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Boot J, Rosser G, Kancheva D, Vinel C, Lim YM, Pomella N, Zhang X, Guglielmi L, Sheer D, Barnes M, Brandner S, Nelander S, Movahedi K, Marino S. Global hypo-methylation in a proportion of glioblastoma enriched for an astrocytic signature is associated with increased invasion and altered immune landscape. eLife 2022; 11:e77335. [PMID: 36412091 PMCID: PMC9681209 DOI: 10.7554/elife.77335] [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: 01/25/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
Abstract
We describe a subset of glioblastoma, the most prevalent malignant adult brain tumour, harbouring a bias towards hypomethylation at defined differentially methylated regions. This epigenetic signature correlates with an enrichment for an astrocytic gene signature, which together with the identification of enriched predicted binding sites of transcription factors known to cause demethylation and to be involved in astrocytic/glial lineage specification, point to a shared ontogeny between these glioblastomas and astroglial progenitors. At functional level, increased invasiveness, at least in part mediated by SRPX2, and macrophage infiltration characterise this subset of glioblastoma.
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Affiliation(s)
- James Boot
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary UniversityLondonUnited Kingdom
| | - Gabriel Rosser
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary UniversityLondonUnited Kingdom
| | - Dailya Kancheva
- Laboratory for Molecular and Cellular Therapy, Vrije Universiteit BrusselBrusselsBelgium
| | - Claire Vinel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary UniversityLondonUnited Kingdom
| | - Yau Mun Lim
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, and Department of Neurodegenerative Disease, Queen Square, Institute of Neurology, University College LondonLondonUnited Kingdom
| | - Nicola Pomella
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary UniversityLondonUnited Kingdom
| | - Xinyu Zhang
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary UniversityLondonUnited Kingdom
| | - Loredana Guglielmi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary UniversityLondonUnited Kingdom
| | - Denise Sheer
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary UniversityLondonUnited Kingdom
| | - Michael Barnes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | - Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, and Department of Neurodegenerative Disease, Queen Square, Institute of Neurology, University College LondonLondonUnited Kingdom
| | - Sven Nelander
- Department of Immunology Genetics and Pathology, Uppsala UniversityUppsalaSweden
| | - Kiavash Movahedi
- Laboratory for Molecular and Cellular Therapy, Vrije Universiteit BrusselBrusselsBelgium
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary UniversityLondonUnited Kingdom
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2
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Woodward L, Jones TA, Patel A, Dokal AD, Stone TJ, Rajeeve V, Cutillas PR, Jones DTW, Hargrave D, Jacques TS, Sheer D. LGG-44. Multi-omic analysis reveals integrated signalling networks in paediatric low-grade glioma. Neuro Oncol 2022. [PMCID: PMC9165225 DOI: 10.1093/neuonc/noac079.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Paediatric low-grade gliomas (pLGGs) are the most common type of childhood CNS tumours. Our study included pilocytic astrocytomas (PAs; KIAA1549:BRAF), glioneuronal tumours (GNTs; BRAFV600E) and location-matched controls. We initially performed kinase substrate enrichment analysis (KSEA) to infer differential kinase activity, which allowed us to identify altered signalling networks in the two tumour types. Here we report the integration of these kinase signalling networks together with total proteomics, transcription factor enrichment analysis (TFEA) and transcriptomics (coding and non-coding). Total proteomic profiling confirmed an increase in proteins involved in cell cycle, inflammatory response and signal transduction in PAs, whilst there was an increase in proteins promoting cell growth, immune response and inflammation in GNTs. TFEA was performed using the DoRothEA database to identify master transcriptional regulators. We observed significant activation of transcription factors (TFs) that are direct targets of MAPK signalling in both tumour types. Notable differences include the higher activation of NF-kB/STAT TFs in PAs and the increased activation of RFX1/2 in GNTs. Next, we constructed kinase-TF networks and identified multiple kinases targeting STAT3 in PAs and STAT1/3 in GNTs. Pathway analysis of RNA-Sequencing data showed enrichment of NF-kB in both tumours and repression of E2F target genes (PA) and reduced expression of MYC target genes (GNT). We developed a BRAF-OIS signature and found 23 genes commonly enriched in both tumour types, highlighting shared senescence-associated targets. MicroRNA profiling identified upregulation of microRNAs that target MAPK and NF-kB signalling networks, and many down-regulated microRNAs with tumour suppressive roles. Finally, we identified several lncRNAs known to be differentially expressed in glioma and, whilst their mechanism(s) of action are varied, they are thought to act with other well-established regulators to fine-tune cellular processes. Taken together, we present a comprehensive signalling network as a framework for studying pLGGs.
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Affiliation(s)
- Lewis Woodward
- Barts and the London School of Medicine and Dentistry , London , United Kingdom
| | - Tania A Jones
- Barts and the London School of Medicine and Dentistry , London , United Kingdom
| | - Ankit Patel
- Barts and the London School of Medicine and Dentistry , London , United Kingdom
| | | | - Thomas J Stone
- UCL Great Ormond Street Institute of Child Health , London , United Kingdom
- Great Ormond Street Hospital for Children NHS Foundation Trust , London , United Kingdom
| | | | | | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Pediatric Glioma Research Group, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Darren Hargrave
- Great Ormond Street Hospital for Children NHS Foundation Trust , London , United Kingdom
| | - Thomas S Jacques
- UCL Great Ormond Street Institute of Child Health , London , United Kingdom
- Great Ormond Street Hospital for Children NHS Foundation Trust , London , United Kingdom
| | - Denise Sheer
- Barts and the London School of Medicine and Dentistry , London , United Kingdom
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3
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Vinel C, Rosser G, Guglielmi L, Constantinou M, Pomella N, Zhang X, Boot JR, Jones TA, Millner TO, Dumas AA, Rakyan V, Rees J, Thompson JL, Vuononvirta J, Nadkarni S, El Assan T, Aley N, Lin YY, Liu P, Nelander S, Sheer D, Merry CLR, Marelli-Berg F, Brandner S, Marino S. Comparative epigenetic analysis of tumour initiating cells and syngeneic EPSC-derived neural stem cells in glioblastoma. Nat Commun 2021; 12:6130. [PMID: 34675201 PMCID: PMC8531305 DOI: 10.1038/s41467-021-26297-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 03/02/2021] [Accepted: 09/23/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms which play an essential role in normal developmental processes, such as self-renewal and fate specification of neural stem cells (NSC) are also responsible for some of the changes in the glioblastoma (GBM) genome. Here we develop a strategy to compare the epigenetic and transcriptional make-up of primary GBM cells (GIC) with patient-matched expanded potential stem cell (EPSC)-derived NSC (iNSC). Using a comparative analysis of the transcriptome of syngeneic GIC/iNSC pairs, we identify a glycosaminoglycan (GAG)-mediated mechanism of recruitment of regulatory T cells (Tregs) in GBM. Integrated analysis of the transcriptome and DNA methylome of GBM cells identifies druggable target genes and patient-specific prediction of drug response in primary GIC cultures, which is validated in 3D and in vivo models. Taken together, we provide a proof of principle that this experimental pipeline has the potential to identify patient-specific disease mechanisms and druggable targets in GBM.
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Affiliation(s)
- Claire Vinel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Gabriel Rosser
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Loredana Guglielmi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Myrianni Constantinou
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Nicola Pomella
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Xinyu Zhang
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - James R Boot
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Tania A Jones
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Thomas O Millner
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Anaelle A Dumas
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Vardhman Rakyan
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Jeremy Rees
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
| | - Jamie L Thompson
- Stem Cell Glycobiology Group, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Juho Vuononvirta
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Suchita Nadkarni
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Tedani El Assan
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
| | - Natasha Aley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Yung-Yao Lin
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
- Stem Cell Laboratory, National Bowel Research Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 2 Newark Street, London, UK
| | - Pentao Liu
- Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sven Nelander
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Denise Sheer
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Catherine L R Merry
- Stem Cell Glycobiology Group, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Federica Marelli-Berg
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Sebastian Brandner
- Division of Neuropathology, The 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
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK.
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4
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Adiutori R, Puentes F, Bremang M, Lombardi V, Zubiri I, Leoni E, Aarum J, Sheer D, McArthur S, Pike I, Malaspina A. Analysis of circulating protein aggregates as a route of investigation into neurodegenerative disorders. Brain Commun 2021; 3:fcab148. [PMID: 34396108 PMCID: PMC8361415 DOI: 10.1093/braincomms/fcab148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 03/08/2021] [Accepted: 04/22/2021] [Indexed: 11/22/2022] Open
Abstract
Plasma proteome composition reflects the inflammatory and metabolic state of the organism and can be predictive of system-level and organ-specific pathologies. Circulating protein aggregates are enriched with neurofilament heavy chain-axonal proteins involved in brain aggregate formation and recently identified as biomarkers of the fatal neuromuscular disorder amyotrophic lateral sclerosis. Using unbiased proteomic methods, we have fully characterized the content in neuronal proteins of circulating protein aggregates from amyotrophic lateral sclerosis patients and healthy controls, with reference to brain protein aggregate composition. We also investigated circulating protein aggregate protein aggregation propensity, stability to proteolytic digestion and toxicity for neuronal and endothelial cell lines. Circulating protein aggregates separated by ultracentrifugation are visible as electron-dense macromolecular particles appearing as either large globular or as small filamentous formations. Analysis by mass spectrometry revealed that circulating protein aggregates obtained from patients are enriched with proteins involved in the proteasome system, possibly reflecting the underlying basis of dysregulated proteostasis seen in the disease, while those from healthy controls show enrichment of proteins involved in metabolism. Compared to the whole human proteome, proteins within circulating protein aggregates and brain aggregates show distinct chemical features of aggregation propensity, which appear dependent on the tissue or fluid of origin and not on the health status. Neurofilaments' two high-mass isoforms (460 and 268 kDa) showed a strong differential expression in amyotrophic lateral sclerosis compared to healthy control circulating protein aggregates, while aggregated neurofilament heavy chain was also partially resistant to enterokinase proteolysis in patients, demonstrated by immunoreactive bands at 171 and 31 kDa fragments not seen in digested healthy controls samples. Unbiased proteomics revealed that a total of 4973 proteins were commonly detected in circulating protein aggregates and brain, including 24 expressed from genes associated with amyotrophic lateral sclerosis. Interestingly, 285 circulating protein aggregate proteins (5.7%) were regulated (P < 0.05) and are present in biochemical pathways linked to disease pathogenesis and protein aggregation. Biologically, circulating protein aggregates from both patients and healthy controls had a more pronounced effect on the viability of hCMEC/D3 endothelial and PC12 neuronal cells compared to immunoglobulins extracted from the same plasma samples. Furthermore, circulating protein aggregates from patients exerted a more toxic effect than healthy control circulating protein aggregates on both cell lines at lower concentrations (P: 0.03, in both cases). This study demonstrates that circulating protein aggregates are significantly enriched with brain proteins which are representative of amyotrophic lateral sclerosis pathology and a potential source of biomarkers and therapeutic targets for this incurable disorder.
