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Wallis R, Bishop CL. Death-seq and ye shall find: A novel screening strategy for dying cells. Cell Metab 2023; 35:1675-1676. [PMID: 37793342 DOI: 10.1016/j.cmet.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023]
Abstract
Killing senescent cells to improve health-span holds great promise. However, screening for senescence-regulating genes and molecules is challenging because these cells do not proliferate. In this issue, Colville and Liu et al. develop Death-seq, a positive selection screening tool that overcomes this hurdle to offer broad genetic and pharmacological utility.
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Affiliation(s)
- Ryan Wallis
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Cleo L Bishop
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
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2
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Hughes BK, Wallis R, Bishop CL. Yearning for machine learning: applications for the classification and characterisation of senescence. Cell Tissue Res 2023; 394:1-16. [PMID: 37016180 PMCID: PMC10558380 DOI: 10.1007/s00441-023-03768-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/05/2023] [Indexed: 04/06/2023]
Abstract
Senescence is a widely appreciated tumour suppressive mechanism, which acts as a barrier to cancer development by arresting cell cycle progression in response to harmful stimuli. However, senescent cell accumulation becomes deleterious in aging and contributes to a wide range of age-related pathologies. Furthermore, senescence has beneficial roles and is associated with a growing list of normal physiological processes including wound healing and embryonic development. Therefore, the biological role of senescent cells has become increasingly nuanced and complex. The emergence of sophisticated, next-generation profiling technologies, such as single-cell RNA sequencing, has accelerated our understanding of the heterogeneity of senescence, with distinct final cell states emerging within models as well as between cell types and tissues. In order to explore data sets of increasing size and complexity, the senescence field has begun to employ machine learning (ML) methodologies to probe these intricacies. Most notably, ML has been used to aid the classification of cells as senescent, as well as to characterise the final senescence phenotypes. Here, we provide a background to the principles of ML tasks, as well as some of the most commonly used methodologies from both traditional and deep ML. We focus on the application of these within the context of senescence research, by addressing the utility of ML for the analysis of data from different laboratory technologies (microscopy, transcriptomics, proteomics, methylomics), as well as the potential within senolytic drug discovery. Together, we aim to highlight both the progress and potential for the application of ML within senescence research.
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Affiliation(s)
- Bethany K Hughes
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Ryan Wallis
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Cleo L Bishop
- Blizard Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
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3
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Wallis R, Milligan D, Hughes B, Mizen H, López-Domínguez JA, Eduputa U, Tyler EJ, Serrano M, Bishop CL. Senescence-associated morphological profiles (SAMPs): an image-based phenotypic profiling method for evaluating the inter and intra model heterogeneity of senescence. Aging (Albany NY) 2022; 14:4220-4246. [PMID: 35580013 PMCID: PMC9186762 DOI: 10.18632/aging.204072] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 11/13/2021] [Accepted: 04/22/2022] [Indexed: 01/10/2023]
Abstract
Senescence occurs in response to a number of damaging stimuli to limit oncogenic transformation and cancer development. As no single, universal senescence marker has been discovered, the confident classification of senescence induction requires the parallel assessment of a series of hallmarks. Therefore, there is a growing need for “first-pass” tools of senescence identification to streamline experimental workflows and complement conventional markers. Here, we utilise a high content, multidimensional phenotypic profiling-based approach, to assess the morphological profiles of senescent cells induced via a range of stimuli. In the context of senescence, we refer to these as senescence-associated morphological profiles (SAMPs), as they facilitate distinction between senescent and proliferating cells. The complexity of the profiles generated also allows exploration of the heterogeneity both between models of senescence and within an individual senescence model, providing a level of insight at the single cell level. Furthermore, we also demonstrate that these models are applicable to the assessment of senescence in vivo, which remains a key challenge for the field. Therefore, we believe SAMPs has the potential to serve as a useful addition in the repertoire of senescence researchers, either as a first-pass tool or as part of the established senescence hallmarks.
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Affiliation(s)
- Ryan Wallis
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Deborah Milligan
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Bethany Hughes
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Hannah Mizen
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - José Alberto López-Domínguez
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ugochim Eduputa
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eleanor J Tyler
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Cleo L Bishop
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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4
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Palmer A, Epton S, Crawley E, Straface M, Gammon L, Edgar MM, Xu Y, Elahi S, Chin-Aleong J, Martin JE, Bishop CL, Knowles CH, Sanger GJ. Expression of p16 Within Myenteric Neurons of the Aged Colon: A Potential Marker of Declining Function. Front Neurosci 2021; 15:747067. [PMID: 34690683 PMCID: PMC8529329 DOI: 10.3389/fnins.2021.747067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 07/26/2021] [Accepted: 09/14/2021] [Indexed: 01/31/2023] Open
Abstract
Human colonic neuromuscular functions decline among the elderly. The aim was to explore the involvement of senescence. A preliminary PCR study looked for age-dependent differences in expression of CDKN1A (encoding the senescence-related p21 protein) and CDKN2A (encoding p16 and p14) in human ascending and descending colon (without mucosa) from 39 (approximately 50: 50 male: female) adult (aged 27–60 years) and elderly donors (70–89 years). Other genes from different aging pathways (e.g., inflammation, oxidative stress, autophagy) and cell-types (e.g., neurons, neuron axonal transport) were also examined. Unlike CDKN1A, CDKN2A (using primers for p16 and p14 but not when using p14-specific primers) was upregulated in both regions of colon. Compared with the number of genes appearing to upregulate in association with temporal age, more genes positively associated with increased CDKN2A expression (respectively, 16 and five of 44 genes studied for ascending and descending colon). Confirmation of increased expression of CDKN2A was sought by immunostaining for p16 in the myenteric plexus of colon from 52 patients, using a semi-automated software protocol. The results showed increased staining not within the glial cells (S100 stained), but in the cytoplasm of myenteric nerve cell bodies (MAP2 stained, with identified nucleus) of ascending, but not descending colon of the elderly, and not in the cell nucleus of either region or age group (5,710 neurons analyzed: n = 12–14 for each group). It was concluded that increased p16 staining within the cytoplasm of myenteric nerve cell bodies of elderly ascending (but not descending) colon, suggests a region-dependent, post-mitotic cellular senescence-like activity, perhaps involved with aging of enteric neurons within the colon.
