18 results on '"Cleo L. Bishop"'
Search Results
2. A multidimensional systems biology analysis of cellular senescence in aging and disease
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Roberto A. Avelar, Javier Gómez Ortega, Robi Tacutu, Eleanor J. Tyler, Dominic Bennett, Paolo Binetti, Arie Budovsky, Kasit Chatsirisupachai, Emily Johnson, Alex Murray, Samuel Shields, Daniela Tejada-Martinez, Daniel Thornton, Vadim E. Fraifeld, Cleo L. Bishop, and João Pedro de Magalhães
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Biogerontology ,Cancer ,Genetics ,Longevity ,Transcriptome ,Biology (General) ,QH301-705.5 ,QH426-470 - Abstract
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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- 2020
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3. Expression of p16 Within Myenteric Neurons of the Aged Colon: A Potential Marker of Declining Function
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Alexandra Palmer, Sarah Epton, Ellie Crawley, Marilisa Straface, Luke Gammon, Meghan M. Edgar, Yichen Xu, Shezan Elahi, Joanne Chin-Aleong, Joanne E. Martin, Cleo L. Bishop, Charles H. Knowles, and Gareth J. Sanger
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senescence ,p16 ,aging ,human ,colon ,myenteric neuron ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - 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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- 2021
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4. Current Understanding of the Role of Senescent Melanocytes in Skin Ageing
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Bethany K. Hughes and Cleo L. Bishop
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melanocyte ,senescence ,skin ,ageing ,UV ,Biology (General) ,QH301-705.5 - Abstract
Melanocytes reside within the basal epidermis of human skin, and function to protect the skin from ultraviolet light through the production of melanin. Prolonged exposure of the skin to UV light can induce irreparable DNA damage and drive cells into senescence, a sustained cell cycle arrest that prevents the propagation of this damage. Senescent cells can also be detrimental and contribute to skin ageing phenotypes through their senescence-associated secretory phenotype. Senescent cells can act in both an autocrine and paracrine manner to produce widespread tissue inflammation and skin ageing. Recently, melanocytes have been identified as the main senescent cell population within the epidermis and have been linked to a variety of skin ageing phenotypes, such as epidermal thinning and the presence of wrinkles. However, the literature surrounding melanocyte senescence is limited and tends to focus on the role of senescence in the prevention of melanoma. Therefore, this review aims to explore the current understanding of the contribution of senescent melanocytes to human skin ageing.
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- 2022
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5. Isolation methodology is essential to the evaluation of the extracellular vesicle component of the senescence‐associated secretory phenotype
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Ryan Wallis, Natasa Josipovic, Hannah Mizen, Arturo Robles‐Tenorio, Eleanor J. Tyler, Argyris Papantonis, and Cleo L. Bishop
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ageing ,exosomes ,extracellular vesicles ,paracrine senescence ,senescence‐associated secretory phenotype ,senescence ,Cytology ,QH573-671 - Abstract
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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- 2021
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6. Senescence-associated morphological profiles (SAMPs): an image-based phenotypic profiling method for evaluating the inter and intra model heterogeneity of senescence
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Ryan Wallis, Deborah Milligan, Bethany Hughes, Hannah Mizen, José Alberto López-Domínguez, Ugochim Eduputa, Eleanor J. Tyler, Manuel Serrano, and Cleo L. Bishop