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Affiliation(s)
- Rocco Adiutori
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Fabiola Puentes
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Michael Bremang
- Proteome Sciences R&D GmbH & Co. KG, Frankfurt am Main 60438, Germany
| | - Vittoria Lombardi
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Irene Zubiri
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Emanuela Leoni
- Proteome Sciences R&D GmbH & Co. KG, Frankfurt am Main 60438, Germany
| | - Johan Aarum
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm 171 76, Sweden
| | - Denise Sheer
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Simon McArthur
- Institute of Dentistry, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Ian Pike
- Proteome Sciences plc, Hamilton House, Mabledon Place, London WC1H 9BB, UK
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
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5
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Patel A, Jones T, Woodward L, Dokal A, Rajeeve V, Cutillas P, Stone T, Jacques T, Sheer D. LGG-57. SIGNALLING MECHANISMS IN PAEDIATRIC LOW-GRADE GLIOMA. Neuro Oncol 2020. [PMCID: PMC7715376 DOI: 10.1093/neuonc/noaa222.435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Paediatric low-grade gliomas (pLGGs) constitute the largest group of childhood CNS tumours. They often cause significant disability and morbidity, despite their indolent growth and the good survival rate of patients. The most common genetic alterations in these tumours, KIAA1549:BRAF fusion and BRAFV600E mutation, lead to abnormal activation of MAPK signalling. The central role of this pathway in pLGG development is emphasized by the occasional presence of other MAPK-activating alterations such as RTK mutations. It is not known how these different aberrations can induce the variety of clinical phenotypes seen in pLGG. Here, we compared pilocytic astrocytomas (PAs) containing the KIAA1549:BRAF fusion with glioneuronal tumours (GNTs) containing the BRAFV600E mutation, to identify differentially activated downstream targets of the MAPK pathway. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used as a multi-proteomic approach. Kinase Set Enrichment Analysis (KSEA) using PhosphositePlus and NetworkIN was used to determine relative enrichment of kinase activity in the tumours compared to healthy control brain tissue. Significant similarities and differences were found in the two tumour types. For example, more robust MAPK activation was found in the GNTs than in PAs. However, while PI3K/AKT1/mTOR signalling was active in both PAs and GNTs, there was statistically higher activation in the PAs. In both tumour types, there was significant reduction in casein kinase 2 activity, which likely affects nuclear translocation of ERK and, in turn, alters the range of its phosphorylated substrates. We will present these data together with transcriptomics to further characterise the downstream targets of these genetic alterations.
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Affiliation(s)
- Ankit Patel
- Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Tania Jones
- Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Lewis Woodward
- Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Arran Dokal
- Barts Cancer Institute, London, United Kingdom
| | | | | | - Thomas Stone
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Thomas Jacques
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Denise Sheer
- Barts and the London School of Medicine and Dentistry, London, United Kingdom
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6
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Aarum J, Cabrera CP, Jones TA, Rajendran S, Adiutori R, Giovannoni G, Barnes MR, Malaspina A, Sheer D. Enzymatic degradation of RNA causes widespread protein aggregation in cell and tissue lysates. EMBO Rep 2020; 21:e49585. [PMID: 32945072 PMCID: PMC7534620 DOI: 10.15252/embr.201949585] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/28/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Most proteins in cell and tissue lysates are soluble. We show here that in lysate from human neurons, more than 1,300 proteins are maintained in a soluble and functional state by association with endogenous RNA, as degradation of RNA invariably leads to protein aggregation. The majority of these proteins lack conventional RNA‐binding domains. Using synthetic oligonucleotides, we identify the importance of nucleic acid structure, with single‐stranded pyrimidine‐rich bulges or loops surrounded by double‐stranded regions being particularly efficient in the maintenance of protein solubility. These experiments also identify an apparent one‐to‐one protein‐nucleic acid stoichiometry. Furthermore, we show that protein aggregates isolated from brain tissue from Amyotrophic Lateral Sclerosis patients can be rendered soluble after refolding by both RNA and synthetic oligonucleotides. Together, these findings open new avenues for understanding the mechanism behind protein aggregation and shed light on how certain proteins remain soluble.
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Affiliation(s)
- Johan Aarum
- Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Claudia P Cabrera
- Barts and The London NIHR Cardiovascular Biomedical Research Centre, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Tania A Jones
- Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Shiron Rajendran
- Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Rocco Adiutori
- Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Gavin Giovannoni
- Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Michael R Barnes
- Barts and The London NIHR Cardiovascular Biomedical Research Centre, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Andrea Malaspina
- Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
| | - Denise Sheer
- Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK
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Dumas AA, Pomella N, Rosser G, Guglielmi L, Vinel C, Millner TO, Rees J, Aley N, Sheer D, Wei J, Marisetty A, Heimberger AB, Bowman RL, Brandner S, Joyce JA, Marino S. Microglia promote glioblastoma via mTOR-mediated immunosuppression of the tumour microenvironment. EMBO J 2020; 39:e103790. [PMID: 32567735 PMCID: PMC7396846 DOI: 10.15252/embj.2019103790] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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: 10/20/2019] [Revised: 05/03/2020] [Accepted: 05/08/2020] [Indexed: 12/31/2022] Open
Abstract
Tumour-associated microglia/macrophages (TAM) are the most numerous non-neoplastic populations in the tumour microenvironment in glioblastoma multiforme (GBM), the most common malignant brain tumour in adulthood. The mTOR pathway, an important regulator of cell survival/proliferation, is upregulated in GBM, but little is known about the potential role of this pathway in TAM. Here, we show that GBM-initiating cells induce mTOR signalling in the microglia but not bone marrow-derived macrophages in both in vitro and in vivo GBM mouse models. mTOR-dependent regulation of STAT3 and NF-κB activity promotes an immunosuppressive microglial phenotype. This hinders effector T-cell infiltration, proliferation and immune reactivity, thereby contributing to tumour immune evasion and promoting tumour growth in mouse models. The translational value of our results is demonstrated in whole transcriptome datasets of human GBM and in a novel in vitro model, whereby expanded-potential stem cells (EPSC)-derived microglia-like cells are conditioned by syngeneic patient-derived GBM-initiating cells. These results raise the possibility that microglia could be the primary target of mTOR inhibition, rather than the intrinsic tumour cells in GBM.
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Affiliation(s)
- Anaelle A Dumas
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University LondonLondonUK
| | - Nicola Pomella
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University LondonLondonUK
| | - Gabriel Rosser
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University LondonLondonUK
| | - Loredana Guglielmi
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University LondonLondonUK
| | - Claire Vinel
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University LondonLondonUK
| | - Thomas O Millner
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University LondonLondonUK
| | - Jeremy Rees
- National Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
| | - Natasha Aley
- Division of NeuropathologyDepartment of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
| | - Denise Sheer
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University LondonLondonUK
| | - Jun Wei
- Department of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Anantha Marisetty
- Department of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Amy B Heimberger
- Department of NeurosurgeryThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Robert L Bowman
- Human Oncology and Pathogenesis ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Sebastian Brandner
- National Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
| | - Johanna A Joyce
- Department of OncologyLudwig Institute for Cancer ResearchUniversity of LausanneLausanneSwitzerland
| | - Silvia Marino
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University LondonLondonUK
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8
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Merve A, Zhang X, Pomella N, Acquati S, Hoeck JD, Dumas A, Rosser G, Li Y, Jeyapalan J, Vicenzi S, Fan Q, Yang ZJ, Sabò A, Sheer D, Behrens A, Marino S. Correction to: c-MYC overexpression induces choroid plexus papillomas through a T-cell mediated inflammatory mechanism. Acta Neuropathol Commun 2019; 7:179. [PMID: 31727166 PMCID: PMC6854732 DOI: 10.1186/s40478-019-0835-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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9
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Merve A, Zhang X, Pomella N, Acquati S, Hoeck J, Dumas A, Rosser G, Li Y, Jeyapalan J, Vicenzi S, Sabò A, Sheer D, Behrens A, Marino S. Choroid plexus papillomas are induced by c-Myc overexpression in the choroid plexus via a T-cell inflammatory mechanism. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz167.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Choroid plexus tumours (CPT) account for up to 20% of brain tumours in children under 2 years of age. Histologically CPTs are classified into three categories - Choroid Plexus Papilloma (CPP), Atypical Choroid Plexus Papilloma (ACPP) and Choroid Plexus Carcinoma (CPC). Recent literature demonstrates that CPP and ACPP are molecularly distinct from CPC. Initial management for CPT include surgery followed by adjuvant therapy in selected patients. Currently there are no disease-specific chemotherapeutic agents available, possibly because of their rarity and paucity of faithful pre-clinical experimental models.
In this study we show that c-Myc overexpression in the choroid plexus epithelium induces T-cell inflammation-dependent choroid plexus papillomas in a mouse model. We demonstrate that c-MYC is expressed in a substantial proportion of human choroid plexus tumours and that this subgroup of tumours is characterised by an inflammatory transcriptome and significant inflammatory infiltrates. We observed that triple transgenic compound mutant mouse model with c-Myc overexpression in an immune-suppressed background led to a decreased incidence of CPP and reduced tumour bulk. A reduced tumour size was also observed when c-Myc overexpressing mice were treated with anti-CD3 antibodies.
Our data raise the possibility that benign choroid plexus tumours expressing c-MYC could be amenable to medical therapy with anti-inflammatory drugs.
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Affiliation(s)
- Ashirwad Merve
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Xinyu Zhang
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Nicola Pomella
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Serena Acquati
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Joerg Hoeck
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Anaelle Dumas
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Gabriel Rosser
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Yichen Li
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Jennie Jeyapalan
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Silvia Vicenzi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Arianna Sabò
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Denise Sheer
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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10
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Caley M, Marsh S, Martins V, Corbett-Jones T, Chen M, Di W, Sheer D, McGrath J, Barnes M, O’Toole E. 298 Defective DNA Repair and Chromosomal Instability in RDEB. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Merve A, Zhang X, Pomella N, Acquati S, Hoeck JD, Dumas A, Rosser G, Li Y, Jeyapalan J, Vicenzi S, Fan Q, Yang ZJ, Sabò A, Sheer D, Behrens A, Marino S. c-MYC overexpression induces choroid plexus papillomas through a T-cell mediated inflammatory mechanism. Acta Neuropathol Commun 2019; 7:95. [PMID: 31142360 PMCID: PMC6540455 DOI: 10.1186/s40478-019-0739-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Choroid plexus tumours (CPTs) account for 2–5% of brain tumours in children. They can spread along the neuraxis and can recur after treatment. Little is known about the molecular mechanisms underlying their formation and only few high fidelity mouse models of p53-deficient malignant CPTs are available. We show here that c-MYC overexpression in the choroid plexus epithelium induces T-cell inflammation-dependent choroid plexus papillomas in a mouse model. We demonstrate that c-MYC is expressed in a substantial proportion of human choroid plexus tumours and that this subgroup of tumours is characterised by an inflammatory transcriptome and significant inflammatory infiltrates. In compound mutant mice, overexpression of c-MYC in an immunodeficient background led to a decreased incidence of CPP and reduced tumour bulk. Finally, reduced tumour size was also observed upon T-cell depletion in CPP-bearing mice. Our data raise the possibility that benign choroid plexus tumours expressing c-MYC could be amenable to medical therapy with anti-inflammatory drugs.
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12
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Fedorova L, Kost-Alimova M, Gizatullin R, Alimov A, Zabarovska V, Szeles A, Protopopov A, Vorobieva N, Kashuba VI, Klein G, Zelenin A, Sheer D, Zabarovsky E. Assignment and Ordering of Twenty-Three Unique NotI-Linking Clones Containing Expressed Genes Including the Guanosine 5'-Monophosphate Synthetase Gene to Human Chromosome 3. Eur J Hum Genet 2019. [DOI: 10.1159/000484744] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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13
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Adiutori R, Aarum J, Zubiri I, Bremang M, Jung S, Sheer D, Pike I, Malaspina A. The proteome of neurofilament-containing protein aggregates in blood. Biochem Biophys Rep 2018; 14:168-177. [PMID: 29872749 PMCID: PMC5986704 DOI: 10.1016/j.bbrep.2018.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/15/2018] [Accepted: 04/26/2018] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation in biofluids is a poorly understood phenomenon. Under normal physiological conditions, fluid-borne aggregates may contain plasma or cell proteins prone to aggregation. Recent observations suggest that neurofilaments (Nf), the building blocks of neurons and a biomarker of neurodegeneration, are included in high molecular weight complexes in circulation. The composition of these Nf-containing hetero-aggregates (NCH) may change in systemic or organ-specific pathologies, providing the basis to develop novel disease biomarkers. We have tested ultracentrifugation (UC) and a commercially available protein aggregate binder, Seprion PAD-Beads (SEP), for the enrichment of NCH from plasma of healthy individuals, and then characterised the Nf content of the aggregate fractions using gel electrophoresis and their proteome by mass spectrometry (MS). Western blot analysis of fractions obtained by UC showed that among Nf isoforms, neurofilament heavy chain (NfH) was found within SDS-stable high molecular weight aggregates. Shotgun proteomics of aggregates obtained with both extraction techniques identified mostly cell structural and to a lesser extent extra-cellular matrix proteins, while functional analysis revealed pathways involved in inflammatory response, phagosome and prion-like protein behaviour. UC aggregates were specifically enriched with proteins involved in endocrine, metabolic and cell-signalling regulation. We describe the proteome of neurofilament-containing aggregates isolated from healthy individuals biofluids using different extraction methods.