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Affiliation(s)
- Alexandra Palmer
- Center for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Sarah Epton
- Barts Health NHS Trust, Department of Colorectal Surgery and Pathology, The Royal London Hospital, London, United Kingdom
| | - Ellie Crawley
- Center for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Marilisa Straface
- Center for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Luke Gammon
- Center for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Meghan M Edgar
- Gastroenterology Drug Discovery Unit, Takeda Pharmaceuticals, San Diego, CA, United States
| | - Yichen Xu
- Center for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Shezan Elahi
- Center for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Joanne Chin-Aleong
- Barts Health NHS Trust, Department of Colorectal Surgery and Pathology, The Royal London Hospital, London, United Kingdom
| | - Joanne E Martin
- Center for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.,Barts Health NHS Trust, Department of Colorectal Surgery and Pathology, The Royal London Hospital, London, United Kingdom
| | - Cleo L Bishop
- Center for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.,Center for Inflammation and Therapeutic Innovation Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Charles H Knowles
- Center for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.,Barts Health NHS Trust, Department of Colorectal Surgery and Pathology, The Royal London Hospital, London, United Kingdom
| | - Gareth J Sanger
- Center for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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5
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Barkaway A, Rolas L, Joulia R, Bodkin J, Lenn T, Owen-Woods C, Reglero-Real N, Stein M, Vázquez-Martínez L, Girbl T, Poston RN, Golding M, Saleeb RS, Thiriot A, von Andrian UH, Duchene J, Voisin MB, Bishop CL, Voehringer D, Roers A, Rot A, Lämmermann T, Nourshargh S. Age-related changes in the local milieu of inflamed tissues cause aberrant neutrophil trafficking and subsequent remote organ damage. Immunity 2021; 54:1494-1510.e7. [PMID: 34033752 PMCID: PMC8284598 DOI: 10.1016/j.immuni.2021.04.025] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/11/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022]
Abstract
Aging is associated with dysregulated immune functions. Here, we investigated the impact of age on neutrophil diapedesis. Using confocal intravital microscopy, we found that in aged mice, neutrophils adhered to vascular endothelium in inflamed tissues but exhibited a high frequency of reverse transendothelial migration (rTEM). This retrograde breaching of the endothelium by neutrophils was governed by enhanced production of the chemokine CXCL1 from mast cells that localized at endothelial cell (EC) junctions. Increased EC expression of the atypical chemokine receptor 1 (ACKR1) supported this pro-inflammatory milieu in aged venules. Accumulation of CXCL1 caused desensitization of the chemokine receptor CXCR2 on neutrophils and loss of neutrophil directional motility within EC junctions. Fluorescent tracking revealed that in aged mice, neutrophils undergoing rTEM re-entered the circulation and disseminated to the lungs where they caused vascular leakage. Thus, neutrophils stemming from a local inflammatory site contribute to remote organ damage, with implication to the dysregulated systemic inflammation associated with aging.
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Affiliation(s)
- Anna Barkaway
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Loïc Rolas
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Régis Joulia
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jennifer Bodkin
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Tchern Lenn
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Charlotte Owen-Woods
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Natalia Reglero-Real
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Monja Stein
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Laura Vázquez-Martínez
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Tamara Girbl
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Robin N Poston
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Matthew Golding
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Rebecca S Saleeb
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Aude Thiriot
- Department of Immunology and HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, MA 02115, USA; The Ragon Institute of MGH, MIT and Harvard, Cambridge MA 02139, USA
| | - Ulrich H von Andrian
- Department of Immunology and HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, MA 02115, USA; The Ragon Institute of MGH, MIT and Harvard, Cambridge MA 02139, USA
| | - Johan Duchene
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, Munich 80336, Germany
| | - Mathieu-Benoit Voisin
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Cleo L Bishop
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - David Voehringer
- Department of Infection Biology, University Hospital Erlangen and Friedrich-Alexander University Erlangen-Nuremberg (FAU), Erlangen 91054, Germany
| | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden 01069, Germany
| | - Antal Rot
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; Centre for Inflammation and Therapeutic Innovation, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Tim Lämmermann
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Sussan Nourshargh
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; Centre for Inflammation and Therapeutic Innovation, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.
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6
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Tyler EJ, Gutierrez del Arroyo A, Hughes BK, Wallis R, Garbe JC, Stampfer MR, Koh J, Lowe R, Philpott MP, Bishop CL. Early growth response 2 (EGR2) is a novel regulator of the senescence programme. Aging Cell 2021; 20:e13318. [PMID: 33547862 PMCID: PMC7963333 DOI: 10.1111/acel.13318] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 10/03/2019] [Revised: 12/16/2020] [Accepted: 12/31/2020] [Indexed: 12/14/2022] Open
Abstract
Senescence, a state of stable growth arrest, plays an important role in ageing and age-related diseases in vivo. Although the INK4/ARF locus is known to be essential for senescence programmes, the key regulators driving p16 and ARF transcription remain largely underexplored. Using siRNA screening for modulators of the p16/pRB and ARF/p53/p21 pathways in deeply senescent human mammary epithelial cells (DS HMECs) and fibroblasts (DS HMFs), we identified EGR2 as a novel regulator of senescence. EGR2 expression is up-regulated during senescence, and its ablation by siRNA in DS HMECs and HMFs transiently reverses the senescent phenotype. We demonstrate that EGR2 activates the ARF and p16 promoters and directly binds to both the ARF and p16 promoters. Loss of EGR2 down-regulates p16 levels and increases the pool of p16- p21- 'reversed' cells in the population. Moreover, EGR2 overexpression is sufficient to induce senescence. Our data suggest that EGR2 is a direct transcriptional activator of the p16/pRB and ARF/p53/p21 pathways in senescence and a novel marker of senescence.
