublin, Ireland
| | - Francesca M Brett
- Department of Neuropathology, Beaumont Hospital, D09V2N0 Dublin, Ireland
| | - Michael A Farrell
- Department of Neuropathology, Beaumont Hospital, D09V2N0 Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, D09V2N0 Dublin, Ireland
| | - Donncha F O’Brien
- Department of Neurosurgery, Beaumont Hospital, D09V2N0 Dublin, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
| | - Frederik Helmprobst
- Institute of Neuropathology, Philipps-University, 35043 Marburg, Germany
- Core Facility for Mouse Pathology and Electron Microscopy, Philipps-University, 35043 Marburg, Germany
| | - Axel Pagenstecher
- Institute of Neuropathology, Philipps-University, 35043 Marburg, Germany
- Core Facility for Mouse Pathology and Electron Microscopy, Philipps-University, 35043 Marburg, Germany
| | - Ulrich Steinhoff
- Institute for Medical Microbiology and Hygiene, Philipps-University, 35043 Marburg, Germany
| | - Alexander Visekruna
- Institute for Medical Microbiology and Hygiene, Philipps-University, 35043 Marburg, Germany
| | - Tobias Engel
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
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3
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de Diego-Garcia L, Brennan GP, Auer T, Menendez-Mendez A, Parras A, Martin-Gil A, Mitra M, Ollà I, Villalba-Benito L, Gil B, Alves M, Lau K, Delanty N, Beausang A, Cryan J, Brett FM, Farrell MA, O'Brien DF, Mendez R, Carracedo-Rodríguez G, Henshall DC, Lucas JJ, Engel T. CPEB4-CLOCK crosstalk during temporal lobe epilepsy. Epilepsia 2023; 64:2827-2840. [PMID: 37543852 DOI: 10.1111/epi.17736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023]
Abstract
OBJECTIVE Posttranscriptional mechanisms are increasingly recognized as important contributors to the formation of hyperexcitable networks in epilepsy. Messenger RNA (mRNA) polyadenylation is a key regulatory mechanism governing protein expression by enhancing mRNA stability and translation. Previous studies have shown large-scale changes in mRNA polyadenylation in the hippocampus of mice during epilepsy development. The cytoplasmic polyadenylation element-binding protein CPEB4 was found to drive epilepsy-induced poly(A) tail changes, and mice lacking CPEB4 develop a more severe seizure and epilepsy phenotype. The mechanisms controlling CPEB4 function and the downstream pathways that influence the recurrence of spontaneous seizures in epilepsy remain poorly understood. METHODS Status epilepticus was induced in wild-type and CPEB4-deficient male mice via an intra-amygdala microinjection of kainic acid. CLOCK binding to the CPEB4 promoter was analyzed via chromatin immunoprecipitation assay and melatonin levels via high-performance liquid chromatography in plasma. RESULTS Here, we show increased binding of CLOCK to recognition sites in the CPEB4 promoter region during status epilepticus in mice and increased Cpeb4 mRNA levels in N2A cells overexpressing CLOCK. Bioinformatic analysis of CPEB4-dependent genes undergoing changes in their poly(A) tail during epilepsy found that genes involved in the regulation of circadian rhythms are particularly enriched. Clock transcripts displayed a longer poly(A) tail length in the hippocampus of mice post-status epilepticus and during epilepsy. Moreover, CLOCK expression was increased in the hippocampus in mice post-status epilepticus and during epilepsy, and in resected hippocampus and cortex of patients with drug-resistant temporal lobe epilepsy. Furthermore, CPEB4 is required for CLOCK expression after status epilepticus, with lower levels in CPEB4-deficient compared to wild-type mice. Last, CPEB4-deficient mice showed altered circadian function, including altered melatonin blood levels and altered clustering of spontaneous seizures during the day. SIGNIFICANCE Our results reveal a new positive transcriptional-translational feedback loop involving CPEB4 and CLOCK, which may contribute to the regulation of the sleep-wake cycle during epilepsy.
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Affiliation(s)
- Laura de Diego-Garcia
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Ocupharm Group Research, Faculty of Optics and Optometry, University Complutense of Madrid, Madrid, Spain
| | - Gary P Brennan
- School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
- FutureNeuro, Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Theresa Auer
- School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Aida Menendez-Mendez
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Alberto Parras
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Madrid, Spain
| | - Alba Martin-Gil
- Ocupharm Group Research, Faculty of Optics and Optometry, University Complutense of Madrid, Madrid, Spain
| | - Meghma Mitra
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Ivana Ollà
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Madrid, Spain
- Networking Research Center on Neurodegenerative Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Leticia Villalba-Benito
- School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
- FutureNeuro, Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Beatriz Gil
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Mariana Alves
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Kelvin Lau
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro, Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Norman Delanty
- FutureNeuro, Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
- Beaumont Hospital, Dublin, Ireland
| | | | | | | | | | | | - Raúl Mendez
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | | | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro, Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - José J Lucas
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain, Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Madrid, Spain
- Networking Research Center on Neurodegenerative Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Tobias Engel
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro, Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
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4
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Biswas A, Salvucci M, Connor K, Düssmann H, Carberry S, Fichtner M, King E, Murphy B, O'Farrell AC, Cryan J, Beausang A, Heffernan J, Cremona M, Hennessy BT, Clerkin J, Sweeney KJ, MacNally S, Brett F, O'Halloran P, Bacon O, Furney S, Verreault M, Quissac E, Bielle F, Ahmed MH, Idbaih A, Leenstra S, Ntafoulis I, Fabro F, Lamfers M, Golebiewska A, Hertel F, Niclou SP, Yen RTC, Kremer A, Dilcan G, Lodi F, Arijs I, Lambrechts D, Purushothama MK, Kel A, Byrne AT, Prehn JHM. Comparative analysis of deeply phenotyped GBM cohorts of 'short-term' and 'long-term' survivors. J Neurooncol 2023:10.1007/s11060-023-04341-3. [PMID: 37237151 PMCID: PMC10322749 DOI: 10.1007/s11060-023-04341-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Glioblastoma (GBM) is an aggressive brain cancer that typically results in death in the first 15 months after diagnosis. There have been limited advances in finding new treatments for GBM. In this study, we investigated molecular differences between patients with extremely short (≤ 9 months, Short term survivors, STS) and long survival (≥ 36 months, Long term survivors, LTS). METHODS Patients were selected from an in-house cohort (GLIOTRAIN-cohort), using defined inclusion criteria (Karnofsky score > 70; age < 70 years old; Stupp protocol as first line treatment, IDH wild type), and a multi-omic analysis of LTS and STS GBM samples was performed. RESULTS Transcriptomic analysis of tumour samples identified cilium gene signatures as enriched in LTS. Moreover, Immunohistochemical analysis confirmed the presence of cilia in the tumours of LTS. Notably, reverse phase protein array analysis (RPPA) demonstrated increased phosphorylated GAB1 (Y627), SRC (Y527), BCL2 (S70) and RAF (S338) protein expression in STS compared to LTS. Next, we identified 25 unique master regulators (MR) and 13 transcription factors (TFs) belonging to ontologies of integrin signalling and cell cycle to be upregulated in STS. CONCLUSION Overall, comparison of STS and LTS GBM patients, identifies novel biomarkers and potential actionable therapeutic targets for the management of GBM.
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Affiliation(s)
- Archita Biswas
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Kate Connor
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Heiko Düssmann
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Steven Carberry
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Michael Fichtner
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Ellen King
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Brona Murphy
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Alice C O'Farrell
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin 9, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin 9, Dublin, Ireland
| | | | - Mattia Cremona
- Department of Medicine, Royal College of Surgeons in Ireland and Beaumont Hospital, Dublin 9, Dublin, Ireland
| | - Bryan T Hennessy
- Department of Medicine, Royal College of Surgeons in Ireland and Beaumont Hospital, Dublin 9, Dublin, Ireland
| | - James Clerkin
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
- Department of Neurosurgery, Beaumont Hospital, Dublin 9, Dublin, Ireland
| | - Kieron J Sweeney
- Department of Neurosurgery, Beaumont Hospital, Dublin 9, Dublin, Ireland
| | - Steve MacNally
- Department of Neurosurgery, Beaumont Hospital, Dublin 9, Dublin, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin 9, Dublin, Ireland
| | - Philip O'Halloran
- Department of Neurosurgery, Beaumont Hospital, Dublin 9, Dublin, Ireland
| | - Orna Bacon
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Simon Furney
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Maite Verreault
- DMU Neurosciences, Service de Neurologie 2-Mazarin, Sorbonne Université, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Inserm, F-75013, Paris, France
| | - Emie Quissac
- DMU Neurosciences, Service de Neurologie 2-Mazarin, Sorbonne Université, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Inserm, F-75013, Paris, France
| | - Franck Bielle
- DMU Neurosciences, Service de Neurologie 2-Mazarin, Sorbonne Université, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Inserm, F-75013, Paris, France
| | - Mohammed H Ahmed
- DMU Neurosciences, Service de Neurologie 2-Mazarin, Sorbonne Université, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Inserm, F-75013, Paris, France
| | - Ahmed Idbaih
- DMU Neurosciences, Service de Neurologie 2-Mazarin, Sorbonne Université, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Inserm, F-75013, Paris, France
| | - Sieger Leenstra
- Dept of Neurosurgery Brain Tumor Center, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Ioannis Ntafoulis
- Dept of Neurosurgery Brain Tumor Center, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Federica Fabro
- Dept of Neurosurgery Brain Tumor Center, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Martine Lamfers
- Dept of Neurosurgery Brain Tumor Center, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Anna Golebiewska
- NORLUX Neuro-Oncology laboratory, Department of Cancer Research, Luxembourg Institute of Health, 6A, Rue Nicolas-Ernest Barblé, L-1210, Luxembourg, Luxembourg
| | - Frank Hertel
- NORLUX Neuro-Oncology laboratory, Department of Cancer Research, Luxembourg Institute of Health, 6A, Rue Nicolas-Ernest Barblé, L-1210, Luxembourg, Luxembourg
- Faculty of Sciences, Technology and Medicine, University of Luxembourg, L-4365, Esch-sur-Alzette, Luxembourg
| | - Simone P Niclou
- NORLUX Neuro-Oncology laboratory, Department of Cancer Research, Luxembourg Institute of Health, 6A, Rue Nicolas-Ernest Barblé, L-1210, Luxembourg, Luxembourg
- Faculty of Sciences, Technology and Medicine, University of Luxembourg, L-4365, Esch-sur-Alzette, Luxembourg
| | - Romain Tching Chi Yen
- Information Technology for Translational Medicine, 27, Rue Henri Koch - House of BioHealth, L-4354, Esch-sur-Alzette, Luxembourg
| | - Andreas Kremer
- Information Technology for Translational Medicine, 27, Rue Henri Koch - House of BioHealth, L-4354, Esch-sur-Alzette, Luxembourg
| | - Gonca Dilcan
- VIB-KU Leuven Cancer for Cancer Biology, Onderwijs en Navorsing 5, Herestraat, 49, 3000, Leuven, Belgium
| | - Francesca Lodi
- VIB-KU Leuven Cancer for Cancer Biology, Onderwijs en Navorsing 5, Herestraat, 49, 3000, Leuven, Belgium
| | - Ingrid Arijs
- VIB-KU Leuven Cancer for Cancer Biology, Onderwijs en Navorsing 5, Herestraat, 49, 3000, Leuven, Belgium
| | - Diether Lambrechts
- VIB-KU Leuven Cancer for Cancer Biology, Onderwijs en Navorsing 5, Herestraat, 49, 3000, Leuven, Belgium
| | | | - Alexander Kel
- geneXplain GmbH, Am Exer 19b, 38302, Wolfenbüttel, Germany
| | - Annette T Byrne
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Dublin, D02 YN77, Ireland.
