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Damhofer H, Tatar T, Southgate B, Scarneo S, Agger K, Shlyueva D, Uhrbom L, Morrison GM, Hughes PF, Haystead T, Pollard SM, Helin K. TAK1 inhibition leads to RIPK1-dependent apoptosis in immune-activated cancers. Cell Death Dis 2024; 15:273. [PMID: 38632238 PMCID: PMC11024179 DOI: 10.1038/s41419-024-06654-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
Poor survival and lack of treatment response in glioblastoma (GBM) is attributed to the persistence of glioma stem cells (GSCs). To identify novel therapeutic approaches, we performed CRISPR/Cas9 knockout screens and discovered TGFβ activated kinase (TAK1) as a selective survival factor in a significant fraction of GSCs. Loss of TAK1 kinase activity results in RIPK1-dependent apoptosis via Caspase-8/FADD complex activation, dependent on autocrine TNFα ligand production and constitutive TNFR signaling. We identify a transcriptional signature associated with immune activation and the mesenchymal GBM subtype to be a characteristic of cancer cells sensitive to TAK1 perturbation and employ this signature to accurately predict sensitivity to the TAK1 kinase inhibitor HS-276. In addition, exposure to pro-inflammatory cytokines IFNγ and TNFα can sensitize resistant GSCs to TAK1 inhibition. Our findings reveal dependency on TAK1 kinase activity as a novel vulnerability in immune-activated cancers, including mesenchymal GBMs that can be exploited therapeutically.
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Affiliation(s)
- Helene Damhofer
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Tülin Tatar
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin Southgate
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Scott Scarneo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Karl Agger
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Daria Shlyueva
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gillian M Morrison
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Philip F Hughes
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Timothy Haystead
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Steven M Pollard
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Kristian Helin
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
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2
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Derby SJ, Dutton L, Strathdee KE, Stevenson K, Koessinger A, Jackson M, Tian Y, Yu W, Mclay K, Misquitta J, Alsharif S, Clarke CJ, Gilmour L, Thomason P, McGhee E, McGarrity-Cottrell CL, Vanderlinden A, Collis SJ, Rominyi O, Lemgruber L, Solecki G, Olson M, Winkler F, Carlin LM, Heiland DH, Inman GJ, Chalmers AJ, Norman JC, Carruthers R, Birch JL. Inhibition of ATR opposes glioblastoma invasion through disruption of cytoskeletal networks and integrin internalization via macropinocytosis. Neuro Oncol 2024; 26:625-639. [PMID: 37936324 PMCID: PMC10995506 DOI: 10.1093/neuonc/noad210] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Glioblastomas have highly infiltrative growth patterns that contribute to recurrence and poor survival. Despite infiltration being a critical therapeutic target, no clinically useful therapies exist that counter glioblastoma invasion. Here, we report that inhibition of ataxia telangiectasia and Rad 3 related kinase (ATR) reduces invasion of glioblastoma cells through dysregulation of cytoskeletal networks and subsequent integrin trafficking. METHODS Glioblastoma motility and invasion were assessed in vitro and in vivo in response to ATR inhibition (ATRi) and ATR overexpression using time-lapse microscopy, two orthotopic glioblastoma models, and intravital imaging. Disruption to cytoskeleton networks and endocytic processing were investigated via high-throughput, super-resolution and intravital imaging. RESULTS High ATR expression was associated with significantly poorer survival in clinical datasets while histological, protein expression, and spatial transcriptomics using glioblastoma tumor specimens revealed higher ATR expression at infiltrative margins. Pharmacological inhibition with two different compounds and RNAi targeting of ATR opposed the invasion of glioblastoma, whereas overexpression of ATR drove migration. Subsequent investigation revealed that cytoskeletal dysregulation reduced macropinocytotic internalization of integrins at growth-cone-like structures, resulting in a tumor microtube retraction defect. The biological relevance and translational potential of these findings were confirmed using two orthotopic in vivo models of glioblastoma and intravital imaging. CONCLUSIONS We demonstrate a novel role for ATR in determining invasion in glioblastoma cells and propose that pharmacological targeting of ATR could have far-reaching clinical benefits beyond radiosensitization.
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Affiliation(s)
- Sarah J Derby
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Louise Dutton
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Karen E Strathdee
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Katrina Stevenson
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Anna Koessinger
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- CRUK Scotland Institute, Glasgow, UK
| | - Mark Jackson
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Yuling Tian
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Wenxi Yu
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kathy Mclay
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Josette Misquitta
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Sama Alsharif
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Lesley Gilmour
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | | | - Aurelie Vanderlinden
- Department of Oncology and Metabolism, The University of Sheffield Medical School, Sheffield, UK
| | - Spencer J Collis
- Department of Oncology and Metabolism, The University of Sheffield Medical School, Sheffield, UK
| | - Ola Rominyi
- Department of Oncology and Metabolism, The University of Sheffield Medical School, Sheffield, UK
| | - Leandro Lemgruber
- Cellular Analysis Facility, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Gergely Solecki
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Olson
- Department of Chemistry and Biology, Ryeson University, Toronto, Ontario, Canada
| | - Frank Winkler
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leo M Carlin
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- CRUK Scotland Institute, Glasgow, UK
| | | | - Gareth J Inman
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- CRUK Scotland Institute, Glasgow, UK
| | - Anthony J Chalmers
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jim C Norman
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- CRUK Scotland Institute, Glasgow, UK
| | - Ross Carruthers
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Joanna L Birch
- Wolfson Wohl Translational Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
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3
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Lopes DM, Wells JA, Ma D, Wallis L, Park D, Llewellyn SK, Ahmed Z, Lythgoe MF, Harrison IF. Glymphatic inhibition exacerbates tau propagation in an Alzheimer's disease model. Alzheimers Res Ther 2024; 16:71. [PMID: 38576025 PMCID: PMC10996277 DOI: 10.1186/s13195-024-01439-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND The aggregation and spread of misfolded amyloid structured proteins, such as tau and α-synuclein, are key pathological features associated with neurodegenerative disorders, including Alzheimer's and Parkinson's disease. These proteins possess a prion-like property, enabling their transmission from cell to cell leading to propagation throughout the central and peripheral nervous systems. While the mechanisms underlying their intracellular spread are still being elucidated, targeting the extracellular space has emerged as a potential therapeutic approach. The glymphatic system, a brain-wide pathway responsible for clearing extracellular metabolic waste from the central nervous system, has gained attention as a promising target for removing these toxic proteins. METHODS In this study, we investigated the impact of long-term modulation of glymphatic function on tau aggregation and spread by chronically treating a mouse model of tau propagation with a pharmacological inhibitor of AQP4, TGN-020. Thy1-hTau.P301S mice were intracerebrally inoculated with tau into the hippocampus and overlying cortex, and subsequently treated with TGN-020 (3 doses/week, 50 mg/kg TGN-020, i.p.) for 10-weeks. During this time, animal memory was studied using cognitive behavioural tasks, and structural MR images were acquired of the brain in vivo prior to brain extraction for immunohistochemical characterisation. RESULTS Our findings demonstrate increased tau aggregation in the brain and transhemispheric propagation in the hippocampus following the inhibition of glymphatic clearance. Moreover, disruption of the glymphatic system aggravated recognition memory in tau inoculated mice and exacerbated regional changes in brain volume detected in the model. When initiation of drug treatment was delayed for several weeks post-inoculation, the alterations were attenuated. CONCLUSIONS These results indicate that by modulating AQP4 function and, consequently, glymphatic clearance, it is possible to modify the propagation and pathological impact of tau in the brain, particularly during the initial stages of the disease. These findings highlight the critical role of the glymphatic system in preserving healthy brain homeostasis and offer valuable insights into the therapeutic implications of targeting this system for managing neurodegenerative diseases characterized by protein aggregation and spread.
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Affiliation(s)
- Douglas M Lopes
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Jack A Wells
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Da Ma
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Lauren Wallis
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Daniel Park
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Sophie K Llewellyn
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Zeshan Ahmed
- Neuroscience Next Generation Therapeutics (NGTx), Eli Lilly and Company, Cambridge, MA, USA
| | - Mark F Lythgoe
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
| | - Ian F Harrison
- Centre for Advanced Biomedical Imaging, Department of Imaging, Division of Medicine, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK.
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4
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Rimmer B, Balla M, Dutton L, Williams S, Araújo-Soares V, Gallagher P, Finch T, Lewis J, Burns R, Menger F, Sharp L. Barriers and facilitators to self-management in people living with a lower-grade glioma. J Cancer Surviv 2024:10.1007/s11764-024-01572-9. [PMID: 38512564 DOI: 10.1007/s11764-024-01572-9] [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: 02/21/2024] [Accepted: 03/16/2024] [Indexed: 03/23/2024]
Abstract
PURPOSE Self-management can have clinical and quality-of-life benefits. However, people with lower-grade gliomas (LGG) may face chronic tumour- and/or treatment-related symptoms and impairments (e.g. cognitive deficits, seizures), which could influence their ability to self-manage. Our study aimed to identify and understand the barriers and facilitators to self-management in people with LGG. METHODS We conducted semi-structured interviews with 28 people with LGG across the United Kingdom, who had completed primary treatment. Sixteen participants were male, mean age was 50.4 years, and mean time since diagnosis was 8.7 years. Interviews were audio-recorded and transcribed. Following inductive open coding, we deductively mapped codes to Schulman-Green et al.'s framework of factors influencing self-management, developed in chronic illness. RESULTS Data suggested extensive support for all five framework categories ('Personal/lifestyle characteristics', 'Health status', 'Resources', 'Environmental characteristics', 'Healthcare system'), encompassing all 18 factors influencing self-management. How people with LGG experience many of these factors appears somewhat distinct from other cancers; participants described multiple, often co-occurring, challenges, primarily with knowledge and acceptance of their incurable condition, the impact of seizures and cognitive deficits, transport difficulties, and access to (in)formal support. Several factors were on a continuum, for example, sufficient knowledge was a facilitator, whereas lack thereof, was a barrier to self-management. CONCLUSIONS People with LGG described distinctive experiences with wide-ranging factors influencing their ability to self-manage. IMPLICATIONS FOR CANCER SURVIVORS These findings will improve awareness of the potential challenges faced by people with LGG around self-management and inform development of self-management interventions for this population.
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Affiliation(s)
- Ben Rimmer
- Population Health Sciences Institute, Newcastle University, Newcastle University Centre for Cancer, Ridley Building 1, Newcastle Upon Tyne, NE1 7RU, England.
| | - Michelle Balla
- Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, England
| | - Lizzie Dutton
- Population Health Sciences Institute, Newcastle University, Newcastle University Centre for Cancer, Ridley Building 1, Newcastle Upon Tyne, NE1 7RU, England
| | - Sophie Williams
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, England
| | - Vera Araújo-Soares
- Population Health Sciences Institute, Newcastle University, Newcastle University Centre for Cancer, Ridley Building 1, Newcastle Upon Tyne, NE1 7RU, England
- Centre for Preventive Medicine and Digital Health, Department for Prevention, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | | | - Tracy Finch
- Department of Nursing, Midwifery and Health, Northumbria University, Newcastle Upon Tyne, England
| | - Joanne Lewis
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, England
| | - Richéal Burns
- Faculty of Science, Atlantic Technological University, Sligo, Ireland
- Health and Biomedical Strategic Research Centre, Atlantic Technological University, Sligo, Ireland
| | - Fiona Menger
- School of Education, Communication and Language Sciences, Newcastle University, Newcastle Upon Tyne, England
| | - Linda Sharp
- Population Health Sciences Institute, Newcastle University, Newcastle University Centre for Cancer, Ridley Building 1, Newcastle Upon Tyne, NE1 7RU, England
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5
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Jones CG, Vanderlinden A, Rominiyi O, Collis SJ. Development and Optimisation of Tumour Treating Fields (TTFields) Delivery within 3D Primary Glioma Stem Cell-like Models of Spatial Heterogeneity. Cancers (Basel) 2024; 16:863. [PMID: 38473223 DOI: 10.3390/cancers16050863] [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: 01/17/2024] [Revised: 02/08/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Glioblastoma is an aggressive, incurable brain cancer with poor five-year survival rates of around 13% despite multimodal treatment with surgery, DNA-damaging chemoradiotherapy and the recent addition of Tumour Treating Fields (TTFields). As such, there is an urgent need to improve our current understanding of cellular responses to TTFields using more clinically and surgically relevant models, which reflect the profound spatial heterogeneity within glioblastoma, and leverage these biological insights to inform the rational design of more effective therapeutic strategies incorporating TTFields. We have recently reported the use of preclinical TTFields using the inovitroTM system within 2D glioma stem-like cell (GSC) models and demonstrated significant cytotoxicity enhancement when co-applied with a range of therapeutically approved and preclinical DNA damage response inhibitors (DDRi) and chemoradiotherapy. Here we report the development and optimisation of preclinical TTFields delivery within more clinically relevant 3D scaffold-based primary GSC models of spatial heterogeneity, and highlight some initial enhancement of TTFields potency with temozolomide and clinically approved PARP inhibitors (PARPi). These studies, therefore, represent an important platform for further preclinical assessment of TTFields-based therapeutic strategies within clinically relevant 3D GSC models, aimed towards accelerating clinical trial implementation and the ultimate goal of improving the persistently dire survival rates for these patients.
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Affiliation(s)
- Callum G Jones
- Division of Clinical Medicine, University of Sheffield Medical School, Sheffield S10 2RX, UK
| | - Aurelie Vanderlinden
- Division of Clinical Medicine, University of Sheffield Medical School, Sheffield S10 2RX, UK
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ola Rominiyi
- Division of Clinical Medicine, University of Sheffield Medical School, Sheffield S10 2RX, UK
- Division of Neuroscience, University of Sheffield Medical School, Sheffield S10 2HQ, UK
- Department of Neurosurgery, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Spencer J Collis
- Division of Clinical Medicine, University of Sheffield Medical School, Sheffield S10 2RX, UK
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Liam-Or R, Faruqu FN, Walters A, Han S, Xu L, Wang JTW, Oberlaender J, Sanchez-Fueyo A, Lombardi G, Dazzi F, Mailaender V, Al-Jamal KT. Cellular uptake and in vivo distribution of mesenchymal-stem-cell-derived extracellular vesicles are protein corona dependent. Nat Nanotechnol 2024:10.1038/s41565-023-01585-y. [PMID: 38366223 DOI: 10.1038/s41565-023-01585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/27/2023] [Indexed: 02/18/2024]
Abstract
Extracellular vesicles (EVs) derived from mesenchymal stem cells are promising nanotherapeutics in liver diseases due to their regenerative and immunomodulatory properties. Nevertheless, a concern has been raised regarding the rapid clearance of exogenous EVs by phagocytic cells. Here we explore the impact of protein corona on EVs derived from two culturing conditions in which specific proteins acquired from media were simultaneously adsorbed on the EV surface. Additionally, by incubating EVs with serum, simulating protein corona formation upon systemic delivery, further resolved protein corona-EV complex patterns were investigated. Our findings reveal the potential influences of corona composition on EVs under in vitro conditions and their in vivo kinetics. Our data suggest that bound albumin creates an EV signature that can retarget EVs from hepatic macrophages. This results in markedly improved cellular uptake by hepatocytes, liver sinusoidal endothelial cells and hepatic stellate cells. This phenomenon can be applied as a camouflage strategy by precoating EVs with albumin to fabricate the albumin-enriched protein corona-EV complex, enhancing non-phagocytic uptake in the liver. This work addresses a critical challenge facing intravenously administered EVs for liver therapy by tailoring the protein corona-EV complex for liver cell targeting and immune evasion.
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Affiliation(s)
- Revadee Liam-Or
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Farid N Faruqu
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, UK
- Pharmacology Department, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Adam Walters
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Shunping Han
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Lizhou Xu
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Julie Tzu-Wen Wang
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Jennifer Oberlaender
- Max Planck Institute for Polymer Research, Mainz, Germany
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Alberto Sanchez-Fueyo
- Institute of Liver Studies, King's College London University and King's College Hospital, London, UK
| | - Giovanna Lombardi
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Francesco Dazzi
- Comprehensive Cancer Centre, King's College London, London, UK
| | - Volker Mailaender
- Max Planck Institute for Polymer Research, Mainz, Germany
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Khuloud T Al-Jamal
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, UK.
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van Essen MJ, Apsley EJ, Riepsaame J, Xu R, Northcott PA, Cowley SA, Jacob J, Becker EBE. PTCH1-mutant human cerebellar organoids exhibit altered neural development and recapitulate early medulloblastoma tumorigenesis. Dis Model Mech 2024; 17:dmm050323. [PMID: 38411252 PMCID: PMC10924233 DOI: 10.1242/dmm.050323] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Patched 1 (PTCH1) is the primary receptor for the sonic hedgehog (SHH) ligand and negatively regulates SHH signalling, an essential pathway in human embryogenesis. Loss-of-function mutations in PTCH1 are associated with altered neuronal development and the malignant brain tumour medulloblastoma. As a result of differences between murine and human development, molecular and cellular perturbations that arise from human PTCH1 mutations remain poorly understood. Here, we used cerebellar organoids differentiated from human induced pluripotent stem cells combined with CRISPR/Cas9 gene editing to investigate the earliest molecular and cellular consequences of PTCH1 mutations on human cerebellar development. Our findings demonstrate that developmental mechanisms in cerebellar organoids reflect in vivo processes of regionalisation and SHH signalling, and offer new insights into early pathophysiological events of medulloblastoma tumorigenesis without the use of animal models.