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Aging ,Carcinogenesis ,Envelliment ,Neoplasms ,Humans ,Cell Biology ,Oncogenes ,Morphology (Biology) ,Morfologia (Biologia) ,Biomarkers ,Cellular Senescence - 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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- 2022
7. Early growth response 2 (EGR2) is a novel regulator of the senescence programme
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Eleanor J. Tyler, Ryan Wallis, Robert Lowe, Martha R. Stampfer, Cleo L. Bishop, Bethany K. Hughes, Ana Gutierrez del Arroyo, Michael P. Philpott, James C. Garbe, and Jim Koh
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0301 basic medicine ,Aging ,senescence ,Regulator ,p16 ,Medical and Health Sciences ,Retinoblastoma Protein ,0302 clinical medicine ,Transcription (biology) ,2.1 Biological and endogenous factors ,cellular senescence ,RNA, Small Interfering ,transcription factor ,Cells, Cultured ,education.field_of_study ,Cultured ,Biological Sciences ,Ink4a ,Phenotype ,Mammary Glands ,Cell biology ,Up-Regulation ,Gene Knockdown Techniques ,EGR2 ,Human ,Protein Binding ,Senescence ,Adult ,Cyclin-Dependent Kinase Inhibitor p21 ,Adolescent ,Cells ,1.1 Normal biological development and functioning ,Population ,Biology ,Small Interfering ,03 medical and health sciences ,Young Adult ,Genetics ,Humans ,replicative lifespan ,education ,Mammary Glands, Human ,Transcription factor ,Cyclin-Dependent Kinase Inhibitor p16 ,Early Growth Response Protein 2 ,Original Paper ,Promoter ,Epithelial Cells ,Cell Biology ,Original Articles ,Fibroblasts ,030104 developmental biology ,Ageing ,RNA ,Tumor Suppressor Protein p53 ,030217 neurology & neurosurgery ,Developmental Biology - 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., Deep senescence is reversible in normal adult human fibroblasts. Loss of early growth response 2 (EGR2) reverses epithelial and fibroblast senescence. EGR2 levels are up‐regulated in multiple models of senescence and prolonged expression of EGR2 induces fibroblast senescence. Early growth response 2 (EGR2) is a novel master transcriptional regulator of the INK/ARF locus and the senescence programme.
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- 2021
8. The bright and dark side of extracellular vesicles in the senescence-associated secretory phenotype
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Ryan Wallis, Cleo L. Bishop, and Hannah Mizen
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0301 basic medicine ,Senescence ,Aging ,Inflammation ,Biology ,SASP ,Extracellular vesicles ,Article ,Malignant transformation ,03 medical and health sciences ,Extracellular Vesicles ,0302 clinical medicine ,microRNA ,medicine ,Humans ,EVs ,Cellular Senescence ,miRNA ,Senescence-Associated Secretory Phenotype ,fungi ,Phenotype ,Cell biology ,Ageing ,030104 developmental biology ,sense organs ,medicine.symptom ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Highlights • Extracellular vesicles (EVs) are key mediators within the senescence-associated secretory phenotype (SASP). • Increased EV production has been demonstrated following senescence induction. • Changes in EVs cargoes including proteins, nucleic acids and lipids have been demonstrated following senescence induction. • EVs have been demonstrated to contribute to both the beneficial (Bright) and detrimental (Dark) sides of the SASP., Senescence is a state of proliferative arrest which has been described as a protective mechanism against the malignant transformation of cells. However, senescent cells have also been demonstrated to accumulate with age and to contribute to a variety of age-related pathologies. These pathological effects have been attributed to the acquisition of an enhanced secretory profile geared towards inflammatory molecules and tissue remodelling agents – known as the senescence-associated secretory phenotype (SASP). Whilst the SASP has long been considered to be comprised predominantly of soluble mediators, growing evidence has recently emerged for the role of extracellular vesicles (EVs) as key players within the secretome of senescent cells. This review is intended to consolidate recent evidence for the roles of senescent cell-derived EVs to both the beneficial (Bright) and detrimental (Dark) effects of the SASP.