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Lockhart A, Heffernan J, Kennedy A, Walsh A, Heeney C, Cheung R, Howley R, Cryan J, Beausang A, Farrell M, Brett F. Brain biopsy in neurological disease of unknown etiology: A single-center 12-year retrospective analysis. Clin Neuropathol 2023; 42:93-99. [PMID: 36970952 DOI: 10.5414/np301517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 03/29/2023] Open
Abstract
There are no international guidelines for brain biopsy in neurological disease of unknown etiology, yet most practicing neurologists will encounter difficult cases in which biopsy is considered. This patient cohort is heterogenous, and it is unclear in which circumstances biopsy is most useful. We performed an audit of brain biopsies reviewed in our neuropathology department from 2010 to 2021. Of 9,488 biopsies, 331 biopsies undertaken for an undiagnosed neurological disease were identified. Where documented, the commonest symptoms were hemorrhage, encephalopathy, and dementia. 29% of biopsies were non-diagnostic. The most common clinically relevant findings on biopsy were infection, cerebral amyloid angiopathy with or without angiitis, and demyelination. Rarer conditions included CNS vasculitis, non-infectious encephalitis, and Creutzfeldt Jakob Disease. We highlight the value of brain biopsy in the workup of cryptogenic neurological disease despite recent advances in less invasive diagnostics.
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6
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White K, Connor K, Meylan M, Bougoüin A, Salvucci M, Bielle F, O'Farrell AC, Sweeney K, Weng L, Bergers G, Dicker P, Ashley DM, Lipp ES, Low JT, Zhao J, Wen P, Prins R, Verreault M, Idbaih A, Biswas A, Prehn JHM, Lambrechts D, Arijs I, Lodi F, Dilcan G, Lamfers M, Leenstra S, Fabro F, Ntafoulis I, Kros JM, Cryan J, Brett F, Quissac E, Beausang A, MacNally S, O'Halloran P, Clerkin J, Bacon O, Kremer A, Chi Yen RT, Varn FS, Verhaak RGW, Sautès-Fridman C, Fridman WH, Byrne AT. Identification, validation and biological characterisation of novel glioblastoma tumour microenvironment subtypes: implications for precision immunotherapy. Ann Oncol 2023; 34:300-314. [PMID: 36494005 DOI: 10.1016/j.annonc.2022.11.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND New precision medicine therapies are urgently required for glioblastoma (GBM). However, to date, efforts to subtype patients based on molecular profiles have failed to direct treatment strategies. We hypothesised that interrogation of the GBM tumour microenvironment (TME) and identification of novel TME-specific subtypes could inform new precision immunotherapy treatment strategies. MATERIALS AND METHODS A refined and validated microenvironment cell population (MCP) counter method was applied to >800 GBM patient tumours (GBM-MCP-counter). Specifically, partition around medoids (PAM) clustering of GBM-MCP-counter scores in the GLIOTRAIN discovery cohort identified three novel patient clusters, uniquely characterised by TME composition, functional orientation markers and immune checkpoint proteins. Validation was carried out in three independent GBM-RNA-seq datasets. Neoantigen, mutational and gene ontology analysis identified mutations and uniquely altered pathways across subtypes. The longitudinal Glioma Longitudinal AnalySiS (GLASS) cohort and three immunotherapy clinical trial cohorts [treatment with neoadjuvant/adjuvant anti-programmed cell death protein 1 (PD-1) or PSVRIPO] were further interrogated to assess subtype alterations between primary and recurrent tumours and to assess the utility of TME classifiers as immunotherapy biomarkers. RESULTS TMEHigh tumours (30%) displayed elevated lymphocyte, myeloid cell immune checkpoint, programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 transcripts. TMEHigh/mesenchymal+ patients featured tertiary lymphoid structures. TMEMed (46%) tumours were enriched for endothelial cell gene expression profiles and displayed heterogeneous immune populations. TMELow (24%) tumours were manifest as an 'immune-desert' group. TME subtype transitions upon recurrence were identified in the longitudinal GLASS cohort. Assessment of GBM immunotherapy trial datasets revealed that TMEHigh patients receiving neoadjuvant anti-PD-1 had significantly increased overall survival (P = 0.04). Moreover, TMEHigh patients treated with adjuvant anti-PD-1 or oncolytic virus (PVSRIPO) showed a trend towards improved survival. CONCLUSIONS We have established a novel TME-based classification system for application in intracranial malignancies. TME subtypes represent canonical 'termini a quo' (starting points) to support an improved precision immunotherapy treatment approach.
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Affiliation(s)
- K White
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - K Connor
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - M Meylan
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - A Bougoüin
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - M Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - F Bielle
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - A C O'Farrell
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - K Sweeney
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - L Weng
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, Leuven, Belgium
| | - G Bergers
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, Leuven, Belgium
| | - P Dicker
- Epidemiology & Public Health, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - D M Ashley
- Duke Cancer Institute, Duke University, Durham, USA
| | - E S Lipp
- Duke Cancer Institute, Duke University, Durham, USA
| | - J T Low
- Duke Cancer Institute, Duke University, Durham, USA
| | - J Zhao
- Department of Systems Biology at Columbia University, New York, USA
| | - P Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - R Prins
- Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - M Verreault
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - A Idbaih
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière-Charles Foix, Paris, France
| | - A Biswas
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - J H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - D Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - I Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - F Lodi
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - G Dilcan
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - M Lamfers
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - S Leenstra
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - F Fabro
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - I Ntafoulis
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - J M Kros
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - J Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - F Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - E Quissac
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - A Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - S MacNally
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - P O'Halloran
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - J Clerkin
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - O Bacon
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - A Kremer
- Information Technology for Translational Medicine (ITTM), Luxembourg, Luxembourg
| | - R T Chi Yen
- Information Technology for Translational Medicine (ITTM), Luxembourg, Luxembourg
| | - F S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - R G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, USA; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Medical Center, Amsterdam, the Netherlands
| | - C Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - W H Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - A T Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Connor K, Conroy E, White K, Shiels L, Keek S, Ibrahim A, Gallagher W, Clerkin J, Sweeney K, O'Brien D, Cryan J, Heffernan J, Brett F, Lambin P, Woodruff H, Byrne A. MODL-24. ESTABLISHING A CLINICALLY RELEVANT CT AND ASSOCIATED RADIOMICS PIPELINE FOR INTRACRANIAL RODENT TUMOUR MODELS. Neuro Oncol 2022. [PMCID: PMC9661278 DOI: 10.1093/neuonc/noac209.1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
While magnetic resonance imaging (MRI) is the predominant imaging modality for glioblastoma (GBM), pre-clinical MRI scanner availability is limited. As pre-clinical CT is more widely available and cost-effective, this study aimed to 1) establish preclinical-GBM CT and CT-radiomic workflows, 2) identify whether CE-CT could detect murine orthotopic GBM tumours on two CT instruments [TRIUMPHX-O-CT; IVISSPECTRUM-CT], 3) assess whether CT-radiomic features could distinguish tumour from normal tissue, and support earlier detection of tumours, 4) verify translation of pre-clinical CT-radiomic pipelines to, and assess pre-clinical CT-features in, clinical CE-CT scans.U87R-Luc2(n=25) and NFpp10a-Luc2(n=10) orthotopic GBM models were established and tumours monitored via bioluminescence imaging (BLI). Concurrently, mice underwent CE-CT (IV-iodine/300mg/mL/50kV-scan). Extracted radiomic features (PyRadiomics) underwent dimensionality reduction (Spearman correlation; >0.85). Remaining features were analysed (Recursive feature elimination (RFE)/RepeatedCV/randomforest) in normal and tumour tissue and across timepoints (TRIUMPHX-O-CT-Wk3vsWk6,Wk6vsWk9/12; IVISSPECTRUM-CT-Wk6vsWk9/12).CE-CT and radiomic pipelines were successfully established for orthotopic GBM models, using both CT-systems. On visual assessment of images, BLI was significantly more sensitive, with tumours detectable at Wk1 (BLI) vs Wk9 (CE-CT). However, RFE analysis identified CT-radiomic features (first_order&glcm) which differentiated tumour from normal tissue (TRIUMPHX-O-CT). A subsequent feature set (first_order,glcm,gldm&glzm) were identified (TRIUMPHX-O-CT/IVISSPECTRUM-CT), detecting tumours earlier (Wk3&Wk6) than possible by visual assessment of CTs. Preclinical radiomic methods were successfully applied to exploratory clinical CE-CT scans(n=10). Here, several preclinical CT-features (e.g. Zone_Entropy) showed increased intensity in tumour regions. Overall experimental BLI is the most sensitive method for pre-clinical intracranial tumour detection. However, analysis of clinically relevant CT-radiomic features may facilitate tumour identification and earlier tumour detection (Wk3/Wk6-TRIUMPHX-O-CT/Wk6-IVISSPECTRUM-CT) than possible by visual assessment of CT (Wk9). Clinically relevant CT-derived radiomic features may therefore support intracranial rodent tumour assessment. Importantly, preclinical radiomic methods successfully translate to clinical CT-radiomic analysis. Parallel trends in tumour-specific feature intensities across pre-clinical and clinical scans suggest species conservation of features.
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Affiliation(s)
- Kate Connor
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Emer Conroy
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, , Dublin , Ireland
| | - Kieron White
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Liam Shiels
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Simon Keek
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht , Maastricht , Netherlands
| | - Abdalla Ibrahim
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht , Maastricht , Netherlands
| | - William Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin , Ireland
| | - James Clerkin
- Department of Neurosurgery, Beaumont hospital, Dublin Ireland , Dublin , Ireland
| | - Kieron Sweeney
- Department of Neurosurgery, Beaumont hospital , Dublin , Ireland
| | - David O'Brien
- Department of Neurosurgery, Beaumont hospital, Dublin , Dublin , Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital , Dublin , Ireland
| | | | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital , Dublin , Ireland
| | - Philippe Lambin
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University , Maastricht , Netherlands
| | - Henry Woodruff
- The D-Lab: Department of Precision Medicine, GROW - School for Oncology, Maastricht University, Maastricht , Maastricht , Netherlands
| | - Annette Byrne
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
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8
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Imlau M, Saeed M, Cryan J, Hoey S, McKenna M, Jahns H, Kelly P. Dysplastic gangliocytoma of the cerebellum in a cat. Vet Pathol 2022; 59:459-462. [PMID: 35130805 PMCID: PMC9109245 DOI: 10.1177/03009858221075594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A 2.5-year-old cat presented with progressive ataxia and lethargy. Magnetic resonance imaging (MRI) showed enlargement of the cerebellum and herniation of cerebellar vermis. Postmortem examination confirmed the MRI findings, and histopathology showed numerous large dysplastic neurons populating and displacing the Purkinje cell layer and extending into the molecular and granular layers of the cerebellum. The lesion was diagnosed as dysplastic gangliocytoma of the cerebellum. In humans, this tumor is often associated with Cowden syndrome, a genetic disorder characterized by multiple hamartomas and an increased risk of developing certain neoplasms, known to be linked to a germline mutation of the phosphatase and tensin homolog (PTEN) gene. Reduction in PTEN nuclear and cytoplasmic immunohistochemical labeling of dysplastic neurons in this case suggested a possible PTEN mutation involved in the tumorigenesis. This report provides a detailed pathology description of the tumor and the use of neuronal and PTEN markers which will help guide pathologists presented with this rare condition in the future.
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9
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Jagust P, Varešlija D, Cocchiglia S, O'Haloran PJ, Dablouk MO, Brett FM, Cryan J, Beausang A, Hudson L, Hill ADK, Young L. O50: DEVELOPMENT OF A PATIENT-DERIVED TUMOUR ORGANOIDS FROM METASTATIC BREAST CANCER FOR ASSESSMENT OF NOVEL CLINICALLY ACTIONABLE TARGETS. Br J Surg 2021. [DOI: 10.1093/bjs/znab117.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Introduction
Metastatic breast cancer (MBC) is the main source of mortality in breast cancer patients largely due to lack of effective treatments. Our previous results suggest that tumour transcriptional heterogeneity drives therapy resistance and cancer relapse. While traditional in vitro human cancer cell line models have been widely used for disease modelling, they do not faithfully recapitulate the pathophysiology of MBC.
Method
In this study we developed patient-derived tumour organoid cultures from frozen patient-derived (PDX) models of MBC. Using those models we performed preclinical drug screening of investigational and FDA approved therapeutics previously uncovered by us as potentially clinically actionable in MBC.
Result
Our results reveal high heterogeneity in the responses to various targeted therapies among tested MBC organoids, which makes them a valuable tool for studying intra-tumor heterogeneity and drug response. Moreover, drug screening identified a divergent set of the breast to brain metastatic MBC organoids that showed high sensitivity to a new class of tyrosine kinase receptors, RET.