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Affiliation(s)
- Eleanor J. Tyler
- Blizard InstituteBarts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondonUK
| | - Ana Gutierrez del Arroyo
- Translational Medicine & TherapeuticsWilliam Harvey Research InstituteBarts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Bethany K. Hughes
- Blizard InstituteBarts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondonUK
| | - Ryan Wallis
- Blizard InstituteBarts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondonUK
| | - James C. Garbe
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Martha R. Stampfer
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Jim Koh
- Division of General SurgeryDepartment of SurgeryUCSFSan FranciscoCaliforniaUSA
| | - Robert Lowe
- Blizard InstituteBarts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondonUK
| | - Michael P. Philpott
- Blizard InstituteBarts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondonUK
| | - Cleo L. Bishop
- Blizard InstituteBarts and The London School of Medicine and Dentistry, Queen Mary University of LondonLondonUK
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7
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Wallis R, Josipovic N, Mizen H, Robles‐Tenorio A, Tyler EJ, Papantonis A, Bishop CL. Isolation methodology is essential to the evaluation of the extracellular vesicle component of the senescence-associated secretory phenotype. J Extracell Vesicles 2021; 10:e12041. [PMID: 33659050 PMCID: PMC7892802 DOI: 10.1002/jev2.12041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 09/03/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
A hallmark of senescence is the acquisition of an enhanced secretome comprising inflammatory mediators and tissue remodelling agents - the senescence-associated secretory phenotype (SASP). Through the SASP, senescent cells are hypothesised to contribute to both ageing and pathologies associated with age. Whilst soluble factors have been the most widely investigated components of the SASP, there is growing evidence that small extracellular vesicles (EVs) comprise functionally important constituents. Thus, dissecting the contribution of the soluble SASP from the vesicular component is crucial to elucidating the functional significance of senescent cell derived EVs. Here, we take advantage of a systematic proteomics based approach to determine that soluble SASP factors co-isolate with EVs following differential ultracentrifugation (dUC). We present size-exclusion chromatography (SEC) as a method for separation of the soluble and vesicular components of the senescent secretome and thus EV purification. Furthermore, we demonstrate that SEC EVs isolated from senescent cells contribute to non-cell autonomous paracrine senescence. Therefore, this work emphasises the requirement for methodological rigor due to the propensity of SASP components to co-isolate during dUC and provides a framework for future investigations of the vesicular component of the SASP.
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Affiliation(s)
- Ryan Wallis
- Blizard Institute of Cell and Molecular ScienceBarts and The London School of Medicine and DentistryLondonUK
| | - Natasa Josipovic
- Institute of PathologyUniversity Medical Centre GöttingenGöttingenGermany
| | - Hannah Mizen
- Blizard Institute of Cell and Molecular ScienceBarts and The London School of Medicine and DentistryLondonUK
| | - Arturo Robles‐Tenorio
- Blizard Institute of Cell and Molecular ScienceBarts and The London School of Medicine and DentistryLondonUK
| | - Eleanor J. Tyler
- Blizard Institute of Cell and Molecular ScienceBarts and The London School of Medicine and DentistryLondonUK
| | - Argyris Papantonis
- Institute of PathologyUniversity Medical Centre GöttingenGöttingenGermany
| | - Cleo L. Bishop
- Blizard Institute of Cell and Molecular ScienceBarts and The London School of Medicine and DentistryLondonUK
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8
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Almeida FV, Gammon L, Laly AC, Pundel OJ, Bishop CL, Connelly JT. High-Content Analysis of Cell Migration Dynamics within a Micropatterned Screening Platform. ACTA ACUST UNITED AC 2020; 3:e1900011. [PMID: 32648701 DOI: 10.1002/adbi.201900011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/31/2019] [Indexed: 01/04/2023]
Abstract
Cell migration is a fundamental biological process that is dynamically regulated by complex interactions between the microenvironment and intrinsic gene expression programs. Here, a high-throughput cell migration assay is developed using micropatterned and dynamically adhesive polymer brush substrates, which support highly precise and consistent control over cell-matrix interactions within a 96-well cell culture plate format. This system is combined with automated imaging and quantitation of both cell motility and organization of the F-actin cytoskeleton for high-content analysis of cell migration phenotypes. Using this platform to screen a library of 147 epigenetic inhibitors identifies a set of EZH2-specific compounds that promote cytoskeletal remodeling and accelerates keratinocyte migration through derepression of an epithelial to mesenchymal transition-like gene expression program. Together, these studies establish the high-throughput, micropatterned assay as a powerful tool for discovery of novel therapeutic targets and for dissecting complex gene-environment interactions involved in wound repair.
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Affiliation(s)
- Filipe V Almeida
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Luke Gammon
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ana C Laly
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Oscar J Pundel
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Cleo L Bishop
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - John T Connelly
- Centre for Cell Biology and Cutaneous Research, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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9
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Milligan DA, Tyler EJ, Bishop CL. Tissue engineering to better understand senescence: Organotypics come of age. Mech Ageing Dev 2020; 190:111261. [PMID: 32461142 PMCID: PMC7493709 DOI: 10.1016/j.mad.2020.111261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 05/04/2020] [Accepted: 05/08/2020] [Indexed: 12/01/2022]
Abstract
The recent advent of 'organs in a dish' has revolutionised the research landscape. These 3D culture systems have paved the way for translational, post genomics research by enabling scientists to model diseases in the laboratory, grow patient-derived organoids, and unite this technology with other cutting-edge methodologies such as drug discovery. Fields such as dermatology and neuroscience have revolutionised the development of robust 3D models, which faithfully recapitulate native physiology in vivo to provide important functional and mechanistic insights. These models have underpinned a rapid growth in the number of organs and myriad of human diseases that can be modelled in 3D, which currently includes breast, cerebral cortex, heart, intestine, kidney, liver, lung, neural tube, pancreas, prostate, skin and stomach, as well as patient derived tumours. However, so far, they have not yet been employed extensively in the study of fundamental cellular programmes such as senescence. Thus, tissue engineering and 3D culture offer an exciting opportunity to further understand the bright and dark sides of senescence in a more complex and physiologically relevant environment. Below, we will discuss previous approaches to investigating senescence and ageing using organotypic models, and some potential opportunities for future research.
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Affiliation(s)
- Deborah A Milligan
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, UK
| | - Eleanor J Tyler
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, UK
| | - Cleo L Bishop
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, UK.