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- 2020
9. Chondrocyte expansion is associated with loss of primary cilia and disrupted hedgehog signalling
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A.K. Wann, Cleo L. Bishop, Pavel Novák, J C Plant, J.P. Chapple, Hannah M. Mitchison, Clare L. Thompson, PL Beales, and Martin M. Knight
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0301 basic medicine ,Cartilage, Articular ,medicine.medical_specialty ,Indian hedgehog ,lcsh:Diseases of the musculoskeletal system ,hedgehog ,cilium ,lcsh:Surgery ,Ligands ,Chondrocyte ,Polymerization ,Weight-Bearing ,03 medical and health sciences ,Chondrocytes ,primary cilia ,Microtubule ,GLI1 ,re-differentiation ,Internal medicine ,medicine ,Animals ,Hedgehog Proteins ,Cilia ,Cytoskeleton ,Hedgehog ,lithium chloride ,Cell Proliferation ,biology ,Cilium ,dedifferentiation ,Wnt signaling pathway ,lcsh:RD1-811 ,Cell Dedifferentiation ,biology.organism_classification ,Actins ,Cell biology ,030104 developmental biology ,medicine.anatomical_structure ,Endocrinology ,Phenotype ,biology.protein ,Cattle ,lcsh:RC925-935 ,Signal Transduction - 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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- 2017
10. Ribosomal stress-induced senescence as a novel pro-senescence strategy for p16 positive basal-like breast cancer
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James C. Garbe, Jim Koh, Dreger S, Lee W. Jones, Cleo L. Bishop, Martha R. Stampfer, M. Moore, Luke Gammon, and Michael P. Philpott
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Senescence ,Gene knockdown ,Breast cancer ,Ribosomal protein ,DNA damage ,Cancer research ,medicine ,Cancer ,Endogeny ,Ribosomal RNA ,Biology ,medicine.disease - Abstract
Re-engaging the senescent programme represents an attractive yet underexplored strategy for cancer therapy, particularly for those tumour subtypes where targeted agents are limited or unavailable. Here, we identify a specific subset of ribosomal proteins as novel pro-senescence therapeutic targets for a highly aggressive subtype of breast cancer, p16 positive basal-like breast cancer. Mechanistically, ribosomal stress-induced senescence generates a stable cell cycle arrest, is dependent on endogenous p16 triggering a resensitisation to the p16/RB tumour suppressor axis, followed by establishment of a senescence-associated secretory phenotype, and is independent of DNA damage. Conversely, ribosomal protein knockdown in a p16 negative breast cancer model results in caspase-mediated apoptosis. Importantly, individual ribosomal protein loss is well tolerated by a panel of normal human cells. We demonstrate a reciprocal feedback loop between loss of RPS3A and RPS7 at both the transcriptional and post-transcriptional level during ribosomal stress-induced senescence. Further, our ribosomal hits are co-ordinately dysregulated in breast cancer, with elevated expression associated with a poor prognosis. Clinical relevance is demonstrated in tissue microarrays, and a RPS3AHIGHRPS7HIGHsignature is associated with an earlier disease onset and synergises with p16 to further worsen patient outcome. We conclude that dysregulation of ribosomal proteins constitutes a cancer cell-specific mechanism of senescence evasion and that engaging ribosomal stress-induced senescence may be relevant for future pro-senescence therapies.
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- 2018
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11. Remodelling of microRNAs in colorectal cancer by hypoxia alters metabolism profiles and 5-fluorouracil resistance
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Alexandra Parker, Mohamed A. Thaha, Sarah McDonald, Roger Feakins, Nirosha Suraweera, Robert Lowe, Aisha Jalaly, Cleo L. Bishop, Amy Lewis, Hannah Thompson, Luke Gammon, Tomoyoshi Soga, David Propper, Anke Nijhuis, Jacob G. Bundy, Rosemary Jeffery, Andrew Silver, and Julie Adam