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Affiliation(s)
- Max J. van Essen
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Elizabeth J. Apsley
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Joey Riepsaame
- Genome Engineering Oxford, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Ruijie Xu
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Paul A. Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Sally A. Cowley
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - John Jacob
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Esther B. E. Becker
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
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8
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Rimmer B, Balla M, Dutton L, Lewis J, Burns R, Gallagher P, Williams S, Araújo-Soares V, Finch T, Sharp L. 'A Constant Black Cloud': The Emotional Impact of Informal Caregiving for Someone With a Lower-Grade Glioma. Qual Health Res 2024; 34:227-238. [PMID: 37967320 PMCID: PMC10768339 DOI: 10.1177/10497323231204740] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Those closest to people with lower-grade gliomas (LGGs) often assume the role of informal caregiver (IC). The additional responsibilities mean ICs of people with cancer can experience adverse impacts on their own lives. We explored the emotional impact of informal caregiving for people with LGGs. This was a descriptive qualitative study within the multi-method Ways Ahead project. We conducted semi-structured interviews with individuals from the United Kingdom, who currently, or in the past 5 years, informally cared for someone with an LGG. Interviews encompassed experiences of emotional impact as a consequence of caregiving for someone with an LGG. Inductive thematic analysis was undertaken. We interviewed 19 ICs (mean age 54.6 years; 14 females, 5 males). Participants reported substantial emotional impact. Four themes and associated subthemes were generated: Emotional responses to the illness (e.g. feeling helpless), Emotional responses to the unknown (e.g. anxiety about future uncertainty), Emotional consequences of care recipient changes (e.g. challenges of changed relationship dynamics), and Emotional weight of the responsibility (e.g. feeling burnout). Emotional impact in one area often exacerbated impact in another (e.g. future uncertainty impacted feelings of helplessness). Participants detailed the factors that helped them manage the emotional impact (e.g. being resilient). ICs of people with LGGs can experience wide-ranging emotional responses to and impacts of the illness, uncertain prognosis, care recipient changes, and the toll of caregiving. Adjustment and resilience are key protective factors, though further consideration of ways to identify and fulfil the emotional support needs of ICs of people with LGGs is required.
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Affiliation(s)
- Ben Rimmer
- Population Health Sciences Institute, Newcastle University, Newcastle University Centre for Cancer, Newcastle upon Tyne, England
| | - Michelle Balla
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
| | - Lizzie Dutton
- Population Health Sciences Institute, Newcastle University, Newcastle University Centre for Cancer, Newcastle upon Tyne, England
| | - Joanne Lewis
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, England
| | - Richéal Burns
- Faculty of Science, Atlantic Technological University, Sligo, Ireland
- Health and Biomedical Strategic Research Centre, Atlantic Technological University, Sligo, Ireland
| | | | - Sophie Williams
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, England
| | - Vera Araújo-Soares
- Population Health Sciences Institute, Newcastle University, Newcastle University Centre for Cancer, Newcastle upon Tyne, England
- Centre for Preventive Medicine and Digital Health, Department for Prevention of Cardiovascular and Metabolic Disease, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Tracy Finch
- Department of Nursing, Midwifery and Health, Northumbria University, Newcastle upon Tyne, England
| | - Linda Sharp
- Population Health Sciences Institute, Newcastle University, Newcastle University Centre for Cancer, Newcastle upon Tyne, England
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Bhaskaran D, Savage J, Patel A, Collinson F, Mant R, Boele F, Brazil L, Meade S, Buckle P, Lax S, Billingham L, Short SC. A randomised phase II trial of temozolomide with or without cannabinoids in patients with recurrent glioblastoma (ARISTOCRAT): protocol for a multi-centre, double-blind, placebo-controlled trial. BMC Cancer 2024; 24:83. [PMID: 38225549 PMCID: PMC10790538 DOI: 10.1186/s12885-023-11792-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common adult malignant brain tumour, with an incidence of 5 per 100,000 per year in England. Patients with tumours showing O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation represent around 40% of newly diagnosed GBM. Relapse/tumour recurrence is inevitable. There is no agreed standard treatment for patients with GBM, therefore, it is aimed at delaying further tumour progression and maintaining health-related quality of life (HRQoL). Limited clinical trial data exist using cannabinoids in combination with temozolomide (TMZ) in this setting, but early phase data demonstrate prolonged overall survival compared to TMZ alone, with few additional side effects. Jazz Pharmaceuticals (previously GW Pharma Ltd.) have developed nabiximols (trade name Sativex®), an oromucosal spray containing a blend of cannabis plant extracts, that we aim to assess for preliminary efficacy in patients with recurrent GBM. METHODS ARISTOCRAT is a phase II, multi-centre, double-blind, placebo-controlled, randomised trial to assess cannabinoids in patients with recurrent MGMT methylated GBM who are suitable for treatment with TMZ. Patients who have relapsed ≥ 3 months after completion of initial first-line treatment will be randomised 2:1 to receive either nabiximols or placebo in combination with TMZ. The primary outcome is overall survival time defined as the time in whole days from the date of randomisation to the date of death from any cause. Secondary outcomes include overall survival at 12 months, progression-free survival time, HRQoL (using patient reported outcomes from QLQ-C30, QLQ-BN20 and EQ-5D-5L questionnaires), and adverse events. DISCUSSION Patients with recurrent MGMT promoter methylated GBM represent a relatively good prognosis sub-group of patients with GBM. However, their median survival remains poor and, therefore, more effective treatments are needed. The phase II design of this trial was chosen, rather than phase III, due to the lack of data currently available on cannabinoid efficacy in this setting. A randomised, double-blind, placebo-controlled trial will ensure an unbiased robust evaluation of the treatment and will allow potential expansion of recruitment into a phase III trial should the emerging phase II results warrant this development. TRIAL REGISTRATION ISRCTN: 11460478. CLINICALTRIALS Gov: NCT05629702.
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Affiliation(s)
- Divyalakshmi Bhaskaran
- School of Medicine, University of Leeds, LS2 9JT, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Joshua Savage
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Amit Patel
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Fiona Collinson
- School of Medicine, University of Leeds, LS2 9JT, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rhys Mant
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Florien Boele
- School of Medicine, University of Leeds, LS2 9JT, Leeds, UK
| | - Lucy Brazil
- Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sara Meade
- University Hospitals Birmingham Foundation Trust, Birmingham, UK
| | | | - Siân Lax
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Lucinda Billingham
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Susan C Short
- School of Medicine, University of Leeds, LS2 9JT, Leeds, UK.
- Leeds Teaching Hospitals NHS Trust, Leeds, UK.
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10
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Brown EJ, Balaguer-Lluna L, Cribbs AP, Philpott M, Campo L, Browne M, Wong JF, Oppermann U, Carcaboso ÁM, Bullock AN, Farnie G. PRMT5 inhibition shows in vitro efficacy against H3K27M-altered diffuse midline glioma, but does not extend survival in vivo. Sci Rep 2024; 14:328. [PMID: 38172189 PMCID: PMC10764357 DOI: 10.1038/s41598-023-48652-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
H3K27-altered Diffuse Midline Glioma (DMG) is a universally fatal paediatric brainstem tumour. The prevalent driver mutation H3K27M creates a unique epigenetic landscape that may also establish therapeutic vulnerabilities to epigenetic inhibitors. However, while HDAC, EZH2 and BET inhibitors have proven somewhat effective in pre-clinical models, none have translated into clinical benefit due to either poor blood-brain barrier penetration, lack of efficacy or toxicity. Thus, there remains an urgent need for new DMG treatments. Here, we performed wider screening of an epigenetic inhibitor library and identified inhibitors of protein arginine methyltransferases (PRMTs) among the top hits reducing DMG cell viability. Two of the most effective inhibitors, LLY-283 and GSK591, were targeted against PRMT5 using distinct binding mechanisms and reduced the viability of a subset of DMG cells expressing wild-type TP53 and mutant ACVR1. RNA-sequencing and phenotypic analyses revealed that LLY-283 could reduce the viability, clonogenicity and invasion of DMG cells in vitro, representing three clinically important phenotypes, but failed to prolong survival in an orthotopic xenograft model. Together, these data show the challenges of DMG treatment and highlight PRMT5 inhibitors for consideration in future studies of combination treatments.
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Affiliation(s)
- Elizabeth J Brown
- Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Leire Balaguer-Lluna
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Adam P Cribbs
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, UK
| | - Martin Philpott
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, UK
| | - Leticia Campo
- Department of Oncology, Experimental Cancer Medicine Centre, University of Oxford, Oxford, UK
| | - Molly Browne
- Department of Oncology, Experimental Cancer Medicine Centre, University of Oxford, Oxford, UK
| | - Jong Fu Wong
- Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Udo Oppermann
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, UK
| | - Ángel M Carcaboso
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona, Spain
| | - Alex N Bullock
- Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, UK.
| | - Gillian Farnie
- Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, UK.
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, UK.
- Cancer Research Horizons, The Francis Crick Institute, London, UK.
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11
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Schmassmann P, Roux J, Dettling S, Hogan S, Shekarian T, Martins TA, Ritz MF, Herter S, Bacac M, Hutter G. Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation. eLife 2023; 12:RP92678. [PMID: 38127790 PMCID: PMC10735226 DOI: 10.7554/elife.92678] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Glioblastoma (GBM) harbors a highly immunosuppressive tumor microenvironment (TME) which influences glioma growth. Major efforts have been undertaken to describe the TME on a single-cell level. However, human data on regional differences within the TME remain scarce. Here, we performed high-depth single-cell RNA sequencing (scRNAseq) on paired biopsies from the tumor center, peripheral infiltration zone and blood of five primary GBM patients. Through analysis of >45,000 cells, we revealed a regionally distinct transcription profile of microglia (MG) and monocyte-derived macrophages (MdMs) and an impaired activation signature in the tumor-peripheral cytotoxic-cell compartment. Comparing tumor-infiltrating CD8+ T cells with circulating cells identified CX3CR1high and CX3CR1int CD8+ T cells with effector and memory phenotype, respectively, enriched in blood but absent in the TME. Tumor CD8+ T cells displayed a tissue-resident memory phenotype with dysfunctional features. Our analysis provides a regionally resolved mapping of transcriptional states in GBM-associated leukocytes, serving as an additional asset in the effort towards novel therapeutic strategies to combat this fatal disease.
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Affiliation(s)
- Philip Schmassmann
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Julien Roux
- Bioinformatics Core Facility, Department of Biomedicine, University of BaselBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Steffen Dettling
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center MunichPenzbergGermany
| | - Sabrina Hogan
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Tala Shekarian
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Tomás A Martins
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Marie-Françoise Ritz
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Sylvia Herter
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center ZürichSchlierenSwitzerland
| | - Marina Bacac
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center ZürichSchlierenSwitzerland
| | - Gregor Hutter
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of BaselBaselSwitzerland
- Department of Neurosurgery, University Hospital BaselBaselSwitzerland
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12
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Rimmer B, Brown MC, Sotire T, Beyer F, Bolnykh I, Balla M, Richmond C, Dutton L, Williams S, Araújo-Soares V, Finch T, Gallagher P, Lewis J, Burns R, Sharp L. Characteristics and Components of Self-Management Interventions for Improving Quality of Life in Cancer Survivors: A Systematic Review. Cancers (Basel) 2023; 16:14. [PMID: 38201442 PMCID: PMC10777971 DOI: 10.3390/cancers16010014] [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: 10/30/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
Self-management can improve clinical and psychosocial outcomes in cancer survivors. Which intervention characteristics and components are beneficial is unclear, hindering implementation into practice. We systematically searched six databases from inception to 17 November 2021 for studies evaluating self-management interventions for adult cancer survivors post-treatment. Independent reviewers screened for eligibility. Data extraction included population and study characteristics, intervention characteristics (TIDieR) and components (PRISMS), (associations with) quality of life (QoL), self-efficacy, and economic outcomes. Study quality was appraised, and narrative synthesis was conducted. We identified 53 papers reporting 32 interventions. Studies had varying quality. They were most often randomised controlled trials (n = 20), targeted at survivors of breast (n = 10), prostate (n = 7), or mixed cancers (n = 11). Intervention characteristics (e.g., provider, location) varied considerably. On average, five (range 1-10) self-management components were delivered, mostly "Information about condition and its management" (n = 26). Twenty-two studies reported significant QoL improvements (6 also reported significant self-efficacy improvements); these were associated most consistently with combined individual and group delivery. Economic evaluations were limited and inconclusive. Self-management interventions showed promise for improving QoL, but study quality was variable, with substantial heterogeneity in intervention characteristics and components. By identifying what to adapt from existing interventions, these findings can inform development and implementation of self-management interventions in cancer.
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Affiliation(s)
- Ben Rimmer
- Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Morven C. Brown
- Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Tumi Sotire
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Fiona Beyer
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Iakov Bolnykh
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Michelle Balla
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Catherine Richmond
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Lizzie Dutton
- Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Sophie Williams
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Vera Araújo-Soares
- Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
- Centre for Preventive Medicine and Digital Health, Department for Prevention, Medical Faculty Mannheim, Heidelberg University, 69117 Heidelberg, Germany
| | - Tracy Finch
- Department of Nursing, Midwifery and Health, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Pamela Gallagher
- School of Psychology, Dublin City University, D09 N920 Dublin, Ireland
| | - Joanne Lewis
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Richéal Burns
- Faculty of Science, Atlantic Technological University, F91 YW50 Sligo, Ireland
- Health and Biomedical Strategic Research Centre, Atlantic Technological University, F91 YW50 Sligo, Ireland
| | - Linda Sharp
- Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
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13
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Baillache DJ, Valero T, Lorente-Macías Á, Bennett DJ, Elliott RJR, Carragher NO, Unciti-Broceta A. Discovery of pyrazolopyrimidines that selectively inhibit CSF-1R kinase by iterative design, synthesis and screening against glioblastoma cells. RSC Med Chem 2023; 14:2611-2624. [PMID: 38099057 PMCID: PMC10718585 DOI: 10.1039/d3md00454f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/09/2023] [Indexed: 12/17/2023] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive type of brain cancer in adults, with an average life expectancy under treatment of approx. 15 months. GBM is characterised by a complex set of genetic alterations that results in significant disruption of receptor tyrosine kinase (RTK) signaling. We report here an exploration of the pyrazolo[3,4-d]pyrimidine scaffold in search for antiproliferative compounds directed to GBM treatment. Small compound libraries were synthesised and screened against GBM cells to build up structure-antiproliferative activity-relationships (SAARs) and inform further rounds of design, synthesis and screening. 76 novel compounds were generated through this iterative process that found low micromolar potencies against selected GBM lines, including patient-derived stem cells. Phenomics analysis demonstrated preferential activity against glioma cells of the mesenchymal subtype, whereas kinome screening identified colony stimulating factor-1 receptor (CSF-1R) as the lead's target, a RTK implicated in the tumourigenesis and progression of different cancers and the immunoregulation of the GBM microenvironment.
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Affiliation(s)
- Daniel J Baillache
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | - Teresa Valero
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | - Álvaro Lorente-Macías
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | | | - Richard J R Elliott
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | - Neil O Carragher
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | - Asier Unciti-Broceta
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
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14
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Wu Y, Derks SHAE, Wood TC, de Blois E, van der Veldt AAM, Smits M, Warnert EAH. Improved postprocessing of dynamic glucose-enhanced CEST MRI for imaging brain metastases at 3 T. Eur Radiol Exp 2023; 7:78. [PMID: 38066225 PMCID: PMC10709288 DOI: 10.1186/s41747-023-00390-5] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/14/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Dynamic glucose-enhanced (DGE) chemical exchange saturation transfer (CEST) has the potential to characterize glucose metabolism in brain metastases. Since the effect size of DGE CEST is small at 3 T (< 1%), measurements of signal-to-noise ratios are challenging. To improve DGE detection, we developed an acquisition pipeline and extended image analysis for DGE CEST on a hybrid 3-T positron emission tomography/magnetic resonance imaging system. METHODS This cross-sectional study was conducted after local ethical approval. Static Z-spectra (from -100 to 100 ppm) were acquired to compare the use of 1.2 versus 2 ppm to calculate static glucose-enhanced (glucoCEST) maps in 10 healthy volunteers before and after glucose infusion. Dynamic CEST images were acquired during glucose infusion. Image analysis was optimized using motion correction, dynamic B0 correction, and principal component analysis (PCA) to improve the detection of DGE CEST in the sagittal sinus, cerebrospinal fluid, and grey and white matter. The developed DGE CEST pipeline was applied to four patients diagnosed with brain metastases. RESULTS GlucoCEST was strongest in healthy tissues at 2 ppm. Correcting for motion, B0, and use of PCA locally improved DGE maps. A larger contrast between healthy tissues and enhancing regions in brain metastases was found when dynamic B0 correction and PCA denoising were applied. CONCLUSION We demonstrated the feasibility of DGE CEST with our developed acquisition and analysis pipeline at 3 T in patients with brain metastases. This work enables a direct comparison of DGE CEST to 18F-fluoro-deoxy-D-glucose positron emission tomography of glucose metabolism in patients with brain metastases. RELEVANCE STATEMENT Contrast between brain metastasis and healthy brain tissue in DGE CEST MR images is improved by including principle component analysis and dynamic magnetic field correction during postprocessing. This approach enables the detection of increased DGE CEST signal in brain metastasis, if present. KEY POINTS • Despite the low signal-to-noise ratio, dynamic glucose-enhanced CEST MRI is feasible at 3 T. • Principal component analyses and dynamic magnetic field correction improve DGE CEST MRI. • DGE CEST MRI does not consequently show changes in brain metastases compared to healthy brain tissue. • Increased DGE CEST MRI in brain metastases, if present, shows overlap with contrast enhancement on T1-weighted images.