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10
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Avelar RA, Ortega JG, Tacutu R, Tyler EJ, Bennett D, Binetti P, Budovsky A, Chatsirisupachai K, Johnson E, Murray A, Shields S, Tejada-Martinez D, Thornton D, Fraifeld VE, Bishop CL, de Magalhães JP. A multidimensional systems biology analysis of cellular senescence in aging and disease. Genome Biol 2020; 21:91. [PMID: 32264951 PMCID: PMC7333371 DOI: 10.1186/s13059-020-01990-9] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [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: 10/17/2019] [Accepted: 03/08/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of aging and has been linked to aging-related diseases. Many genes play a role in cellular senescence, yet a comprehensive understanding of its pathways is still lacking. RESULTS We develop CellAge (http://genomics.senescence.info/cells), a manually curated database of 279 human genes driving cellular senescence, and perform various integrative analyses. Genes inducing cellular senescence tend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and tumor-suppressor genes, while genes inhibiting cellular senescence overlap with pro-longevity and oncogenes. Furthermore, cellular senescence genes are strongly conserved in mammals but not in invertebrates. We also build cellular senescence protein-protein interaction and co-expression networks. Clusters in the networks are enriched for cell cycle and immunological processes. Network topological parameters also reveal novel potential cellular senescence regulators. Using siRNAs, we observe that all 26 candidates tested induce at least one marker of senescence with 13 genes (C9orf40, CDC25A, CDCA4, CKAP2, GTF3C4, HAUS4, IMMT, MCM7, MTHFD2, MYBL2, NEK2, NIPA2, and TCEB3) decreasing cell number, activating p16/p21, and undergoing morphological changes that resemble cellular senescence. CONCLUSIONS Overall, our work provides a benchmark resource for researchers to study cellular senescence, and our systems biology analyses reveal new insights and gene regulators of cellular senescence.
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Affiliation(s)
- Roberto A Avelar
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Javier Gómez Ortega
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Robi Tacutu
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
- Computational Biology of Aging Group, Institute of Biochemistry, Romanian Academy, 060031, Bucharest, Romania
- Chronos Biosystems SRL, 060117, Bucharest, Romania
| | - Eleanor J Tyler
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Dominic Bennett
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Paolo Binetti
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Arie Budovsky
- Research and Development Authority, Barzilai Medical Center, Ashkelon, Israel
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Emily Johnson
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Alex Murray
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Samuel Shields
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Daniela Tejada-Martinez
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
- Doctorado en Ciencias mención Ecología y Evolución, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 631, Valdivia, Chile
| | - Daniel Thornton
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Vadim E Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | - Cleo L Bishop
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK.
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11
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Thompson CL, Plant JC, Wann AK, Bishop CL, Novak P, Mitchison HM, Beales PL, Chapple JP, Knight MM. Chondrocyte expansion is associated with loss of primary cilia and disrupted hedgehog signalling. Eur Cell Mater 2017; 34:128-141. [PMID: 28929469 DOI: 10.22203/ecm.v034a09] [Citation(s) in RCA: 28] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Tissue engineering-based therapies targeting cartilage diseases, such as osteoarthritis, require in vitro expansion of articular chondrocytes. A major obstacle for these therapies is the dedifferentiation and loss of phenotype accompanying chondrocyte expansion. Recent studies suggest that manipulation of hedgehog signalling may be used to promote chondrocyte re-differentiation. Hedgehog signalling requires the primary cilium, a microtubule-based signalling compartment, the integrity of which is linked to the cytoskeleton. We tested the hypothesis that alterations in cilia expression occurred as consequence of chondrocyte dedifferentiation and influenced hedgehog responsiveness. In vitro chondrocyte expansion to passage 5 (P5) was associated with increased actin stress fibre formation, dedifferentiation and progressive loss of primary cilia, compared to primary (P0) cells. P5 chondrocytes exhibited ~50 % fewer cilia with a reduced mean length. Cilia loss was associated with disruption of ligand-induced hedgehog signalling, such that P5 chondrocytes did not significantly regulate the expression of hedgehog target genes (GLI1 and PTCH1). This phenomenon could be recapitulated by applying 24 h cyclic tensile strain, which reduced cilia prevalence and length in P0 cells. LiCl treatment rescued cilia loss in P5 cells, partially restoring hedgehog signalling, so that GLI1 expression was significantly increased by Indian hedgehog. This study demonstrated that monolayer expansion disrupted primary cilia structure and hedgehog signalling associated with chondrocyte dedifferentiation. This excluded the possibility to use hedgehog ligands to stimulate re-differentiation without first restoring cilia expression. Furthermore, primary cilia loss during chondrocyte expansion would likely impact other cilia pathways important for cartilage health and tissue engineering, including transforming growth factor (TGF), Wnt and mechanosignalling.
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Affiliation(s)
- C L Thompson
- Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary, University of London, Mile End Road, London E1 4NS,
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12
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Nijhuis A, Thompson H, Adam J, Parker A, Gammon L, Lewis A, Bundy JG, Soga T, Jalaly A, Propper D, Jeffery R, Suraweera N, McDonald S, Thaha MA, Feakins R, Lowe R, Bishop CL, Silver A. Remodelling of microRNAs in colorectal cancer by hypoxia alters metabolism profiles and 5-fluorouracil resistance. Hum Mol Genet 2017; 26:1552-1564. [PMID: 28207045 PMCID: PMC5393147 DOI: 10.1093/hmg/ddx059] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 12/19/2016] [Accepted: 02/13/2017] [Indexed: 12/25/2022] Open
Abstract
Solid tumours have oxygen gradients and areas of near and almost total anoxia. Hypoxia reduces sensitivity to 5-fluorouracil (5-FU)-chemotherapy for colorectal cancer (CRC). MicroRNAs (miRNAs) are hypoxia sensors and were altered consistently in six CRC cell lines (colon cancer: DLD-1, HCT116 and HT29; rectal cancer: HT55, SW837 and VACO4S) maintained in hypoxia (1 and 0.2% oxygen) compared with normoxia (20.9%). CRC cell lines also showed altered amino acid metabolism in hypoxia and hypoxia-responsive miRNAs were predicted to target genes in four metabolism pathways: beta-alanine; valine, leucine, iso-leucine; aminoacyl-tRNA; and alanine, aspartate, glutamate. MiR-210 was increased in hypoxic areas of CRC tissues and hypoxia-responsive miR-21 and miR-30d, but not miR-210, were significantly increased in 5-FU resistant CRCs. Treatment with miR-21 and miR-30d antagonists sensitized hypoxic CRC cells to 5-FU. Our data highlight the complexity and tumour heterogeneity caused by hypoxia. MiR-210 as a hypoxic biomarker, and the targeting of miR-21 and miR-30d and/or the amino acid metabolism pathways may offer translational opportunities.