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0301 basic medicine ,Colorectal cancer ,Apoptosis ,THERAPY ,TUMOR HYPOXIA ,0302 clinical medicine ,Amino Acids ,11 Medical and Health Sciences ,Genetics (clinical) ,GENE-EXPRESSION ,Genetics & Heredity ,Articles ,General Medicine ,CHEMOTHERAPY ,Cell Hypoxia ,Gene Expression Regulation, Neoplastic ,030220 oncology & carcinogenesis ,ACID ,Fluorouracil ,medicine.symptom ,Leucine ,Colorectal Neoplasms ,Life Sciences & Biomedicine ,CHEMORADIOTHERAPY IN-VITRO ,Biochemistry & Molecular Biology ,Tumour heterogeneity ,Biology ,CARBONIC-ANHYDRASE-IX ,CHEMORADIOTHERAPY ,Genetic Heterogeneity ,03 medical and health sciences ,POOR-PROGNOSIS ,Valine ,microRNA ,Genetics ,medicine ,BREAST-CANCER ,Humans ,Molecular Biology ,RECTAL-CANCER ,Science & Technology ,Tumor hypoxia ,06 Biological Sciences ,Hypoxia (medical) ,HCT116 Cells ,medicine.disease ,MIR-210 ,digestive system diseases ,Oxygen ,MicroRNAs ,030104 developmental biology ,Drug Resistance, Neoplasm ,CELLS ,Cancer research ,OVEREXPRESSION - 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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- 2018
12. Low Stress Ion Conductance Microscopy of Sub-Cellular Stiffness
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Alexander Zhukov, Kirill E. Volynski, Cleo L. Bishop, Richard W. Clarke, David Klenerman, Eleanor J. Tyler, Owen Richards, Pavel Novák, Anna Drews, Marife Cano-Jaimez, Klenerman, David [0000-0001-7116-6954], and Apollo - University of Cambridge Repository
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0301 basic medicine ,musculoskeletal diseases ,Cytoplasm ,Materials science ,animal structures ,FOS: Physical sciences ,Condensed Matter - Soft Condensed Matter ,Cell Line ,Glycocalyx ,Stress (mechanics) ,03 medical and health sciences ,Animals ,Humans ,Physics - Biological Physics ,Cytoskeleton ,health care economics and organizations ,Cells, Cultured ,Ions ,Neurons ,Microscopy ,Cell Membrane ,Conductance ,Ion current ,General Chemistry ,Fibroblasts ,Condensed Matter Physics ,Compression (physics) ,equipment and supplies ,Rats ,Chemistry ,030104 developmental biology ,Membrane ,Biological Physics (physics.bio-ph) ,Biophysics ,Soft Condensed Matter (cond-mat.soft) ,Intracellular - Abstract
Directly examining subcellular mechanics whilst avoiding excessive strain of a live cell requires the precise control of light stress on very small areas, which is fundamentally difficult. Here we use a glass nanopipet out of contact with the plasma membrane to both exert the stress on the cell and also accurately monitor cellular compression. This allows the mapping of cell stiffness at a lateral resolution finer than 100 nm. We calculate the stress a nanopipet exerts on a cell as the sum of the intrinsic pressure between the tip face and the plasma membrane plus its direct pressure on any glycocalyx, both evaluated from the gap size in terms of the ion current decrease. A survey of cell types confirms that an intracellular pressure of approximately 120 Pa begins to detach the plasma membrane from the cytoskeleton and reveals that the first 0.66 ± 0.09 μm of compression of a neuron cell body is much softer than previous methods have been able to detect., Biotechnology and Biological Sciences Research Council (Grant ID: BB/L006227/1), Engineering and Physical Sciences Research Council (Grant ID: EP/H01098X/1), Medical Research Council (Grant IDs: G0701057, MR/K501372/1), Herchel Smith Postdoctoral Fellowship, Royal Society of Chemistry Analytical Chemistry Trust Fund
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- 2016
13. Brief report: isogenic induced pluripotent stem cell lines from an adult with mosaic down syndrome model accelerated neuronal ageing and neurodegeneration
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Cleo L. Bishop, Mamoru Hasegawa, Dean Nizetic, Franca Dagna-Bricarelli, Aoife Murray, Frédérique Sloan-Béna, Trevor G. Smart, David Ballard, Denise Syndercombe Court, Noemi Fusaki, Audrey Letourneau, Robert Abrehart, C. Baldo, Pollyanna Goh, Stefania Gimelli, Saad Hannan, Claudia Canzonetta, Shuhui Lim, Stylianos E. Antonarakis, Martin Mortensen, Jürgen Groet, Elisavet Stathaki, and Lee Kong Chian School of Medicine (LKCMedicine)