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Affiliation(s)
- Rocco Adiutori
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and The School of Medicine and Dentistry, London, United Kingdom
| | - Johan Aarum
- Centre for Genomics and Child Health, Queen Mary University of London, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Irene Zubiri
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and The School of Medicine and Dentistry, London, United Kingdom
| | - Michael Bremang
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Stephan Jung
- ProteomeSciencesR&DGmbH&Co.KG, Frankfurt, Germany
| | - Denise Sheer
- Centre for Genomics and Child Health, Queen Mary University of London, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Ian Pike
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and The School of Medicine and Dentistry, London, United Kingdom
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14
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Jeyapalan JN, Doctor GT, Jones TA, Alberman SN, Tep A, Haria CM, Schwalbe EC, Morley ICF, Hill AA, LeCain M, Ottaviani D, Clifford SC, Qaddoumi I, Tatevossian RG, Ellison DW, Sheer D. DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas. Acta Neuropathol Commun 2016; 4:54. [PMID: 27229157 PMCID: PMC4882864 DOI: 10.1186/s40478-016-0323-6] [Citation(s) in RCA: 16] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/04/2016] [Indexed: 12/30/2022] Open
Abstract
Low-grade gliomas (LGGs) account for about a third of all brain tumours in children. We conducted a detailed study of DNA methylation and gene expression to improve our understanding of the biology of pilocytic and diffuse astrocytomas. Pilocytic astrocytomas were found to have a distinctive signature at 315 CpG sites, of which 312 were hypomethylated and 3 were hypermethylated. Genomic analysis revealed that 182 of these sites are within annotated enhancers. The signature was not present in diffuse astrocytomas, or in published profiles of other brain tumours and normal brain tissue. The AP-1 transcription factor was predicted to bind within 200 bp of a subset of the 315 differentially methylated CpG sites; the AP-1 factors, FOS and FOSL1 were found to be up-regulated in pilocytic astrocytomas. We also analysed splice variants of the AP-1 target gene, CCND1, which encodes cell cycle regulator cyclin D1. CCND1a was found to be highly expressed in both pilocytic and diffuse astrocytomas, but diffuse astrocytomas have far higher expression of the oncogenic variant, CCND1b. These findings highlight novel genetic and epigenetic differences between pilocytic and diffuse astrocytoma, in addition to well-described alterations involving BRAF, MYB and FGFR1.
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Affiliation(s)
- Jennie N Jeyapalan
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Gabriel T Doctor
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Tania A Jones
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Samuel N Alberman
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Alexander Tep
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Chirag M Haria
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Edward C Schwalbe
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Isabel C F Morley
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Alfred A Hill
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Magdalena LeCain
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Diego Ottaviani
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Steven C Clifford
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Ibrahim Qaddoumi
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ruth G Tatevossian
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA.
| | - Denise Sheer
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
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15
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Noor DAM, Jeyapalan JN, Alhazmi S, Carr M, Squibb B, Wallace C, Tan C, Cusack M, Hughes J, Reader T, Shipley J, Sheer D, Scotting PJ. Genome-wide methylation analysis identifies genes silenced in non-seminoma cell lines. NPJ Genom Med 2016; 1:15009. [PMID: 29263807 PMCID: PMC5685295 DOI: 10.1038/npjgenmed.2015.9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/09/2015] [Accepted: 11/06/2015] [Indexed: 01/13/2023] Open
Abstract
Silencing of genes by DNA methylation is a common phenomenon in many types of cancer. However, the genome-wide effect of DNA methylation on gene expression has been analysed in relatively few cancers. Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. Previous analyses have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. The genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours’ biology have not yet been established. In this study, genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data from primary tumours to address this question. Genome methylation was analysed using the Illumina infinium HumanMethylome450 bead chip system and gene expression was analysed using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Regulation by methylation was confirmed by demethylation using 5-aza-2-deoxycytidine and reverse transcription–quantitative PCR. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested played a role in their silencing in yolk sac tumour cells and many of these genes were also differentially expressed in primary tumours. Genes silenced by methylation in the various GCT cell lines were identified. Several pluripotency-associated genes were identified as a major functional group of silenced genes.
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Affiliation(s)
- Dzul Azri Mohamed Noor
- School of Life Sciences, University of Nottingham, Nottingham, UK.,School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Jennie N Jeyapalan
- School of Life Sciences, University of Nottingham, Nottingham, UK.,The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
| | - Safiah Alhazmi
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Biology Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Matthew Carr
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Benjamin Squibb
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Claire Wallace
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Christopher Tan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Martin Cusack
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Jaime Hughes
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Tom Reader
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Denise Sheer
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
| | - Paul J Scotting
- School of Life Sciences, University of Nottingham, Nottingham, UK
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Jones TA, Jeyapalan JN, Forshew T, Tatevossian RG, Lawson ARJ, Patel SN, Doctor GT, Mumin MA, Picker SR, Phipps KP, Michalski A, Jacques TS, Sheer D. Molecular analysis of pediatric brain tumors identifies microRNAs in pilocytic astrocytomas that target the MAPK and NF-κB pathways. Acta Neuropathol Commun 2015; 3:86. [PMID: 26682910 PMCID: PMC4683939 DOI: 10.1186/s40478-015-0266-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 12/05/2015] [Indexed: 12/17/2022] Open
Abstract
Introduction Pilocytic astrocytomas are slow-growing tumors that usually occur in the cerebellum or in the midline along the hypothalamic/optic pathways. The most common genetic alterations in pilocytic astrocytomas activate the ERK/MAPK signal transduction pathway, which is a major driver of proliferation but is also believed to induce senescence in these tumors. Here, we have conducted a detailed investigation of microRNA and gene expression, together with pathway analysis, to improve our understanding of the regulatory mechanisms in pilocytic astrocytomas. Results Pilocytic astrocytomas were found to have distinctive microRNA and gene expression profiles compared to normal brain tissue and a selection of other pediatric brain tumors. Several microRNAs found to be up-regulated in pilocytic astrocytomas are predicted to target the ERK/MAPK and NF-κB signaling pathways as well as genes involved in senescence-associated inflammation and cell cycle control. Furthermore, IGFBP7 and CEBPB, which are transcriptional inducers of the senescence-associated secretory phenotype (SASP), were also up-regulated together with the markers of senescence and inflammation, CDKN1A (p21), CDKN2A (p16) and IL1B. Conclusion These findings provide further evidence of a senescent phenotype in pilocytic astrocytomas. In addition, they suggest that the ERK/MAPK pathway, which is considered the major driver of these tumors, is regulated not only by genetic aberrations but also by microRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s40478-015-0266-3) contains supplementary material, which is available to authorized users.
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Jeyapalan JN, Haria CM, Jones TA, Tatevossian RG, Qaddoumi I, Ellison DW, Sheer D. PO77EXPRESSION OF THE ONCOGENIC SPLICE VARIANT OF CYCLIN D1, CCND1B, IN PAEDIATRIC LOW GRADE GLIOMAS. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov284.68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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18
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Takousis P, Johonnett P, Williamson J, Sasieni P, Warnes G, Forshew T, Azuara V, Fisher A, Wu PJ, Jones T, Vatcheva R, Beck S, Sheer D. Replication Timing Profile Reflects the Distinct Functional and Genomic Features of the MHC Class II Region. Cell Cycle 2014; 6:2393-8. [DOI: 10.4161/cc.6.19.4762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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19
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Abstract
The male hormone androgen, working through the androgen receptor (AR), plays a major role in physiological process and disease development. Previous studies of AR mainly focus on its transcriptional activity. Here, we found that androgen-induced TMPRSS2 and ERG gene proximity is mediated by AR control of DNA replication rather than gene transcription. We demonstrate that, in both AR transactivation-positive and -negative prostate cells, androgen regulates DNA replication and androgen-induced gene proximity relies on both DNA replication-licensing and actual DNA replication activity. Androgen stimulation advances DNA replication timing of certain genomic regions, which may potentially increase gene proximity through sharing the same replication factory at a similar time. Therefore, we have revealed novel mechanisms of AR biological function, which will stimulate new research directions.
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Affiliation(s)
| | | | - Bryan D Young
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK and
| | - Denise Sheer
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
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Jeyapalan JN, Jones TA, Tatevossian RG, Qaddoumi I, Ellison DW, Sheer D. OP17 * MICRORNA PROFILING USING SMALL RNA-SEQ IN PAEDIATRIC LOW GRADE GLIOMAS. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou251.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Ogunkolade BW, Jones TA, Aarum J, Szary J, Owen N, Ottaviani D, Mumin MA, Patel S, Pieri CA, Silver AR, Sheer D. BORIS/CTCFL is an RNA-binding protein that associates with polysomes. BMC Cell Biol 2013; 14:52. [PMID: 24279897 PMCID: PMC4219345 DOI: 10.1186/1471-2121-14-52] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/19/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND BORIS (CTCFL), a paralogue of the multifunctional and ubiquitously expressed transcription factor CTCF, is best known for its role in transcriptional regulation. In the nucleus, BORIS is particularly enriched in the nucleolus, a crucial compartment for ribosomal RNA and RNA metabolism. However, little is known about cytoplasmic BORIS, which represents the major pool of BORIS protein. RESULTS We show, firstly, that BORIS has a putative nuclear export signal in the C-terminal domain. Furthermore, BORIS associates with mRNA in both neural stem cells and young neurons. The majority of the BORIS-associated transcripts are different in the two cell types. Finally, by using polysome profiling we show that BORIS is associated with actively translating ribosomes. CONCLUSION We have demonstrated the RNA binding properties of cellular BORIS and its association with actively translating ribosomes. We suggest that BORIS is involved in gene expression at both the transcriptional and post-transcriptional levels.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Denise Sheer
- Centre for Neuroscience and Trauma, Queen Mary University of London, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, E1 2AT, UK.
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Henriquez NV, Forshew T, Tatevossian R, Ellis M, Richard-Loendt A, Rogers H, Jacques TS, Reitboeck PG, Pearce K, Sheer D, Grundy RG, Brandner S. Comparative expression analysis reveals lineage relationships between human and murine gliomas and a dominance of glial signatures during tumor propagation in vitro. Cancer Res 2013; 73:5834-44. [PMID: 23887970 DOI: 10.1158/0008-5472.can-13-1299] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Brain tumors are thought to originate from stem/progenitor cell populations that acquire specific genetic mutations. Although current preclinical models have relevance to human pathogenesis, most do not recapitulate the histogenesis of the human disease. Recently, a large series of human gliomas and medulloblastomas were analyzed for genetic signatures of prognosis and therapeutic response. Using a mouse model system that generates three distinct types of intrinsic brain tumors, we correlated RNA and protein expression levels with human brain tumors. A combination of genetic mutations and cellular environment during tumor propagation defined the incidence and phenotype of intrinsic murine tumors. Importantly, in vitro passage of cancer stem cells uniformly promoted a glial expression profile in culture and in brain tumors. Gene expression profiling revealed that experimental gliomas corresponded to distinct subclasses of human glioblastoma, whereas experimental supratentorial primitive neuroectodermal tumors (sPNET) correspond to atypical teratoid/rhabdoid tumor (AT/RT), a rare childhood tumor.