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Affiliation(s)
- Yulun Wu
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands
- Brain Tumor Centre, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Sophie H A E Derks
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands
- Departments of Neurology, Erasmus MC, Rotterdam, Netherlands
- Departments of Medical Oncology, Erasmus MC, Rotterdam, Netherlands
| | - Tobias C Wood
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Erik de Blois
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands
| | - Astrid A M van der Veldt
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands
- Departments of Medical Oncology, Erasmus MC, Rotterdam, Netherlands
| | - Marion Smits
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands
- Brain Tumor Centre, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Medical Delta, Delft, Netherlands
| | - Esther A H Warnert
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, Netherlands.
- Brain Tumor Centre, Erasmus MC Cancer Institute, Rotterdam, Netherlands.
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15
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Hardin EC, Schmid S, Sommerkamp A, Bodden C, Heipertz AE, Sievers P, Wittmann A, Milde T, Pfister SM, von Deimling A, Horn S, Herz NA, Simon M, Perera AA, Azizi A, Cruz O, Curry S, Van Damme A, Garami M, Hargrave D, Kattamis A, Kotnik BF, Lähteenmäki P, Scheinemann K, Schouten-van Meeteren AYN, Sehested A, Viscardi E, Wormdal OM, Zapotocky M, Ziegler DS, Koch A, Hernáiz Driever P, Witt O, Capper D, Sahm F, Jones DTW, van Tilburg CM. LOGGIC Core BioClinical Data Bank: Added clinical value of RNA-Seq in an international molecular diagnostic registry for pediatric low-grade glioma patients. Neuro Oncol 2023; 25:2087-2097. [PMID: 37075810 PMCID: PMC10628936 DOI: 10.1093/neuonc/noad078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 01/01/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The international, multicenter registry LOGGIC Core BioClinical Data Bank aims to enhance the understanding of tumor biology in pediatric low-grade glioma (pLGG) and provide clinical and molecular data to support treatment decisions and interventional trial participation. Hence, the question arises whether implementation of RNA sequencing (RNA-Seq) using fresh frozen (FrFr) tumor tissue in addition to gene panel and DNA methylation analysis improves diagnostic accuracy and provides additional clinical benefit. METHODS Analysis of patients aged 0 to 21 years, enrolled in Germany between April 2019 and February 2021, and for whom FrFr tissue was available. Central reference histopathology, immunohistochemistry, 850k DNA methylation analysis, gene panel sequencing, and RNA-Seq were performed. RESULTS FrFr tissue was available in 178/379 enrolled cases. RNA-Seq was performed on 125 of these samples. We confirmed KIAA1549::BRAF-fusion (n = 71), BRAF V600E-mutation (n = 12), and alterations in FGFR1 (n = 14) as the most frequent alterations, among other common molecular drivers (n = 12). N = 16 cases (13%) presented rare gene fusions (eg, TPM3::NTRK1, EWSR1::VGLL1, SH3PXD2A::HTRA1, PDGFB::LRP1, GOPC::ROS1). In n = 27 cases (22%), RNA-Seq detected a driver alteration not otherwise identified (22/27 actionable). The rate of driver alteration detection was hereby increased from 75% to 97%. Furthermore, FGFR1 internal tandem duplications (n = 6) were only detected by RNA-Seq using current bioinformatics pipelines, leading to a change in analysis protocols. CONCLUSIONS The addition of RNA-Seq to current diagnostic methods improves diagnostic accuracy, making precision oncology treatments (MEKi/RAFi/ERKi/NTRKi/FGFRi/ROSi) more accessible. We propose to include RNA-Seq as part of routine diagnostics for all pLGG patients, especially when no common pLGG alteration was identified.
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Affiliation(s)
- Emily C Hardin
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- Heidelberg Medical Faculty, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Simone Schmid
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alexander Sommerkamp
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Paediatrics and Adolescent Medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Carina Bodden
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK)
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Anna-Elisa Heipertz
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- Heidelberg Medical Faculty, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andrea Wittmann
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Till Milde
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Saint Luc University Hospital, Brussels, Belgium
| | - Svea Horn
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, HIT-LOGGIC German Registry for children and adolescents with low-grade glioma, Berlin, Germany
| | - Nina A Herz
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, HIT-LOGGIC German Registry for children and adolescents with low-grade glioma, Berlin, Germany
| | - Michèle Simon
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, HIT-LOGGIC German Registry for children and adolescents with low-grade glioma, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ashwyn A Perera
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Heidelberg Medical Faculty, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Amedeo Azizi
- Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Ofelia Cruz
- Neuro-Oncology Unit, Pediatric Cancer Center, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Sarah Curry
- Department of Haematology and Oncology, Children’s Health Ireland at Crumlin, Dublin, Ireland
| | - An Van Damme
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Saint Luc University Hospital, Brussels, Belgium
| | - Miklos Garami
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Darren Hargrave
- Great Ormond Street Hospital for Children NHS Trust London, London, UK
| | - Antonis Kattamis
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- First Department of Paediatrics, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Barbara Faganel Kotnik
- Department of Haematology and Oncology, University Children’s Hospital, University Medical Centre Ljubljana (UMC), Ljubljana, Slovenia
| | - Päivi Lähteenmäki
- Turku University and University Hospital, Turku, Finland
- Swedish Childhood Cancer Registry, Karolinska Institutet, Stockholm, Sweden
| | - Katrin Scheinemann
- Division of Pediatric Oncology – Hematology, Department of Pediatrics, Kantonsspital Aarau, Aarau, Switzerland
- Department of Health Sciences and Medicine, University of Lucerne, Lucerne, Switzerland
- Department of Paediatrics, McMaster Children’s Hospital and McMaster University, Hamilton, Canada
| | | | - Astrid Sehested
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Paediatrics and Adolescent Medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | | | - Ole Mikal Wormdal
- Section of Pediatric Oncology, UNN University Hospital of Northern Norway, Tromsø, Norway
| | - Michal Zapotocky
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, University Hospital Motol, Charles University, Prague, Czech Republic
| | - David S Ziegler
- Kids Cancer Centre, Sydney Children’s Hospital, High St, Randwick, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Arend Koch
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- First Department of Paediatrics, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Pablo Hernáiz Driever
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, HIT-LOGGIC German Registry for children and adolescents with low-grade glioma, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Olaf Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cornelis M van Tilburg
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK)
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
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16
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Vanderlinden A, Jones CG, Myers KN, Rominiyi O, Collis SJ. DNA damage response inhibitors enhance tumour treating fields (TTFields) potency in glioma stem-like cells. Br J Cancer 2023; 129:1829-1840. [PMID: 37777579 PMCID: PMC10667536 DOI: 10.1038/s41416-023-02454-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND High-grade gliomas are primary brain cancers with unacceptably low and persistent survival rates of 10-16 months for WHO grade 4 gliomas over the last 40 years, despite surgical resection and DNA-damaging chemo-radiotherapy. More recently, tumour-treating fields therapy (TTFields) has demonstrated modest survival benefit and been clinically approved in several countries. TTFields is thought to mediate anti-cancer activity by primarily disrupting mitosis. However, recent data suggest that TTFields may also attenuate DNA damage repair and replication fork dynamics, providing a potential platform for therapeutic combinations incorporating standard-of-care treatments and targeted DNA damage response inhibitors (DDRi). METHODS We have used patient-derived, typically resistant, glioma stem-like cells (GSCs) in combination with the previously validated preclinical Inovitro™ TTFields system together with a number of therapeutic DDRi. RESULTS We show that TTFields robustly activates PARP- and ATR-mediated DNA repair (including PARylation and CHK1 phosphorylation, respectively), whilst combining TTFields with PARP1 or ATR inhibitor treatment leads to significantly reduced clonogenic survival. The potency of each of these strategies is further enhanced by radiation treatment, leading to increased amounts of DNA damage with profound delay in DNA damage resolution. CONCLUSION To our knowledge, our findings represent the first report of TTFields applied with clinically approved or in-trial DDRi in GSC models and provides a basis for translational studies toward multimodal DDRi/TTFields-based therapeutic strategies for patients with these currently incurable tumours.
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Affiliation(s)
- Aurelie Vanderlinden
- Division of Clinical Medicine, The University of Sheffield, School of Medicine and Population Health, Sheffield, S10 2RX, UK
| | - Callum G Jones
- Division of Clinical Medicine, The University of Sheffield, School of Medicine and Population Health, Sheffield, S10 2RX, UK
| | - Katie N Myers
- Division of Clinical Medicine, The University of Sheffield, School of Medicine and Population Health, Sheffield, S10 2RX, UK
| | - Ola Rominiyi
- Division of Clinical Medicine, The University of Sheffield, School of Medicine and Population Health, Sheffield, S10 2RX, UK.
- Division of Neuroscience, The University of Sheffield, School of Medicine and Population Health, Sheffield, S10 2RX, UK.
- Department of Neurosurgery, Royal Hallamshire Hospital, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, S10 2JF, UK.
| | - Spencer J Collis
- Division of Clinical Medicine, The University of Sheffield, School of Medicine and Population Health, Sheffield, S10 2RX, UK.
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17
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Wu Y, Wood TC, Derks SHAE, Pruis IJ, van der Voort S, van Zanten SEMV, Smits M, Warnert EAH. Reproducibility of APT-weighted CEST-MRI at 3T in healthy brain and tumor across sessions and scanners. Sci Rep 2023; 13:18115. [PMID: 37872418 PMCID: PMC10593824 DOI: 10.1038/s41598-023-44891-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/17/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Amide proton transfer (APT)-weighted chemical exchange saturation transfer (CEST) imaging is a recent MRI technique making its way into clinical application. In this work, we investigated whether APT-weighted CEST imaging can provide reproducible measurements across scan sessions and scanners. Within-session, between-session and between scanner reproducibility was calculated for 19 healthy volunteers and 7 patients with a brain tumor on two 3T MRI scanners. The APT-weighted CEST effect was evaluated by calculating the Lorentzian Difference (LD), magnetization transfer ratio asymmetry (MTRasym), and relaxation-compensated inverse magnetization transfer ratio (MTRREX) averaged in whole brain white matter (WM), enhancing tumor and necrosis. Within subject coefficient of variation (COV) calculations, Bland-Altman plots and mixed effect modeling were performed to assess the repeatability and reproducibility of averaged values. The group median COVs of LD APT were 0.56% (N = 19), 0.84% (N = 6), 0.80% (N = 9) in WM within-session, between-session and between-scanner respectively. The between-session COV of LD APT in enhancing tumor (N = 6) and necrotic core (N = 3) were 4.57% and 5.67%, respectively. There were no significant differences in within session, between session and between scanner comparisons of the APT effect. The COVs of LD and MTRREX were consistently lower than MTRasym in all experiments, both in healthy tissues and tumor. The repeatability and reproducibility of APT-weighted CEST was clinically acceptable across scan sessions and scanners. Although MTRasym is simple to acquire and compute and sufficient to provide robust measurement, it is beneficial to include LD and MTRREX to obtain higher reproducibility for detecting minor signal difference in different tissue types.
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Affiliation(s)
- Yulun Wu
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Tobias C Wood
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Sophie H A E Derks
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Medical Oncology, Erasmus MC-University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Ilanah J Pruis
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Sebastian van der Voort
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Medical Delta, Delft, The Netherlands
| | - Sophie E M Veldhuijzen van Zanten
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marion Smits
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Medical Delta, Delft, The Netherlands
| | - Esther A H Warnert
- Department of Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands.
- Brain Tumour Centre, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
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18
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Walker H, Rimmer B, Dutton L, Finch T, Gallagher P, Lewis J, Burns R, Araújo-Soares V, Williams S, Sharp L. Experiences of work for people living with a grade 2/3 oligodendroglioma: a qualitative analysis within the Ways Ahead study. BMJ Open 2023; 13:e074151. [PMID: 37770270 PMCID: PMC10546132 DOI: 10.1136/bmjopen-2023-074151] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/07/2023] [Indexed: 09/30/2023] Open
Abstract
OBJECTIVES This study aimed to explore the work experiences of people living with an oligodendroglioma. DESIGN This was a descriptive qualitative study. One-time semi-structured interviews exploring supportive care needs were conducted; work was discussed at various points throughout each interview. An inductive thematic analysis was undertaken. SETTING Participants were recruited across the UK through four National Health Service hospitals and the Brain Tumour Charity research involvement networks. PARTICIPANTS 19 people with grade 2 or 3 oligodendroglioma (mean age 52 years; male n=11). At diagnosis, 16 participants were working, 2 studying and 1 retired. At the interview (mean time since diagnosis 9.6 years; range 1-18 years), seven participants were working, eight retired (four on medical grounds) and four unable to work due to illness. RESULTS Seven themes were constructed: (1) physical and cognitive limitations; (2) work ability and productivity; (3) work accommodations; (4) changing roles; (5) attitudes of clients and coworkers; (6) feelings and ambitions; and (7) financial implications. Fatigue, seizures and cognitive deficits influenced work ability. A stressful work environment could exacerbate symptoms. Changes in job roles and work environment were often required. Employer and coworker support were integral to positive experiences. Work changes could result in financial stress and strain. CONCLUSIONS This study has highlighted, for the first time, influences on work experiences in this understudied population. These findings have implications for clinicians and employers, when considering the importance of work in rehabilitation for people with oligodendrogliomas, and the individually assessed adjustments required to accommodate them, should employment be desired.
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Affiliation(s)
- Hayley Walker
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ben Rimmer
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lizzie Dutton
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tracy Finch
- Department of Nursing, Midwifery, and Health, Northumbria University, Newcastle upon Tyne, UK
| | | | - Joanne Lewis
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Richéal Burns
- Faculty of Science, Atlantic Technological University, Sligo, Ireland
- Health and Biomedical Strategic Research Centre, Atlantic Technological University, Sligo, Ireland
| | - Vera Araújo-Soares
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Centre for Preventive Medicine and Digital Health, Department for Prevention of Cardiovascular and Metabolic Disease, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Sophie Williams
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Linda Sharp
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
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19
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Kanev GK, Zhang Y, Kooistra AJ, Bender A, Leurs R, Bailey D, Würdinger T, de Graaf C, de Esch IJP, Westerman BA. Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks. PLoS Comput Biol 2023; 19:e1011301. [PMID: 37669273 PMCID: PMC10508635 DOI: 10.1371/journal.pcbi.1011301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2023] [Accepted: 06/25/2023] [Indexed: 09/07/2023] Open
Abstract
Many therapies in clinical trials are based on single drug-single target relationships. To further extend this concept to multi-target approaches using multi-targeted drugs, we developed a machine learning pipeline to unravel the target landscape of kinase inhibitors. This pipeline, which we call 3D-KINEssence, uses a new type of protein fingerprints (3D FP) based on the structure of kinases generated through a 3D convolutional neural network (3D-CNN). These 3D-CNN kinase fingerprints were matched to molecular Morgan fingerprints to predict the targets of each respective kinase inhibitor based on available bioactivity data. The performance of the pipeline was evaluated on two test sets: a sparse drug-target set where each drug is matched in most cases to a single target and also on a densely-covered drug-target set where each drug is matched to most if not all targets. This latter set is more challenging to train, given its non-exclusive character. Our model's root-mean-square error (RMSE) based on the two datasets was 0.68 and 0.8, respectively. These results indicate that 3D FP can predict the target landscape of kinase inhibitors at around 0.8 log units of bioactivity. Our strategy can be utilized in proteochemometric or chemogenomic workflows by consolidating the target landscape of kinase inhibitors.