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Affiliation(s)
- Anke Nijhuis
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Hannah Thompson
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Julie Adam
- Radcliffe Department of Medicine, OCDEM, University of Oxford, Oxford OX3 7LJ, UK
| | - Alexandra Parker
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Luke Gammon
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Amy Lewis
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Jacob G Bundy
- Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Aisha Jalaly
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - David Propper
- Department of Medical Oncology, St Bartholomew's Hospital, Gloucester House, Little Britain, London EC1A 7BE, UK
| | - Rosemary Jeffery
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Nirosha Suraweera
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Sarah McDonald
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Mohamed A Thaha
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK.,Academic Surgical Unit, The Royal London Hospital, Whitechapel, London E1 1BB, UK
| | - Roger Feakins
- Department of Histopathology, Royal London Hospital, Whitechapel, London, UK
| | - Robert Lowe
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Cleo L Bishop
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Andrew Silver
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, London E1 2AT, UK
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13
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Nijhuis A, Curciarello R, Mehta S, Feakins R, Bishop CL, Lindsay JO, Silver A. MCL-1 is modulated in Crohn's disease fibrosis by miR-29b via IL-6 and IL-8. Cell Tissue Res 2017; 368:325-335. [PMID: 28190086 PMCID: PMC5397660 DOI: 10.1007/s00441-017-2576-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 11/10/2016] [Accepted: 01/03/2017] [Indexed: 12/15/2022]
Abstract
The miR-29 family is involved in fibrosis in multiple organs, including the intestine where miR-29b facilitates TGF-β-mediated up-regulation of collagen in mucosal fibroblasts from Crohn’s disease (CD) patients. Myeloid cell leukemia-1 (MCL-1), a member of the B-cell CLL/Lymphoma 2 (BCL-2) apoptosis family, is involved in liver fibrosis and is targeted by miR-29b via its 3’-UTR in cultured cell lines. We investigate the role of MCL-1 and miR-29b in primary intestinal fibroblasts and tissue from stricturing CD patients. Transfection of CD intestinal fibroblasts with pre-miR-29b resulted in a significant increase in the mRNA expression of MCL-1 isoforms [MCL-1Long (L)/Extra Short (ES) and MCL-1Short (S)], although MCL-1S was expressed at significantly lower levels. Western blotting predominantly detected the anti-apoptotic MCL-1L isoform, and immunofluorescence showed that staining was localised in discrete nuclear foci. Transfection with pre-miR-29b or anti-miR-29b resulted in a significant increase or decrease, respectively, in MCL-1L foci. CD fibroblasts treated with IL-6 and IL-8, inflammatory cytokines upstream of MCL-1, increased the total mass of MCL-1L-positive foci. Furthermore, transfection of intestinal fibroblasts with pre-miR-29b resulted in an increase in mRNA and protein levels of IL-6 and IL-8. Finally, immunohistochemistry showed reduced MCL-1 protein expression in fibrotic CD samples compared to non-stricturing controls. Together, our findings suggest that induction of MCL-1 by IL-6/IL-8 may surmount any direct down-regulation by miR-29b via its 3’-UTR. We propose that an anti-fibrotic miR-29b/IL-6 IL-8/MCL-1L axis may influence intestinal fibrosis in CD. In the future, therapeutic modulation of this pathway might contribute to the management of fibrosis in CD.
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Affiliation(s)
- Anke Nijhuis
- Centre for Genomics and Child Health and National Centre for Bowel Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark St, Whitechapel, E1 2AT, London, UK
| | - Renata Curciarello
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark St, Whitechapel, E1 2AT, London, UK
| | - Shameer Mehta
- Centre for Genomics and Child Health and National Centre for Bowel Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark St, Whitechapel, E1 2AT, London, UK
| | - Roger Feakins
- Department of Histopathology, The Royal London Hospital, London, UK
| | - Cleo L Bishop
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - James O Lindsay
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark St, Whitechapel, E1 2AT, London, UK.
| | - Andrew Silver
- Centre for Genomics and Child Health and National Centre for Bowel Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark St, Whitechapel, E1 2AT, London, UK.
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14
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Lowe R, Overhoff MG, Ramagopalan SV, Garbe JC, Koh J, Stampfer MR, Beach DH, Rakyan VK, Bishop CL. The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans. Genome Biol 2015; 16:194. [PMID: 26381124 PMCID: PMC4574115 DOI: 10.1186/s13059-015-0748-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 05/20/2015] [Accepted: 08/10/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Cellular senescence is a stable arrest of proliferation and is considered a key component of processes associated with carcinogenesis and other ageing-related phenotypes. Here, we perform methylome analysis of actively dividing and deeply senescent normal human epithelial cells. RESULTS We identify senescence-associated differentially methylated positions (senDMPs) from multiple experiments using cells from one donor. We find that human senDMP epigenetic signatures are positively and significantly correlated with both cancer and ageing-associated methylation dynamics. We also identify germline genetic variants, including those associated with the p16INK4A locus, which are associated with the presence of in vivo senDMP signatures. Importantly, we also demonstrate that a single senDMP signature can be effectively reversed in a newly-developed protocol of transient senescence reversal. CONCLUSIONS The senDMP signature has significant potential for understanding some of the key (epi)genetic etiological factors that may lead to cancer and age-related diseases in humans.