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Affiliation(s)
- Nico V Henriquez
- Authors' Affiliations: Division of Neuropathology, Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology; Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London; Department of Histopathology, Neural Development Unit, and UCL Genomics, UCL Institute of Child Health, Great Ormond Street Hospital, London; and Children's Brain Tumour Research Centre, Queen's Medical Centre, Nottingham, United Kingdom
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Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet 2013; 45:602-12. [PMID: 23583981 PMCID: PMC3727232 DOI: 10.1038/ng.2611] [Citation(s) in RCA: 579] [Impact Index Per Article: 52.6] [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: 12/19/2012] [Accepted: 03/21/2013] [Indexed: 12/28/2022]
Abstract
The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62%) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53% of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100% penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.
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Affiliation(s)
- Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Birks S, Altinkaya M, Altinkaya A, Pilkington G, Kurian KM, Crosby C, Hopkins K, Williams M, Donovan L, Birks S, Eason A, Bosak V, Pilkington G, Birks S, Holliday J, Corbett I, Pilkington G, Keeling M, Bambrough J, Simpson J, Higgins S, Dogra H, Pilkington G, Kurian KM, Zhang Y, Bradley M, Schmidberger C, Hafizi S, Noorani I, Price S, Dubocq A, Jaunky T, Chatelain C, Evans L, Gaissmaier T, Pilkington GJ, An Q, Hurwitz V, Logan J, Bhangoo R, Ashkan K, Gullan A, Beaney R, Brazil L, Kokkinos S, Blake R, Singleton A, Shaw A, Iyer V, Kurian KM, Jeyapalan JN, Morley IC, Hill AA, Mumin MA, Tatevossian RG, Qaddoumi I, Ellison DW, Sheer D, Frary A, Price S, Jefferies S, Harris F, Burnet N, Jena R, Watts C, Haylock B, Leow-Dyke S, Rathi N, Wong H, Dunn J, Baborie A, Crooks D, Husband D, Shenoy A, Brodbelt A, Walker C, Bahl A, Larsen J, Craven I, Metherall P, McKevitt F, Romanowski C, Hoggard N, Jellinek DA, Bell S, Murray E, Muirhead R, James A, Hanzely Z, Jackson R, Stewart W, O'Brien A, Young A, Bell S, Hanzely Z, Stewart W, Shepherd S, Cavers D, Wallace L, Hacking B, Scott S, Bowyer D, Elmahdi A, Frary AJ, O'Donovan DG, Price SJ, Kia A, Przystal JM, Nianiaris N, Mazarakis ND, Mintz PJ, Hajitou A, Karakoula K, Phipps K, Harkness W, Hayward R, Thompson D, Jacques T, Harding B, Darling J, Warr T, Leow-Dyke S, Rathi N, Haylock B, Crooks D, Jenkinson M, Walker C, Brodbelt A, Zhou L, Ercolano E, Ammoun S, Schmid MC, Barczyk M, Hanemann CO, Rowther F, Dawson T, Ashton K, Darling J, Warr T, Maherally Z, Hatherell KE, Kroese K, Hafizi S, Pilkington GJ, Singh P, McQuaid S, Al-Rashid S, Prise K, Herron B, Healy E, Shoakazemi A, Donnelly M, McConnell R, Harney J, Conkey D, McGrath E, Lunsford L, Kondziolka D, Niranjan A, Kano H, Hamilton R, Flannery T, Majani Y, Smith S, Grundy R, Rahman R, Saini S, Hall G, Davis C, Rowther F, Lawson T, Ashton K, Potter N, Goessl E, Darling J, Warr T, Brodbelt A, Jenkinson M, Walker C, Leow-Dyke S, Haylock B, Dunn J, Wilkins S, Smith T, Petinou V, Nicholl I, Singh J, Lea R, Welsby P, Spiteri I, Sottoriva A, Marko N, Tavare S, Collins P, Price SJ, Watts C, Su Z, Gerhard A, Hinz R, Roncaroli F, Coope D, Thompson G, Karabatsou K, Sofat A, Leggate J, du Plessis D, Turkheimer F, Jackson A, Brodbelt A, Jenkinson M, Das K, Crooks D, Herholz K, Price SJ, Whittle IR, Ashkan K, Grundy P, Cruickshank G, Berry V, Elder D, Iyer V, Hopkins K, Cohen N, Tavare J, Zilidis G, Tibarewal P, Spinelli L, Leslie NR, Coope DJ, Karabatsou K, Green S, Wall G, Bambrough J, Brennan P, Baily J, Diaz M, Ironside J, Sansom O, Brunton V, Frame M, Young A, Thomas O, Mohsen L, Frary A, Lupson V, McLean M, Price S, Arora M, Shaw L, Lawrence C, Alder J, Dawson T, Hall G, Rada L, Chen K, Shivane A, Ammoun S, Parkinson D, Hanemann C, Pangeni RP, Warr TJ, Morris MR, Mackinnon M, Williamson A, James A, Chalmers A, Beckett V, Joannides A, Brock R, McCarthy K, Price S, Singh A, Karakoula K, Dawson T, Ashton K, Darling J, Warr T, Kardooni H, Morris M, Rowther F, Darling J, Warr T, Watts C, Syed N, Roncaroli F, Janczar K, Singh P, O'Neil K, Nigro CL, Lattanzio L, Coley H, Hatzimichael E, Bomalaski J, Szlosarek P, Crook T, Pullen NA, Anand M, Birks S, Van Meter T, Pullen NA, Anand M, Williams S, Boissinot M, Steele L, Williams S, Chiocca EA, Lawler S, Al Rashid ST, Mashal S, Taggart L, Clarke E, Flannery T, Prise KM. Abstracts from the 2012 BNOS Conference. Neuro Oncol 2012. [DOI: 10.1093/neuonc/nos198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Shih CS, Ekoma S, Ho C, Pradhan K, Hwang E, Jakacki R, Fisher M, Kilburn L, Horn M, Vezina G, Rood B, Packer R, Mittal R, Omar S, Khalifa N, Bedir R, Avery R, Hwang E, Acosta M, Hutcheson K, Santos D, Zand D, Kilburn L, Rosenbaum K, Rood B, Packer R, Kalin-Hajdu E, Ospina L, Carret AS, Marzouki M, Decarie JC, Freeman E, Hershon L, Warmuth-Metz M, Zurakowski D, Bison B, Falkenstein F, Gnekow A, Ehrstedt C, Laurencikas E, Bjorklund AC, Stromberg B, Hedborg F, Pfeifer S, Bertin D, Packer RJ, Vallero S, Basso ME, Romano E, Peretta P, Morra I, D'Alonzo G, Fagioli F, Toledano H, Laviv Y, Dratviman-Storobinsky O, Michowiz S, Yaniv I, Cohen IJ, Goldenberg-Cohen N, Muller K, Gnekow A, Warmuth-Metz M, Pietsch T, Zwiener I, Falkenstein F, Meyer FM, Micke O, Hoffmann W, Kortmann RD, Shofty B, Ben-Sira L, Roth J, Constantini S, Shofty B, Weizmann L, Joskowicz L, Kesler A, Ben-Bashat D, Yalon M, Dvir R, Freedman S, Roth J, Ben-Sira L, Constantini S, Bandopadhayay P, Dagi L, Robison N, Goumnerova L, Ullrich N, Opocher E, De Salvo GL, De Paoli A, Simmons I, Sehested A, Walker DA, Picton SV, Gnekow A, Grill J, Driever PH, Azizi AA, Viscardi E, Perilongo G, Cappellano AM, Bouffet E, Silva F, Paiva P, Cavalheiro S, Seixas MT, Silva NS, Antony R, Fraser K, Lin J, Falkenstein F, Kwiecien R, Mirow C, Thieme B, von Hornstein S, Pietsch T, Faldum A, Warmuth-Metz M, Kortmann RD, Gnekow AK, Shofty B, Bokshtein F, Kesler A, Ben-Sira L, Freedman S, Constantini S, Panandiker AP, Klimo P, Thompson C, Armstrong G, Kun L, Boop F, Sanford A, Orge F, Laschinger K, Gold D, Bangert B, Stearns D, Cappellano AM, Senerchia A, Paiva P, Cavalheiro S, Silva F, Silva NS, Gnekow AK, Falkenstein F, Walker D, Perilongo G, Picton S, Grill J, Kortmann RD, Stokland T, van Meeteren AS, Slavc I, Faldum A, de Salvo GL, Fernandez KS, Antony R, Lulla RR, Flores M, Benavides VC, Mitchell C, AlKofide A, Hassonah M, Khafagh Y, Ayas MA, AlFawaz I, Anas M, Barria M, Siddiqui K, Al-Shail E, Fisher MJ, Ullrich NJ, Ferner RE, Gutmann DH, Listernick R, Packer RJ, Tabori U, Hoffman RO, Ardern-Holmes SL, Hummel TR, Hargrave DR, Charrow J, Loguidice M, Balcer LJ, Liu GT, Fisher MJ, Listernick R, Gutmann DH, Ferner RE, Packer RJ, Ullrich NJ, Tabori U, Hoffman RO, Ardern-Holmes SL, Hummel TR, Hargrave DR, Loguidice M, Balcer LJ, Liu GT, Jeeva I, Nelson O, Guy D, Damani A, Gogi D, Picton S, Simmons I, Jeeva I, Picton S, Guy D, Nelson O, Dewsbery S, Gogi D, Simmons I, Sievert AJ, Lang SS, Boucher K, Slaunwhite E, Brewington D, Madsen P, Storm PB, Resnick AC, Hemenway M, Madden J, Macy M, Foreman N, Rush S, Mascelli S, Raso A, Barla A, Nozza P, Biassoni R, Pignatelli S, Cama A, Verri A, Capra V, Garre M, Bergthold G, Piette C, Raquin MA, Dufour C, Varlet P, Dhermain F, Puget S, Sainte-Rose C, Abely M, Canale S, Grill J, Terashima K, Chow K, Jones J, Ahern C, Jo