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Affiliation(s)
- Georgi K. Kanev
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Yaran Zhang
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Albert J. Kooistra
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Bender
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - David Bailey
- The WINDOW consortium, www.window-consortium.org
- IOTA Pharmaceuticals Ltd, St Johns Innovation Centre, Cambridge, United Kingdom
| | - Thomas Würdinger
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
- The WINDOW consortium, www.window-consortium.org
| | - Chris de Graaf
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Bart A. Westerman
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
- The WINDOW consortium, www.window-consortium.org
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20
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Suppree JS, Patel A, Keshwara SM, Krishna ST, Gillespie CS, Richardson GE, Mustafa MA, Hart S, Islim AI, Jenkinson MD, Millward CP. Assessing the reporting quality of adult neuro-oncology protocols, abstracts, and trials: Adherence to the SPIRIT and CONSORT statements. Neurooncol Pract 2023; 10:391-401. [PMID: 37457230 PMCID: PMC10346400 DOI: 10.1093/nop/npad017] [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] [Indexed: 07/18/2023] Open
Abstract
Background Comprehensive and transparent reporting of clinical trial activity is important. The Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) 2013 and Consolidated Standards of Reporting Trials (CONSORT) 2010 statements define the items to be reported in clinical trial protocols and randomized controlled trials, respectively. The aim of this methodological review was to assess the reporting quality of adult neuro-oncology trial protocols and trial result articles. Methods Adult primary and secondary brain tumor phase 3 trial protocols and result articles published after the introduction of the SPIRIT 2013 statement, were identified through searches of 4 electronic bibliographic databases. Following extraction of baseline demographic data, the reporting quality of independently included trial protocols and result articles was assessed against the SPIRIT and CONSORT statements respectively. The CONSORT-A checklist, an extension of the CONSORT 2010 statement, was used to specifically assess the abstract accompanying the trial results article. Percentage adherence (standard deviation [SD]) was calculated for each article. Results Seven trial protocols, and 36 trial result articles were included. Mean adherence of trial protocols to the SPIRIT statement was 79.4% (SD: 0.11). Mean adherence of trial abstracts to CONSORT-A was 75.3% (SD: 0.12) and trial result articles to CONSORT was 74.5% (SD: 0.10). Conclusion The reporting quality of adult neuro-oncology trial protocols and trial result articles requires improvement to ensure comprehensive and transparent communication of planned neuro-oncology clinical trials and results within the literature. Raising awareness by clinical triallists and implementing mandatory evidence of proof of adherence by journals should improve reporting quality.
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Affiliation(s)
- Joshua S Suppree
- School of Medicine, University of Liverpool, Liverpool, United Kingdom
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Avni Patel
- School of Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sumirat M Keshwara
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | | | - Conor S Gillespie
- School of Medicine, University of Liverpool, Liverpool, United Kingdom
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - George E Richardson
- School of Medicine, University of Liverpool, Liverpool, United Kingdom
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Mohammad A Mustafa
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Sophia Hart
- School of Medicine, University of Liverpool, Liverpool, United Kingdom
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Abdurrahman I Islim
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michael D Jenkinson
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Christopher P Millward
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
- Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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21
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Sigaud R, Albert TK, Hess C, Hielscher T, Winkler N, Kocher D, Walter C, Münter D, Selt F, Usta D, Ecker J, Brentrup A, Hasselblatt M, Thomas C, Varghese J, Capper D, Thomale UW, Hernáiz Driever P, Simon M, Horn S, Herz NA, Koch A, Sahm F, Hamelmann S, Faria-Andrade A, Jabado N, Schuhmann MU, Schouten-van Meeteren AYN, Hoving E, Brummer T, van Tilburg CM, Pfister SM, Witt O, Jones DTW, Kerl K, Milde T. MAPK inhibitor sensitivity scores predict sensitivity driven by the immune infiltration in pediatric low-grade gliomas. Nat Commun 2023; 14:4533. [PMID: 37500667 PMCID: PMC10374577 DOI: 10.1038/s41467-023-40235-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
Pediatric low-grade gliomas (pLGG) show heterogeneous responses to MAPK inhibitors (MAPKi) in clinical trials. Thus, more complex stratification biomarkers are needed to identify patients likely to benefit from MAPKi therapy. Here, we identify MAPK-related genes enriched in MAPKi-sensitive cell lines using the GDSC dataset and apply them to calculate class-specific MAPKi sensitivity scores (MSSs) via single-sample gene set enrichment analysis. The MSSs discriminate MAPKi-sensitive and non-sensitive cells in the GDSC dataset and significantly correlate with response to MAPKi in an independent PDX dataset. The MSSs discern gliomas with varying MAPK alterations and are higher in pLGG compared to other pediatric CNS tumors. Heterogenous MSSs within pLGGs with the same MAPK alteration identify proportions of potentially sensitive patients. The MEKi MSS predicts treatment response in a small set of pLGG patients treated with trametinib. High MSSs correlate with a higher immune cell infiltration, with high expression in the microglia compartment in single-cell RNA sequencing data, while low MSSs correlate with low immune infiltration and increased neuronal score. The MSSs represent predictive tools for the stratification of pLGG patients and should be prospectively validated in clinical trials. Our data supports a role for microglia in the response to MAPKi.
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Affiliation(s)
- Romain Sigaud
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| | - Thomas K Albert
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Caroline Hess
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Faculty of Biochemistry, Heidelberg University, Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Nadine Winkler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Daniela Kocher
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Carolin Walter
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Daniel Münter
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Diren Usta
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Angela Brentrup
- Neurosurgery Dept., University Hospital Münster, Münster, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - David Capper
- Berlin Institute of Health, Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany
| | - Ulrich W Thomale
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Pediatric Neurosurgery, Berlin, Germany
| | - Pablo Hernáiz Driever
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, German HIT-LOGGIC-Registry for pLGG in children and adolescents, Department of Pediatric Oncology and Hematology, Berlin, Germany
| | - Michèle Simon
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, German HIT-LOGGIC-Registry for pLGG in children and adolescents, Department of Pediatric Oncology and Hematology, Berlin, Germany
| | - Svea Horn
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, German HIT-LOGGIC-Registry for pLGG in children and adolescents, Department of Pediatric Oncology and Hematology, Berlin, Germany
| | - Nina Annika Herz
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, German HIT-LOGGIC-Registry for pLGG in children and adolescents, Department of Pediatric Oncology and Hematology, Berlin, Germany
| | - Arend Koch
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Hamelmann
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC, H4A 3J1, Canada
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Martin U Schuhmann
- Section of Pediatric Neurosurgery, Department of Neurosurgery, University Hospital Tübingen, Tübingen, Germany
| | | | - Eelco Hoving
- Princess Màxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Freiburg, Germany, Centre for Biological Signaling Studies BIOSS, University of Freiburg and German Consortium for Translational Cancer Research (DKTK), Freiburg, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cornelis M van Tilburg
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
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22
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Rimmer B, Balla M, Dutton L, Lewis J, Brown MC, Burns R, Gallagher P, Williams S, Araújo-Soares V, Finch T, Menger F, Sharp L. Identifying and understanding how people living with a lower-grade glioma engage in self-management. J Cancer Surviv 2023:10.1007/s11764-023-01425-x. [PMID: 37450254 DOI: 10.1007/s11764-023-01425-x] [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: 03/28/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
PURPOSE Lower-grade gliomas (LGG) are mostly diagnosed in working-aged adults and rarely cured. LGG patients may face chronic impairments (e.g. fatigue, cognitive deficits). Self-management can improve clinical and psychosocial outcomes, yet how LGG patients self-manage the consequences of their tumour and its treatment is not fully understood. This study, therefore, aimed to identify and understand how LGG patients engage in the self-management of their condition. METHODS A diverse group of 28 LGG patients (age range 22-69 years; male n = 16, female n = 12; mean time since diagnosis = 8.7 years) who had completed primary treatment, were recruited from across the United Kingdom. Semi-structured interviews were conducted. Informed by a self-management strategy framework developed in cancer, directed content analysis identified and categorised self-management types and strategies used by patients. RESULTS Overall, 20 self-management strategy types, comprising 123 self-management strategies were reported; each participant detailed extensive engagement in self-management. The most used strategy types were 'using support' (n = 28), 'creating a healthy environment' (n = 28), 'meaning making' (n = 27), and 'self-monitoring' (n = 27). The most used strategies were 'accepting the tumour and its consequences' (n = 26), 'receiving support from friends (n = 24) and family' (n = 24), and 'reinterpreting negative consequences' (n = 24). CONCLUSIONS This study provides a comprehensive understanding of the strategies used by LGG patients to self-manage their health and wellbeing, with a diverse, and substantial number of self-management strategies reported. IMPLICATIONS FOR CANCER SURVIVORS The findings will inform the development of a supported self-management intervention for LGG patients, which will be novel for this patient group.
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Affiliation(s)
- Ben Rimmer
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle Upon Tyne, England.
| | - Michelle Balla
- Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, England
| | - Lizzie Dutton
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle Upon Tyne, England
| | - Joanne Lewis
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, England
| | - Morven C Brown
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle Upon Tyne, England
| | - Richéal Burns
- Faculty of Science, Atlantic Technological University, Sligo, Ireland
- Health and Biomedical Strategic Research Centre, Atlantic Technological University, Sligo, Ireland
| | | | - Sophie Williams
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, England
| | - Vera Araújo-Soares
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle Upon Tyne, England
- Centre for Preventive Medicine and Digital Health, Department for Prevention of Cardiovascular and Metabolic Disease, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Tracy Finch
- Department of Nursing, Midwifery and Health, Northumbria University, Newcastle Upon Tyne, England
| | - Fiona Menger
- School of Education, Communication and Language Sciences, Newcastle University, Newcastle Upon Tyne, England
| | - Linda Sharp
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle Upon Tyne, England
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23
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Andrieux G, Das T, Griffin M, Straehle J, Paine SML, Beck J, Boerries M, Heiland DH, Smith SJ, Rahman R, Chakraborty S. Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence. Genome Med 2023; 15:48. [PMID: 37434262 PMCID: PMC10337060 DOI: 10.1186/s13073-023-01207-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 07/01/2022] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Spatiotemporal heterogeneity originating from genomic and transcriptional variation was found to contribute to subtype switching in isocitrate dehydrogenase-1 wild-type glioblastoma (GBM) prior to and upon recurrence. Fluorescence-guided neurosurgical resection utilizing 5-aminolevulinic acid (5ALA) enables intraoperative visualization of infiltrative tumors outside the magnetic resonance imaging contrast-enhanced regions. The cell population and functional status of tumor responsible for enhancing 5ALA-metabolism to fluorescence-active PpIX remain elusive. The close spatial proximity of 5ALA-metabolizing (5ALA +) cells to residual disease remaining post-surgery renders 5ALA + biology an early a priori proxy of GBM recurrence, which is poorly understood. METHODS We performed spatially resolved bulk RNA profiling (SPRP) analysis of unsorted Core, Rim, Invasive margin tissue, and FACS-isolated 5ALA + /5ALA - cells from the invasive margin across IDH-wt GBM patients (N = 10) coupled with histological, radiographic, and two-photon excitation fluorescence microscopic analyses. Deconvolution of SPRP followed by functional analyses was performed using CIBEROSRTx and UCell enrichment algorithms, respectively. We further investigated the spatial architecture of 5ALA + enriched regions by analyzing spatial transcriptomics from an independent IDH-wt GBM cohort (N = 16). Lastly, we performed survival analysis using Cox Proportinal-Hazards model on large GBM cohorts. RESULTS SPRP analysis integrated with single-cell and spatial transcriptomics uncovered that the GBM molecular subtype heterogeneity is likely to manifest regionally in a cell-type-specific manner. Infiltrative 5ALA + cell population(s) harboring transcriptionally concordant GBM and myeloid cells with mesenchymal subtype, -active wound response, and glycolytic metabolic signature, was shown to reside within the invasive margin spatially distinct from the tumor core. The spatial co-localization of the infiltrating MES GBM and myeloid cells within the 5ALA + region indicates PpIX fluorescence can effectively be utilized to resect the immune reactive zone beyond the tumor core. Finally, 5ALA + gene signatures were associated with poor survival and recurrence in GBM, signifying that the transition from primary to recurrent GBM is not discrete but rather a continuum whereby primary infiltrative 5ALA + remnant tumor cells more closely resemble the eventual recurrent GBM. CONCLUSIONS Elucidating the unique molecular and cellular features of the 5ALA + population within tumor invasive margin opens up unique possibilities to develop more effective treatments to delay or block GBM recurrence, and warrants commencement of such treatments as early as possible post-surgical resection of the primary neoplasm.
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Affiliation(s)
- Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tonmoy Das
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Systems Cell-Signaling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Michaela Griffin
- Children's Brain Tumour Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Jakob Straehle
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Simon M L Paine
- Children's Brain Tumour Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Jürgen Beck
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Microenvironment and Immunology Research Laboratory, Medical Center - University of Freiburg, Freiburg, Germany
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Stuart J Smith
- Children's Brain Tumour Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK
| | - Ruman Rahman
- Children's Brain Tumour Research Centre, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham, UK.
| | - Sajib Chakraborty
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Systems Cell-Signaling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.
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24
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Kratz CP, Smirnov D, Autry R, Jäger N, Waszak SM, Großhennig A, Berutti R, Wendorff M, Hainaut P, Pfister SM, Prokisch H, Ripperger T, Malkin D. Reply to Li and Colleagues. J Natl Cancer Inst 2023; 115:760-761. [PMID: 37004196 PMCID: PMC10248829 DOI: 10.1093/jnci/djad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 04/03/2023] Open
Affiliation(s)
- Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Dmitrii Smirnov
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Robert Autry
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic European Molecular Biology Laboratory (EMBL) Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Anika Großhennig
- Institute of Biostatistics, Hannover Medical School, Hannover, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Inserm 1209 CNRS 5309 UGA, Grenoble, France
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - David Malkin
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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25
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Gonzalez-Meljem JM, Ivins S, Andoniadou CL, Le Tissier P, Scambler P, Martinez-Barbera JP. An expression and function analysis of the CXCR4/SDF-1 signalling axis during pituitary gland development. PLoS One 2023; 18:e0280001. [PMID: 36800350 PMCID: PMC9937476 DOI: 10.1371/journal.pone.0280001] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 12/19/2022] [Indexed: 02/18/2023] Open
Abstract
The chemokine SDF-1 (CXCL12) and its receptor CXCR4 control several processes during embryonic development such as the regulation of stem cell proliferation, differentiation, and migration. However, the role of this pathway in the formation of the pituitary gland is not understood. We sought to characterise the expression patterns of CXCR4, SDF-1 and CXCR7 at different stages of pituitary gland development. Our expression profiling revealed that SDF-1 is expressed in progenitor-rich regions of the pituitary anterior lobe, that CXCR4 and CXCR7 have opposite expression domains and that CXCR4 expression is conserved between mice and human embryos. We then assessed the importance of this signalling pathway in the development and function of the murine pituitary gland through conditional deletion of CXCR4 in embryonic pituitary progenitors. Successful and specific ablation of CXCR4 expression in embryonic pituitary progenitors did not lead to observable embryonic nor postnatal defects but allowed the identification of stromal CXCR4+ cells not derived from HESX1+ progenitors. Further analysis of constitutive SDF-1, CXCR7 and CXCR4 mutants of the pathway indicates that CXCR4 expression in HESX1+ cells and their descendants is not essential for normal pituitary development in mice.
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Affiliation(s)
- Jose Mario Gonzalez-Meljem
- Tecnologico de Monterrey, School of Engineering and Sciences, Mexico City, Mexico
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL-Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sarah Ivins
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL-Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Cynthia Lilian Andoniadou
- Division of Craniofacial Development and Stem Cell Biology, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Paul Le Tissier
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Scambler
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL-Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Juan Pedro Martinez-Barbera
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL-Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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26
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Keck MK, Sill M, Wittmann A, Joshi P, Stichel D, Beck P, Okonechnikow K, Sievers P, Wefers AK, Roncaroli F, Avula S, McCabe MG, Hayden JT, Wesseling P, Øra I, Nistér M, Kranendonk MEG, Tops BBJ, Zapotocky M, Zamecnik J, Vasiljevic A, Fenouil T, Meyronet D, von Hoff K, Schüller U, Loiseau H, Figarella-Branger D, Kramm CM, Sturm D, Scheie D, Rauramaa T, Pesola J, Gojo J, Haberler C, Brandner S, Jacques T, Sexton Oates A, Saffery R, Koscielniak E, Baker SJ, Yip S, Snuderl M, Ud Din N, Samuel D, Schramm K, Blattner-Johnson M, Selt F, Ecker J, Milde T, von Deimling A, Korshunov A, Perry A, Pfister SM, Sahm F, Solomon DA, Jones DTW. Amplification of the PLAG-family genes-PLAGL1 and PLAGL2-is a key feature of the novel tumor type CNS embryonal tumor with PLAGL amplification. Acta Neuropathol 2023; 145:49-69. [PMID: 36437415 PMCID: PMC9807491 DOI: 10.1007/s00401-022-02516-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/23/2022] [Accepted: 10/24/2022] [Indexed: 11/28/2022]
Abstract
Pediatric central nervous system (CNS) tumors represent the most common cause of cancer-related death in children aged 0-14 years. They differ from their adult counterparts, showing extensive clinical and molecular heterogeneity as well as a challenging histopathological spectrum that often impairs accurate diagnosis. Here, we use DNA methylation-based CNS tumor classification in combination with copy number, RNA-seq, and ChIP-seq analysis to characterize a newly identified CNS tumor type. In addition, we report histology, patient characteristics, and survival data in this tumor type. We describe a biologically distinct pediatric CNS tumor type (n = 31 cases) that is characterized by focal high-level amplification and resultant overexpression of either PLAGL1 or PLAGL2, and an absence of recurrent genetic alterations characteristic of other pediatric CNS tumor types. Both genes act as transcription factors for a regulatory subset of imprinted genes (IGs), components of the Wnt/β-Catenin pathway, and the potential drug targets RET and CYP2W1, which are also specifically overexpressed in this tumor type. A derived PLAGL-specific gene expression signature indicates dysregulation of imprinting control and differentiation/development. These tumors occurred throughout the neuroaxis including the cerebral hemispheres, cerebellum, and brainstem, and were predominantly composed of primitive embryonal-like cells lacking robust expression of markers of glial or neuronal differentiation (e.g., GFAP, OLIG2, and synaptophysin). Tumors with PLAGL1 amplification were typically diagnosed during adolescence (median age 10.5 years), whereas those with PLAGL2 amplification were diagnosed during early childhood (median age 2 years). The 10-year overall survival was 66% for PLAGL1-amplified tumors, 25% for PLAGL2-amplified tumors, 18% for male patients, and 82% for female patients. In summary, we describe a new type of biologically distinct CNS tumor characterized by PLAGL1/2 amplification that occurs predominantly in infants and toddlers (PLAGL2) or adolescents (PLAGL1) which we consider best classified as a CNS embryonal tumor and which is associated with intermediate survival. The cell of origin and optimal treatment strategies remain to be defined.