Conclusion
Taken together, our novel MBC models and methodology applied here provides an important modelling tool to assess the contribution of intra-tumour heterogeneity and microenvironment to drug response as they recapitulate the cellular, structural and biochemical complexity previously observed in our genomic characterisation of MBCs. Application of this type of translational research will enhance the development of new targeted precision medicine strategies and prelude stratification for clinical trials. Abbreviations MBC- Metastatic Breast Cancer; PDX- Patient-Derived Xenografts; FDA- Food and Drug Administration; RET- Receptor Tyrosine Kinase
Take-home message
Patient-derived tumour organoid cultures provide an important modelling tool to assess the contribution of intra-tumour heterogeneity and microenvironment to drug response as they recapitulate the cellular, structural and biochemical complexity previously observed in genomic characterisation of metastatic breast cancer.
SURGICAL EDUCATION AND TRAINING
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Affiliation(s)
- P Jagust
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland,
| | - D Varešlija
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland,
| | - S Cocchiglia
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland,
| | - PJ O'Haloran
- Department of Neurosurgery, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland,
| | - MO Dablouk
- Department of Neurosurgery, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland,
| | - FM Brett
- Department of Neuropathology, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland
| | - J Cryan
- Department of Neuropathology, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland
| | - A Beausang
- Department of Neuropathology, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland
| | - L Hudson
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland,
| | - ADK Hill
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland,
| | - L Young
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland,
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10
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Varešlija D, Ward E, Purcell SP, Cosgrove NS, Cocchiglia S, O'Halloran PJ, Charmsaz S, Bane FT, Brett FM, Farrell M, Cryan J, Beausang A, Hudson L, Turnbul AK, Dixon JM, Hill ADK, Priedigkeit N, Oesterreich S, Lee AV, Sims AH, Redmond AM, Carroll JS, Young LS. Comparative analysis of the AIB1 interactome in breast cancer reveals MTA2 as a repressive partner which silences E-Cadherin to promote EMT and associates with a pro-metastatic phenotype. Oncogene 2021; 40:1318-1331. [PMID: 33420368 PMCID: PMC7892341 DOI: 10.1038/s41388-020-01606-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/20/2020] [Accepted: 12/07/2020] [Indexed: 02/08/2023]
Abstract
Steroid regulated cancer cells use nuclear receptors and associated regulatory proteins to orchestrate transcriptional networks to drive disease progression. In primary breast cancer, the coactivator AIB1 promotes estrogen receptor (ER) transcriptional activity to enhance cell proliferation. The function of the coactivator in ER+ metastasis however is not established. Here we describe AIB1 as a survival factor, regulator of pro-metastatic transcriptional pathways and a promising actionable target. Genomic alterations and functional expression of AIB1 associated with reduced disease-free survival in patients and enhanced metastatic capacity in novel CDX and PDX ex-vivo models of ER+ metastatic disease. Comparative analysis of the AIB1 interactome with complementary RNAseq characterized AIB1 as a transcriptional repressor. Specifically, we report that AIB1 interacts with MTA2 to form a repressive complex, inhibiting CDH1 (encoding E-cadherin) to promote EMT and drive progression. We further report that pharmacological and genetic inhibition of AIB1 demonstrates significant anti-proliferative activity in patient-derived models establishing AIB1 as a viable strategy to target endocrine resistant metastasis. This work defines a novel role for AIB1 in the regulation of EMT through transcriptional repression in advanced cancer cells with a considerable implication for prognosis and therapeutic interventions.
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Affiliation(s)
- Damir Varešlija
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Elspeth Ward
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Siobhan P Purcell
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Nicola S Cosgrove
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sinéad Cocchiglia
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Philip J O'Halloran
- Department of Neurosurgery, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland
| | - Sara Charmsaz
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Fiona T Bane
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Francesca M Brett
- Department of Neuropathology, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland
| | - Michael Farrell
- Department of Neuropathology, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, National Neurosurgical Center, Beaumont Hospital, Dublin, Ireland
| | - Lance Hudson
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Arran K Turnbul
- Breast Cancer Now Research Laboratories, Edinburgh, EH4 2XU, UK
| | - J Michael Dixon
- Breast Cancer Now Research Laboratories, Edinburgh, EH4 2XU, UK
| | - Arnold D K Hill
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Nolan Priedigkeit
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Women's Cancer Research Center, Magee-Women's Research Institute, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Women's Cancer Research Center, Magee-Women's Research Institute, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew H Sims
- Applied Bioinformatics of Cancer Group, University of Edinburgh Cancer Research UK Centre, MRC Institute of Genetics & Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - Aisling M Redmond
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Leonie S Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland.
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11
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Fearon C, Loftus T, Byrne AL, Heffernan J, Cooney M, Heeney C, Walsh A, Lorigan J, Beausang A, Cryan J, Farrell M, Brett F. Impact of the 2016 World Health Organization Classification of Tumours of the Central Nervous System: an Irish experience. Ir J Med Sci 2019; 189:799-803. [PMID: 31797204 DOI: 10.1007/s11845-019-02144-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/15/2019] [Indexed: 01/26/2023]
Abstract
The 2016 World Health Organization Classification of Tumours of the Central Nervous System Tumours represents the most significant update to neuro-oncological tumour classification to date, compared with previous updates. This update reflects the substantial advances in molecular and genetic understanding of both adult and childhood brain tumours which have occurred in recent years. These advances have meant that an increasing array of molecular tests are required to definitively classify a tumour, allowing for a more precise integrated pathological diagnosis, but at the expense of a more challenging pathology workup. We review the changes incorporated into the 2016 classification and describe the impact of these changes in an Irish neuropathology laboratory.
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Affiliation(s)
- Conor Fearon
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Teresa Loftus
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Amber Lynn Byrne
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | | | - Maeve Cooney
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Ciara Heeney
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Andrea Walsh
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Jennifer Lorigan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Michael Farrell
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland.
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12
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O’Halloran P, Cleary A, Cryan J, Caird J. SURG-10. MELANOMA CEREBRAL METASTASES IN IRELAND- GETTING UNDER THE SKIN. Neurooncol Adv 2019. [PMCID: PMC7213406 DOI: 10.1093/noajnl/vdz014.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND: Ireland has the highest rate of melanoma related deaths in Europe. Despite the incidence of melanoma reaching record highs there remains a paucity of information in Ireland regarding the factors associated with melanoma brain metastasis (MBM). METHODS: Patients diagnosed with MBM in Ireland were retrospectively identified in Beaumont Hospital between 1999 and 2018. Patient demographics; year of detection of MBM, age at diagnosis of primary melanoma, age at detection of MBM, anatomical location of primary melanoma, BRAF mutation analysis and the number of metastases were investigated. Follow up data was also derived, including overall survival (OS). RESULTS: The incidence of malignant melanoma has increased by 158% over the past 20 years with 1,092 and 422 cases diagnosed in 2018 and 1999, respectively.128 patients with melanoma brain metastases were identified during this period. The median OS after detection of MBM was 5 months (95% CI 0.641–9.359 months). There was a male predominance (n= 77/128; 60%) with a median age of death at 58 years (n=67; range 16–82 years). Although females had a significantly longer time between diagnosis of primary melanoma and detection of MBM compared to males, 4 and 2 years respectively (p=0.02442), there was no significant age difference at death between males and females (p= 0.41294). BRAF mutation was an independent prognostic factor with an improved overall survival compared to those without the mutation, of 8 months and 3.5 months respectively (p=0.0012). Although non significant, the primary location of melanoma, leptomeningeal disease and number of cerebral metastases were all important considerations in this group. CONCLUSIONS: Male predominance and BRAF mutation represent important factors in this population group. The results of this study add to our knowledge concerning outcomes in melanoma brain metastases in Ireland, and may be useful in clinical planning, educational programs and future treatments.
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Affiliation(s)
| | - Anna Cleary
- Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - John Caird
- Department of Neurosurgery, Beaumont Hospital, Dublin, Ireland
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13
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Kearney H, Price T, Cryan J, Beausang A, Looby S, Brett FM, Farrell M. Acute multiple sclerosis lesion pathology does not predict subsequent clinical course-a biopsy study. Ir J Med Sci 2019; 188:1427-1434. [PMID: 30771138 DOI: 10.1007/s11845-019-01983-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/04/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Knowledge of the clinical outcome in tumefactive demyelination remains limited. AIMS This study aims to characterise the natural history of biopsy-proven, pathogen-free, cerebral demyelination in an adult Irish population. METHODS We identified all patients with biopsy-proven demyelination in a single neuropathology centre between 1999 and 2017. A baseline, and at least one follow-up MRI scan was available in each instance (mean of 3 scans per patient), together with both the presenting and most recent clinical details including disability level and disease-modifying drugs. RESULTS In 21 patients, white matter biopsies showed the following: macrophages with myelin debris, myelin-axonal dissociation, reactive astrocytes and occasional lymphocytes. During a mean follow-up time of 8 years (± 4.4), 17 patients developed MS, confirmed both clinically and on MRI, using the 2010 McDonald criteria: 11 relapsing remitting (RR) MS, four secondary progressive and two primary progressive MS. Four patients had a monophasic illness with lesion regression, without clinical or radiological evidence of any further disease activity on follow-up. The patients with progressive MS had significantly higher levels of physical disability than either the RRMS or monophasic patients. CONCLUSION Uniform white matter subacute demyelination is associated with a diverse clinical course ranging from a monophasic illness to progressive MS, suggesting that extraneous factors distinct from the basic pathology significantly influence the clinical course in MS.
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Affiliation(s)
- Hugh Kearney
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin, Ireland.
| | - Tucker Price
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin, Ireland
| | - Seamus Looby
- Department of Neuroradiology, Beaumont Hospital, Dublin, Ireland
| | - Francesca M Brett
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin, Ireland
| | - Michael Farrell
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin, Ireland
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14
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Tsoli M, Shen H, Mayoh C, Franshaw L, Ehteda A, Upton D, Carvalho D, Vinci M, Meel MH, van Vuurden D, Plessier A, Castel D, Drissi R, Farrell M, Cryan J, Crimmins D, Caird J, Pears J, Francis S, Ludlow LEA, Carai A, Mastronuzzi A, Liu B, Hansford J, Gottardo N, Hassall T, Kirby M, Fouladi M, Hawkins C, Monje M, Grill J, Jones C, Hulleman E, Ziegler DS. International experience in the development of patient-derived xenograft models of diffuse intrinsic pontine glioma. J Neurooncol 2019; 141:253-263. [PMID: 30446898 DOI: 10.1007/s11060-018-03038-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/24/2018] [Indexed: 10/27/2022]
Abstract
PURPOSE Diffuse intrinsic pontine glioma is the most aggressive form of high grade glioma in children with no effective therapies. There have been no improvements in survival in part due poor understanding of underlying biology, and lack of representative in vitro and in vivo models. Recently, it has been found feasible to use both biopsy and autopsy tumors to generate cultures and xenograft models. METHODS To further model development, we evaluated the collective international experience from 8 collaborating centers to develop DIPG pre-clinical models from patient-derived autopsies and biopsies. Univariate and multivariate analysis was performed to determine key factors associated with the success of in vitro and in vivo PDX development. RESULTS In vitro cultures were successfully established from 57% of samples (84.2% of biopsies and 38.2% of autopsies). Samples transferred in DMEM media were more likely to establish successful culture than those transported in Hibernate A. In vitro cultures were more successful from biopsies (84.2%) compared with autopsies (38.2%) and as monolayer on laminin-coated plates than as neurospheres. Primary cultures successfully established from autopsy samples were more likely to engraft in animal models than cultures established from biopsies (86.7% vs. 47.4%). Collectively, tumor engraftment was more successful when DIPG samples were directly implanted in mice (68%), rather than after culturing (40.7%). CONCLUSION This multi-center study provides valuable information on the success rate of establishing patient-derived pre-clinical models of DIPG. The results can lead to further optimization of DIPG model development and ultimately assist in the investigation of new therapies for this aggressive pediatric brain tumor.