E, Ellezam B, Paulino A, Okcu MF, Su J, Adesina A, Mahajan A, Dauser R, Whitehead W, Lau C, Chintagumpala M, Kebudi R, Tuncer S, Cakir FB, Gorgun O, Agaoglu FY, Ayan I, Darendeliler E, Wolf D, Cohen K, Jeyapalan JN, Morley ICF, Hill AA, Tatevossian RG, Qaddoumi I, Ellison DW, Sheer D, Donson A, Barton V, Birks D, Kleinschmidt-DeMasters BK, Hemenway M, Handler M, Foreman N, Rush S, Tatevossian R, Qaddoumi I, Tang B, Dalton J, Shurtleff S, Punchihewa C, Orisme W, Neale G, Gajjar A, Baker S, Sheer D, Ellison D, Gilheeney S, Jamzadeh A, Winchester M, Yataghene K, De Braganca K, Khakoo Y, Lyden D, Dunkel I, Terasaki M, Eto T, Morioka M, Ho CY, Bar E, Giannini C, Karajannis MA, Zagzag D, Eberhart CG, Rodriguez FJ, Lee Y, Bartels U, Tabori U, Huang A, Bouffet E, Zaky W, Bluml S, Grimm J, Wong K, McComb G, Gilles F, Finlay J, Dhall G, Chen HH, Chen YW, Chang FC, Lin SC, Chang KP, Ho DM, Wong TT, Lee CC, Azizi AA, Fox R, Grill J, Mirow C, Gnekow A, Walker D, Perilongo G, Opocher E, Wheatley K, van Meeteren AYS, Phuakpet K, Tabori U, Bartels U, Huang A, Kulkarni A, Laperriere N, Bouffet E, Epari S, Nair V, Gupta T, Patil P, Moiyadi A, Shetty P, Kane S, Jalali R, Dorris K, Nadi M, Sutton M, Wang L, Stogner K, Li D, Hurwitz B, Stevenson C, Miles L, Kim MO, Fuller C, Hawkins C, Bouffet E, Jones B, Drake J, Fouladi M, Fontebasso AM, Shirinian M, Jones DTW, Quang DAK, Jacob K, Cin H, Witt H, Gerges N, Montpetit A, Brunet S, Lepage P, Klekner A, Lambert S, Kwan T, Hawkins C, Tabori U, Collins VP, Albrecht S, Pfister SM, Jabado N, Arrington D, Manley P, Kieran M, Chi S, Robison N, Chordas C, Ullrich N. LOW GRADE GLIOMAS. Neuro Oncol 2012; 14:i69-i81. [PMCID: PMC3483338 DOI: 10.1093/neuonc/nos092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
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Leonard A, Wolff J, Sengupta R, Marassa J, Piwnica-Worms D, Rubin J, Pollack I, Jakacki R, Butterfield L, Okada H, Fangusaro J, Warren KE, Mullins C, Jurgen P, Julia S, Friedrich CC, Keir S, Saling J, Roskoski M, Friedman H, Bigner D, Moertel C, Olin M, Dahlheimer T, Gustafson M, Sumstad D, McKenna D, Low W, Nascene D, Dietz A, Ohlfest J, Sturm D, Witt H, Hovestadt V, Quan DAK, Jones DTW, Konermann C, Pfaff E, Korshunov A, Rizhova M, Milde T, Witt O, Zapatka M, Collins VP, Kool M, Reifenberger G, Lichter P, Lindroth AM, Plass C, Jabado N, Pfister SM, Pizer B, Salehzadeh A, Brodbelt A, Mallucci C, Brassesco M, Pezuk J, Morales A, de Oliveira J, Roberto G, Umezawa K, Valera E, Rego E, Scrideli C, Tone L, Veringa SJE, Van Vuurden DG, Wesseling P, Vandertop WP, Noske DP, Wurdinger T, Kaspers GJL, Hulleman E, Wright K, Broniscer A, Bendel A, Bowers D, Crawford J, Fisher P, Hassall T, Armstrong G, Baker J, Qaddoumi I, Robinson G, Wetmore C, Klimo P, Boop F, Onar-Thomas A, Ellison D, Gajjar A, Cruz O, de Torres C, Sunol M, Rodriguez E, Alonso L, Parareda A, Cardesa T, Salvador H, Celis V, Guillen A, Garcia G, Muchart J, Trampal C, Martin ML, Rebollo M, Mora J, Piotrowski A, Kowalska A, Coyle P, Smith S, Rogers H, Macarthur D, Grundy R, Puccetti D, Salamat S, Kennedy T, Fangusaro J, Patel N, Bradley K, Casey K, Iskandar B, Nakano Y, Okada K, Osugi Y, Yamasaki K, Fujisaki H, Fukushima H, Inoue T, Matsusaka Y, Sakamoto H, Hara J, De Vleeschouwer S, Ardon H, Van Calenbergh F, Sciot R, Wilms G, Van Loon J, Goffin J, Van Gool S, Puccetti D, Salamat S, Rusinak D, Patel N, Bradley K, Casey K, Knight P, Onel K, Wargowski D, Stettner A, Iskandar B, Al-Ghafari A, Punjaruk W, Coyle B, Kerr I, Xipell E, Rodriguez M, Gonzalez-Huarriz M, Tunon MT, Zazpe I, Tejada-Solis S, Diez-Valle R, Fueyo J, Gomez-Manzano C, Alonso MM, Pastakia D, McCully C, Murphy R, Bacher J, Thomas M, Steffen-Smith E, Saleem K, Waldbridge S, Widemann B, Warren K, Miele E, Buttarelli F, Arcella A, Begalli F, Po A, Baldi C, Carissimo G, Antonelli M, Donofrio V, Morra I, Nozza P, Gulino A, Giangaspero F, Ferretti E, Elens I, De Vleeschouwer S, Pauwels F, Van Gool S, Fritzell S, Eberstal S, Sanden E, Visse E, Darabi A, Siesjo P, McDonald P, Wrogemann J, Krawitz S, Del Bigio M, Eisenstat D, Wolff J, Kwiecien R, Pietsch T, Faldum A, Kortmann RD, Warmuth-Metz M, Rutkowski S, Slavc I, Kramm CM, Uparkar U, Geyer R, Ermoian R, Ellenbogen R, Leary S, Triscott J, Hu K, Fotovati A, Yip S, Kast R, Toyota B, Dunn S, Hegde M, Corder A, Chow K, Mukherjee M, Ashoori A, Brawley V, Heslop H, Gottschalk S, Yvon E, Ahmed N, Wong TT, Yang FY, Lu M, Liang HF, Wang HE, Liu RS, Teng MC, Yen CC, Agnihotri S, Ternamian C, Jones C, Zadeh G, Rutka J, Hawkins C, Filipek I, Drogosiewicz M, Perek-Polnik M, Swieszkowska E, Baginska BD, Jurkiewicz E, Perek D, Kuehn A, Falkenstein F, Wolff J, Kwiecien R, Pietsch T, Gnekow A, Kramm C, Brooks MD, Jackson E, Piwnica-Worms D, Mitra RD, Rubin JB, Liu XY, Korshunov A, Schwartzentruber J, Jones DTW, Pfaff E, Sturm D, Fontebasso AM, Quang DAK, Albrecht S, Kool M, Dong Z, Siegel P, Von Diemling A, Faury D, Tabori U, Lichter P, Plass C, Majewski J, Pfister SM, Jabado N, Lulla R, Echevarria M, Alden T, DiPatri A, Tomita T, Goldman S, Fangusaro J, Qaddoumi I, Lin T, Merchant TE, Kocak M, Panandiker AP, Armstrong GT, Wetmore C, Gajjar A, Broniscer A, Gielen GH, Muehlen AZ, Kramm C, Pietsch T, Hubert C, Ding Y, Toledo C, Paddison P, Olson J, Nandhabalan M, Bjerke L, Bax D, Carvalho D, Bajrami I, Ashworth A, Lord C, Hargrave D, Reis R, Workman P, Jones C, Little S, Popov S, Jury A, Burford A, Doey L, Al-Sarraj S, Jurgensmeier J, Jones C, Carvalho D, Bjerke L, Bax D, Chen L, Kozarewa I, Baker S, Grundy R, Ashworth A, Lord C, Hargrave D, Reis R, Jones C, Bjerke L, Perryman L, Burford A, Bax D, Jury A, Popov S, Box G, Raynaud F, Hargrave D, Eccles S, Jones C, Viana-Pereira M, Pereira M, Burford A, Jury A, Popov S, Perryman L, Bax D, Forshew T, Tatevossian R, Sheer D, Pimental J, Pires M, Reis R, Jones C, Sarkar C, Jha P, Patrick IRP, Somasundaram K, Pathak P, Sharma MC, Suri V, Suri A, Gerges N, Haque T, Nantel A, Faury D, Jabado N, Lee C, Fotovati A, Triscott J, Chen J, Venugopal C, Singhal A, Dunham C, Kerr J, Verreault M, Yip S, Wakimoto H, Jones C, Jayanthan A, Narendran A, Singh S, Dunn S, Giraud G, Holm S, Gustavsson B, Van Gool S, Kizyma R, Kizyma Z, Dvornyak L, Kotsay B, Epari S, Sharma P, Gurav M, Gupta T, Shetty P, Moiyadi A, Kane S, Jalali R. HIGH GRADE GLIOMAS. Neuro Oncol 2012; 14:i56-i68. [PMCID: PMC3483348 DOI: 10.1093/neuonc/nos102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023] Open
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Ottaviani D, Lever E, Mao S, Christova R, Ogunkolade BW, Jones TA, Szary J, Aarum J, Mumin MA, Pieri CA, Krawetz SA, Sheer D. CTCF binds to sites in the major histocompatibility complex that are rapidly reconfigured in response to interferon-gamma. Nucleic Acids Res 2012; 40:5262-70. [PMID: 22367884 PMCID: PMC3384298 DOI: 10.1093/nar/gks158] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Activation of the major histocompatibility complex (MHC) by interferon-gamma (IFN−γ) is a fundamental step in the adaptive immune response to pathogens. Here, we show that reorganization of chromatin loop domains in the MHC is evident within the first 30 min of IFN−γ treatment of fibroblasts, and that further dynamic alterations occur up to 6 h. These very rapid changes occur at genomic sites which are occupied by CTCF and are close to IFN−γ-inducible MHC genes. Early responses to IFN−γ are thus initiated independently of CIITA, the master regulator of MHC class II genes and prepare the MHC for subsequent induction of transcription.