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Affiliation(s)
- Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Marita G Overhoff
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Sreeram V Ramagopalan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - James C Garbe
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - James Koh
- Division of Surgical Sciences, Department of Surgery, Duke University Medical School, Durham, NC, 27710, USA
| | - Martha R Stampfer
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David H Beach
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
| | - Cleo L Bishop
- The 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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Abstract
p16 is a key regulator of cellular senescence, yet the drivers of this stable state of proliferative arrest are not well understood. Here, we identify 22 senescence-associated microRNAs (SA-miRNAs) in normal human mammary epithelial cells. We show that SA-miRNAs-26b, 181a, 210 and 424 function in concert to directly repress expression of Polycomb group (PcG) proteins CBX7, embryonic ectoderm development (EED), enhancer of zeste homologue 2 (EZH2) and suppressor of zeste 12 homologue (Suz12), thereby activating p16. We demonstrate the existence of a tight positive feedback loop in which SA-miRNAs activate and re-enforce the expression of other SA-miRNA members. In contrast, PcG members restrain senescence by epigenetically repressing the expression of these SA-miRNAs. Importantly, loss of p16 leads to repression of SA-miRNA expression, intimately coupling this effector of senescence to the SA-miRNA/PcG self-regulatory loop. Taken together, our findings illuminate an important regulatory axis that underpins the transition from proliferation to cellular senescence.
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Affiliation(s)
- Marita G Overhoff
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK, Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and Division of Surgical Sciences, Department of Surgery, Duke University Medical School, Durham, NC 27710, USA
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16
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Liu L, Oliveira NMM, Cheney KM, Pade C, Dreja H, Bergin AMH, Borgdorff V, Beach DH, Bishop CL, Dittmar MT, McKnight A. A whole genome screen for HIV restriction factors. Retrovirology 2011; 8:94. [PMID: 22082156 PMCID: PMC3228845 DOI: 10.1186/1742-4690-8-94] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [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: 08/08/2011] [Accepted: 11/14/2011] [Indexed: 01/01/2023] Open
Abstract
Background Upon cellular entry retroviruses must avoid innate restriction factors produced by the host cell. For human immunodeficiency virus (HIV) human restriction factors, APOBEC3 (apolipoprotein-B-mRNA-editing-enzyme), p21 and tetherin are well characterised. Results To identify intrinsic resistance factors to HIV-1 replication we screened 19,121 human genes and identified 114 factors with significant inhibition of infection. Those with a known function are involved in a broad spectrum of cellular processes including receptor signalling, vesicle trafficking, transcription, apoptosis, cross-nuclear membrane transport, meiosis, DNA damage repair, ubiquitination and RNA processing. We focused on the PAF1 complex which has been previously implicated in gene transcription, cell cycle control and mRNA surveillance. Knockdown of all members of the PAF1 family of proteins enhanced HIV-1 reverse transcription and integration of provirus. Over-expression of PAF1 in host cells renders them refractory to HIV-1. Simian Immunodeficiency Viruses and HIV-2 are also restricted in PAF1 expressing cells. PAF1 is expressed in primary monocytes, macrophages and T-lymphocytes and we demonstrate strong activity in MonoMac1, a monocyte cell line. Conclusions We propose that the PAF1c establishes an anti-viral state to prevent infection by incoming retroviruses. This previously unrecognised mechanism of restriction could have implications for invasion of cells by any pathogen.
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Affiliation(s)
- Li Liu
- Centre for Immunology and Infectious Disease, 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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17
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Glenzer SH, MacGowan BJ, Meezan NB, Adams PA, Alfonso JB, Alger ET, Alherz Z, Alvarez LF, Alvarez SS, Amick PV, Andersson KS, Andrews SD, Antonini GJ, Arnold PA, Atkinson DP, Auyang L, Azevedo SG, Balaoing BNM, Baltz JA, Barbosa F, Bardsley GW, Barker DA, Barnes AI, Baron A, Beeler RG, Beeman BV, Belk LR, Bell JC, Bell PM, Berger RL, Bergonia MA, Bernardez LJ, Berzins LV, Bettenhausen RC, Bezerides L, Bhandarkar SD, Bishop CL, Bond EJ, Bopp DR, Borgman JA, Bower JR, Bowers GA, Bowers MW, Boyle DT, Bradley DK, Bragg JL, Braucht J, Brinkerhoff DL, Browning DF, Brunton GK, Burkhart SC, Burns SR, Burns KE, Burr B, Burrows LM, Butlin RK, Cahayag NJ, Callahan DA, Cardinale PS, Carey RW, Carlson JW, Casey AD, Castro C, Celeste JR, Chakicherla AY, Chambers FW, Chan C, Chandrasekaran H, Chang C, Chapman RF, Charron K, Chen Y, Christensen MJ, Churby AJ, Clancy TJ, Cline BD, Clowdus LC, Cocherell DG, Coffield FE, Cohen SJ, Costa RL, Cox JR, Curnow GM, Dailey MJ, Danforth PM, Darbee R, Datte PS, Davis JA, Deis GA, Demaret RD, Dewald EL, Di Nicola P, Di Nicola JM, Divol L, Dixit S, Dobson DB, Doppner T, Driscoll JD, Dugorepec J, Duncan JJ, Dupuy PC, Dzenitis EG, Eckart MJ, Edson SL, Edwards GJ, Edwards MJ, Edwards OD, Edwards PW, Ellefson JC, Ellerbee CH, Erbert GV, Estes CM, Fabyan