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Affiliation(s)
- Michaela-Kristina Keck
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea Wittmann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Piyush Joshi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pengbo Beck
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Konstantin Okonechnikow
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Federico Roncaroli
- Geoffrey Jefferson Brain Research Centre, Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shivaram Avula
- Department of Radiology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Martin G McCabe
- Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - James T Hayden
- Department of Pediatric Hematology and Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers, Location VUmc and Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Ingrid Øra
- Department of Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Michal Zapotocky
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Josef Zamecnik
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Alexandre Vasiljevic
- Institut de Pathologie Multisite-Site Est, Groupement Hospitalier Est, Hospices Civils de Lyon, Lyon, France
| | - Tanguy Fenouil
- Institut de Pathologie Multisite-Site Est, Groupement Hospitalier Est, Hospices Civils de Lyon, Lyon, France
| | - David Meyronet
- Institut de Pathologie Multisite-Site Est, Groupement Hospitalier Est, Hospices Civils de Lyon, Lyon, France
| | - Katja von Hoff
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Hugues Loiseau
- University of Bordeaux, Bordeaux Institute of Oncology (BRIC)-INSERM U1312 Université de Bordeaux, 146 rue Leo Saignat, Case 76, 33076, Bordeaux, France
| | - Dominique Figarella-Branger
- Aix-Marseille Univ, APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Marseille, France
| | - Christof M Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | - Tuomas Rauramaa
- Department of Clinical Pathology, Kuopio University Hospital and Unit of Pathology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jouni Pesola
- Department of Pediatrics, Pediatric Hematology and Oncology Ward, Kuopio University Hospital and Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Comprehensive Cancer Center and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090, Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Sebastian Brandner
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Tom Jacques
- Department of Developmental Biology and Cancer, UCL GOS Institute of Child Health, University College London, London, UK
| | - Alexandra Sexton Oates
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Australia
| | - Ewa Koscielniak
- Department of Pediatric Oncology/Hematology/Immunology, Olgahospital, Klinikum Stuttgart, Stuttgart, Germany
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, The University of British Colombia, Vancouver, Canada
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY, USA
| | - Nasir Ud Din
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - David Samuel
- Department of Pediatric Hematology-Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Kathrin Schramm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Arie Perry
- Division of Neuropathology, Department of Pathology, University of California San Francisco (UCSF), 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David A Solomon
- Division of Neuropathology, Department of Pathology, University of California San Francisco (UCSF), 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA.
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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Giczewska A, Pastuszak K, Houweling M, Abdul KU, Faaij N, Wedekind L, Noske D, Wurdinger T, Supernat A, Westerman BA. Longitudinal drug synergy assessment using convolutional neural network image-decoding of glioblastoma single-spheroid cultures. Neurooncol Adv 2023; 5:vdad134. [PMID: 38047207 PMCID: PMC10691443 DOI: 10.1093/noajnl/vdad134] [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] [Indexed: 12/05/2023] Open
Abstract
Background In recent years, drug combinations have become increasingly popular to improve therapeutic outcomes in various diseases, including difficult to cure cancers such as the brain cancer glioblastoma. Assessing the interaction between drugs over time is critical for predicting drug combination effectiveness and minimizing the risk of therapy resistance. However, as viability readouts of drug combination experiments are commonly performed as an endpoint where cells are lysed, longitudinal drug-interaction monitoring is currently only possible through combined endpoint assays. Methods We provide a method for massive parallel monitoring of drug interactions for 16 drug combinations in 3 glioblastoma models over a time frame of 18 days. In our assay, viabilities of single neurospheres are to be estimated based on image information taken at different time points. Neurosphere images taken on the final day (day 18) were matched to the respective viability measured by CellTiter-Glo 3D on the same day. This allowed to use of machine learning to decode image information to viability values on day 18 as well as for the earlier time points (on days 8, 11, and 15). Results Our study shows that neurosphere images allow us to predict cell viability from extrapolated viabilities. This enables to assess of the drug interactions in a time window of 18 days. Our results show a clear and persistent synergistic interaction for several drug combinations over time. Conclusions Our method facilitates longitudinal drug-interaction assessment, providing new insights into the temporal-dynamic effects of drug combinations in 3D neurospheres which can help to identify more effective therapies against glioblastoma.
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Affiliation(s)
- Anna Giczewska
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Krzysztof Pastuszak
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
- Center of Biostatistics and Bioinformatics, Medical University of Gdańsk, Gdańsk, Poland
- Department of Algorithms and System Modeling, Gdansk University of Technology, Gdańsk, Poland
| | - Megan Houweling
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- The WINDOW Consortium (www.window-consortium.org)
| | - Kulsoom U Abdul
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- The WINDOW Consortium (www.window-consortium.org)
| | - Noa Faaij
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Laurine Wedekind
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - David Noske
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- The WINDOW Consortium (www.window-consortium.org)
| | - Anna Supernat
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
- Center of Biostatistics and Bioinformatics, Medical University of Gdańsk, Gdańsk, Poland
| | - Bart A Westerman
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- The WINDOW Consortium (www.window-consortium.org)
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Jørgensen ACS, Ghosh A, Sturrock M, Shahrezaei V. Efficient Bayesian inference for stochastic agent-based models. PLoS Comput Biol 2022; 18:e1009508. [PMID: 36197919 PMCID: PMC9576090 DOI: 10.1371/journal.pcbi.1009508] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/17/2022] [Accepted: 09/21/2022] [Indexed: 11/14/2022] Open
Abstract
The modelling of many real-world problems relies on computationally heavy simulations of randomly interacting individuals or agents. However, the values of the parameters that underlie the interactions between agents are typically poorly known, and hence they need to be inferred from macroscopic observations of the system. Since statistical inference rests on repeated simulations to sample the parameter space, the high computational expense of these simulations can become a stumbling block. In this paper, we compare two ways to mitigate this issue in a Bayesian setting through the use of machine learning methods: One approach is to construct lightweight surrogate models to substitute the simulations used in inference. Alternatively, one might altogether circumvent the need for Bayesian sampling schemes and directly estimate the posterior distribution. We focus on stochastic simulations that track autonomous agents and present two case studies: tumour growths and the spread of infectious diseases. We demonstrate that good accuracy in inference can be achieved with a relatively small number of simulations, making our machine learning approaches orders of magnitude faster than classical simulation-based methods that rely on sampling the parameter space. However, we find that while some methods generally produce more robust results than others, no algorithm offers a one-size-fits-all solution when attempting to infer model parameters from observations. Instead, one must choose the inference technique with the specific real-world application in mind. The stochastic nature of the considered real-world phenomena poses an additional challenge that can become insurmountable for some approaches. Overall, we find machine learning approaches that create direct inference machines to be promising for real-world applications. We present our findings as general guidelines for modelling practitioners.
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Affiliation(s)
| | | | - Marc Sturrock
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Vahid Shahrezaei
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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29
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Retzer A, Sivell S, Scott H, Nelson A, Bulbeck H, Seddon K, Grant R, Adams R, Watts C, Aiyegbusi OL, Kearns P, Cruz Rivera S, Dirven L, Baddeley E, Calvert M, Byrne A. Development of a core outcome set and identification of patient-reportable outcomes for primary brain tumour trials: protocol for the COBra study. BMJ Open 2022; 12:e057712. [PMID: 36180121 PMCID: PMC9528585 DOI: 10.1136/bmjopen-2021-057712] [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] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 07/18/2022] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Primary brain tumours, specifically gliomas, are a rare disease group. The disease and treatment negatively impacts on patients and those close to them. The high rates of physical and cognitive morbidity differ from other cancers causing reduced health-related quality of life. Glioma trials using outcomes that allow holistic analysis of treatment benefits and risks enable informed care decisions. Currently, outcome assessment in glioma trials is inconsistent, hindering evidence synthesis. A core outcome set (COS) - an agreed minimum set of outcomes to be measured and reported - may address this. International initiatives focus on defining core outcomes assessments across brain tumour types. This protocol describes the development of a COS involving UK stakeholders for use in glioma trials, applicable across glioma types, with provision to identify subsets as required. Due to stakeholder interest in data reported from the patient perspective, outcomes from the COS that can be patient-reported will be identified. METHODS AND ANALYSIS Stage I: (1) trial registry review to identify outcomes collected in glioma trials and (2) systematic review of qualitative literature exploring glioma patient and key stakeholder research priorities. Stage II: semi-structured interviews with glioma patients and caregivers. Outcome lists will be generated from stages I and II. Stage III: study team will remove duplicate items from the outcome lists and ensure accessible terminology for inclusion in the Delphi survey. Stage IV: a two-round Delphi process whereby the outcomes will be rated by key stakeholders. Stage V: a consensus meeting where participants will finalise the COS. The study team will identify the COS outcomes that can be patient-reported. Further research is needed to match patient-reported outcomes to available measures. ETHICS AND DISSEMINATION Ethical approval was obtained (REF SMREC 21/59, Cardiff University School of Medicine Research Ethics Committee). Study findings will be disseminated widely through conferences and journal publication. The final COS will be adopted and promoted by patient and carer groups and its use by funders encouraged. PROSPERO REGISTRATION NUMBER CRD42021236979.
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Affiliation(s)
- Ameeta Retzer
- Centre for Patient Reported Outcomes Research, Institute for Applied Health Research, University of Birmingham, Birmingham, UK
- National Institute for Health and Care Research (NIHR) Applied Research Centre, West Midlands, Birmingham, UK
| | - Stephanie Sivell
- Marie Curie Palliative Care Research Centre, Division of Population Medicine, Cardiff University School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Hannah Scott
- Cambridge Public Health, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Annmarie Nelson
- Marie Curie Palliative Care Research Centre, Division of Population Medicine, Cardiff University School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | | | | | - Robin Grant
- Department of Clinical Neurosciences, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Richard Adams
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - Colin Watts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Olalekan Lee Aiyegbusi
- Centre for Patient Reported Outcomes Research, Institute for Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
| | - Pamela Kearns
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
| | - Samantha Cruz Rivera
- Centre for Patient Reported Outcomes Research, Institute for Applied Health Research, University of Birmingham, Birmingham, UK
- Birmingham Health Partners Centre for Regulatory Science and Innovation, University of Birmingham, Birmingham, UK
| | - Linda Dirven
- Department of Neurology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
- Department of Neurology, Medical Centre Haaglanden, Den Haag, The Netherlands
| | - Elin Baddeley
- Marie Curie Palliative Care Research Centre, Division of Population Medicine, Cardiff University School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Melanie Calvert
- Centre for Patient Reported Outcomes Research, Institute for Applied Health Research, University of Birmingham, Birmingham, UK
- National Institute for Health and Care Research (NIHR) Applied Research Centre, West Midlands, Birmingham, UK
| | - Anthony Byrne
- Marie Curie Palliative Care Research Centre, Division of Population Medicine, Cardiff University School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
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Watts C, Savage J, Patel A, Mant R, Wykes V, Pohl U, Bulbeck H, Apps J, Sharpe R, Thompson G, Waldman AD, Ansorge O, Billingham L. Protocol for the Tessa Jowell BRAIN MATRIX Platform Study. BMJ Open 2022; 12:e067123. [PMID: 36378622 PMCID: PMC9462095 DOI: 10.1136/bmjopen-2022-067123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 08/07/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION Gliomas are the most common primary tumour of the central nervous system (CNS), with an estimated annual incidence of 6.6 per 100 000 individuals in the USA and around 14 deaths per day from brain tumours in the UK. The genomic and biological landscape of brain tumours has been increasingly defined and, since 2016, the WHO classification of tumours of the CNS incorporates molecular data, along with morphology, to define tumour subtypes more accurately. The Tessa Jowell BRAIN MATRIX Platform (TJBM) study aims to create a transformative clinical research infrastructure that leverages UK National Health Service resources to support research that is patient centric and attractive to both academic and commercial investors. METHODS AND ANALYSIS The TJBM study is a programme of work with the principal purpose to improve the knowledge of glioma and treatment for patients with glioma. The programme includes a platform study and subsequent interventional clinical trials (as separate protocols). The platform study described here is the backbone data-repository of disease, treatment and outcome data from clinical, imaging and pathology data being collected in patients with glioma from secondary care hospitals. The primary outcome measure of the platform is time from biopsy to integrated histological-molecular diagnosis using whole-genome sequencing and epigenomic classification. Secondary outcome measures include those that are process centred, patient centred and framework based. Target recruitment for the study is 1000 patients with interim analyses at 100 and 500 patients. ETHICS AND DISSEMINATION The study will be performed in accordance with the recommendations guiding physicians in biomedical research involving human subjects, adopted by the 18th World Medical Association General Assembly, Helsinki, Finland and stated in the respective participating countries' laws governing human research, and Good Clinical Practice. The protocol was initially approved on 18 February 2020 by West Midlands - Edgbaston Research Ethics Committee; the current protocol (v3.0) was approved on 15 June 2022. Participants will be required to provide written informed consent. A meeting will be held after the end of the study to allow discussion of the main results among the collaborators prior to publication. The results of this study will be disseminated through national and international presentations and peer-reviewed publications. Manuscripts will be prepared by the Study Management Group and authorship will be determined by mutual agreement. TRIAL REGISTRATION NUMBER NCT04274283, 18-Feb-2020; ISRCTN14218060, 03-Feb-2020.
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Affiliation(s)
- Colin Watts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Neurosurgery, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Joshua Savage
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Birmingham, UK
| | - Amit Patel
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Birmingham, UK
| | - Rhys Mant
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Birmingham, UK
| | - Victoria Wykes
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Neurosurgery, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Ute Pohl
- Pathology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - John Apps
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Birmingham, UK
| | - Rowena Sharpe
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Birmingham, UK
| | - Gerard Thompson
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Adam D Waldman
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Lucinda Billingham
- Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Birmingham, UK
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Ritzmann TA, Chapman RJ, Kilday JP, Thorp N, Modena P, Dineen RA, Macarthur D, Mallucci C, Jaspan T, Pajtler KW, Giagnacovo M, Jacques TS, Paine SML, Ellison DW, Bouffet E, Grundy RG. SIOP Ependymoma I: Final results, long-term follow-up, and molecular analysis of the trial cohort-A BIOMECA Consortium Study. Neuro Oncol 2022; 24:936-948. [PMID: 35018471 PMCID: PMC9159435 DOI: 10.1093/neuonc/noac012] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND SIOP Ependymoma I was a non-randomised trial assessing event free and overall survival (EFS/OS) of non-metastatic intracranial ependymoma in children aged 3-21 years treated with a staged management strategy. A further aim was to assess the response rate (RR) of subtotally resected (STR) ependymoma to vincristine, etoposide, and cyclophosphamide (VEC). We report final results with 12-year follow-up and post hoc analyses of recently described biomarkers. METHODS Seventy-four participants were eligible. Children with gross total resection (GTR) received radiotherapy, whilst those with STR received VEC before radiotherapy. DNA methylation, 1q, hTERT, ReLA, Tenascin-C, H3K27me3, and pAKT status were evaluated. RESULTS Five- and ten-year EFS was 49.5% and 46.7%, OS was 69.3% and 60.5%. GTR was achieved in 33/74 (44.6%) and associated with improved EFS (P = .003, HR = 2.6, 95% confidence interval (CI) 1.4-5.1). Grade 3 tumours were associated with worse OS (P = .005, HR = 2.8, 95%CI 1.3-5.8). 1q gain and hTERT expression were associated with poorer EFS (P = .003, HR = 2.70, 95%CI 1.49-6.10 and P = .014, HR = 5.8, 95%CI 1.2-28) and H3K27me3 loss with worse OS (P = .003, HR = 4.6, 95%CI 1.5-13.2). Methylation profiles showed expected patterns. 12 participants with STR did not receive chemotherapy; a protocol violation. However, best chemotherapy RR was 65.5% (19/29, 95%CI 45.7-82.1), exceeding the prespecified 45%. CONCLUSIONS Participants with totally resected ependymoma had the best outcomes. RR of STR to VEC exceeded the pre-specified efficacy criterion. However, cases of inaccurate stratification highlighted the need for rapid central review. 1q gain, H3K27me3 loss, and hTERT expression were all associated with poorer survival outcomes.