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Affiliation(s)
- Diego Ottaviani
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Newark St, London E1 2AT, UK
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Pavel H, Ajeawung N, Faure R, Poirier D, Kamnasaran D, Ajeawung N, Joshi H, Kamnasaran D, Poirier D, Ajeawung N, Kamnasaran D, Lun X, Zemp F, Sun B, Stechishin O, Luchman A, Kelly JJ, Weiss S, Hamilton MG, Cairncross G, Senger DL, Bell J, McFadden G, Forsyth PA, Tzeng SY, Guerrero-Cazares H, Martinez EE, Young NP, Sunshine JC, Quinones-Hinojosa A, Green JJ, Lei L, D'Amico R, Sisti J, Leung R, Sonabend AM, Guarnieri P, Rosenfeld SS, Bruce JN, Canoll P, Baichwal VR, Reeves L, Chad BL, Zavitz KH, Beelen AP, Mather GG, Carlson RO, Manton C, Chandra J, Keir ST, Reardon DA, Saling JR, Gray LS, Bigner DD, Friedman HS, Zhang J, Brun J, Ogbomo H, Zemp F, Wang Z, Stojdl DJ, Lun X, Forsyth PA, Kong LY, Hatiboglu MA, Wei J, Wang Y, McEnery KA, Fuller GN, Qiao W, Davies MA, Priebe W, Heimberger AB, Amendolara B, Gil O, Lei L, Ivkovic S, Bruce J, Canoll P, Rosenfeld S, Finniss S, Perlstein B, Miller C, Okhrimenko H, Kazimirsky G, Cazacu S, Lemke N, Brodie S, Rempel SA, Rosenblum M, Mikkelsen T, Margel S, Brodie C, Guvenc H, Demir H, Gupta S, Mazumder S, Ray-Chaundhury A, Li T, Li C, Nakano I, Rahman R, Rahman C, Smith S, Macarthur D, Rose F, Shakesheff K, Grundy RG, Brenner AJ, Goins B, Bao A, Miller J, Trevino A, Zuniga R, Phillips WT, Gilg AG, Bowers KG, Toole BP, Maria BL, Leung GK, Sun S, Wong ST, Zhang XQ, Pu JK, Lui WM, Marino AM, Hussaini IM, Amos S, Simpson K, Redpath GT, Lyons C, Dipierro C, Grant GA, Wilson C, Salami S, Macaroni P, Li S, Park JY, Needham D, Bigner D, Dewhirst M, Ohlfest J, Gallardo J, Argawal S, Mittapalli R, Donelson R, Elmquist WF, Nicolaides T, Hariono S, Barkovich K, Hashizume R, Rowitch D, Weiss W, Sheer D, Baker S, Paugh B, Waldman T, Li H, Jones C, Forshew T, James D, Caroline H, Patrick R, Katrin L, Karl F, Ghazaleh T, Michael W, Albrecht V, Thorsteinsdottir J, Wagner E, Tonn JC, Ogris M, Schichor C, Charest G, Paquette B, Sanche L, Mathieu D, Fortin D, Qi X, Cuttitta F, Chu Z, Celerier J, Pakradouni J, Rixe O, Hashizume R, Gragg A, Muller S, Banerjee A, Phillips J, Prados M, Haas-Kogan D, Gupta N, James D, Florence L, Gwendoline VG, Veronique M, Robert K, Agarwal S, Mittapalli RK, Cen L, Carlson BL, Elmquist WF, Sarkaria JN, Sengupta S, Weeraratne SD, Rallapalli S, Amani V, Pierre-Francois J, Teider N, Rotenberg A, Cook J, Pomeroy SL, Jenses F, Cho YJ, Hjouj M, Last D, Guez D, Daniels D, Lavee J, Rubinsky B, Mardor Y, Serwer LP, Noble CO, Michaud K, Drummond DC, Ozawa T, Zhou Y, Marks JD, Bankiewicz K, Park JW, James D, Wang W, Cho H, Weintraub M, Jhaveri N, Torres S, Petasis N, Schonthal AH, Louie SG, Hofman FM, Chen TC, Grada Z, Hegde M, Schaffer DR, Ghazi A, Byrd T, Dotti G, Wels W, Heslop HE, Gottschalk S, Baker M, Ahmed N, Hamblett KJ, Kozlosky CJ, Liu H, Siu S, Arora T, Retter MW, Matsuda K, Hill JS, Fanslow WC, Diaz RJ, Etame A, Meaghan O, Mainprize T, Smith C, Hynynen K, Rutka J, Pradarelli J, Yoo JY, Kaka A, Alvarez-Breckenridge C, Pan Q, Chiocca EA, Teknos T, Kaur B, Lee SY, Slagle-Webb B, Sheehan JM, Connor JR, Cote J, Lepage M, Gobeil F, Fortin D, Kleijn A, Balvers R, Kloezeman J, Dirven C, Lamfers M, Leenstra S, See W, Tan IL, Nicolaides T, Pieper R, Jiang H, White E, Rios-Vicil CI, Yung WKA, Gomez-Manzano C, Fueyo J, Zemp FJ, McKenzie BA, Lun X, McFadden G, Forsyth PA, Mueller S, Yang X, Hashizume R, Gragg A, Smirnov I, Prados M, James DC, Phillips JJ, Berger MS, Rowitch DH, Gupta N, Haas-Kogan DH, D'Amico R, Lei L, Kennedy B, Rosenfeld SS, Canoll P, Bruce JN, Gopalakrishnan V, Das C, Taylor P, Kommagani R, Su X, Aguilera D, Thomas A, Wolff J, Flores E, Kadakia M, Alkins R, Broderson P, Sodhi R, Hynynen K, Chung SA, McDonald KL, Shen H, Day BW, Stringer BW, Johns T, Decollogne S, Teo C, Hogg PJ, Dilda PJ, Patel TR, Zhou J, Piepmeier JM, Saltzman WM, Vogelbaum MA, Agarwal S, Manchanda P, Ohlfest JR, Elmquist WF, Kitange GJ, Mladek AC, Carlson BL, Schroeder MA, Pokorny JL, Sarkaria JN, Ogbomo H, Lun X, Zhang J, McFadden G, Mody C, Forsyth P, Dasgupta T, Yang X, Hashizume R, Gragg A, Prados M, Nicolaides T, James CD, Haas-Kogan D, Madhankumar AB, Webb BS, Park A, Harbaugh K, Sheehan J, Connor JR. PRECLINICAL EXPERIMENTAL THERAPEUTICS AND PHARMACOLOGY. Neuro Oncol 2011. [DOI: 10.1093/neuonc/nor158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ammoun S, Zhou L, Barczyk M, Hilton D, Hafizi S, Hanemann C, Lehnus KS, Donovan LK, Pilkington GJ, An Q, Anderson IA, Thomson S, Bailey M, Lekka E, Law J, Davis C, Banfill K, Loughrey C, Hatfield P, Bax D, Elliott R, Bishop R, Taylor K, Marshall L, Gaspar N, Viana-Pereira M, Reis R, Renshaw J, Ashworth A, Lord C, Jones C, Bellamy C, Shaw L, Alder J, Shorrocks A, Lea R, Birks S, Burnet M, Pilkington G, Bruch JD, Ho J, Watts C, Price SJ, Camp S, Apostolopoulos V, Mehta A, Roncaroli F, Nandi D, Clark B, Mackinnon M, MacLeod N, Stewart W, Chalmers A, Cole A, Hanna G, Bailie K, Conkey D, Harney J, Darlow C, Chapman S, Mohsen L, Price S, Donovan L, Birks S, Pilkington G, Dyer H, Lord H, Fletcher K, das Nair R, MacNiven J, Basu S, Byrne P, Glancz L, Critchley G, Grech-Sollars M, Saunders D, Phipps K, Clayden J, Clark C, Greco A, Acquati S, Marino S, Hammouche S, Wilkins SP, Smith T, Brodbelt A, Hammouche S, Clark S, Wong AHL, Eldridge P, Farah JO, Ho J, Bruch J, Watts C, Price S, Lamb G, Smith S, James A, Glegg M, Jeffcote T, Boulos S, Robbins P, Knuckey N, Banigo A, Brodbelt AR, Jenkinson MD, Jeyapalan JN, Mumin MA, Forshew T, Lawson AR, Tatevossian RG, Jacques TS, Sheer D, Kilday J, Wright K, Leavy S, Lowe J, Schwalbe E, Clifford S, Gilbertson R, Coyle B, Grundy R, Kinsella P, Clynes M, Amberger-Murphy V, Barron N, Lambert SR, Jones D, Pearson D, Ichimura I, Collins V, Steele L, Sinha P, Chumas P, Tyler J, Ogawa D, Chiocca E, DeLay M, Bronisz A, Nowicki M, Godlewski J, Lawler S, Lee MK, Javadpour M, Jenkinson MD, Lekka E, Abel P, Dawson T, Lea B, Davis C, Lim CSK, Grundy PL, Pendleton M, Lord H, Mackinnon M, Williamson A, James A, Stewart W, Clark B, Chalmers A, Merve A, Zhang X, Marino S, Miller S, Rogers HA, Lyon P, Rand V, Adamowicz-Brice M, Clifford SC, Hayden JT, Dyer S, Pfister S, Korshunov A, Brundler MA, Lowe J, Coyle B, Grundy RG, Nankivell M, Mulvenna P, Barton R, Wilson P, Faivre-Finn C, Pugh C, Langley R, Ngoga D, Tennant D, Williams A, Moss P, Cruickshank G, Owusu-Agyemang K, Bell S, Stewart W, St.George J, Piccirillo SG, Watts C, Qadri S, Pirola E, Jenkinson M, Brodbelt A, Rahman R, Rahman C, Smith S, MacArthur D, Rose F, Shakesheff K, Grundy R, Carroll C, Watson P, Hawkins M, Spoudeas H, Walker D, Holland T, Ring H, Rooney A, McNamara S, Mackinnon M, Fraser M, Rampling R, Carson A, Grant R, Royds J, Al Nadaf S, Ahn A, Chen YJ, Wiles A, Jellinek D, Braithwaite A, Baguley B, MacFarlane M, Hung N, Slatter T, Rusbridge S, Walmsley N, Griffiths S, Wilford P, Rees J, Ryan D, Watts C, Liu P, Galavotti S, Shaked-Rabi M, Tulchinsky E, Brandner S, Jones C, Salomoni P, Schulte A, Gunther HS, Zapf S, Riethdorf S, Westphal M, Lamszus K, Selvanathan SK, Hammouche S, Salminen HJ, Jenkinson MD, Setua S, Watts C, Welland ME, Shevtsov M, Khachatryan W, Kim A, Samochernych K, Pozdnyakov A, Guzhova IV, Romanova IV, Margulis B, Smith S, Rahman R, Rahman C, Barrow J, Macarthur D, Rose F, Grundy R, Smith S, Long A, Barrow J, Macarthur D, Coyle B, Grundy R, Maherally Z, Smith JR, Dickson L, Pilkington GJ, Prabhu S, Harris F, Lea R, Snape TJ, Sussman M, Wilne S, Whitehouse W, Chow G, Liu JF, Walker D, Snape T, Karakoula A, Rowther F, Warr T, Williamson A, Mackinnon M, Zisakis A, Varsos V, Panteli A, Karypidou O, Zampethanis A, Fotovati A, Abu-Ali S, Wang PS, Deleyrolle L, Lee C, Triscott J, Chen JY, Franciosi S, Nakamura Y, Sugita Y, Uchiumi T, Kuwano M, Leavitt BR, Singh SK, Jury A, Jones C, Wakimoto H, Reynolds BA, Pallen CJ, Dunn SE, Shepherd S, Scott S, Bowyer D, Wallace L, Hacking B, Mohsen L, Jena R, Gillard J, Price S, Lee C, Fotovati A, Verraeult M, Wakimoto H, Reynolds B, Dunham C, Bally M, Hukin J, Singhal S, Singh S, Dunn S. Abstracts from the 2011 BNOS Conference, June 29 - July 1, 2011, Homerton College, Cambridge. Neuro Oncol 2011. [DOI: 10.1093/neuonc/nor144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Jones TA, Ogunkolade BW, Szary J, Aarum J, Mumin MA, Patel S, Pieri CA, Sheer D. Widespread expression of BORIS/CTCFL in normal and cancer cells. PLoS One 2011; 6:e22399. [PMID: 21811597 PMCID: PMC3139640 DOI: 10.1371/journal.pone.0022399] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [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: 03/18/2011] [Accepted: 06/21/2011] [Indexed: 01/23/2023] Open
Abstract
BORIS (CTCFL) is the paralog of CTCF (CCCTC-binding factor; NM_006565), a ubiquitously expressed DNA-binding protein with diverse roles in gene expression and chromatin organisation. BORIS and CTCF have virtually identical zinc finger domains, yet display major differences in their respective C- and N-terminal regions. Unlike CTCF, BORIS expression has been reported only in the testis and certain malignancies, leading to its classification as a “cancer-testis” antigen. However, the expression pattern of BORIS is both a significant and unresolved question in the field of DNA binding proteins. Here, we identify BORIS in the cytoplasm and nucleus of a wide range of normal and cancer cells. We compare the localization of CTCF and BORIS in the nucleus and demonstrate enrichment of BORIS within the nucleolus, inside the nucleolin core structure and adjacent to fibrillarin in the dense fibrillar component. In contrast, CTCF is not enriched in the nucleolus. Live imaging of cells transiently transfected with GFP tagged BORIS confirmed the nucleolar accumulation of BORIS. While BORIS transcript levels are low compared to CTCF, its protein levels are readily detectable. These findings show that BORIS expression is more widespread than previously believed, and suggest a role for BORIS in nucleolar function.
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Affiliation(s)
- Tania A. Jones
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Babatunji W. Ogunkolade
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Jaroslaw Szary
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Johan Aarum
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Muhammad A. Mumin
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Shyam Patel
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Christopher A. Pieri
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Denise Sheer
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
- * E-mail:
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Lawson ARJ, Hindley GFL, Forshew T, Tatevossian RG, Jamie GA, Kelly GP, Neale GA, Ma J, Jones TA, Ellison DW, Sheer D. RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology. Genome Res 2011; 21:505-14. [PMID: 21393386 DOI: 10.1101/gr.115782.110] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Gene fusions involving members of the RAF family of protein kinases have recently been identified as characteristic aberrations of low-grade astrocytomas, the most common tumors of the central nervous system in children. While it has been shown that these fusions cause constitutive activation of the ERK/MAPK pathway, very little is known about their formation. Here, we present a detailed analysis of RAF gene fusion breakpoints from a well-characterized cohort of 43 low-grade astrocytomas. Our findings show that the rearrangements that generate these RAF gene fusions may be simple or complex and that both inserted nucleotides and microhomology are common at the DNA breakpoints. Furthermore, we identify novel enrichment of microhomologous sequences in the regions immediately flanking the breakpoints. We thus provide evidence that the tandem duplications responsible for these fusions are generated by microhomology-mediated break-induced replication (MMBIR). Although MMBIR has previously been implicated in the pathogenesis of other diseases and the evolution of eukaryotic genomes, we demonstrate here that the proposed details of MMBIR are consistent with a recurrent rearrangement in cancer. Our analysis of repetitive elements, Z-DNA and sequence motifs in the fusion partners identified significant enrichment of the human minisatellite conserved sequence/χ-like element at one side of the breakpoint. Therefore, in addition to furthering our understanding of low-grade astrocytomas, this study provides insights into the molecular mechanistic details of MMBIR and the sequence of events that occur in the formation of genomic rearrangements.