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Affiliation(s)
- Maria Tsoli
- Children's Cancer Institute, Randwick, NSW, 2031, Australia
| | - Han Shen
- Children's Cancer Institute, Randwick, NSW, 2031, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Randwick, NSW, 2031, Australia
| | - Laura Franshaw
- Children's Cancer Institute, Randwick, NSW, 2031, Australia
| | - Anahid Ehteda
- Children's Cancer Institute, Randwick, NSW, 2031, Australia
| | - Danielle Upton
- Children's Cancer Institute, Randwick, NSW, 2031, Australia
| | - Diana Carvalho
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Maria Vinci
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Michael H Meel
- Department of Pediatric Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Dannis van Vuurden
- Department of Pediatric Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Alexander Plessier
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique (CNRS) et Departement de Cancerologie de l'Enfant et de l'Adolescent, Gustave Roussy et Universite Paris-Saclay, Villejuif, France
| | - David Castel
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique (CNRS) et Departement de Cancerologie de l'Enfant et de l'Adolescent, Gustave Roussy et Universite Paris-Saclay, Villejuif, France
| | - Rachid Drissi
- Brain Tumor Center, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, USA
| | - Michael Farrell
- Histopathology Department, Beaumont Hospital, Dublin, Ireland
| | - Jane Cryan
- Histopathology Department, Beaumont Hospital, Dublin, Ireland
| | - Darach Crimmins
- Department of Neurosurgery, Temple Street Children's University Hospital, Dublin, Ireland
| | - John Caird
- Department of Neurosurgery, Temple Street Children's University Hospital, Dublin, Ireland
| | - Jane Pears
- Our Lady's Children's Hospital, Dublin, Ireland
| | - Stephanie Francis
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, 2052, Australia
| | - Louise E A Ludlow
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, VIC, 3052, Australia
| | - Andrea Carai
- Neurosurgery Unit, Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children's Hospital, Rome, Italy
| | - Angela Mastronuzzi
- Neuro-Oncology Unit, Department of Hemato-Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, Rome, Italy
| | - Bing Liu
- Children's Cancer Institute, Randwick, NSW, 2031, Australia
| | - Jordan Hansford
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, VIC, 3052, Australia
| | - Nick Gottardo
- Department of Oncology, Princess Margaret Hospital, Perth, WA, Australia
| | - Tim Hassall
- Lady Cilento Children's Hospital, Brisbane, Australia
| | - Maria Kirby
- Department of Haematology-Oncology, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Maryam Fouladi
- Brain Tumor Center, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, USA
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michelle Monje
- Stanford University and Lucile Packard Children's Hospital, Palo Alto, CA, USA
| | - Jacques Grill
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique (CNRS) et Departement de Cancerologie de l'Enfant et de l'Adolescent, Gustave Roussy et Universite Paris-Saclay, Villejuif, France
| | - Chris Jones
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Esther Hulleman
- Unite Mixte de Recherche 8203 du Centre National de la Recherche Scientifique (CNRS) et Departement de Cancerologie de l'Enfant et de l'Adolescent, Gustave Roussy et Universite Paris-Saclay, Villejuif, France
| | - David S Ziegler
- Children's Cancer Institute, Randwick, NSW, 2031, Australia.
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, 2052, Australia.
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15
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Lorigan J, Kearney H, Grimes B, Heffernan J, Beausang A, Cryan J, Farrell MA, Brett FM. Evaluation of the specificity of the central diagnostic criterion for chronic traumatic encephalopathy. Ir J Med Sci 2018; 188:993-998. [PMID: 30506345 DOI: 10.1007/s11845-018-1943-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/22/2018] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Chronic traumatic encephalopathy (CTE) is a postmortem diagnosis. Consensus postmortem, but not antemortem, diagnostic criteria have been established. A key factor in these criteria is evidence of phosphorylated-tau (p-tau) around sulcal vessels in the cortex. However, this sign has been observed anecdotally in a diverse range of neurodegenerative diseases (NDD). We therefore hypothesise that this criterion may lack specificity. METHODS To test this, we assessed patients with NDD, but no documented history of brain trauma, for sulcal p-tau. Tissue was retrieved from Dublin Brain Bank (known NDD n = 17; control with no diagnosed NDD n = 6; CTE n = 1), and slides were prepared from three sites with a predilection for trauma: superior frontal gyrus, temporal pole, and superior temporal gyrus. We stained the resulting anonymised slides with both hemotoxylin and eosin (H&E) and p-tau. Three neuropathologists, blinded to the clinical history and neuropathological diagnosis in each instance, evaluated each case for sulcal p-tau. We calculated the interrater agreement, using Fleiss's kappa, and the specificity of this neuropathological sign. RESULTS Sulcal p-tau was highly specific to diagnosed CTE cases (specificity 0.98), with moderate interrater agreement (κ = 0.45). CONCLUSION In conclusion, therefore, we observed sulcal p-tau to be a sign highly specific to CTE when compared with NDD cases in the absence of head trauma.
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Affiliation(s)
- Jennifer Lorigan
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland.
| | - Hugh Kearney
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Bryan Grimes
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Josephine Heffernan
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Michael A Farrell
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Francesca M Brett
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
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16
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De Looze C, Beausang A, Cryan J, Loftus T, Buckley PG, Farrell M, Looby S, Reilly R, Brett F, Kearney H. Machine learning: a useful radiological adjunct in determination of a newly diagnosed glioma's grade and IDH status. J Neurooncol 2018; 139:491-499. [PMID: 29770897 DOI: 10.1007/s11060-018-2895-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/02/2018] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Machine learning methods have been introduced as a computer aided diagnostic tool, with applications to glioma characterisation on MRI. Such an algorithmic approach may provide a useful adjunct for a rapid and accurate diagnosis of a glioma. The aim of this study is to devise a machine learning algorithm that may be used by radiologists in routine practice to aid diagnosis of both: WHO grade and IDH mutation status in de novo gliomas. METHODS To evaluate the status quo, we interrogated the accuracy of neuroradiology reports in relation to WHO grade: grade II 96.49% (95% confidence intervals [CI] 0.88, 0.99); III 36.51% (95% CI 0.24, 0.50); IV 72.9% (95% CI 0.67, 0.78). We derived five MRI parameters from the same diagnostic brain scans, in under two minutes per case, and then supplied these data to a random forest algorithm. RESULTS Machine learning resulted in a high level of accuracy in prediction of tumour grade: grade II/III; area under the receiver operating characteristic curve (AUC) = 98%, sensitivity = 0.82, specificity = 0.94; grade II/IV; AUC = 100%, sensitivity = 1.0, specificity = 1.0; grade III/IV; AUC = 97%, sensitivity = 0.83, specificity = 0.97. Furthermore, machine learning also facilitated the discrimination of IDH status: AUC of 88%, sensitivity = 0.81, specificity = 0.77. CONCLUSIONS These data demonstrate the ability of machine learning to accurately classify diffuse gliomas by both WHO grade and IDH status from routine MRI alone-without significant image processing, which may facilitate usage as a diagnostic adjunct in clinical practice.
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Affiliation(s)
- Céline De Looze
- Trinity Centre for Bioengineering, Trinity College Dublin, Dublin, Ireland.,School of Engineering, Trinity College Dublin, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Teresa Loftus
- Department of Molecular Pathology, Beaumont Hospital, Dublin, Ireland
| | - Patrick G Buckley
- Department of Molecular Pathology, Beaumont Hospital, Dublin, Ireland.,Genomics Medicine Ireland, Dublin, Ireland
| | - Michael Farrell
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Seamus Looby
- Department of Neuroradiology, Beaumont Hospital, Dublin, Ireland
| | - Richard Reilly
- Trinity Centre for Bioengineering, Trinity College Dublin, Dublin, Ireland.,Institute of Neurosciences, Trinity College Dublin, Dublin, Ireland.,School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Hugh Kearney
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland.
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17
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Capper D, Jones DTW, Sill M, Hovestadt V, Schrimpf D, Sturm D, Koelsche C, Sahm F, Chavez L, Reuss DE, Kratz A, Wefers AK, Huang K, Pajtler KW, Schweizer L, Stichel D, Olar A, Engel NW, Lindenberg K, Harter PN, Braczynski AK, Plate KH, Dohmen H, Garvalov BK, Coras R, Hölsken A, Hewer E, Bewerunge-Hudler M, Schick M, Fischer R, Beschorner R, Schittenhelm J, Staszewski O, Wani K, Varlet P, Pages M, Temming P, Lohmann D, Selt F, Witt H, Milde T, Witt O, Aronica E, Giangaspero F, Rushing E, Scheurlen W, Geisenberger C, Rodriguez FJ, Becker A, Preusser M, Haberler C, Bjerkvig R, Cryan J, Farrell M, Deckert M, Hench J, Frank S, Serrano J, Kannan K, Tsirigos A, Brück W, Hofer S, Brehmer S, Seiz-Rosenhagen M, Hänggi D, Hans V, Rozsnoki S, Hansford JR, Kohlhof P, Kristensen BW, Lechner M, Lopes B, Mawrin C, Ketter R, Kulozik A, Khatib Z, Heppner F, Koch A, Jouvet A, Keohane C, Mühleisen H, Mueller W, Pohl U, Prinz M, Benner A, Zapatka M, Gottardo NG, Driever PH, Kramm CM, Müller HL, Rutkowski S, von Hoff K, Frühwald MC, Gnekow A, Fleischhack G, Tippelt S, Calaminus G, Monoranu CM, Perry A, Jones C, Jacques TS, Radlwimmer B, Gessi M, Pietsch T, Schramm J, Schackert G, Westphal M, Reifenberger G, Wesseling P, Weller M, Collins VP, Blümcke I, Bendszus M, Debus J, Huang A, Jabado N, Northcott PA, Paulus W, Gajjar A, Robinson GW, Taylor MD, Jaunmuktane Z, Ryzhova M, Platten M, Unterberg A, Wick W, Karajannis MA, Mittelbronn M, Acker T, Hartmann C, Aldape K, Schüller U, Buslei R, Lichter P, Kool M, Herold-Mende C, Ellison DW, Hasselblatt M, Snuderl M, Brandner S, Korshunov A, von Deimling A, Pfister SM. DNA methylation-based classification of central nervous system tumours. Nature 2018; 555:469-474. [PMID: 29539639 PMCID: PMC6093218 DOI: 10.1038/nature26000] [Citation(s) in RCA: 1580] [Impact Index Per Article: 263.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 02/13/2018] [Indexed: 02/07/2023]
Abstract
Accurate pathological diagnosis is crucial for optimal management of patients with cancer. For the approximately 100 known tumour types of the central nervous system, standardization of the diagnostic process has been shown to be particularly challenging-with substantial inter-observer variability in the histopathological diagnosis of many tumour types. Here we present a comprehensive approach for the DNA methylation-based classification of central nervous system tumours across all entities and age groups, and demonstrate its application in a routine diagnostic setting. We show that the availability of this method may have a substantial impact on diagnostic precision compared to standard methods, resulting in a change of diagnosis in up to 12% of prospective cases. For broader accessibility, we have designed a free online classifier tool, the use of which does not require any additional onsite data processing. Our results provide a blueprint for the generation of machine-learning-based tumour classifiers across other cancer entities, with the potential to fundamentally transform tumour pathology.