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Affiliation(s)
- Timothy A Ritzmann
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rebecca J Chapman
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - John-Paul Kilday
- Children’s Brain Tumour Research Network (CBTRN), Royal Manchester Children’s Hospital, Manchester, UK
- The Centre for Paediatric, Teenage and Young Adult Cancer, University of Manchester, Manchester, UK
| | - Nicola Thorp
- The Clatterbridge Cancer Centre, Liverpool, UK
- The Christie Hospital Proton Beam Therapy Centre, Manchester, UK
| | | | - Robert A Dineen
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham, UK
| | - Donald Macarthur
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Conor Mallucci
- Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Timothy Jaspan
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Thomas S Jacques
- UCL GOS Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Simon M L Paine
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - David W Ellison
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Eric Bouffet
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Richard G Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
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Scott JI, Mendive-Tapia L, Gordon D, Barth ND, Thompson EJ, Cheng Z, Taggart D, Kitamura T, Bravo-Blas A, Roberts EW, Juarez-Jimenez J, Michel J, Piet B, de Vries IJ, Verdoes M, Dawson J, Carragher NO, Connor RAO, Akram AR, Frame M, Serrels A, Vendrell M. A fluorogenic probe for granzyme B enables in-biopsy evaluation and screening of response to anticancer immunotherapies. Nat Commun 2022; 13:2366. [PMID: 35501326 PMCID: PMC9061857 DOI: 10.1038/s41467-022-29691-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 05/30/2021] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
Immunotherapy promotes the attack of cancer cells by the immune system; however, it is difficult to detect early responses before changes in tumor size occur. Here, we report the rational design of a fluorogenic peptide able to detect picomolar concentrations of active granzyme B as a biomarker of immune-mediated anticancer action. Through a series of chemical iterations and molecular dynamics simulations, we synthesize a library of FRET peptides and identify probe H5 with an optimal fit into granzyme B. We demonstrate that probe H5 enables the real-time detection of T cell-mediated anticancer activity in mouse tumors and in tumors from lung cancer patients. Furthermore, we show image-based phenotypic screens, which reveal that the AKT kinase inhibitor AZD5363 shows immune-mediated anticancer activity. The reactivity of probe H5 may enable the monitoring of early responses to anticancer treatments using tissue biopsies.
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Affiliation(s)
- Jamie I Scott
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Lorena Mendive-Tapia
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Doireann Gordon
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Nicole D Barth
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Emily J Thompson
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Zhiming Cheng
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - David Taggart
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Takanori Kitamura
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | | | | | - Jordi Juarez-Jimenez
- EaStChem School of Chemistry, Joseph Black Building, The University of Edinburgh, Edinburgh, UK
| | - Julien Michel
- EaStChem School of Chemistry, Joseph Black Building, The University of Edinburgh, Edinburgh, UK
| | - Berber Piet
- Department of Pulmonary Diseases, Radboud University Medical Centre, Nijmegen, Netherlands
| | - I Jolanda de Vries
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Martijn Verdoes
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, Netherlands
| | - John Dawson
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Richard A O' Connor
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Ahsan R Akram
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Margaret Frame
- Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh, UK
| | - Alan Serrels
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Marc Vendrell
- Centre for Inflammation Research, Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, UK.
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Patel A, Dogan H, Payne A, Krause E, Sievers P, Schoebe N, Schrimpf D, Blume C, Stichel D, Holmes N, Euskirchen P, Hench J, Frank S, Rosenstiel-Goidts V, Ratliff M, Etminan N, Unterberg A, Dieterich C, Herold-Mende C, Pfister SM, Wick W, Loose M, von Deimling A, Sill M, Jones DTW, Schlesner M, Sahm F. Rapid-CNS 2: rapid comprehensive adaptive nanopore-sequencing of CNS tumors, a proof-of-concept study. Acta Neuropathol 2022; 143:609-612. [PMID: 35357562 PMCID: PMC9038836 DOI: 10.1007/s00401-022-02415-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 01/01/2023]
Affiliation(s)
- Areeba Patel
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Helin Dogan
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Alexander Payne
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Elena Krause
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Natalie Schoebe
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, 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), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Christina Blume
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Nadine Holmes
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Philipp Euskirchen
- Department of Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jürgen Hench
- Division of Neuropathology, Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Stephan Frank
- Division of Neuropathology, Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Miriam Ratliff
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - Nima Etminan
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Christoph Dieterich
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
| | | | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schlesner
- Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
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Pfister SM, Reyes-Múgica M, Chan JKC, Hasle H, Lazar AJ, Rossi S, Ferrari A, Jarzembowski JA, Pritchard-Jones K, Hill DA, Jacques TS, Wesseling P, López Terrada DH, von Deimling A, Kratz CP, Cree IA, Alaggio R. A Summary of the Inaugural WHO Classification of Pediatric Tumors: Transitioning from the Optical into the Molecular Era. Cancer Discov 2022; 12:331-355. [PMID: 34921008 PMCID: PMC9401511 DOI: 10.1158/2159-8290.cd-21-1094] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [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: 08/19/2021] [Revised: 10/28/2021] [Accepted: 11/18/2021] [Indexed: 01/07/2023]
Abstract
Pediatric tumors are uncommon, yet are the leading cause of cancer-related death in childhood. Tumor types, molecular characteristics, and pathogenesis are unique, often originating from a single genetic driver event. The specific diagnostic challenges of childhood tumors led to the development of the first World Health Organization (WHO) Classification of Pediatric Tumors. The classification is rooted in a multilayered approach, incorporating morphology, IHC, and molecular characteristics. The volume is organized according to organ sites and provides a single, state-of-the-art compendium of pediatric tumor types. A special emphasis was placed on "blastomas," which variably recapitulate the morphologic maturation of organs from which they originate. SIGNIFICANCE: In this review, we briefly summarize the main features and updates of each chapter of the inaugural WHO Classification of Pediatric Tumors, including its rapid transition from a mostly microscopic into a molecularly driven classification systematically taking recent discoveries in pediatric tumor genomics into account.
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Affiliation(s)
- Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Miguel Reyes-Múgica
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Division of Pediatric Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong, SAR China
| | - Henrik Hasle
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Jason A Jarzembowski
- Department of Pathology, Children's Wisconsin and Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Kathy Pritchard-Jones
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - D Ashley Hill
- Department of Pathology, Children's National Hospital, Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Thomas S Jacques
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Pieter Wesseling
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Pathology, Amsterdam University Medical Centers/VUmc, Amsterdam, the Netherlands
| | - Dolores H López Terrada
- Department of Pathology, Texas Children's Hospital and Baylor College of Medicine, Houston, Texas
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Ian A Cree
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rita Alaggio
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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35
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Abstract
Despite the growing evidence base for supported self-management for the improvement of quality of life, there is a lack of widespread implementation of self-management interventions for cancer survivors. We propose five key areas that, if addressed, would optimise the development and evaluation of these interventions, namely: (1) improving intervention adaptability to different survivor populations; (2) establishing intervention acceptability (and feasibility); (3) ensuring systematic description of interventions, their content, and active ingredients; (4) conducting process evaluations; and (5) assessing cost-effectiveness. These areas are an essential prerequisite for translation of self-management interventions from research into routine cancer care.
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Affiliation(s)
- Ben Rimmer
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Ridley Building 1, Newcastle upon Tyne, NE1 7RU, England, UK.
| | - Linda Sharp
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Ridley Building 1, Newcastle upon Tyne, NE1 7RU, England, UK
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36
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Alhalabi KT, Stichel D, Sievers P, Peterziel H, Sommerkamp AC, Sturm D, Wittmann A, Sill M, Jäger N, Beck P, Pajtler KW, Snuderl M, Jour G, Delorenzo M, Martin AM, Levy A, Dalvi N, Hansford JR, Gottardo NG, Uro-Coste E, Maurage CA, Godfraind C, Vandenbos F, Pietsch T, Kramm C, Filippidou M, Kattamis A, Jones C, Øra I, Mikkelsen TS, Zapotocky M, Sumerauer D, Scheie D, McCabe M, Wesseling P, Tops BBJ, Kranendonk MEG, Karajannis MA, Bouvier N, Papaemmanuil E, Dohmen H, Acker T, von Hoff K, Schmid S, Miele E, Filipski K, Kitanovski L, Krskova L, Gojo J, Haberler C, Alvaro F, Ecker J, Selt F, Milde T, Witt O, Oehme I, Kool M, von Deimling A, Korshunov A, Pfister SM, Sahm F, Jones DTW. PATZ1 fusions define a novel molecularly distinct neuroepithelial tumor entity with a broad histological spectrum. Acta Neuropathol 2021; 142:841-857. [PMID: 34417833 PMCID: PMC8500868 DOI: 10.1007/s00401-021-02354-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 02/20/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022]
Abstract
Large-scale molecular profiling studies in recent years have shown that central nervous system (CNS) tumors display a much greater heterogeneity in terms of molecularly distinct entities, cellular origins and genetic drivers than anticipated from histological assessment. DNA methylation profiling has emerged as a useful tool for robust tumor classification, providing new insights into these heterogeneous molecular classes. This is particularly true for rare CNS tumors with a broad morphological spectrum, which are not possible to assign as separate entities based on histological similarity alone. Here, we describe a molecularly distinct subset of predominantly pediatric CNS neoplasms (n = 60) that harbor PATZ1 fusions. The original histological diagnoses of these tumors covered a wide spectrum of tumor types and malignancy grades. While the single most common diagnosis was glioblastoma (GBM), clinical data of the PATZ1-fused tumors showed a better prognosis than typical GBM, despite frequent relapses. RNA sequencing revealed recurrent MN1:PATZ1 or EWSR1:PATZ1 fusions related to (often extensive) copy number variations on chromosome 22, where PATZ1 and the two fusion partners are located. These fusions have individually been reported in a number of glial/glioneuronal tumors, as well as extracranial sarcomas. We show here that they are more common than previously acknowledged, and together define a biologically distinct CNS tumor type with high expression of neural development markers such as PAX2, GATA2 and IGF2. Drug screening performed on the MN1:PATZ1 fusion-bearing KS-1 brain tumor cell line revealed preliminary candidates for further study. In summary, PATZ1 fusions define a molecular class of histologically polyphenotypic neuroepithelial tumors, which show an intermediate prognosis under current treatment regimens.
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Affiliation(s)
- Karam T Alhalabi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heike Peterziel
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Alexander C Sommerkamp
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andrea Wittmann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Martin Sill
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pengbo Beck
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Matija Snuderl
- Division of Neuropathology, NYU Langone Health, New York, NY, USA
| | - George Jour
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | | | - Allison M Martin
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Adam Levy
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Nagma Dalvi
- Isabel Rapin Division of Child Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jordan R Hansford
- Department of Pediatrics, Children's Cancer Centre, Royal Children's Hospital, Murdoch Children's Research Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas G Gottardo
- Department of Oncology and Haematology, Perth Children's Hospital, Perth, WA, Australia
| | - Emmanuelle Uro-Coste
- Department of Pathology, IUCT-Oncopole, Toulouse University Hospital, Toulouse, France
- INSERM U1037, Team 11, Cancer Research Center of Toulouse (CRCT), Toulouse, France
| | - Claude-Alain Maurage
- Department of Pathology, Lille University Hospital, Lille, France
- INSERM U837 UMR-S1172, Centre de Recherche Jean Pierre Aubert, Team 1, Lille, France
| | - Catherine Godfraind
- Laboratory of Pathology, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
- University Clermont-Auvergne, M2iSH UMR1071, Clermont-Ferrand, France
| | - Fanny Vandenbos
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Department of Pathology, CHU Gabriel Montpied, Clermont-Ferrand, France
| | - Torsten Pietsch
- Institute of Neuropathology, Brain Tumor Reference Center of the Society for Neuropathology and Neuroanatomy, University of Bonn Medical Center, Bonn, Germany
| | - Christof Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Gottingen, Germany
| | - Maria Filippidou
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Antonis Kattamis
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Ingrid Øra
- Children's Hospital, Paediatric Oncology, Skåne University Hospital, Lund, Sweden
| | - Torben Stamm Mikkelsen
- Paediatric and Adolescent Medicine, Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michal Zapotocky
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, University Hospital Motol, Charles University, Prague, Czech Republic
| | - David Sumerauer
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, University Hospital Motol, Charles University, Prague, Czech Republic
| | - David Scheie
- Department of Clinical Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Martin McCabe
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Pieter Wesseling
- Department of Pathology, Brain Tumor Center Amsterdam University Medical Center, Amsterdam Universities Medical Centers/VUmc, Amsterdam, The Netherlands
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bastiaan B J Tops
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mariëtte E G Kranendonk
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Nancy Bouvier
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hildegard Dohmen
- Department of Neuropathology, University Giessen, Giessen, Germany
| | - Till Acker
- Department of Neuropathology, University Giessen, Giessen, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology and Hematology, Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Simone Schmid
- Department of Pediatric Oncology and Hematology, Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Evelina Miele
- Department of Oncology, Hematology, Cell Therapy, Gene Therapy and Haemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Katharina Filipski
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt, Germany
| | - Lidija Kitanovski
- Division of Paediatrics, Department of Haematooncology, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Lenka Krskova
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Johannes Gojo
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Frank Alvaro
- University of Newcastle, Newcastle, NSW, Australia
- John Hunter Children's Hospital Newcastle, Newcastle, NSW, Australia
| | - Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ina Oehme
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Andreas von Deimling
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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37
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Peirsman A, Blondeel E, Ahmed T, Anckaert J, Audenaert D, Boterberg T, Buzas K, Carragher N, Castellani G, Castro F, Dangles-Marie V, Dawson J, De Tullio P, De Vlieghere E, Dedeyne S, Depypere H, Diosdi A, Dmitriev RI, Dolznig H, Fischer S, Gespach C, Goossens V, Heino J, Hendrix A, Horvath P, Kunz-Schughart LA, Maes S, Mangodt C, Mestdagh P, Michlíková S, Oliveira MJ, Pampaloni F, Piccinini F, Pinheiro C, Rahn J, Robbins SM, Siljamäki E, Steigemann P, Sys G, Takayama S, Tesei A, Tulkens J, Van Waeyenberge M, Vandesompele J, Wagemans G, Weindorfer C, Yigit N, Zablowsky N, Zanoni M, Blondeel P, De Wever O. MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity. Nat Methods 2021; 18:1294-1303. [PMID: 34725485 PMCID: PMC8566242 DOI: 10.1038/s41592-021-01291-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 06/07/2020] [Accepted: 09/09/2021] [Indexed: 01/21/2023]
Abstract
Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase that assembles the experimental parameters of 3,058 published spheroid-related experiments. Interrogation of this knowledgebase identified heterogeneity in the methodological setup of spheroids. Empirical evaluation and interlaboratory validation of selected variations in spheroid methodology revealed diverse impacts on spheroid metrics. To facilitate interpretation, stimulate transparency and increase awareness, the Consortium defines the MISpheroID string, a minimum set of experimental parameters required to report spheroid research. Thus, MISpheroID combines a valuable resource and a tool for three-dimensional cellular models to mine experimental parameters and to improve reproducibility.