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Affiliation(s)
- Andrew R J Lawson
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London, United Kingdom
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Tatevossian RG, Tang B, Dalton J, Forshew T, Lawson AR, Ma J, Neale G, Shurtleff SA, Bailey S, Gajjar A, Baker SJ, Sheer D, Ellison DW. MYB upregulation and genetic aberrations in a subset of pediatric low-grade gliomas. Acta Neuropathol 2010; 120:731-43. [PMID: 21046410 DOI: 10.1007/s00401-010-0763-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [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: 09/21/2010] [Revised: 10/16/2010] [Accepted: 10/19/2010] [Indexed: 12/18/2022]
Abstract
Recent studies of genetic abnormalities in pediatric low-grade gliomas (LGGs) have focused on activation of the ERK/MAPK pathway by KIAA1549-BRAF gene fusions in the majority of pilocytic astrocytomas (PAs) and by rare mutations in elements of the pathway across histopathologically diverse LGGs. This study reports that MYB, an oncogene not previously implicated in gliomagenesis, is activated in a diverse subset of pediatric LGGs. The study cohort comprised 57 pediatric LGGs and a comparative cohort of 59 pediatric high-grade gliomas (HGGs). The LGG cohort included 34 PAs and 23 diffuse gliomas; fibrillary astrocytomas (n = 14), oligodendroglial tumors (n = 7), and angiocentric gliomas (n = 2). MYB copy number abnormalities were disclosed using Affymetrix 6.0 SNP arrays and confirmed using interphase fluorescence in situ hybridization. Novel MYB amplifications that upregulate MYB RNA and protein expression were demonstrated in 2/14 diffuse astrocytomas. In addition, focal deletion of the terminal region of MYB was seen in 1 of 2 angiocentric gliomas (AGs). Increased expression of MYB was demonstrated by quantitative RT-PCR and immunohistochemistry. MYB upregulation at the protein level was demonstrated in a proportion of diffuse LGGs (60%), pilocytic astrocytomas (41%), and HGGs (19%), but abnormalities at the genomic level were only a feature of diffuse gliomas. Our data suggest that MYB may have a role in a subset of pediatric gliomas, through a variety of mechanisms in addition to MYB amplification and deletion.
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Affiliation(s)
- Ruth G Tatevossian
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Lawson ARJ, Tatevossian RG, Phipps KP, Picker SR, Michalski A, Sheer D, Jacques TS, Forshew T. RAF gene fusions are specific to pilocytic astrocytoma in a broad paediatric brain tumour cohort. Acta Neuropathol 2010; 120:271-3. [PMID: 20454969 DOI: 10.1007/s00401-010-0693-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 04/29/2010] [Accepted: 04/29/2010] [Indexed: 11/24/2022]
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Reynolds LE, Watson AR, Baker M, Jones TA, D’Amico G, Robinson SD, Joffre C, Garrido-Urbani S, Rodriguez-Manzaneque JC, Martino-Echarri E, Aurrand-Lions M, Sheer D, Dagna-Bricarelli F, Nizetic D, McCabe CJ, Turnell AS, Kermorgant S, Imhof BA, Adams RH, Fisher EMC, Tybulewicz VLJ, Hart IR, Hodivala-Dilke KM. Erratum: Tumour angiogenesis is reduced in the Tc1 mouse model of Down’s syndrome. Nature 2010. [DOI: 10.1038/nature09281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
The functional significance of changes in nuclear structure and organization in transformed cells remains one of the most enigmatic questions in cancer biology. In this review, we discuss relationships between nuclear organization and transcription in terms of the three-dimensional arrangement of genes in the interphase cancer nucleus and the regulatory functions of nuclear matrix proteins. We also analyse the role of nuclear topology in the generation of gene fusions. We speculate that this type of multi-layered analysis will one day provide a framework for a more comprehensive understanding of the genetic origins of cancer and the identification of new therapeutic targets.
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Affiliation(s)
- Elliott Lever
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
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Tatevossian RG, Lawson ARJ, Forshew T, Hindley GFL, Ellison DW, Sheer D. MAPK pathway activation and the origins of pediatric low-grade astrocytomas. J Cell Physiol 2010; 222:509-14. [PMID: 19937730 DOI: 10.1002/jcp.21978] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Low-grade astrocytomas (LGAs) are the most common type of brain tumor in children. Until recently, very little was known about the underlying biology and molecular genetics of these tumors. However, within the past year a number of studies have shown that the MAPK pathway is constitutively activated in a high proportion of LGAs. Several genetic aberrations which generate this deregulation of the MAPK pathway have been identified, most notably gene fusions between KIAA1549 and BRAF. In this review we summarize these findings, discuss how these gene fusions may arise and consider possible implications for diagnosis and treatment.
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Affiliation(s)
- Ruth G Tatevossian
- Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, London, UK
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Forshew T, Tatevossian RG, Lawson ARJ, Ma J, Neale G, Ogunkolade BW, Jones TA, Aarum J, Dalton J, Bailey S, Chaplin T, Carter RL, Gajjar A, Broniscer A, Young BD, Ellison DW, Sheer D. Activation of the ERK/MAPK pathway: a signature genetic defect in posterior fossa pilocytic astrocytomas. J Pathol 2009; 218:172-81. [PMID: 19373855 DOI: 10.1002/path.2558] [Citation(s) in RCA: 216] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We report genetic aberrations that activate the ERK/MAP kinase pathway in 100% of posterior fossa pilocytic astrocytomas, with a high frequency of gene fusions between KIAA1549 and BRAF among these tumours. These fusions were identified from analysis of focal copy number gains at 7q34, detected using Affymetrix 250K and 6.0 SNP arrays. PCR and sequencing confirmed the presence of five KIAA1549-BRAF fusion variants, along with a single fusion between SRGAP3 and RAF1. The resulting fusion genes lack the auto-inhibitory domains of BRAF and RAF1, which are replaced in-frame by the beginning of KIAA1549 and SRGAP3, respectively, conferring constitutive kinase activity. An activating mutation of KRAS was identified in the single pilocytic astrocytoma without a BRAF or RAF1 fusion. Further fusions and activating mutations in BRAF were identified in 28% of grade II astrocytomas, highlighting the importance of the ERK/MAP kinase pathway in the development of paediatric low-grade gliomas.
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Affiliation(s)
- Tim Forshew
- Neuroscience Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Institute of Cell and Molecular Science, London, UK
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Bax DA, Little SE, Gaspar N, Perryman L, Marshall L, Viana-Pereira M, Jones TA, Williams RD, Grigoriadis A, Vassal G, Workman P, Sheer D, Reis RM, Pearson ADJ, Hargrave D, Jones C. Molecular and phenotypic characterisation of paediatric glioma cell lines as models for preclinical drug development. PLoS One 2009; 4:e5209. [PMID: 19365568 PMCID: PMC2666263 DOI: 10.1371/journal.pone.0005209] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [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: 01/13/2009] [Accepted: 03/19/2009] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Although paediatric high grade gliomas resemble their adult counterparts in many ways, there appear to be distinct clinical and biological differences. One important factor hampering the development of new targeted therapies is the relative lack of cell lines derived from childhood glioma patients, as it is unclear whether the well-established adult lines commonly used are representative of the underlying molecular genetics of childhood tumours. We have carried out a detailed molecular and phenotypic characterisation of a series of paediatric high grade glioma cell lines in comparison to routinely used adult lines. PRINCIPAL FINDINGS All lines proliferate as adherent monolayers and express glial markers. Copy number profiling revealed complex genomes including amplification and deletions of genes known to be pivotal in core glioblastoma signalling pathways. Expression profiling identified 93 differentially expressed genes which were able to distinguish between the adult and paediatric high grade cell lines, including a number of kinases and co-ordinated sets of genes associated with DNA integrity and the immune response. SIGNIFICANCE These data demonstrate that glioma cell lines derived from paediatric patients show key molecular differences to those from adults, some of which are well known, whilst others may provide novel targets for evaluation in primary tumours. We thus provide the rationale and demonstrate the practicability of using paediatric glioma cell lines for preclinical and mechanistic studies.
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Affiliation(s)
- Dorine A. Bax
- Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Suzanne E. Little
- Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Nathalie Gaspar
- Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Sutton, United Kingdom
- Pharmacology and New Treatments of Cancer, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Lara Perryman
- Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Lynley Marshall
- Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Sutton, United Kingdom
- Paediatric Oncology, The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Marta Viana-Pereira
- Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom
- Life and Health Science Research Institute (ICVS), Universidade do Minho, Braga, Portugal
| | - Tania A. Jones
- Neuroscience Centre, Institute of Cell and Molecular Science, Bart's and The London School of Medicine & Dentistry, London, United Kingdom
| | - Richard D. Williams
- Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Anita Grigoriadis
- Breakthrough Breast Cancer Unit, Guy's Hospital, London, United Kingdom
| | - Gilles Vassal
- Pharmacology and New Treatments of Cancer, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Paul Workman
- Pharmacology and New Treatments of Cancer, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Denise Sheer
- Neuroscience Centre, Institute of Cell and Molecular Science, Bart's and The London School of Medicine & Dentistry, London, United Kingdom
| | - Rui M. Reis
- Life and Health Science Research Institute (ICVS), Universidade do Minho, Braga, Portugal
| | - Andrew D. J. Pearson
- Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom
- Paediatric Oncology, The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Darren Hargrave
- Paediatric Oncology, The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Chris Jones
- Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom
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Ottaviani D, Lever E, Mitter R, Jones T, Forshew T, Christova R, Tomazou EM, Rakyan VK, Krawetz SA, Platts AE, Segarane B, Beck S, Sheer D. Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex. Genome Res 2008; 18:1778-86. [PMID: 18849521 PMCID: PMC2577859 DOI: 10.1101/gr.082313.108] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The folding of chromatin into topologically constrained loop domains is essential for genomic function. We have identified genomic anchors that define the organization of chromatin loop domains across the human major histocompatibility complex (MHC). This locus contains critical genes for immunity and is associated with more diseases than any other region of the genome. Classical MHC genes are expressed in a cell type-specific pattern and can be induced by cytokines such as interferon-gamma (IFNG). Transcriptional activation of the MHC was associated with a reconfiguration of chromatin architecture resulting from the formation of additional genomic anchors. These findings suggest that the dynamic arrangement of genomic anchors and loops plays a role in transcriptional regulation.
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Affiliation(s)
- Diego Ottaviani
- Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, United Kingdom
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Tomazou EM, Rakyan VK, Lefebvre G, Andrews R, Ellis P, Jackson DK, Langford C, Francis MD, Bäckdahl L, Miretti M, Coggill P, Ottaviani D, Sheer D, Murrell A, Beck S. Generation of a genomic tiling array of the human major histocompatibility complex (MHC) and its application for DNA methylation analysis. BMC Med Genomics 2008; 1:19. [PMID: 18513384 PMCID: PMC2430202 DOI: 10.1186/1755-8794-1-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 05/30/2008] [Indexed: 12/25/2022] Open
Abstract
Background The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), array comparative genomic hybridization (aCGH) and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs). Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.