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Affiliation(s)
- David Capper
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Koelsche
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lukas Chavez
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annekathrin Kratz
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristin Huang
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Leonille Schweizer
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
| | - Damian Stichel
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adriana Olar
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Department of Neurosurgery, Medical University of South Carolina, Charleston, South Carolina 29425, USA
- Hollings Cancer Center, Charleston, South Carolina 29425, USA
| | - Nils W Engel
- Department of Oncology and Hematology with Sections Bone Marrow Transplant and Pneumology, Hubertus Wald Tumorzentrum/University Cancer Center Hamburg, University Medical Center Hamburg, Hamburg, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University, Munich, Germany
| | - Kerstin Lindenberg
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick N Harter
- Institute of Neurology (Edinger Institute), Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Anne K Braczynski
- Institute of Neurology (Edinger Institute), Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Karl H Plate
- Institute of Neurology (Edinger Institute), Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Hildegard Dohmen
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Boyan K Garvalov
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Roland Coras
- Neuropathological Institute, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Annett Hölsken
- Neuropathological Institute, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Ekkehard Hewer
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schick
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roger Fischer
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rudi Beschorner
- Institute of Pathology and Neuropathology, Department of Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Jens Schittenhelm
- Institute of Pathology and Neuropathology, Department of Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Ori Staszewski
- Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Khalida Wani
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Pascale Varlet
- Department of Neuropathology, Centre Hospitalier Sainte Anne, Paris, France
| | - Melanie Pages
- Department of Neuropathology, Centre Hospitalier Sainte Anne, Paris, France
| | - Petra Temming
- Pediatrics III, Pediatric Oncology and Hematology, University Hospital Essen, Essen, Germany
| | - Dietmar Lohmann
- Eye Cancer Research Group, Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - Florian Selt
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
- CCU Pediatric Oncology (G340), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Hendrik Witt
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
- CCU Pediatric Oncology (G340), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
- CCU Pediatric Oncology (G340), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Academic Medisch Centrum (AMC), University of Amsterdam, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Amsterdam, The Netherlands
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Elisabeth Rushing
- Department of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | | | - Christoph Geisenberger
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Fausto J Rodriguez
- Division of Neuropathology of the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Albert Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Matthias Preusser
- Department of Medicine I, Comprehensive Cancer Center Vienna, CNS Unit (CCC-CNS), Medical University of Vienna, Vienna, Austria
| | | | - Rolf Bjerkvig
- Department of Biomedicine, University of Bergen, Bergen, Norway
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Michael Farrell
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Martina Deckert
- Department of Neuropathology, University Hospital of Cologne, Cologne, Germany
| | - Jürgen Hench
- Department of Neuropathology, Institute of Pathology, Basel University Hospital, Basel, Switzerland
| | - Stephan Frank
- Department of Neuropathology, Institute of Pathology, Basel University Hospital, Basel, Switzerland
| | | | | | | | - Wolfgang Brück
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Silvia Hofer
- Division of Oncology, Luzerner Kantonsspital, Luzern, Switzerland
| | - Stefanie Brehmer
- Department of Neurosurgery, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Marcel Seiz-Rosenhagen
- Department of Neurosurgery, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Daniel Hänggi
- Department of Neurosurgery, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Volkmar Hans
- Institut für Neuropathologie, Evangelisches Krankenhaus Bielefeld gGmbH, Bielefeld, Germany
- Institut für Neuropathologie, Universitätskinikum Essen, Essen, Germany
| | - Stephanie Rozsnoki
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Patricia Kohlhof
- Institute for Pathology, Katharinenhospital Stuttgart, Stuttgart, Germany
| | - Bjarne W Kristensen
- Department of Pathology, Odense University Hospital, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Matt Lechner
- University College London Cancer Institute and University College London Hospitals, London, UK
| | - Beatriz Lopes
- Department of Pathology, University of Virginia, Charlottesville, Virginia, USA
| | - Christian Mawrin
- Institute of Neuropathology, Otto-von-Guericke-University, Magdeburg, Germany
| | - Ralf Ketter
- Department of Neurosurgery, University Hospital Saarland, Homburg, Saar, Germany
| | - Andreas Kulozik
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ziad Khatib
- Nicklaus Children's Hospital Brain Institute, Miami, Florida 33155, USA
| | - Frank Heppner
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
- Cluster of Excellence, NeuroCure, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Arend Koch
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
| | - Anne Jouvet
- Département de Pathologie et Neuropathologie, Hôpital Neurologique, Hospices Civils de Lyon, Lyon, France
| | - Catherine Keohane
- Department of Neuropathology, Cork University Hospital, Cork, Ireland
| | - Helmut Mühleisen
- Department of Pathology, Ludwigsburg Hospital, Ludwigsburg, Germany
| | - Wolf Mueller
- Department of Neuropathology, Leipzig University, Leipzig, Germany
| | - Ute Pohl
- Department of Cellular Pathology, Queen's Hospital, Romford, UK
| | - Marco Prinz
- Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nicholas G Gottardo
- Department of Pediatric Oncology and Haematology, Princess Margaret Hospital for Children, GPO Box D184, Perth, Western Australia 6840, Australia
- Telethon Kids Institute, University of Western Australia, PO Box 855, Perth, Western Australia 6872, Australia
- School of Paediatrics and Child Health, University of Western Australia, GPO Box D184, Perth, Western Australia 6840, Australia
| | - Pablo Hernáiz Driever
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christof M Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Hermann L Müller
- Department of Pediatrics and Pediatric Hematology/Oncology, Klinikum Oldenburg AöR, Medical Campus University Oldenburg, 26133 Oldenburg, Germany
| | - Stefan Rutkowski
- Department for Pediatric Hematology and Oncology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department for Pediatric Hematology and Oncology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Michael C Frühwald
- Children's Hospital Augsburg, Swabian Children's Cancer Centre, Augsburg, Germany
| | - Astrid Gnekow
- Children's Hospital Augsburg, Swabian Children's Cancer Centre, Augsburg, Germany
| | - Gudrun Fleischhack
- Pediatrics III, Pediatric Oncology and Hematology, University Hospital Essen, Essen, Germany
| | - Stephan Tippelt
- Pediatrics III, Pediatric Oncology and Hematology, University Hospital Essen, Essen, Germany
| | - Gabriele Calaminus
- Department of Pediatric Hematology/Oncology, University of Bonn Medical Center, Bonn, Germany
| | - Camelia-Maria Monoranu
- Department of Neuropathology, Insitute of Pathology, Comprehensive Cancer Center (CCC) Mainfranken, University of Würzburg, Würzburg, Germany
| | - Arie Perry
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health and Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marco Gessi
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Johannes Schramm
- Medical Faculty, University of Bonn Medical School, Bonn, Germany
| | - Gabriele Schackert
- Department of Neurosurgery, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pieter Wesseling
- Department of Pathology, Princess Máxima Center for Pediatric Oncology and University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Vincent Peter Collins
- Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Cambridge, UK
| | - Ingmar Blümcke
- Neuropathological Institute, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jürgen Debus
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annie Huang
- Department of Pediatrics, Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Nada Jabado
- Division of Hematology/Oncology, McGill University, Montreal, Quebec, Canada
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Amar Gajjar
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Giles W Robinson
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Zane Jaunmuktane
- Division of Neuropathology, UCL Hospitals, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
- Department of Molecular Neuroscience, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
- Department of Neurodegeneration, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
| | | | - Michael Platten
- Department of Neurology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michel Mittelbronn
- Institute of Neurology (Edinger Institute), Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, German Cancer Research Center (DKFZ) Heidelberg, Germany
- NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Luxembourg
- Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Luxembourg Centre of Neuropathology (LCNP), Luxembourg, Luxembourg
| | - Till Acker
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Christian Hartmann
- Department of Neuropathology, Hannover Medical School (MHH), Hannover, Germany
| | - Kenneth Aldape
- Department of Pathology, University of Toronto, Toronto, Ontario, Canada
| | - Ulrich Schüller
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University, Munich, Germany
- Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Rolf Buslei
- Neuropathological Institute, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Section Neuropathology, Institute of Pathology, Sozialstiftung Bamberg, Klinikum am Bruderwald, Bamberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Matija Snuderl
- Division of Neuropathology, Department of Pathology, NYU Langone Medical Center, New York, New York, USA
| | - Sebastian Brandner
- Division of Neuropathology, UCL Hospitals, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
- Department of Neurodegeneration, Institute of Neurology, University College London, Queen Square, WC1N 3BG London, UK
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
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18
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Chang K, Bai HX, Zhou H, Su C, Bi WL, Agbodza E, Kavouridis VK, Senders JT, Boaro A, Beers A, Zhang B, Capellini A, Liao W, Shen Q, Li X, Xiao B, Cryan J, Ramkissoon S, Ramkissoon L, Ligon K, Wen PY, Bindra RS, Woo J, Arnaout O, Gerstner ER, Zhang PJ, Rosen BR, Yang L, Huang RY, Kalpathy-Cramer J. Residual Convolutional Neural Network for the Determination of IDH Status in Low- and High-Grade Gliomas from MR Imaging. Clin Cancer Res 2017; 24:1073-1081. [PMID: 29167275 DOI: 10.1158/1078-0432.ccr-17-2236] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/12/2017] [Accepted: 11/16/2017] [Indexed: 01/23/2023]
Abstract
Purpose: Isocitrate dehydrogenase (IDH) mutations in glioma patients confer longer survival and may guide treatment decision making. We aimed to predict the IDH status of gliomas from MR imaging by applying a residual convolutional neural network to preoperative radiographic data.Experimental Design: Preoperative imaging was acquired for 201 patients from the Hospital of University of Pennsylvania (HUP), 157 patients from Brigham and Women's Hospital (BWH), and 138 patients from The Cancer Imaging Archive (TCIA) and divided into training, validation, and testing sets. We trained a residual convolutional neural network for each MR sequence (FLAIR, T2, T1 precontrast, and T1 postcontrast) and built a predictive model from the outputs. To increase the size of the training set and prevent overfitting, we augmented the training set images by introducing random rotations, translations, flips, shearing, and zooming.Results: With our neural network model, we achieved IDH prediction accuracies of 82.8% (AUC = 0.90), 83.0% (AUC = 0.93), and 85.7% (AUC = 0.94) within training, validation, and testing sets, respectively. When age at diagnosis was incorporated into the model, the training, validation, and testing accuracies increased to 87.3% (AUC = 0.93), 87.6% (AUC = 0.95), and 89.1% (AUC = 0.95), respectively.Conclusions: We developed a deep learning technique to noninvasively predict IDH genotype in grade II-IV glioma using conventional MR imaging using a multi-institutional data set. Clin Cancer Res; 24(5); 1073-81. ©2017 AACR.
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Affiliation(s)
- Ken Chang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Harrison X Bai
- Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hao Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chang Su
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ena Agbodza
- Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Vasileios K Kavouridis
- Department of Neurosurgery, Computational Neuroscience Outcomes Center, Brigham and Women's Hospital, Boston, Massachusetts
| | - Joeky T Senders
- Department of Neurosurgery, Computational Neuroscience Outcomes Center, Brigham and Women's Hospital, Boston, Massachusetts
| | - Alessandro Boaro
- Department of Neurosurgery, Computational Neuroscience Outcomes Center, Brigham and Women's Hospital, Boston, Massachusetts
| | - Andrew Beers
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Biqi Zhang
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Alexandra Capellini
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Weihua Liao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qin Shen
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jane Cryan
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Shakti Ramkissoon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lori Ramkissoon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Keith Ligon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Patrick Y Wen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ranjit S Bindra
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut
| | - John Woo
- Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Omar Arnaout
- Department of Neurosurgery, Computational Neuroscience Outcomes Center, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Paul J Zhang
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bruce R Rosen
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Li Yang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Raymond Y Huang
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Jayashree Kalpathy-Cramer
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts.
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19
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Comerford CM, Morrell R, Johnson D, Javadpour M, Beausang A, Cryan J, Murphy P, Quinn J. Pituitary plasmacytoma—a rare presentation of multiple myeloma. Ir J Med Sci 2017; 187:349-350. [DOI: 10.1007/s11845-017-1690-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/03/2017] [Indexed: 10/18/2022]
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20
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Mackay A, Burford A, Carvalho D, Izquierdo E, Fazal-Salom J, Taylor KR, Bjerke L, Clarke M, Vinci M, Nandhabalan M, Temelso S, Popov S, Molinari V, Raman P, Waanders AJ, Han HJ, Gupta S, Marshall L, Zacharoulis S, Vaidya S, Mandeville HC, Bridges LR, Martin AJ, Al-Sarraj S, Chandler C, Ng HK, Li X, Mu K, Trabelsi S, Brahim DHB, Kisljakov AN, Konovalov DM, Moore AS, Carcaboso AM, Sunol M, de Torres C, Cruz O, Mora J, Shats LI, Stavale JN, Bidinotto LT, Reis RM, Entz-Werle N, Farrell M, Cryan J, Crimmins D, Caird J, Pears J, Monje M, Debily MA, Castel D, Grill J, Hawkins C, Nikbakht H, Jabado N, Baker SJ, Pfister SM, Jones DTW, Fouladi M, von Bueren AO, Baudis M, Resnick A, Jones C. Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma. Cancer Cell 2017; 32:520-537.e5. [PMID: 28966033 PMCID: PMC5637314 DOI: 10.1016/j.ccell.2017.08.017] [Citation(s) in RCA: 621] [Impact Index Per Article: 88.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/14/2017] [Accepted: 08/29/2017] [Indexed: 12/20/2022]
Abstract
We collated data from 157 unpublished cases of pediatric high-grade glioma and diffuse intrinsic pontine glioma and 20 publicly available datasets in an integrated analysis of >1,000 cases. We identified co-segregating mutations in histone-mutant subgroups including loss of FBXW7 in H3.3G34R/V, TOP3A rearrangements in H3.3K27M, and BCOR mutations in H3.1K27M. Histone wild-type subgroups are refined by the presence of key oncogenic events or methylation profiles more closely resembling lower-grade tumors. Genomic aberrations increase with age, highlighting the infant population as biologically and clinically distinct. Uncommon pathway dysregulation is seen in small subsets of tumors, further defining the molecular diversity of the disease, opening up avenues for biological study and providing a basis for functionally defined future treatment stratification.