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Affiliation(s)
- Arne Peirsman
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
| | - Eva Blondeel
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Tasdiq Ahmed
- Wallace H Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Jasper Anckaert
- OncoRNALab, Cancer Research Institute, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Dominique Audenaert
- VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium
| | - Tom Boterberg
- Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Krisztina Buzas
- Department of Immunology, University of Szeged, Faculty of Medicine-Faculty of Science and Informatics, Szeged, Hungary
| | - Neil Carragher
- Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Flávia Castro
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Virginie Dangles-Marie
- Translational Research Department, Institut Curie, PSL Research University, and Faculty of Pharmacy, Paris, France
- Faculty of Pharmacy, Université Paris Descartes, Paris, France
| | - John Dawson
- Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Pascal De Tullio
- Center for Interdisciplinary Research on Medicines (CIRM), Metabolomics Group, Université de Liège, Liège, Belgium
| | - Elly De Vlieghere
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Sándor Dedeyne
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Herman Depypere
- Menopause and Breast Clinic, Ghent University Hospital, Ghent, Belgium
| | - Akos Diosdi
- Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center (BRC), Szeged, Hungary
| | - Ruslan I Dmitriev
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Helmut Dolznig
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Suzanne Fischer
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Christian Gespach
- INSERM U938 Hospital Saint-Antoine Research Center CRSA, Team Céline Prunier, TGFbeta Signaling in Cellular Plasticity and Cancer, Sorbonne University, Paris, France
| | - Vera Goossens
- VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium
| | - Jyrki Heino
- Department of Life Technologies, University of Turku, Turku, Finland
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center (BRC), Szeged, Hungary
| | - Leoni A Kunz-Schughart
- OncoRay - National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Carl Gustav Carus Faculty of Medicine at TU Dresden, and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Sebastiaan Maes
- Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
| | - Christophe Mangodt
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Cancer Research Institute, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Soňa Michlíková
- OncoRay - National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Carl Gustav Carus Faculty of Medicine at TU Dresden, and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Maria José Oliveira
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Francesco Pampaloni
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Filippo Piccinini
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Cláudio Pinheiro
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Jennifer Rahn
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Stephen M Robbins
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Elina Siljamäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Gwen Sys
- Department of Orthopedics and Traumatology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Shuichi Takayama
- Wallace H Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Anna Tesei
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Joeri Tulkens
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | | | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Glenn Wagemans
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Claudia Weindorfer
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Nurten Yigit
- OncoRNALab, Cancer Research Institute, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Michele Zanoni
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Phillip Blondeel
- Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
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Hoogstrate Y, Ghisai SA, de Wit M, de Heer I, Draaisma K, van Riet J, van de Werken HJG, Bours V, Buter J, Vanden Bempt I, Eoli M, Franceschi E, Frenel JS, Gorlia T, Hanse MC, Hoeben A, Kerkhof M, Kros JM, Leenstra S, Lombardi G, Lukacova S, Robe PA, Sepulveda JM, Taal W, Taphoorn M, Vernhout RM, Walenkamp AME, Watts C, Weller M, de Vos FYF, Jenster GW, van den Bent M, French PJ. The EGFRvIII transcriptome in glioblastoma, a meta-omics analysis. Neuro Oncol 2021; 24:429-441. [PMID: 34608482 PMCID: PMC8917407 DOI: 10.1093/neuonc/noab231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Indexed: 11/15/2022] Open
Abstract
Background EGFR is among the genes most frequently altered in glioblastoma, with exons 2-7 deletions (EGFRvIII) being among its most common genomic mutations. There are conflicting reports about its prognostic role and it remains unclear whether and how it differs in signaling compared with wildtype EGFR. Methods To better understand the oncogenic role of EGFRvIII, we leveraged 4 large datasets into 1 large glioblastoma transcriptome dataset (n = 741) alongside 81 whole-genome samples from 2 datasets. Results The EGFRvIII/EGFR expression ratios differ strongly between tumors and range from 1% to 95%. Interestingly, the slope of relative EGFRvIII expression is near-linear, which argues against a more positive selection pressure than EGFR wildtype. An absence of selection pressure is also suggested by the similar survival between EGFRvIII-positive and -negative glioblastoma patients. EGFRvIII levels are inversely correlated with pan-EGFR (all wildtype and mutant variants) expression, which indicates that EGFRvIII has a higher potency in downstream pathway activation. EGFRvIII-positive glioblastomas have a lower CDK4 or MDM2 amplification incidence than EGFRvIII-negative (P = .007), which may point toward crosstalk between these pathways. EGFRvIII-expressing tumors have an upregulation of “classical” subtype genes compared to those with EGFR-amplification only (P = 3.873e−6). Genomic breakpoints of the EGFRvIII deletions have a preference toward the 3′-end of the large intron-1. These preferred breakpoints preserve a cryptic exon resulting in a novel EGFRvIII variant and preserve an intronic enhancer. Conclusions These data provide deeper insights into the complex EGFRvIII biology and provide new insights for targeting EGFRvIII mutated tumors.
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Affiliation(s)
- Youri Hoogstrate
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus MC, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
- Corresponding Author: Youri Hoogstrate, PhD, Department of Neurology, Erasmus MC, PO Box 2040, 3000CA Rotterdam, the Netherlands ()
| | | | - Maurice de Wit
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Iris de Heer
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Kaspar Draaisma
- Department of Neurosurgery, UMC Utrecht, Utrecht, The Netherlands
| | - Job van Riet
- Cancer Computational Biology Center, Erasmus MC, Rotterdam, The Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC, Rotterdam, The Netherlands
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Vincent Bours
- Department of Human Genetics, Université de Liège, Liège, Belgium
| | - Jan Buter
- Department of Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Marica Eoli
- Unit of Molecular Neuro-Oncology, Besta-IRCCS, Milan, Italy
| | - Enrico Franceschi
- IRCCS Istituto Scienze Neurologiche di Bologna, Nervous System Medical Oncology Department, Bologna, Italy
| | | | | | - Monique C Hanse
- Department of Neurology, Catharina Hospital, Eindhoven, The Netherlands
| | - Ann Hoeben
- Department of Medical Oncology, Maastricht UMC+, Maastricht, The Netherlands
| | - Melissa Kerkhof
- Department of Neurology, Haaglanden Medical Center, The Hague, The Netherlands
| | - Johan M Kros
- Department of Medical Oncology, Erasmus MC, Rotterdam, The Netherlands
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Sieger Leenstra
- Department of Neurosurgery, Erasmus MC, Rotterdam, The Netherlands
| | | | - Slávka Lukacova
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Pierre A Robe
- Department of Neurosurgery, UMC Utrecht, Utrecht, The Netherlands
| | | | - Walter Taal
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Martin Taphoorn
- Department of Neurology, Haaglanden Medical Center, The Hague, The Netherlands
| | - René M Vernhout
- Department of Radiotherapy, Erasmus MC, Rotterdam, The Netherlands
| | | | - Colin Watts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Filip Y F de Vos
- Department of Medical Oncology, UMC Utrecht, Utrecht, The Netherlands
| | - Guido W Jenster
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Pim J French
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
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Malins S, Owen R, Wright I, Borrill H, Limond J, Gibson F, Grundy RG, Bailey S, Clifford SC, Lowis S, Lemon J, Hayes L, Thomas S. Acceptance and commitment therapy for young brain tumour survivors: study protocol for an acceptability and feasibility trial. BMJ Open 2021; 11:e051091. [PMID: 34078638 PMCID: PMC8173289 DOI: 10.1136/bmjopen-2021-051091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
INTRODUCTION Survivors of childhood brain tumours have the poorest health-related quality of life of all cancer survivors due to the multiple physical and psychological sequelae of brain tumours and their treatment. Remotely delivered acceptance and commitment therapy (ACT) may be a suitable and accessible psychological intervention to support young people who have survived brain tumours. This study aims to assess the feasibility and acceptability of remotely delivered ACT to improve quality of life among these young survivors. METHODS AND ANALYSIS This study is a two-arm, parallel group, randomised controlled trial comparing ACT with waitlist control at 12-week follow-up as the primary endpoint. Seventy-two participants will be recruited, who are aged 11-24 and have completed brain tumour treatment. Participants will be randomised to receive 12 weeks of ACT either immediately or after a 12-week wait. The DNA-v model of ACT will be employed, which is a developmentally appropriate model for young people. Feasibility will be assessed using the proportion of those showing interest who consent to the trial and complete the intervention. Acceptability will be assessed using participant evaluations of the intervention, alongside qualitative interviews and treatment diaries analysed thematically. A range of clinical outcome measures will also assess physical and mental health, everyday functioning, quality of life and service usage at 12-week follow-up. The durability of treatment effects will be assessed by further follow-up assessments at 24 weeks, 36 weeks and 48 weeks. ETHICS AND DISSEMINATION Ethical approval was given by East Midlands, Nottingham 1 Research Ethics Committee (Reference: 20/EM/0237). Study results will be disseminated in peer-reviewed journals, through public events and relevant third sector organisations. TRIAL REGISTRATION ISRCTN10903290; NCT04722237.
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Affiliation(s)
- Sam Malins
- Nottingham University Hospitals NHS Trust, Nottingham, UK
- Division of Psychiatry and Applied Psychology, University of Nottingham, Nottingham, UK
| | - Ray Owen
- Wye Valley NHS Trust, Hereford, UK
| | - Ingram Wright
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Heather Borrill
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jenny Limond
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Faith Gibson
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
- Great Ormond Street Hospital For Children NHS Foundation Trust, London, UK
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Simon Bailey
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Newcastle University, Newcastle upon Tyne, UK
| | - Steven C Clifford
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Newcastle University, Newcastle upon Tyne, UK
| | - Stephen Lowis
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
- Population Health Sciences, University of Bristol, Bristol, UK
| | | | - Louise Hayes
- DNA-v International, Melbourne, Victoria, Australia
| | - Sophie Thomas
- Nottingham University Hospitals NHS Trust, Nottingham, UK
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Andreou T, Williams J, Brownlie RJ, Salmond RJ, Watson E, Shaw G, Melcher A, Wurdak H, Short SC, Lorger M. Hematopoietic stem cell gene therapy targeting TGFβ enhances the efficacy of irradiation therapy in a preclinical glioblastoma model. J Immunother Cancer 2021; 9:e001143. [PMID: 33707311 PMCID: PMC7957127 DOI: 10.1136/jitc-2020-001143] [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] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Patients with glioblastoma (GBM) have a poor prognosis, and inefficient delivery of drugs to tumors represents a major therapeutic hurdle. Hematopoietic stem cell (HSC)-derived myeloid cells efficiently home to GBM and constitute up to 50% of intratumoral cells, making them highly appropriate therapeutic delivery vehicles. Because myeloid cells are ubiquitously present in the body, we recently established a lentiviral vector containing matrix metalloproteinase 14 (MMP14) promoter, which is active specifically in tumor-infiltrating myeloid cells as opposed to myeloid cells in other tissues, and resulted in a specific delivery of transgenes to brain metastases in HSC gene therapy. Here, we used this novel approach to target transforming growth factor beta (TGFβ) as a key tumor-promoting factor in GBM. Transplantation of HSCs transduced with lentiviral vector expressing green fluorescent protein (GFP) into lethally irradiated recipient mice was followed by intracranial implantation of GBM cells. Tumor-infiltrating HSC progeny was characterized by flow cytometry. In therapy studies, mice were transplanted with HSCs transduced with lentiviral vector expressing soluble TGFβ receptor II-Fc fusion protein under MMP14 promoter. This TGFβ-blocking therapy was compared with the targeted tumor irradiation, the combination of the two therapies, and control. Tumor growth and survival were quantified (statistical significance determined by t-test and log-rank test). T cell memory response was probed through a repeated tumor challenge. Myeloid cells were the most abundant HSC-derived population infiltrating GBM. TGFβ-blocking HSC gene therapy in combination with irradiation significantly reduced tumor burden as compared with monotherapies and the control, and significantly prolonged survival as compared with the control and TGFβ-blocking monotherapy. Long-term protection from GBM was achieved only with the combination treatment (25% of the mice) and was accompanied by a significant increase in CD8+ T cells at the tumor implantation site following tumor rechallenge. We demonstrated a preclinical proof-of-principle for tumor myeloid cell-specific HSC gene therapy in GBM. In the clinic, HSC gene therapy is being successfully used in non-cancerous brain disorders and the feasibility of HSC gene therapy in patients with glioma has been demonstrated in the context of bone marrow protection. This indicates an opportunity for clinical translation of our therapeutic approach.
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Affiliation(s)
| | | | | | | | - Erica Watson
- School of Medicine, University of Leeds, Leeds, UK
| | - Gary Shaw
- School of Medicine, University of Leeds, Leeds, UK
| | - Alan Melcher
- Division of Radiotherapy and Imaging, Institute of Cancer Research, London, UK
| | - Heiko Wurdak
- School of Medicine, University of Leeds, Leeds, UK
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Abstract
Brain tumours are the commonest solid neoplasms in children, accounting for one quarter of all childhood cancers. Our growing knowledge of basic developmental mechanisms has significantly contributed to understanding the pathogenesis of these tumours and is beginning to impact clinical decisions on how children with these diseases are treated.
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Affiliation(s)
- Silvia Marino
- Blizard Institute, Barts Brain Tumour Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Richard J Gilbertson
- Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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Kanev GK, de Graaf C, Westerman BA, de Esch IJP, Kooistra AJ. KLIFS: an overhaul after the first 5 years of supporting kinase research. Nucleic Acids Res 2021; 49:D562-D569. [PMID: 33084889 PMCID: PMC7778968 DOI: 10.1093/nar/gkaa895] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [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: 09/09/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022] Open
Abstract
Kinases are a prime target of drug development efforts with >60 drug approvals in the past two decades. Due to the research into this protein family, a wealth of data has been accumulated that keeps on growing. KLIFS-Kinase-Ligand Interaction Fingerprints and Structures-is a structural database focusing on how kinase inhibitors interact with their targets. The aim of KLIFS is to support (structure-based) kinase research through the systematic collection, annotation, and processing of kinase structures. Now, 5 years after releasing the initial KLIFS website, the database has undergone a complete overhaul with a new website, new logo, and new functionalities. In this article, we start by looking back at how KLIFS has been used by the research community, followed by a description of the renewed KLIFS, and conclude with showcasing the functionalities of KLIFS. Major changes include the integration of approved drugs and inhibitors in clinical trials, extension of the coverage to atypical kinases, and a RESTful API for programmatic access. KLIFS is available at the new domain https://klifs.net.
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Affiliation(s)
- Georgi K Kanev
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Bart A Westerman
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Albert J Kooistra
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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Rimmer B, Dutton L, Lewis J, Burns R, Gallagher P, Williams S, Araujo-Soares V, Finch T, Sharp L. Ways Ahead: developing a supported self-management programme for people living with low- and intermediate-grade gliomas - a protocol for a multi-method study. BMJ Open 2020; 10:e041465. [PMID: 32727741 PMCID: PMC7394298 DOI: 10.1136/bmjopen-2020-041465] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
INTRODUCTION Living with and beyond a diagnosis of a low- and intermediate-grade glioma (LIGG) can adversely impact many aspects of people's lives and their quality of life (QoL). In people with chronic conditions, self-management can improve QoL. This is especially true if people are supported to self-manage. Supported self-management programmes have been developed for several cancers, but the unique challenges experienced by LIGG survivors mean these programmes may not be readily transferable to this group. The Ways Ahead study aims to address this gap by exploring the needs of LIGG survivors to develop a prototype for a supported self-management programme tailored to this group. METHODS AND ANALYSIS Ways Ahead will follow three sequential phases, underpinned by a systematic review of self-management interventions in cancer. In phase 1, qualitative methods will be used to explore and understand the issues faced by LIGG survivors, as well as the barriers and facilitators to self-management. Three sets of interviews will be conducted with LIGG survivors, their informal carers and professionals. Thematic analysis will be conducted with reference to the Theoretical Domains Framework and Normalisation Process Theory. Phase 2 will involve co-production workshops to generate ideas for the design of a supported self-management programme. Workshop outputs will be translated into a design specification for a prototype programme. Finally, phase 3 will involve a health economic assessment to examine the feasibility and benefits of incorporating the proposed programme into the current survivorship care pathway. This prototype will then be ready for testing in a subsequent trial. ETHICS AND DISSEMINATION The study has been reviewed and approved by an National Health Service Research Ethics Committee (REC ref: 20/WA/0118). The findings will be disseminated through peer-reviewed journals, conference presentations, broadcast media, the study website, The Brain Tumour Charity and stakeholder engagement activities.
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Affiliation(s)
- Ben Rimmer
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Lizzie Dutton
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Joanne Lewis
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | | | - Sophie Williams
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Vera Araujo-Soares
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Tracy Finch
- Department of Nursing, Midwifery and Health, Northumbria University, Newcastle upon Tyne, UK
| | - Linda Sharp
- Population Health Sciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
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Andreou T, Rippaus N, Wronski K, Williams J, Taggart D, Cherqui S, Sunderland A, Kartika YD, Egnuni T, Brownlie RJ, Mathew RK, Holmen SL, Fife C, Droop A, Lorger M. Hematopoietic Stem Cell Gene Therapy for Brain Metastases Using Myeloid Cell-Specific Gene Promoters. J Natl Cancer Inst 2020; 112:617-627. [PMID: 31501884 PMCID: PMC7301153 DOI: 10.1093/jnci/djz181] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 09/17/2018] [Revised: 07/16/2019] [Accepted: 09/04/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Brain metastases (BrM) develop in 20-40% of cancer patients and represent an unmet clinical need. Limited access of drugs into the brain because of the blood-brain barrier is at least partially responsible for therapeutic failure, necessitating improved drug delivery systems. METHODS Green fluorescent protein (GFP)-transduced murine and nontransduced human hematopoietic stem cells (HSCs) were administered into mice (n = 10 and 3). The HSC progeny in mouse BrM and in patient-derived BrM tissue (n = 6) was characterized by flow cytometry and immunofluorescence. Promoters driving gene expression, specifically within the BrM-infiltrating HSC progeny, were identified through differential gene-expression analysis and subsequent validation of a series of promoter-green fluorescent protein-reporter constructs in mice (n = 5). One of the promoters was used to deliver tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) to BrM in mice (n = 17/21 for TRAIL vs control group). RESULTS HSC progeny (consisting mostly of macrophages) efficiently homed to macrometastases (mean [SD] = 37.6% [7.2%] of all infiltrating cells for murine HSC progeny; 27.9% mean [SD] = 27.9% [4.9%] of infiltrating CD45+ hematopoietic cells for human HSC progeny) and micrometastases in mice (19.3-53.3% of all macrophages for murine HSCs). Macrophages were also abundant in patient-derived BrM tissue (mean [SD] = 8.8% [7.8%]). Collectively, this provided a rationale to optimize the delivery of gene therapy to BrM within myeloid cells. MMP14 promoter emerged as the strongest promoter construct capable of limiting gene expression to BrM-infiltrating myeloid cells in mice. TRAIL delivered under MMP14 promoter statistically significantly prolonged survival in mice (mean [SD] = 19.0 [3.4] vs mean [SD] = 15.0 [2.0] days for TRAIL vs control group; two-sided P = .006), demonstrating therapeutic and translational potential of our approach. CONCLUSIONS Our study establishes HSC gene therapy using a myeloid cell-specific promoter as a new strategy to target BrM. This approach, with strong translational value, has potential to overcome the blood-brain barrier, target micrometastases, and control multifocal lesions.