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Affiliation(s)
- Eleni M Tomazou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Abstract
Although the principles governing chromosomal architecture are largely unresolved, there is evidence that higher-order chromatin folding is mediated by the anchoring of specific DNA sequences to the nuclear matrix. These genome anchors are also crucial regulators of gene expression and DNA replication, and play a role in pathogenesis.
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Affiliation(s)
- Diego Ottaviani
- Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, UK
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Christova R, Jones T, Wu PJ, Bolzer A, Costa-Pereira AP, Watling D, Kerr IM, Sheer D. P-STAT1 mediates higher-order chromatin remodelling of the human MHC in response to IFNgamma. J Cell Sci 2007; 120:3262-70. [PMID: 17726060 DOI: 10.1242/jcs.012328] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Transcriptional activation of the major histocompatibility complex (MHC) by IFNgamma is a key step in cell-mediated immunity. At an early stage of IFNgamma induction, chromatin carrying the entire MHC locus loops out from the chromosome 6 territory. We show here that JAK/STAT signalling triggers this higher-order chromatin remodelling and the entire MHC locus becomes decondensed prior to transcriptional activation of the classical HLA class II genes. A single point mutation of STAT1 that prevents phosphorylation is sufficient to abolish chromatin remodelling, thus establishing a direct link between the JAK/STAT signalling pathway and human chromatin architecture. The onset of chromatin remodelling corresponds with the binding of activated STAT1 and the chromatin remodelling enzyme BRG1 at specific sites within the MHC, and is followed by RNA-polymerase recruitment and histone hyperacetylation. We propose that the higher-order chromatin remodelling of the MHC locus is an essential step to generate a transcriptionally permissive chromatin environment for subsequent activation of classical HLA genes.
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Affiliation(s)
- Rossitza Christova
- Human Cytogenetics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3PX, UK
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Donev R, Newall A, Thome J, Sheer D. A role for SC35 and hnRNPA1 in the determination of amyloid precursor protein isoforms. Mol Psychiatry 2007; 12:681-90. [PMID: 17353911 PMCID: PMC2684093 DOI: 10.1038/sj.mp.4001971] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [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: 06/19/2006] [Revised: 12/11/2006] [Accepted: 01/09/2007] [Indexed: 11/09/2022]
Abstract
The beta-amyloid peptide (Abeta) that accumulates in senile plaques in Alzheimer's disease is formed by cleavage of the amyloid precursor protein (APP). The APP gene has several intronic Alu elements inserted in either the sense or antisense orientation. In this study, we demonstrate that binding of SC35 and hnRNPA1 to Alu elements on either side of exon 7 in the transcribed pre-mRNA is involved in alternative splicing of APP exons 7 and 8. Neuronal cells transfected with the full-length form of APP secrete higher levels of Abeta than cells transfected with the APP695 isoform lacking exons 7 and 8. Finally, we show that treatment of neuronal cells with estradiol results in increased expression of APP695, SC35 and hnRNPA1, and lowers the level of secreted Abeta. An understanding of the regulation of splicing of APP may lead to the identification of new targets for treating Alzheimer's disease.
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Affiliation(s)
- Rossen Donev
- Human Cytogenetics Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
- Department of Medical Biochemistry & Immunology, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Alistair Newall
- Human Cytogenetics Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
| | - Johannes Thome
- Molecular Psychiatry and Psychopharmacology, School of Medicine, University of Wales Swansea, Grove Building, Singleton Park, Swansea, SA2 8PP, UK
| | - Denise Sheer
- Human Cytogenetics Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London WC2A 3PX, UK
- Neuroscience Centre, Institute of Cell and Molecular Science, Queen Mary School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, UK
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Mulholland PJ, Fiegler H, Mazzanti C, Gorman P, Sasieni P, Adams J, Jones TA, Babbage JW, Vatcheva R, Ichimura K, East P, Poullikas C, Collins VP, Carter NP, Tomlinson IPM, Sheer D. Genomic profiling identifies discrete deletions associated with translocations in glioblastoma multiforme. Cell Cycle 2006; 5:783-91. [PMID: 16582634 DOI: 10.4161/cc.5.7.2631] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [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] [Indexed: 11/19/2022] Open
Abstract
Glioblastoma multiforme is the most common tumor arising in the central nervous system. Patients with these tumors have limited treatment options and their disease is invariably fatal. Molecularly targeted agents offer the potential to improve patient treatment, however the use of these will require a fuller understanding of the genetic changes in these complex tumors. In this study, we identify copy number changes in a series of glioblastoma multiforme tumors and cell lines by applying high-resolution microarray comparative genomic hybridization. Molecular cytogenetic characterization of the cell lines revealed that copy number changes define translocation breakpoints. We focused on chromosome 6 and further characterized three regions of copy number change associated with translocations including a discrete deletion involving IGF2R, PARK2, PACRG and QKI and an unbalanced translocation involving POLH, GTPBP2 and PTPRZ1.
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45
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Abstract
We purified a 68-kDa protein from the mouse nuclear matrix using ion exchange and affinity chromatography. Column fractions were tested for specific binding to mouse minor satellite DNA using a gel mobility shift assay. The protein was identified by mass spectrometry as RNA helicase P68. In fixed cells, P68 was found to shuttle in and out of SC35 domains, forming fibres and granules in a cell-cycle dependent manner. Analysis of the P68 sequence revealed a short potential coiled-coil domain that might be involved in the formation of P68 fibres. Contacts between centromeres and P68 granules were observed during all phases of the cycle but they were most prominent in mitosis. At this stage, P68 was found in both the centromeric regions and the connections between chromosomes. Direct interaction of P68/DEAD box RNA helicase with satellite DNAs in vitro has not been demonstrated for any other members of the RNA helicase family.
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Affiliation(s)
- Natella Enukashvily
- Cell Cultures Department, Institute of Cytology, Tikhoretsky, 4, St Petersburg, 194064, Russia.
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46
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Wang J, Shiels C, Sasieni P, Wu PJ, Islam SA, Freemont PS, Sheer D. Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions. ACTA ACUST UNITED AC 2004; 164:515-26. [PMID: 14970191 PMCID: PMC2171989 DOI: 10.1083/jcb.200305142] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.3] [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] [Indexed: 12/12/2022]
Abstract
The promyelocytic leukemia (PML) protein is aggregated into nuclear bodies that are associated with diverse nuclear processes. Here, we report that the distance between a locus and its nearest PML body correlates with the transcriptional activity and gene density around the locus. Genes on the active X chromosome are more significantly associated with PML bodies than their silenced homologues on the inactive X chromosome. We also found that a histone-encoding gene cluster, which is transcribed only in S-phase, is more strongly associated with PML bodies in S-phase than in G0/G1 phase of the cell cycle. However, visualization of specific RNA transcripts for several genes showed that PML bodies were not themselves sites of transcription for these genes. Furthermore, knock-down of PML bodies by RNA interference did not preferentially change the expression of genes closely associated with PML bodies. We propose that PML bodies form in nuclear compartments of high transcriptional activity, but they do not directly regulate transcription of genes in these compartments.
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Affiliation(s)
- Jayson Wang
- Human Cytogenetics Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, England, UK
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47
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Donev R, Horton R, Beck S, Doneva T, Vatcheva R, Bowen WR, Sheer D. Recruitment of heterogeneous nuclear ribonucleoprotein A1 in vivo to the LMP/TAP region of the major histocompatibility complex. J Biol Chem 2003; 278:5214-26. [PMID: 12435746 DOI: 10.1074/jbc.m206621200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [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] [Indexed: 11/06/2022] Open
Abstract
Sequences containing the matrix recognition signature were identified adjacent to the LMP/TAP gene cluster in the human and mouse major histocompatibility complex class II region. These sequences were shown to function as nuclear matrix attachment regions (MARs). Three of the five human MARs and the single mouse MAR recruit heterogeneous nuclear ribonucleoprotein A1 (hnRNP-A1) in vivo during transcriptional up-regulation of the major histocompatibility complex class II genes. The timing of this recruitment correlates with a rise in mature TAP1 mRNA. Two of the human MARs bind hnRNP-A1 in vitro directly within a 35-bp sequence that shows over 90% similarity to certain Alu repeat sequences. This study shows that MARs recruit and bind hnRNP-A1 upon transcriptional up-regulation.
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Affiliation(s)
- Rossen Donev
- Human Cytogenetics Laboratory, Cancer Research, UK London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, United Kingdom
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48
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Abstract
The heterogeneous nuclear ribonucleoprotein A1 (hnRNP-A1) is known as an RNA- and single-stranded DNA-binding protein involved in alternative splicing of mRNA, RNA transport and maintenance of chromosome telomere length. In this study we tested whether this protein could bind directly to double-stranded DNA (dsDNA). Using PCR amplification of target DNA-sequences from human chromosome 11q13 followed by their incubation with hnRNP-A1 and atomic force microscopy (AFM) of the DNA/protein complexes, we found that this protein bound to DNA within a 36 bp sequence. These results were confirmed by electrophoretic mobility shift assay (EMSA). This sequence was found widely dispersed throughout the genome. There is no overlap between the 36 bp sequence and known target sequences in RNA for binding binRNP-A1.
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Affiliation(s)
- Rossen M Donev
- Human Cytogenetics Laboratory, Cancer Research UK London Research Institute, UK
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Williams RRE, Broad S, Sheer D, Ragoussis J. Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei. Exp Cell Res 2002; 272:163-75. [PMID: 11777341 DOI: 10.1006/excr.2001.5400] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.3] [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] [Indexed: 01/05/2023]
Abstract
The epidermal differentiation complex (EDC) at 1q21 is host to many structurally and functionally related genes coding for proteins involved in the differentiation process of keratinocytes. The grouping together of these genes which share spatial and temporal expression and interrelated functions is a remarkable genomic feature which has led to suggestions that the region may have a coordinated transcription control mechanism. With the growing awareness that the organization of the genome within the interphase nucleus is relevant to transcriptional activity, we have investigated the spatial organization of the EDC in the nuclei of keratinocytes, where the EDC genes are highly expressed, and lymphoblasts, where they are silent. Using 2D and 3D FISH we find that in keratinocyte nuclei the EDC is frequently positioned external to the chromosome 1 territory compared to lymphoblasts where the EDC more often adopts a peripheral or internal location. It has been previously shown that the MHC region can extend from the chromosome 6 territory in relation to transcriptional activity. This study of the EDC thus provides a further example of a gene-dense complex capable of assuming extraterritorial positioning in relation to cell type/transcription status.
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Affiliation(s)
- Ruth R E Williams
- Genomics Laboratory, King's College London, London, SE1 9RT, England, UK.
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Shiels C, Islam SA, Vatcheva R, Sasieni P, Sternberg MJ, Freemont PS, Sheer D. PML bodies associate specifically with the MHC gene cluster in interphase nuclei. J Cell Sci 2001; 114:3705-16. [PMID: 11707522 DOI: 10.1242/jcs.114.20.3705] [Citation(s) in RCA: 24] [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] [Indexed: 12/12/2022] Open
Abstract
Promyelocytic leukemia (PML) bodies are nuclear multi-protein domains. The observations that viruses transcribe their genomes adjacent to PML bodies and that nascent RNA accumulates at their periphery suggest that PML bodies function in transcription. We have used immuno-FISH in primary human fibroblasts to determine the 3D spatial organisation of gene-rich and gene-poor chromosomal regions relative to PML bodies. We find a highly non-random association of the gene-rich major histocompatibilty complex (MHC) on chromosome 6 with PML bodies. This association is specific for the centromeric end of the MHC and extends over a genomic region of at least 1.6 megabases. We also show that PML association is maintained when a subsection of this region is integrated into another chromosomal location. This is the first demonstration that PML bodies have specific chromosomal associations and supports a model for PML bodies as part of a functional nuclear compartment.
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Affiliation(s)
- C Shiels
- Human Cytogenetics Laboratory, Imperial Cancer Research Fund, London, WC2A 3PX, UK
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