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Affiliation(s)
- Alan Mackay
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Anna Burford
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Diana Carvalho
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Elisa Izquierdo
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Janat Fazal-Salom
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Kathryn R Taylor
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK; Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn Bjerke
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Matthew Clarke
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Mara Vinci
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Meera Nandhabalan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Sara Temelso
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Sergey Popov
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK; Department of Cellular Pathology, University Hospital of Wales, Cardiff, UK
| | - Valeria Molinari
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Pichai Raman
- The Center for Data Driven Discovery in Biomedicine (D(3)b), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Angela J Waanders
- The Center for Data Driven Discovery in Biomedicine (D(3)b), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Harry J Han
- The Center for Data Driven Discovery in Biomedicine (D(3)b), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Saumya Gupta
- Institute of Molecular Life Sciences, Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Lynley Marshall
- Pediatric Oncology Drug Development Team, Children and Young People's Unit, Royal Marsden Hospital, Sutton, UK
| | - Stergios Zacharoulis
- Pediatric Oncology Drug Development Team, Children and Young People's Unit, Royal Marsden Hospital, Sutton, UK
| | - Sucheta Vaidya
- Pediatric Oncology Drug Development Team, Children and Young People's Unit, Royal Marsden Hospital, Sutton, UK
| | | | - Leslie R Bridges
- Department of Cellular Pathology, St George's Hospital NHS Trust, London, UK
| | - Andrew J Martin
- Department of Neurosurgery, St George's Hospital NHS Trust, London, UK
| | - Safa Al-Sarraj
- Department of Neuropathology, Kings College Hospital, London, UK
| | | | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Xingang Li
- Department of Neurosurgery, Qilu Hospital of Shandong University and Brain Science Research Institute, Shandong University, Jinan, China
| | - Kun Mu
- Department of Pathology, Shandong University School of Medicine, Jinan, China
| | - Saoussen Trabelsi
- Department of Cytogenetics and Reproductive Biology, Farhat Hached Hospital, Sousse, Tunisia
| | - Dorra H'mida-Ben Brahim
- Department of Cytogenetics and Reproductive Biology, Farhat Hached Hospital, Sousse, Tunisia
| | - Alexei N Kisljakov
- Department of Pathology, Morozov Children's Hospital, Moscow, Russian Federation
| | - Dmitry M Konovalov
- Department of Pathology, Dmitrii Rogachev Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Andrew S Moore
- UQ Child Health Research Centre, The University of Queensland, Brisbane, Australia; Oncology Services Group, Children's Health Queensland Hospital and Health Service, Brisbane, Australia; The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | | | - Mariona Sunol
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | | | - Ofelia Cruz
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Jaume Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Ludmila I Shats
- Division of Oncology, Pediatric Oncology and Radiotherapy, St Petersburg State Pediatric Medical University, St Petersburg, Russian Federation
| | - João N Stavale
- Department of Pathology, Federal University of São Paulo, São Paulo, São Paulo, Brazil
| | - Lucas T Bidinotto
- Molecular Oncology Research Centre, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui M Reis
- Molecular Oncology Research Centre, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal and ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Natacha Entz-Werle
- Pédiatrie Onco-Hématologie - Pédiatrie III, Centre Hospitalier Régional et Universitaire Hautepierre, Strasbourg, France
| | - Michael Farrell
- Histopathology Department, Beaumont Hospital, Dublin, Ireland
| | - Jane Cryan
- Histopathology Department, Beaumont Hospital, Dublin, Ireland
| | - Darach Crimmins
- Department of Neurosurgery, Temple Street Children's University Hospital, Dublin, Ireland
| | - John Caird
- Department of Neurosurgery, Temple Street Children's University Hospital, Dublin, Ireland
| | - Jane Pears
- Department of Paediatric Oncology, Our Lady's Children's Hospital, Dublin, Ireland
| | - Michelle Monje
- Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marie-Anne Debily
- Département de Cancerologie de l'Enfant et de l'Adolescent, Institut Gustav Roussy, Villejuif, France
| | - David Castel
- Département de Cancerologie de l'Enfant et de l'Adolescent, Institut Gustav Roussy, Villejuif, France
| | - Jacques Grill
- Département de Cancerologie de l'Enfant et de l'Adolescent, Institut Gustav Roussy, Villejuif, France
| | - Cynthia Hawkins
- Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
| | - Hamid Nikbakht
- Department of Pediatrics, McGill University, Montreal, Canada
| | - Nada Jabado
- The Center for Data Driven Discovery in Biomedicine (D(3)b), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Stefan M Pfister
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany; Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Maryam Fouladi
- Department of Pediatrics, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - André O von Bueren
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, University Medical Center Goettingen, Goettingen, Germany; Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, University Hospital of Geneva, Geneva, Switzerland; Department of Pediatrics, CANSEARCH Research Laboratory, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Michael Baudis
- Institute of Molecular Life Sciences, Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Adam Resnick
- The Center for Data Driven Discovery in Biomedicine (D(3)b), Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Chris Jones
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK; Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK.
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Affiliation(s)
- David Glynn
- Department of Breast Surgery, Mater Misercordiae University Hospital, Eccles street, Dublin 7, Ireland
| | | | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin 9, Ireland
| | - Donncha O'Brien
- Department of Radiology, Mater Misercordiae University Hospital, Dublin 7, Ireland
| | - Eoin Kavanagh
- Department of Breast Surgery, Mater Misercordiae University Hospital, Eccles street, Dublin 7, Ireland
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Cullinan N, Cryan J, O'Sullivan C, Daly P, Farrell M, Capra M, Pears J, Owens C. CR-13RADIATION-INDUCED GLIOBLASTOMA MULTIFORME WITHIN 4 YEARS OF CRANIAL IRRADIATION FOR PAEDIATRIC CRANIOPHARYNGIOMA - CASE REPORT AND REVIEW OF THE LITERATURE. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now068.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Jack E, Kay E, Cummings R, Buckley P, Brett F, Farrell M, Cryan J. LG-07BRAFV600 MUTATION TESTING IN GLIOMA IN MODERN CLINICAL PRACTICE. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now075.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Yap SM, Farrell M, Cryan J, Smyth S. An irish case of limb-girdle muscular dystrophy 2I with structural eye involvement. Muscle Nerve 2016; 54:509-10. [PMID: 26833294 DOI: 10.1002/mus.25059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/15/2016] [Accepted: 01/22/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Siew Mei Yap
- Department of Neurology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Michael Farrell
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Beaumont Road, Dublin, Ireland
| | - Shane Smyth
- Department of Neurology, Mater Misericordiae University Hospital, Dublin, Ireland
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25
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Cryan J, Power S, Brett F. Two cases of intraventricular hemorrhage in young patients. Brain Pathol 2014; 24:417-8. [PMID: 25083535 DOI: 10.1111/bpa.12154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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O'Rourke DJ, Bergin A, Rotenberg A, Peters J, Gorman M, Poduri A, Cryan J, Lidov H, Madsen J, Harini C. Rasmussen's encephalitis presenting as focal cortical dysplasia. Epilepsy Behav Case Rep 2014; 2:86-9. [PMID: 25667877 PMCID: PMC4307873 DOI: 10.1016/j.ebcr.2014.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Rasmussen's encephalitis is a rare syndrome characterized by intractable seizures, often associated with epilepsia partialis continua and symptoms of progressive hemispheric dysfunction. Seizures are usually the hallmark of presentation, but antiepileptic drug treatment fails in most patients and is ineffective against epilepsia partialis continua, which often requires surgical intervention. Co-occurrence of focal cortical dysplasia has only rarely been described and may have implications regarding pathophysiology and management. We describe a rare case of dual pathology of Rasmussen's encephalitis presenting as a focal cortical dysplasia (FCD) and discuss the literature on this topic.
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Affiliation(s)
- D J O'Rourke
- Dept. of Neurology, Boston Children's Hospital, USA
| | - A Bergin
- Dept. of Neurology, Boston Children's Hospital, USA
| | - A Rotenberg
- Dept. of Neurology, Boston Children's Hospital, USA
| | - J Peters
- Dept. of Neurology, Boston Children's Hospital, USA
| | - M Gorman
- Dept. of Neurology, Boston Children's Hospital, USA
| | - A Poduri
- Dept. of Neurology, Boston Children's Hospital, USA
| | - J Cryan
- Dept. of Neuropathology, Boston Children's Hospital, USA
| | - H Lidov
- Dept. of Neuropathology, Boston Children's Hospital, USA
| | - J Madsen
- Dept. of Neurosurgery, Boston Children's Hospital, USA
| | - C Harini
- Dept. of Neurology, Boston Children's Hospital, USA
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27
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Treacy A, Cryan J, McGarvey C, Devaney D, Matthews TG. Sudden unexplained death in childhood. An audit of the quality of autopsy reporting. Ir Med J 2013; 106:70-72. [PMID: 23951973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cases of sudden unexplained death in childhood (SUDC) in Ireland in children aged > 1 year and < 5 years were examined in order to assess the quality of autopsy reporting. All SUDC cases are notified to and documented by the National Sudden Infant Death Register (NSIDR) in Ireland along with all cases of sudden infant death syndrome (SIDS) referring to sudden infant deaths less than one year of age. The database of the NSIDR in Ireland was interrogated and cases of SIDS and SUDC were compared over a fifteen-year period (1995-2009). SIDS cases whose autopsies were conducted in the same hospital in the same year as the index SUDC case were used for comparison. The autopsy report for each case was examined and modified Rushton (MR) score(s1) calculated. MR scores were compared along with the number of paediatric pathology prosectors and the year of autopsy examination between the two groups. 45 cases were registered as SUDC (age 52 - 152 weeks) between 1995-2009. Autopsy reports were available for 43/45 (95%) of these. 43 SIDS cases from the same year and site of autopsy were used for comparison. Overall MR scores were higher in the SIDS cases, with 29/43 (67%) cases obtaining the minimum arbitrary score (MAS) of > 300 compared to 25/43 (58%) of SUDC cases. Paediatric pathologists in specialist centres carried out similar numbers of SIDS autopsies and SUDC autopsies (46% SIDS, 44% SUDC). Autopsies carried out by paediatric pathologists in specialist centres met the MAS in 19/21 (90%) SIDS cases and 18/19 (95%) SUDC cases. Based on our findings we recommend referral of all SUDC cases to specialist centres for optimal autopsy examination and investigation, and that cases of sudden unexpected death in children over 1 year of age are investigated according to the same guidelines as are used for unexpected death under one year of age.
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Affiliation(s)
- A Treacy
- Department of Histopathology, Children's University Hospital, Temple St, Dublin 1
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28
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McFarland BK, Farrell JP, Berrah N, Bostedt C, Bozek J, Bucksbaum P, Coffee R, Cryan J, Fang L, Feifel R, Gaffney K, Glownia J, Martinez T, Mucke M, Murphy B, Miyabe S, Natan A, Osipov T, Petrovic V, Schorb S, Schultz T, Spector L, Tarantelli F, Tenney I, Wang S, White W, White J, Gühr M. Probing nucleobase photoprotection with soft x-rays. EPJ Web of Conferences 2013. [DOI: 10.1051/epjconf/20134107004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Abstract
BACKGROUND Increasing evidence indicates that childhood trauma is a risk factor for schizophrenia and patients with this syndrome have a pro-inflammatory phenotype. We tested the hypothesis that the pro-inflammatory phenotype in schizophrenia is associated with childhood trauma and that patients without a history of such trauma have a similar immune profile to healthy controls. METHOD We recruited 40 schizophrenia patients and 40 controls, all of whom completed the Childhood Trauma Questionnaire (CTQ). Using enzyme-linked immunosorbent assay (ELISA) techniques, we measured peripheral levels of interleukin (IL)-1β, IL-6, IL-8 and tumour necrosis factor (TNF)-α. These immune parameters were compared in schizophrenia with childhood trauma, schizophrenia without childhood trauma and healthy controls. RESULTS Patients with childhood trauma had higher levels of IL-6 and TNF-α than patients without trauma and healthy controls, and TNF-α levels correlated with the extent of the trauma. Patients with no trauma had similar immune profiles to controls. CONCLUSIONS Childhood trauma drives changes, possibly epigenetic, that generate a pro-inflammatory phenotype.