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Affiliation(s)
| | - Nora Rippaus
- School of Medicine, University of Leeds, Leeds, UK
| | | | | | | | | | | | | | - Teklu Egnuni
- School of Medicine, University of Leeds, Leeds, UK
| | | | - Ryan K Mathew
- School of Medicine, University of Leeds, Leeds, UK
- Department of Neurosurgery, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Sheri L Holmen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | | | - Alastair Droop
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
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Abstract
Polycomb repressive complex 2 (PRC2) is a conserved chromatin regulator that is responsible for the methylation of histone H3 lysine 27 (H3K27). PRC2 is essential for normal development and its loss of function thus results in a range of developmental phenotypes. Here, we review the latest advances in our understanding of mammalian PRC2 activity and present an updated summary of the phenotypes associated with its loss of function in mice. We then discuss recent studies that have highlighted regulatory interplay between the modifications laid down by PRC2 and other chromatin modifiers, including NSD1 and DNMT3A. Finally, we propose a model in which the dysregulation of these modifications at intergenic regions is a shared molecular feature of genetically distinct but highly phenotypically similar overgrowth syndromes in humans.
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Affiliation(s)
- Orla Deevy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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46
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Abstract
Glioblastoma multiforme (GBM) is one of the deadliest human cancers. Despite increasing knowledge of the genetic and epigenetic changes that underlie tumour initiation and growth, the prognosis for GBM patients remains dismal. Genome analysis has failed to lead to success in the clinic. Fresh approaches are needed that can stimulate new discoveries across all levels: cell-intrinsic mechanisms (transcriptional/epigenetic and metabolic), cell-cell signalling, niche and microenvironment, systemic signals, immune regulation, and tissue-level physical forces. GBMs are inherently extremely challenging: tumour detection occurs too late, and cells infiltrate widely, hiding in quiescent states behind the blood-brain barrier. The complexity of the brain tissue also provides varied and complex microenvironments that direct cancer cell fates. Phenotypic heterogeneity is therefore superimposed onto pervasive genetic heterogeneity. Despite this bleak outlook, there are reasons for optimism. A myriad of complementary, and increasingly sophisticated, experimental approaches can now be used across the research pipeline, from simple reductionist models devised to delineate molecular and cellular mechanisms, to complex animal models required for preclinical testing of new therapeutic approaches. No single model can cover the breadth of unresolved questions. This Review therefore aims to guide investigators in choosing the right model for their question. We also discuss the recent convergence of two key technologies: human stem cell and cancer stem cell culture, as well as CRISPR/Cas tools for precise genome manipulations. New functional genetic approaches in tailored models will likely fuel new discoveries, new target identification and new therapeutic strategies to tackle GBM.
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Affiliation(s)
- Faye L Robertson
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research UK Cancer Centre, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Maria-Angeles Marqués-Torrejón
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research UK Cancer Centre, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Gillian M Morrison
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research UK Cancer Centre, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research UK Cancer Centre, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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Ozawa M, Brennan PM, Zienius K, Kurian KM, Hollingworth W, Weller D, Grant R, Hamilton W, Ben-Shlomo Y. The usefulness of symptoms alone or combined for general practitioners in considering the diagnosis of a brain tumour: a case-control study using the clinical practice research database (CPRD) (2000-2014). BMJ Open 2019; 9:e029686. [PMID: 31471440 PMCID: PMC6720478 DOI: 10.1136/bmjopen-2019-029686] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES To evaluate the utility of different symptoms, alone or combined, presented to primary care for an adult brain tumour diagnosis. DESIGN AND SETTING Matched case-control study, using the data from Clinical Practice Research Datalink (2000-2014) from primary care consultations in the UK. METHOD All presentations within 6 months of the index diagnosis date (cases) or equivalent (controls) were coded into 32 symptom groups. Sensitivity, specificity, positive predictive values (PPVs) and positive likelihood ratios were calculated for symptoms and combinations of symptoms with headache and cognitive features. Diagnostic odds ratios were calculated using conditional logistic regression, adjusted for age group, sex and Charlson comorbidity. Stratified analyses were performed for age group, sex and whether the tumour was of primary or secondary origin. RESULTS We included 8,184 cases and 28,110 controls. Seizure had the highest PPV of 1.6% (95% CI 1.4% to 1.7%) followed by weakness 1.5% (1.3 to 1.7) and confusion 1.4% (1.3 to 1.5). Combining headache with other symptoms increased the PPV. For example, headache plus combined cognitive symptoms PPV 7.2% (6.0 to 8.6); plus weakness 4.4% (3.2 to 6.2), compared with headache alone PPV 0.1%. The diagnostic ORs were generally larger for patients <70 years; this was most marked for confusion, seizure and visual symptoms. CONCLUSION We found seizure, weakness and confusion had relatively higher predictive values than many other symptoms. Headache on its own was a weak predictor but this was enhanced when combined with other symptoms especially in younger patients. Clinicians need to actively search for other neurological symptoms such as cognitive problems.
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Affiliation(s)
- Mio Ozawa
- Population Health Sciences, University of Bristol, Bristol, UK
| | - Paul M Brennan
- Department of Clinical Neurosciences, Western General Hospital, Edinburgh, UK
| | - Karolis Zienius
- Department of Clinical Neurosciences, Western General Hospital, Edinburgh, UK
| | | | | | - David Weller
- General Practice, University of Edinburgh, Edinburgh, UK
| | - Robin Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Willie Hamilton
- Primary Care Diagnostics, University of Exeter Medical School, Exeter, UK
| | - Yoav Ben-Shlomo
- Population Health Sciences, University of Bristol, Bristol, UK
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Scott SE, Penfold C, Saji S, Curtis S, Watts C, Hamilton W, Joannides AJ, Walter FM. 'It was nothing that you would think was anything': Qualitative analysis of appraisal and help seeking preceding brain cancer diagnosis. PLoS One 2019; 14:e0213599. [PMID: 30901334 PMCID: PMC6430370 DOI: 10.1371/journal.pone.0213599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 12/12/2018] [Accepted: 02/25/2019] [Indexed: 12/29/2022] Open
Abstract
Background The patient’s interpretation of the events and decisions leading up to consultation with a healthcare professional for symptoms of brain cancer is under researched. The aim of this study was to document responses to noticing the changes preceding a diagnosis of brain cancer and living with them, focusing on appraisal of changes and the decision to seek (and re-seek) help, with attention to the psychological processes underpinning the appraisal and help-seeking intervals. Method In this qualitative study set in Eastern and NW England, in-depth interviews with adult patients recently diagnosed with primary brain cancer and their family members were analysed thematically, using the Model of Pathways to Treatment as a conceptual framework. Results 39 adult patients were interviewed. Regarding the appraisal interval, cognitive heuristics were found to underpin explanations of changes/symptoms. The subtlety and normality of changes often suggested nothing serious was wrong. Common explanations included stress or being busy at work, or age and these did not seem to warrant a visit to a doctor. Explanations and the decision to seek help were made within the social context, with friends, family and work colleagues contributing to appraisal and help-seeking decisions. Regarding the help-seeking interval, barriers to seeking help reflected components of Social Cognitive Theory, and included having other priorities, outcome expectations (e.g. ‘feeling silly’, not sure much can be done about it, not wanting to waste doctors’ time) and accessibility of a preferred healthcare professional. Conclusion Application of psychological theory facilitated understanding of the influences on cognition and behaviour. The study highlights implications for theory, awareness campaigns and potential opportunities promoting more timely help-seeking.
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Affiliation(s)
- Suzanne E. Scott
- Centre for Oral, Clinical & Translational Science, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, Guy’s Hospital, London, United Kingdom
- * E-mail:
| | - Clarissa Penfold
- The Primary Care Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Smiji Saji
- Clinical School, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Curtis
- Centre for Oral, Clinical & Translational Science, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Colin Watts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Willie Hamilton
- Willie Hamilton, St Luke’s Campus, University of Exeter, Exeter, United Kingdom
| | - Alexis J. Joannides
- Department of Clinical Neurosciences, Division of Neurosurgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Fiona M. Walter
- The Primary Care Unit, Department of Public Health & Primary Care, University of Cambridge, Cambridge, United Kingdom
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Apps JR, Carreno G, Gonzalez-Meljem JM, Haston S, Guiho R, Cooper JE, Manshaei S, Jani N, Hölsken A, Pettorini B, Beynon RJ, Simpson DM, Fraser HC, Hong Y, Hallang S, Stone TJ, Virasami A, Donson AM, Jones D, Aquilina K, Spoudeas H, Joshi AR, Grundy R, Storer LCD, Korbonits M, Hilton DA, Tossell K, Thavaraj S, Ungless MA, Gil J, Buslei R, Hankinson T, Hargrave D, Goding C, Andoniadou CL, Brogan P, Jacques TS, Williams HJ, Martinez-Barbera JP. Tumour compartment transcriptomics demonstrates the activation of inflammatory and odontogenic programmes in human adamantinomatous craniopharyngioma and identifies the MAPK/ERK pathway as a novel therapeutic target. Acta Neuropathol 2018. [PMID: 29541918 PMCID: PMC5904225 DOI: 10.1007/s00401-018-1830-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [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] [Indexed: 12/28/2022]
Abstract
Adamantinomatous craniopharyngiomas (ACPs) are clinically challenging tumours, the majority of which have activating mutations in CTNNB1. They are histologically complex, showing cystic and solid components, the latter comprised of different morphological cell types (e.g. β-catenin-accumulating cluster cells and palisading epithelium), surrounded by a florid glial reaction with immune cells. Here, we have carried out RNA sequencing on 18 ACP samples and integrated these data with an existing ACP transcriptomic dataset. No studies so far have examined the patterns of gene expression within the different cellular compartments of the tumour. To achieve this goal, we have combined laser capture microdissection with computational analyses to reveal groups of genes that are associated with either epithelial tumour cells (clusters and palisading epithelium), glial tissue or immune infiltrate. We use these human ACP molecular signatures and RNA-Seq data from two ACP mouse models to reveal that cell clusters are molecularly analogous to the enamel knot, a critical signalling centre controlling normal tooth morphogenesis. Supporting this finding, we show that human cluster cells express high levels of several members of the FGF, TGFB and BMP families of secreted factors, which signal to neighbouring cells as evidenced by immunostaining against the phosphorylated proteins pERK1/2, pSMAD3 and pSMAD1/5/9 in both human and mouse ACP. We reveal that inhibiting the MAPK/ERK pathway with trametinib, a clinically approved MEK inhibitor, results in reduced proliferation and increased apoptosis in explant cultures of human and mouse ACP. Finally, we analyse a prominent molecular signature in the glial reactive tissue to characterise the inflammatory microenvironment and uncover the activation of inflammasomes in human ACP. We validate these results by immunostaining against immune cell markers, cytokine ELISA and proteome analysis in both solid tumour and cystic fluid from ACP patients. Our data support a new molecular paradigm for understanding ACP tumorigenesis as an aberrant mimic of natural tooth development and opens new therapeutic opportunities by revealing the activation of the MAPK/ERK and inflammasome pathways in human ACP.
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Affiliation(s)
- John R Apps
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK.
- Histopathology Department, Great Ormond Street Hospital NHS Trust, London, UK.
| | - Gabriela Carreno
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Jose Mario Gonzalez-Meljem
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Basic Research Department, National Institute of Geriatrics, Mexico City, Mexico
| | - Scott Haston
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Romain Guiho
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Julie E Cooper
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Saba Manshaei
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Nital Jani
- Centre for Translational Omics-GOSgene, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, University College London, London, UK
| | - Annett Hölsken
- Department of Neuropathology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | | | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Deborah M Simpson
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Helen C Fraser
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ying Hong
- Infection, Immunity and Inflammation Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Shirleen Hallang
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Thomas J Stone
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Histopathology Department, Great Ormond Street Hospital NHS Trust, London, UK
| | - Alex Virasami
- Histopathology Department, Great Ormond Street Hospital NHS Trust, London, UK
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David Jones
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian Aquilina
- Neurosurgery Department, Great Ormond Street Hospital NHS Trust, London, UK
| | - Helen Spoudeas
- Endocrinology Department, Great Ormond Street Hospital NHS Trust, London, UK
| | - Abhijit R Joshi
- Laboratory Medicine, Royal Victoria Infirmary, Newcastle, UK
| | - Richard Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Lisa C D Storer
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Márta Korbonits
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University, London, UK
| | - David A Hilton
- Pathology Department, Plymouth Hospitals NHS Trust, Plymouth, UK
| | - Kyoko Tossell
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Selvam Thavaraj
- Head and Neck Pathology, Dental Institute, King's College London, London, UK
| | - Mark A Ungless
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Jesus Gil
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Rolf Buslei
- Department of Neuropathology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Institute of Pathology, Klinikum Sozialstiftung Bamberg, Bamberg, Germany
| | - Todd Hankinson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Darren Hargrave
- Haematology and Oncology Department, Great Ormond Street Hospital NHS Trust, London, UK
| | - Colin Goding
- Ludwig Institute for Cancer Research, Oxford University, Old Road Campus, Headington, Oxford, UK
| | - Cynthia L Andoniadou
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, Floor 27 Tower Wing, London, UK
- Department of Internal Medicine III, Technische Universität Dresden, Fetscherstaße 74, 01307, Dresden, Germany
| | - Paul Brogan
- Infection, Immunity and Inflammation Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Rheumatology Department, Great Ormond Street Hospital NHS Trust, London, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Histopathology Department, Great Ormond Street Hospital NHS Trust, London, UK
| | - Hywel J Williams
- Centre for Translational Omics-GOSgene, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, University College London, London, UK
| | - Juan Pedro Martinez-Barbera
- Developmental Biology and Cancer Programme, Birth Defects Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London, UK.
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50
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Dewari PS, Southgate B, Mccarten K, Monogarov G, O'Duibhir E, Quinn N, Tyrer A, Leitner MC, Plumb C, Kalantzaki M, Blin C, Finch R, Bressan RB, Morrison G, Jacobi AM, Behlke MA, von Kriegsheim A, Tomlinson S, Krijgsveld J, Pollard SM. An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein. eLife 2018; 7:e35069. [PMID: 29638216 PMCID: PMC5947990 DOI: 10.7554/elife.35069] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [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: 01/12/2018] [Accepted: 04/10/2018] [Indexed: 01/09/2023] Open
Abstract
CRISPR/Cas9 can be used for precise genetic knock-in of epitope tags into endogenous genes, simplifying experimental analysis of protein function. However, Cas9-assisted epitope tagging in primary mammalian cell cultures is often inefficient and reliant on plasmid-based selection strategies. Here, we demonstrate improved knock-in efficiencies of diverse tags (V5, 3XFLAG, Myc, HA) using co-delivery of Cas9 protein pre-complexed with two-part synthetic modified RNAs (annealed crRNA:tracrRNA) and single-stranded oligodeoxynucleotide (ssODN) repair templates. Knock-in efficiencies of ~5-30%, were achieved without selection in embryonic stem (ES) cells, neural stem (NS) cells, and brain-tumor-derived stem cells. Biallelic-tagged clonal lines were readily derived and used to define Olig2 chromatin-bound interacting partners. Using our novel web-based design tool, we established a 96-well format pipeline that enabled V5-tagging of 60 different transcription factors. This efficient, selection-free and scalable epitope tagging pipeline enables systematic surveys of protein expression levels, subcellular localization, and interactors across diverse mammalian stem cells.
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Affiliation(s)
- Pooran Singh Dewari
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Benjamin Southgate
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Katrina Mccarten
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - German Monogarov
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Eoghan O'Duibhir
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Niall Quinn
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Ashley Tyrer
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Marie-Christin Leitner
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Colin Plumb
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Maria Kalantzaki
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Carla Blin
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Rebecca Finch
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Raul Bardini Bressan
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Gillian Morrison
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc.CoralvilleUnited States
| | - Alex von Kriegsheim
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Simon Tomlinson
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jeroen Krijgsveld
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Steven M Pollard
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
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