WJ, Fallejo RN, Fedorov M, Felker B, Fink JT, Finney MD, Finnie LF, Fischer MJ, Fisher JM, Fishler BT, Florio JW, Forsman A, Foxworthy CB, Franks RM, Frazier T, Frieder G, Fung T, Gawinski GN, Gibson CR, Giraldez E, Glenn SM, Golick BP, Gonzales H, Gonzales SA, Gonzalez MJ, Griffin KL, Grippen J, Gross SM, Gschweng PH, Gururangan G, Gu K, Haan SW, Hahn SR, Haid BJ, Hamblen JE, Hammel BA, Hamza AV, Hardy DL, Hart DR, Hartley RG, Haynam CA, Heestand GM, Hermann MR, Hermes GL, Hey DS, Hibbard RL, Hicks DG, Hinkel DE, Hipple DL, Hitchcock JD, Hodtwalker DL, Holder JP, Hollis JD, Holtmeier GM, Huber SR, Huey AW, Hulsey DN, Hunter SL, Huppler TR, Hutton MS, Izumi N, Jackson JL, Jackson MA, Jancaitis KS, Jedlovec DR, Johnson B, Johnson MC, Johnson T, Johnston MP, Jones OS, Kalantar DH, Kamperschroer JH, Kauffman RL, Keating GA, Kegelmeyer LM, Kenitzer SL, Kimbrough JR, King K, Kirkwood RK, Klingmann JL, Knittel KM, Kohut TR, Koka KG, Kramer SW, Krammen JE, Krauter KG, Krauter GW, Krieger EK, Kroll JJ, La Fortune KN, Lagin LJ, Lakamsani VK, Landen OL, Lane SW, Langdon AB, Langer SH, Lao N, Larson DW, Latray D, Lau GT, Le Pape S, Lechleiter BL, Lee Y, Lee TL, Li J, Liebman JA, Lindl JD, Locke SF, Loey HK, London RA, Lopez FJ, Lord DM, Lowe-Webb RR, Lown JG, Ludwigsen AP, Lum NW, Lyons RR, Ma T, MacKinnon AJ, Magat MD, Maloy DT, Malsbury TN, Markham G, Marquez RM, Marsh AA, Marshall CD, Marshall SR, Maslennikov IL, Mathisen DG, Mauger GJ, Mauvais MY, McBride JA, McCarville T, McCloud JB, McGrew A, McHale B, MacPhee AG, Meeker JF, Merill JS, Mertens EP, Michel PA, Miller MG, Mills T, Milovich JL, Miramontes R, Montesanti RC, Montoya MM, Moody J, Moody JD, Moreno KA, Morris J, Morriston KM, Nelson JR, Neto M, Neumann JD, Ng E, Ngo QM, Olejniczak BL, Olson RE, Orsi NL, Owens MW, Padilla EH, Pannell TM, Parham TG, Patterson RW, Pavel G, Prasad RR, Pendlton D, Penko FA, Pepmeier BL, Petersen DE, Phillips TW, Pigg D, Piston KW, Pletcher KD, Powell CL, Radousky HB, Raimondi BS, Ralph JE, Rampke RL, Reed RK, Reid WA, Rekow VV, Reynolds JL, Rhodes JJ, Richardson MJ, Rinnert RJ, Riordan BP, Rivenes AS, Rivera AT, Roberts CJ, Robinson JA, Robinson RB, Robison SR, Rodriguez OR, Rogers SP, Rosen MD, Ross GF, Runkel M, Runtal AS, Sacks RA, Sailors SF, Salmon JT, Salmonson JD, Saunders RL, Schaffer JR, Schindler TM, Schmitt MJ, Schneider MB, Segraves KS, Shaw MJ, Sheldrick ME, Shelton RT, Shiflett MK, Shiromizu SJ, Shor M, Silva LL, Silva SA, Skulina KM, Smauley DA, Smith BE, Smith LK, Solomon AL, Sommer S, Soto JG, Spafford NI, Speck DE, Springer PT, Stadermann M, Stanley F, Stone TG, Stout EA, Stratton PL, Strausser RJ, Suter LJ, Sweet W, Swisher MF, Tappero JD, Tassano JB, Taylor JS, Tekle EA, Thai C, Thomas CA, Thomas A, Throop AL, Tietbohl GL, Tillman JM, Town RPJ, Townsend SL, Tribbey KL, Trummer D, Truong J, Vaher J, Valadez M, Van Arsdall P, Van Prooyen AJ, Vergel de Dios EO, Vergino MD, Vernon SP, Vickers JL, Villanueva GT, Vitalich MA, Vonhof SA, Wade FE, Wallace RJ, Warren CT, Warrick AL, Watkins J, Weaver S, Wegner PJ, Weingart MA, Wen J, White KS, Whitman PK, Widmann K, Widmayer CC, Wilhelmsen K, Williams EA, Williams WH, Willis L, Wilson EF, Wilson BA, Witte MC, Work K, Yang PS, Young BK, Youngblood KP, Zacharias RA, Zaleski T, Zapata PG, Zhang H, Zielinski JS, Kline JL, Kyrala GA, Niemann C, Kilkenny JD, Nikroo A, Van Wonterghem BM, Atherton LJ, Moses EI. Demonstration of ignition radiation temperatures in indirect-drive inertial confinement fusion hohlraums. Phys Rev Lett 2011; 106:085004. [PMID: 21405580 DOI: 10.1103/physrevlett.106.085004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Indexed: 05/30/2023]
Abstract
We demonstrate the hohlraum radiation temperature and symmetry required for ignition-scale inertial confinement fusion capsule implosions. Cryogenic gas-filled hohlraums with 2.2 mm-diameter capsules are heated with unprecedented laser energies of 1.2 MJ delivered by 192 ultraviolet laser beams on the National Ignition Facility. Laser backscatter measurements show that these hohlraums absorb 87% to 91% of the incident laser power resulting in peak radiation temperatures of T(RAD)=300 eV and a symmetric implosion to a 100 μm diameter hot core.
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Affiliation(s)
- S H Glenzer
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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Bishop CL, Bergin AMH, Fessart D, Borgdorff V, Hatzimasoura E, Garbe JC, Stampfer MR, Koh J, Beach DH. Primary cilium-dependent and -independent Hedgehog signaling inhibits p16(INK4A). Mol Cell 2010; 40:533-47. [PMID: 21095584 DOI: 10.1016/j.molcel.2010.10.027] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 06/09/2010] [Accepted: 08/27/2010] [Indexed: 01/24/2023]
Abstract
In a genome-wide siRNA analysis of p16(INK4a) (p16) modulators, we identify the Hedgehog (Hh) pathway component SUFU and formally demonstrate that Hh signaling promotes mitogenesis by suppression of p16. A fragment of the Hh-responsive GLI2 transcription factor directly binds and inhibits the p16 promoter and senescence is associated with the loss of nuclear GLI2. Hh components partially reside in the primary cilium (PC), and the small fraction of cells in mass culture that elaborate a PC have the lowest expression of p16. Suppression of p16 is effected by both PC-dependent and -independent routes, and ablation of p16 renders cells insensitive to an Hh inhibitor and increases PC formation. These results directly link a well-established developmental mitogenic pathway with a key tumor suppressor and contribute to the molecular understanding of replicative senescence, Hh-mediated oncogenesis, and potentially the role of p16 in aging.