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Affiliation(s)
- U Dennison
- Department of Psychiatry, University College Cork, Cork, Ireland.
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30
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McGarvey CM, O'Regan M, Cryan J, Treacy A, Hamilton K, Devaney D, Matthews T. Sudden unexplained death in childhood (1-4 years) in Ireland: an epidemiological profile and comparison with SIDS. Arch Dis Child 2012; 97:692-7. [PMID: 22685045 DOI: 10.1136/archdischild-2011-301393] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To examine the incidence of sudden unexplained death in children 1-4 years old (SUDC) in Ireland and to compare the epidemiological profile of SUDC with that of SIDS. DESIGN All cases of sudden unexplained death in children <5 years in Ireland between 1994 and 2008 were reviewed. Epidemiological information obtained from parental questionnaires and post-mortem reports was examined, and data on cases ≥52 weeks compared with cases <52 weeks. RESULTS SUDC accounted for 5% (n=44) of deaths in children aged 1-4 years during 1994-2008. During this period, the SIDS rate dropped from 0.71 to 0.34 per 1000 live births, while the SUDC rate increased from 0.08 to 0.18 deaths per 10 000 population aged 1-4 years. The median age of SUDC cases was 71.5 weeks, and the male/female ratio was 1.3:1. All died during a sleep period, 71% between 10pm and 8am, and more than two-thirds were found prone. Fewest cases occurred during July-September (11%), and a greater proportion occurred at weekends (55%). 52% (17/33) had symptoms (any) in the 48 h before death, and 35% (11/31) visited their general practitioner because of illness in the week preceding death. SUDC differed from SIDS in prevalence of maternal smoking (38% vs 72%, p<0.001), bed-sharing (17% vs 49%, p<0.001), and whether found prone (72% vs 23%, p<0.001). CONCLUSION While SUDC shares some characteristics with SIDS, there are also some important differences. Further data collection will help determine whether SIDS and SUDC represent the same pathophysiological entity. Standardisation of protocols for investigating sudden deaths is urgently required for accurate diagnosis of cases.
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Affiliation(s)
- Cliona M McGarvey
- National Paediatric Mortality Register, Children's University Hospital, Temple St, Dublin 1, Ireland.
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31
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Abstract
This is the case of a 42-year-old female who presented with transient dizziness. Her symptoms and signs progressed to include dysarthria, ataxia and cognitive decline over 2 years, such that she was unable to care for herself. She died 4 years after first presentation without a diagnosis. Investigations revealed a normochromic normocytic anaemia. Cerebrospinal fluid was normal. Serial computed tomography brain showed a wedge-shaped frontal infarct but no progressive changes. Examination at autopsy showed discoloration of the gray and white matter of the brain and spinal cord.Microscopy of leptomeningeal and parenchymal vessels showed they were filled with atypical B lymphocytes confined to the intravascular space with multiple infarcts in the brain, cerebellum and spinal cord. A diagnosis of intravascular B cell lymphoma was made and is discussed.
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Affiliation(s)
- Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
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32
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Bienenstock⁎ J, Karimi K, Forsythe P, Kunze W, Bravo J, Cryan J. What do commensal bacteria have to do with allergy, pain and behaviour? Eur J Pharmacol 2011. [DOI: 10.1016/j.ejphar.2011.09.222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Cryan J, Catháin NO, Curtis M, Cassidy M, Brett FM. The contribution of alcohol to fatal traumatic head injuries in the forensic setting. Ir Med J 2010; 103:303-305. [PMID: 21560501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Excessive drinking increases the risk of dying unnaturally. In the Republic of Ireland such deaths are referred to the State Pathologist. Blood alcohol concentration (BAC) is routinely measured. We created a database of cases presenting to the State Pathologist over a nine year period (2000-2008 inclusive) to evaluate the relationship between alcohol and fatal traumatic brain injuries (FTBI). Of a total of 1778 cases, 332 (275 Male [M]; 57 Female [F]) died of head injuries. Fatalities were highest in males aged 36-50 (N = 97) and 26-35 (N = 73). Assaults (N = 147), falls (N = 95), road traffic accidents (RTA) (N = 50) and suicide (N = 15) were the commonest modes of presentation. A positive blood alcohol concentration (BAC) was found in 36% of assaults, 41% of falls and 40% of suicides. In the RTA group BAC was positive in 59% of pedestrians, 33% of drivers and 14% of passengers. Alcohol clearly plays a significant role in FTBI in the forensic setting.
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Affiliation(s)
- J Cryan
- Department of Neuropathology, Beaumont Hospital, Beaumont, Dublin 9.
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35
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Fang L, Hoener M, Gessner O, Tarantelli F, Pratt ST, Kornilov O, Buth C, Gühr M, Kanter EP, Bostedt C, Bozek JD, Bucksbaum PH, Chen M, Coffee R, Cryan J, Glownia M, Kukk E, Leone SR, Berrah N. Double core-hole production in N2: beating the Auger clock. Phys Rev Lett 2010; 105:083005. [PMID: 20868097 DOI: 10.1103/physrevlett.105.083005] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Indexed: 05/29/2023]
Abstract
We investigate the creation of double K-shell holes in N2 molecules via sequential absorption of two photons on a time scale shorter than the core-hole lifetime by using intense x-ray pulses from the Linac Coherent Light Source free electron laser. The production and decay of these states is characterized by photoelectron spectroscopy and Auger electron spectroscopy. In molecules, two types of double core holes are expected, the first with two core holes on the same N atom, and the second with one core hole on each N atom. We report the first direct observations of the former type of core hole in a molecule, in good agreement with theory, and provide an experimental upper bound for the relative contribution of the latter type.
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Affiliation(s)
- L Fang
- Physics Department, Western Michigan University, Kalamazoo, Michigan 49008, USA.
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36
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Glownia JM, Cryan J, Andreasson J, Belkacem A, Berrah N, Blaga CI, Bostedt C, Bozek J, DiMauro LF, Fang L, Frisch J, Gessner O, Gühr M, Hajdu J, Hertlein MP, Hoener M, Huang G, Kornilov O, Marangos JP, March AM, McFarland BK, Merdji H, Petrovic VS, Raman C, Ray D, Reis DA, Trigo M, White JL, White W, Wilcox R, Young L, Coffee RN, Bucksbaum PH. Time-resolved pump-probe experiments at the LCLS. Opt Express 2010; 18:17620-30. [PMID: 20721148 DOI: 10.1364/oe.18.017620] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The first time-resolved x-ray/optical pump-probe experiments at the SLAC Linac Coherent Light Source (LCLS) used a combination of feedback methods and post-analysis binning techniques to synchronize an ultrafast optical laser to the linac-based x-ray laser. Transient molecular nitrogen alignment revival features were resolved in time-dependent x-ray-induced fragmentation spectra. These alignment features were used to find the temporal overlap of the pump and probe pulses. The strong-field dissociation of x-ray generated quasi-bound molecular dications was used to establish the residual timing jitter. This analysis shows that the relative arrival time of the Ti:Sapphire laser and the x-ray pulses had a distribution with a standard deviation of approximately 120 fs. The largest contribution to the jitter noise spectrum was the locking of the laser oscillator to the reference RF of the accelerator, which suggests that simple technical improvements could reduce the jitter to better than 50 fs.
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Affiliation(s)
- James M Glownia
- The PULSE Institute for Ultrafast Energy Science, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025. USA.
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37
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Hoener M, Fang L, Kornilov O, Gessner O, Pratt ST, Gühr M, Kanter EP, Blaga C, Bostedt C, Bozek JD, Bucksbaum PH, Buth C, Chen M, Coffee R, Cryan J, Dimauro L, Glownia M, Hosler E, Kukk E, Leone SR, McFarland B, Messerschmidt M, Murphy B, Petrovic V, Rolles D, Berrah N. Ultraintense x-ray induced ionization, dissociation, and frustrated absorption in molecular nitrogen. Phys Rev Lett 2010; 104:253002. [PMID: 20867372 DOI: 10.1103/physrevlett.104.253002] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Indexed: 05/11/2023]
Abstract
Sequential multiple photoionization of the prototypical molecule N2 is studied with femtosecond time resolution using the Linac Coherent Light Source (LCLS). A detailed picture of intense x-ray induced ionization and dissociation dynamics is revealed, including a molecular mechanism of frustrated absorption that suppresses the formation of high charge states at short pulse durations. The inverse scaling of the average target charge state with x-ray peak brightness has possible implications for single-pulse imaging applications.
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Affiliation(s)
- M Hoener
- Western Michigan University Physics Department, Kalamazoo, Michigan 49008, USA
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Cryan J, O’Grady A, Allen D, Kay E. Tissue microarray technology in the routine assessment of HER2 status in invasive breast cancer. Histopathology 2009; 54:901. [DOI: 10.1111/j.1365-2559.2009.03304.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Fitzgerald P, Cassidy Eugene M, Clarke G, Scully P, Barry S, Quigley Eamonn MM, Shanahan F, Cryan J, Dinan Timothy G. Tryptophan catabolism in females with irritable bowel syndrome: relationship to interferon-gamma, severity of symptoms and psychiatric co-morbidity. Neurogastroenterol Motil 2008; 20:1291-7. [PMID: 18823288 DOI: 10.1111/j.1365-2982.2008.01195.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Irritable bowel syndrome (IBS) has been linked with abnormal serotonin functioning and immune activation. Tryptophan forms the substrate for serotonin biosynthesis, but it can alternatively be catabolized to kynurenine (Kyn) by the enzyme indoleamine 2,3-dioxygenase (IDO), the main inducer of which is interferon-gamma. The primary aim of this study was to test the hypothesis that IBS is associated with increased tryptophan (Trp) catabolism along the Kyn pathway due to increased IFN-gamma levels. Plasma Kyn, Trp and IFN-gamma levels were measured in 41 female IBS subjects and 33 controls. Indoleamine 2,3-dioxygenase activity was assessed using the Kyn to Trp ratio. Psychiatric co-morbidity was assessed using the Patient Health Questionnaire, and severity of IBS assessed using self-report ordinal scales. Irritable bowel syndrome subjects had increased Kyn concentrations compared with controls (P = 0.039) and there was a trend for Kyn:Trp to be increased in the IBS group (P = 0.09). There was a positive correlation between IBS severity and Kyn:Trp (r = 0.57, P < 0.001). Those with severe IBS symptoms had increased Kyn:Trp (P < 0.005) compared to those with less severe symptoms and controls, and were over twice as likely to have depression or anxiety compared to those with less severe IBS (RR = 2.2, 95% CI 1.2-3.9). No difference in IFN-gamma levels was observed between groups; however, IFN-gamma was positively correlated with Kyn:Trp in IBS (r = 0.58, P = 0.005) but not controls (r = 0.12, P = 0.5). Females with IBS have abnormal Trp catabolism. The Kyn:Trp is related to symptom severity, and those with severe IBS symptoms have increased shunting of Trp along the Kyn pathway which contributes to the abnormal serotonergic functioning in this syndrome.
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Affiliation(s)
- P Fitzgerald
- Department of Psychiatry, University College Cork, Wilton, Cork, Ireland.
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40
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Hauri CP, Lopez-Martens RB, Blaga CI, Schultz KD, Cryan J, Chirla R, Colosimo P, Doumy G, March AM, Roedig C, Sistrunk E, Tate J, Wheeler J, Dimauro LF, Power EP. Intense self-compressed, self-phase-stabilized few-cycle pulses at 2 microm from an optical filament. Opt Lett 2007; 32:868-70. [PMID: 17339964 DOI: 10.1364/ol.32.000868] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We report the compression of intense, carrier-envelope phase stable mid-IR pulses down to few-cycle duration using an optical filament. A filament in xenon gas is formed by using self-phase stabilized 330 microJ 55 fs pulses at 2 microm produced via difference-frequency generation in a Ti:sapphire-pumped optical parametric amplifier. The ultrabroadband 2 microm carrier-wavelength output is self-compressed below 3 optical cycles and has a 270 microJ pulse energy. The self-locked phase offset of the 2 microm difference-frequency field is preserved after filamentation. This is to our knowledge the first experimental realization of pulse compression in optical filaments at mid-IR wavelengths (lambda>0.8 microm).
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Affiliation(s)
- C P Hauri
- Laboratorie d'Optique Appliquée, ENSTA Ecole Polytechnique, CNRS UMR 7639, Palaiseau, France.
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41
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Dumont FJ, Ok H, Lin S, Kastner CA, Cryan J, Martin MM, Wiederrecht G, Staruch MJ. Mixed agonist/antagonist activity of an FK-506-related immunosuppressant: biological and biochemical characterization. J Pharmacol Exp Ther 1996; 276:1078-88. [PMID: 8786538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
FK-506 blocks T cell activation by preventing lymphokine gene transcription through formation of a complex with FKBP12 that inhibits calcineurin phosphatase activity. Immunosuppressive FK-506 analogs (agonists) have been generated whose potency correlates with calcineurin inhibition. Nonimmunosuppressive antagonist analogs have also been identified, including L-685,818, which binds to FKBP12 but does not inhibit calcineurin. We describe a novel property of FK-506 analog, characterized as a mixed agonist/antagonist immunosuppressive activity. It is displayed by L-688,617, the 32 O-methoxyethoxymethyl derivative of the agonist L-683,590 (C21-ethyl). Although it binds to FKBP12 similarly to L-683,590, L-688,617 incompletely suppressed T cell proliferation induced by optimal activation and enhanced that induced by supraoptimal activation. In the latter situation, L-688,617 suppressed IL-2 production only partially but blocked activation-driven cell death. Moreover, a 1000-fold molar excess of L-688,617 antagonized the immunosuppressive activity of L-683,590. L-688,617 inhibited calcineurin phosphatase activity in cells only partially. The unique agonist/antagonist activity of L-688,617 may therefore reflect its high affinity for FKBP12, combined with a reduced ability of the drug-FKBP12 complex to inhibit calcineurin function. However, in a cell-free system, L-688,617 completely blocked this function when a large excess of FKBP12 over calcineurin was present, suggesting that the intracellular concentration of FKBP12 may be a limiting factor that prevents full agonist activity of L-688,617 in cells.
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Affiliation(s)
- F J Dumont
- Department of Immunology, Merck Research Laboratories, Rahway, New Jersey, USA
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42
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Zhang BW, Zimmer G, Chen J, Ladd D, Li E, Alt FW, Wiederrecht G, Cryan J, O'Neill EA, Seidman CE, Abbas AK, Seidman JG. T cell responses in calcineurin A alpha-deficient mice. J Exp Med 1996; 183:413-20. [PMID: 8627154 PMCID: PMC2192457 DOI: 10.1084/jem.183.2.413] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have created embryonic stem (ES) cells and mice lacking the predominant isoform (alpha) of the calcineurin A subunit (CNA alpha) to study the role of this serine/threonine phosphatase in the immune system. T and B cell maturation appeared to be normal in CNA alpha -/- mice. CNA alpha -/- T cells responded normally to mitogenic stimulation (i.e., PMA plus ionomycin, concanavalin A, and anti-CD3 epsilon antibody). However, CNA alpha -/- mice generated defective antigen-specific T cell responses in vivo. Mice produced from CNA alpha -/- ES cells injected into RAG-2-deficient blastocysts had a similar defective T cell response, indicating that CNA alpha is required for T cell function per se, rather than for an activity of other cell types involved in the immune response. CNA alpha -/- T cells remained sensitive to both cyclosporin A and FK506, suggesting that CNA beta or another CNA-like molecule can mediate the action of these immunosuppressive drugs. CNA alpha -/- mice provide an animal model for dissecting the physiologic functions of calcineurin as well as the effects of FK506 and CsA.
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Affiliation(s)
- B W Zhang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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43
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Ballor DL, Harvey-Berino JR, Ades PA, Cryan J, Calles-Escandon J. Contrasting effects of resistance and aerobic training on body composition and metabolism after diet-induced weight loss. Metabolism 1996; 45:179-83. [PMID: 8596486 DOI: 10.1016/s0026-0495(96)90050-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This study examined whether exercise training facilitates maintenance of body weight at reduced levels following weight loss by attenuating weight loss-induced reductions in resting metabolism and fat oxidation. The effects of 12 weeks (three times per week) of either aerobic or weight training exercise on body weight, body composition, and energy metabolism during rest and following a meal in 18 older (mean +/- SE, 61 +/- 1 years; range, 56 to 70) subjects who had recently lost a mean of 9 +/- 1 kg were studied. During the exercise training period, the aerobic training group (five women, four men) had a significant (P < .05) reduction in body weight (-2.5 +/- 0.6 kg) as compared with the weight training group (five women, four men) (0.4 +/- 0.9 kg). Eight of nine aerobic training subjects lost additional weight, while six of nine weight training subjects gained weight. Neither type of training reversed the depressions in resting metabolism or fat oxidation rates (ie, resting or postprandial) that had occurred as a consequence of the prior weight loss. Thus, alterations in resting metabolism or fat oxidation (resting or postprandial) do not appear to be the mechanism(s) by which exercise training facilitates maintenance of diet-induced weight loss.
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Affiliation(s)
- D L Ballor
- Sims Obesity Research Center, University of Vermont, Burlington, USA
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44
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Ballor DL, Harvey-Berino JR, Ades PA, Cryan J, Calles-Escandon J. Decrease in fat oxidation following a meal in weight-reduced individuals: a possible mechanism for weight recidivism. Metabolism 1996; 45:174-8. [PMID: 8596485 DOI: 10.1016/s0026-0495(96)90049-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This study examined the effect that dietary-induced weight loss has on body composition, energy metabolism, and substrate oxidation at rest and during the 5-hour period following a meal. Twenty older (age:mean +/- SE, 61 +/- 1 years; range, 56 to 70 y) obese (body mass index > 32 kg/m2) subjects (12 women, eight men) completed an 11-week dietary restriction program in which they lost 9 +/- l kg. Fat and fat-free mass were reduced (P < .05) by 15% and 5%, respectively. Resting metabolic rate decreased by 15% (P < .05). Overall, weight loss did not alter the percentage of energy derived from fat sources (approximately 47% of energy) under resting conditions. In contrast, the percentage of calories derived from fat during the 5-hour postmeal period decreased from baseline to post-weight loss from 38% +/- 3% to 26% +/- 4% (P < .05) of total calories expended. The reduction in fat oxidation subsequent to a meal may facilitate fat storage, and may be one mechanism by which one regains weight following weight loss.
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Affiliation(s)
- D L Ballor
- Sims Obesity Research Center, University of Vermont, Burlington, USA
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45
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Sewell TJ, Lam E, Martin MM, Leszyk J, Weidner J, Calaycay J, Griffin P, Williams H, Hung S, Cryan J. Inhibition of calcineurin by a novel FK-506-binding protein. J Biol Chem 1994; 269:21094-102. [PMID: 7520438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
FK-506, a potent immunosuppressive drug, acts during the commitment phase of T-lymphocyte activation to block a subset of calcium-associated events necessary for transcription of certain early lymphokine genes. The drug binds to an abundant, cytosolic 11.8-kDa protein termed the FK-506-binding protein (FKBP12). The FKBP12.FK-506 complex inhibits calcineurin, a calcium-dependent phosphatase that is a component of the signal transduction pathway leading to early lymphokine gene transcription. FKBP12 is one member of a growing gene family. Prior to this report, all other FKBP family members had been irrelevant to the mechanism of action of FK-506 because no other FKBP.FK-506 complexes were able to bind and inhibit calcineurin. Here, we report the purification and characterization of a novel FK-506-binding protein, FKBP12.6. Having 85% amino acid sequence identity to FKBP12, FKBP12.6 is, among the FKBPs, most closely related to FKBP12. When complexed with FK-506, FKBP12.6 binds to and inhibits calcineurin, making it only the second FKBP discovered thus far to do so. The ability to inhibit calcineurin establishes the potential relevance of FKBP12.6 to the immunosuppressive or toxic side effects of FK-506.
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Affiliation(s)
- T J Sewell
- Department of Immunology Research, Merck Research Laboratories, Rahway, New Jersey 07065
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46
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Sewell T, Lam E, Martin M, Leszyk J, Weidner J, Calaycay J, Griffin P, Williams H, Hung S, Cryan J. Inhibition of calcineurin by a novel FK-506-binding protein. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31934-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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47
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Siekierka JJ, Wiederrecht G, Cryan J, Hung SH, Comisky M, Sigal NH. Potential roles of other FK 506-binding proteins in mediating the effects of FK 506. Transplant Proc 1991; 23:2720-1. [PMID: 1721256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- J J Siekierka
- Department of Immunology Research, Merck, Sharp & Dohme Research Laboratories, Rahway, NJ 07065
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48
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Cryan J, Hung SH, Wiederrecht G, Sigal NH, Siekierka JJ. FKBP, the binding protein for the immunosuppressive drug, FK-506, is not an inhibitor of protein kinase C activity. Biochem Biophys Res Commun 1991; 180:846-52. [PMID: 1719972 DOI: 10.1016/s0006-291x(05)81142-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recently, the amino acid sequence of a 12 Kd endogenous protein inhibitor of protein kinase C (PKC-I 2) has been shown to be identical to that of the 12 KDa receptor for the immunosuppressive drug, FK-506. In view of this observation we examined the effects of recombinant and native human FKBP on protein kinase C (PKC) activity. FKBP, at molar concentrations up to 1900-fold over that of PKC, failed to inhibit PKC phosphorylation of histone H1 and failed to block the auto-phosphorylation of PKC. Interestingly, FKBP is phosphorylated by PKC in these reactions. The phosphorylation of FKBP by PKC appears to be specific since the catalytic subunit of cAMP-dependent protein kinase fails to phosphorylate the binding protein. Our results fail to support a role for FKBP as an inhibitor of protein kinase C.
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Affiliation(s)
- J Cryan
- Department of Immunology Research Merck, Sharp and Dohme Research Laboratories, Rahway, New Jersey
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49
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Siekierka JJ, Wiederrecht G, Greulich H, Boulton D, Hung SH, Cryan J, Hodges PJ, Sigal NH. The cytosolic-binding protein for the immunosuppressant FK-506 is both a ubiquitous and highly conserved peptidyl-prolyl cis-trans isomerase. J Biol Chem 1990; 265:21011-5. [PMID: 1701173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have recently isolated an abundant cytosolic protein from human T-cells which specifically binds the immunosuppressive agent, FK-506. The FK-506-binding protein (FKBP) is a member of a novel class of proteins possessing peptidyl-prolyl cis-trans isomerase activity. These proteins are believed to play an important role in accelerating the rate at which proteins fold into their native conformations. In the present study, we demonstrate that FKBP is not a lymphoid-specific protein, but is widely distributed and phylogenically conserved. FKBP, purified from three sources (a human T-lymphocyte cell line JURKAT, bovine calf thymus, and Saccharomyces cerevisiae) exhibit identical molecular weights, immunological cross-reactivities, and a high degree of NH2-terminal amino acid sequence homology. In addition, FKBP from all sources possesses peptidyl-prolyl cis-trans isomerase activity which can be specifically inhibited by FK-506. We conclude that FKBP may serve an important biological function in all eukaryotic cells.
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Affiliation(s)
- J J Siekierka
- Department of Immunology Research, Merck, Sharp & Dohme Research Laboratories, Rahway, New Jersey 07065
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50
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Siekierka JJ, Wiederrecht G, Greulich H, Boulton D, Hung SH, Cryan J, Hodges PJ, Sigal NH. The cytosolic-binding protein for the immunosuppressant FK-506 is both a ubiquitous and highly conserved peptidyl-prolyl cis-trans isomerase. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)45319-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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