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Affiliation(s)
- Cleo L Bishop
- Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, UK.
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Bishop CL, Ulas S, Baena-Gonzalez E, Aro EM, Purton S, Nugent JHA, Mäenpää P. The PsbZ subunit of Photosystem II in Synechocystis sp. PCC 6803 modulates electron flow through the photosynthetic electron transfer chain. Photosynth Res 2007; 93:139-47. [PMID: 17516144 DOI: 10.1007/s11120-007-9182-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 04/19/2007] [Indexed: 05/15/2023]
Abstract
The psbZ gene of Synechocystis sp. PCC 6803 encodes the approximately 6.6 kDa photosystem II (PSII) subunit. We here report biophysical, biochemical and in vivo characterization of Synechocystis sp. PCC 6803 mutants lacking psbZ. We show that these mutants are able to perform wild-type levels of light-harvesting, energy transfer, PSII oxygen evolution, state transitions and non-photochemical quenching (NPQ) under standard growth conditions. The mutants grow photoautotrophically; however, their growth rate is clearly retarded under low-light conditions and they are not capable of photomixotrophic growth. Further differences exist in the electron transfer properties between the mutants and wild type. In the absence of PsbZ, electron flow potentially increased through photosystem I (PSI) without a change in the maximum electron transfer capacity of PSII. Further, rereduction of P700(+) is much faster, suggesting faster cyclic electron flow around PSI. This implies a role for PsbZ in the regulation of electron transfer, with implication for photoprotection.
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Affiliation(s)
- Cleo L Bishop
- Photosynthesis Research Group, Department of Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
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Bishop CL, Ramalho M, Nadkarni N, May Kong W, Higgins CF, Krauzewicz N. Role for centromeric heterochromatin and PML nuclear bodies in the cellular response to foreign DNA. Mol Cell Biol 2006; 26:2583-94. [PMID: 16537904 PMCID: PMC1430340 DOI: 10.1128/mcb.26.7.2583-2594.2006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nuclear spatial positioning plays an important role in the epigenetic regulation of eukaryotic gene expression. Here we show a role for nuclear spatial positioning in regulating episomal transgenes that are delivered by virus-like particles (VLPs). VLPs mediate the delivery of plasmid DNA (pDNA) to cell nuclei but lack viral factors involved in initiating and regulating transcription. By tracking single fluorescently labeled VLPs, coupled with luciferase reporter gene assays, we found that VLPs transported pDNA to cell nuclei efficiently but transgenes were immediately silenced by the cell. An investigation of the nuclear location of fluorescent VLPs revealed that the pDNAs were positioned next to centromeric heterochromatin. The activation of transcription by providing viral factors or inhibiting histone deacetylase activity resulted in the localization to euchromatin regions. Further, the activation of transcription induced the recruitment of PML nuclear bodies (PML-NBs) to the VLPs. This association did not play a role in regulating transgene expression, but PML protein was necessary for the inhibition of transgene expression with alpha interferon (IFN-alpha). These results support a model whereby cells can prevent foreign gene expression at two levels: by positioning transgenes next to centromeric heterochromatin or, if that is overcome, via the type I IFN response facilitated by PML-NB recruitment.
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Affiliation(s)
- Cleo L Bishop
- MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom
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Bishop CL, Purton S, Nugent JHA. Molecular analysis of the Chlamydomonas nuclear gene encoding PsbW and demonstration that PsbW is a subunit of photosystem II, but not photosystem I. Plant Mol Biol 2003; 52:285-289. [PMID: 12856936 DOI: 10.1023/a:1023963113290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
PsbW is a nuclear-encoded protein located in the thylakoid membrane of the chloroplast. Studies in higher plants have provided substantial evidence that PsbW is a core component of photosystem II. However, recent data have been presented to suggest that PsbW is also a subunit of photosystem I. Such a sharing of subunits between the two photosystems would represent a novel phenomenon. To investigate this, we have cloned and characterized the psbW gene from the green alga Chlamydomonas reinhardtii. The gene is split by five introns and encodes a polypeptide of 115 residues comprising the 6.1 kDa mature PsbW protein preceded by a 59 amino acid bipartite transit sequence. Using antibodies raised to PsbW we have examined: (1) C. reinhardtii mutants lacking either photosystem and (2) purified photosystem preparations. We find that PsbW is a subunit of photosystem II, but not photosystem I.
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Affiliation(s)
- Cleo L Bishop
- Photosynthesis Research Group, Department of Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK
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Bishop CL. Amino-acid cycling drives nitrogen fixation. Genome Biol 2003. [DOI: 10.1186/gb-spotlight-20030422-04] [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: 11/10/2022] Open
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Bishop CL. Bacteria help plants grow. Genome Biol 2003. [DOI: 10.1186/gb-spotlight-20030402-01] [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: 11/10/2022] Open
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Bishop CL. JAW miRNAs regulate plant development. Genome Biol 2003. [DOI: 10.1186/gb-spotlight-20030821-02] [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: 11/10/2022] Open
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Bishop CL. Life cycle control of Chlamydomonas reinhardtii. Genome Biol 2003. [DOI: 10.1186/gb-spotlight-20030423-01] [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: 11/10/2022] Open
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Bishop CL. Arabidopsis insertional mutant database. Genome Biol 2003. [DOI: 10.1186/gb-spotlight-20030801-02] [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: 11/10/2022] Open
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Bishop CL. Gene acquisition in eukaryotes. Genome Biol 2003. [DOI: 10.1186/gb-spotlight-20030528-01] [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: 11/10/2022] Open
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Bishop CL. Plant-to-plant horizontal gene transfer. Genome Biol 2003. [DOI: 10.1186/gb-spotlight-20030710-01] [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: 11/10/2022] Open
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Bishop CL, Flack JD. Proceedings: The use of drugs to elucidate the mechanism of luteolysis in the pseudopregnant rat. J Reprod Fertil 1973; 35:597-8. [PMID: 4202471 DOI: 10.1530/jrf.0.0350597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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