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Science::Biological sciences::Human anatomy and physiology::Neurobiology [DRNTU] ,Down syndrome ,Aging ,Cellular differentiation ,Neurogenesis ,Induced Pluripotent Stem Cells ,Mitochondrion ,Biology ,Embryonic Stem Cells/Induced Pluripotent Stem Cells ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Animals ,Humans ,ddc:576.5 ,Progenitor cell ,Neurodegeneration ,Induced pluripotent stem cell ,Cells, Cultured ,030304 developmental biology ,Genetics ,Neurons ,0303 health sciences ,Cell Differentiation ,Cell Biology ,Fibroblasts ,medicine.disease ,3. Good health ,Cell biology ,Mitochondria ,Neuronal differentiation ,Molecular Medicine ,Reprogramming ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Trisomy 21 (T21), Down Syndrome (DS) is the most common genetic cause of dementia and intellectual disability. Modeling DS is beginning to yield pharmaceutical therapeutic interventions for amelioration of intellectual disability, which are currently being tested in clinical trials. DS is also a unique genetic system for investigation of pathological and protective mechanisms for accelerated ageing, neurodegeneration, dementia, cancer, and other important common diseases. New drugs could be identified and disease mechanisms better understood by establishment of well-controlled cell model systems. We have developed a first nonintegration-reprogrammed isogenic human induced pluripotent stem cell (iPSC) model of DS by reprogramming the skin fibroblasts from an adult individual with constitutional mosaicism for DS and separately cloning multiple isogenic T21 and euploid (D21) iPSC lines. Our model shows a very low number of reprogramming rearrangements as assessed by a high-resolution whole genome CGH-array hybridization, and it reproduces several cellular pathologies seen in primary human DS cells, as assessed by automated high-content microscopic analysis. Early differentiation shows an imbalance of the lineage-specific stem/progenitor cell compartments: T21 causes slower proliferation of neural and faster expansion of hematopoietic lineage. T21 iPSC-derived neurons show increased production of amyloid peptide-containing material, a decrease in mitochondrial membrane potential, and an increased number and abnormal appearance of mitochondria. Finally, T21-derived neurons show significantly higher number of DNA double-strand breaks than isogenic D21 controls. Our fully isogenic system therefore opens possibilities for modeling mechanisms of developmental, accelerated ageing, and neurodegenerative pathologies caused by T21. Stem Cells 2015;33:2077–2084 Video Highlight: https://youtu.be/MoMwXg2azGo
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- 2015
14. A whole genome screen for HIV restriction factors
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Hanna Dreja, Ann Marie H. Bergin, Cleo L. Bishop, David H. Beach, Áine McKnight, Corinna Pade, Matthias T. Dittmar, Kelly M. Cheney, Li Liu, Nidia M M Oliveira, Viola Borgdorff, and Apollo - University of Cambridge Repository
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lcsh:Immunologic diseases. Allergy ,HIV Infections ,Biology ,Virus Replication ,Cell Line ,03 medical and health sciences ,Transcription (biology) ,Virology ,Humans ,Transcription factor ,030304 developmental biology ,0303 health sciences ,Gene knockdown ,Genome, Human ,Research ,030302 biochemistry & molecular biology ,HIV ,Nuclear Proteins ,Proteins ,Provirus ,Reverse transcriptase ,mRNA surveillance ,3. Good health ,Infectious Diseases ,Viral replication ,Host-Pathogen Interactions ,Commentary ,Tetherin ,Interferon ,Therapy ,Host restriction factors ,lcsh:RC581-607 ,Transcription Factors - 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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- 2011
15. Role for Centromeric Heterochromatin and PML Nuclear Bodies in the Cellular Response to Foreign DNA
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Cleo L. Bishop, Nachiket A. Nadkarni, N Krauzewicz, Christopher F. Higgins, Wing May Kong, and Michal Ramalho
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Euchromatin ,Transcription, Genetic ,Heterochromatin ,Transgene ,viruses ,Centromere ,Alpha interferon ,Biology ,Hydroxamic Acids ,Virus Replication ,Mice ,Transcription (biology) ,Gene expression ,Chlorocebus aethiops ,Gene silencing ,Animals ,Humans ,Gene Silencing ,Transgenes ,Molecular Biology ,Cells, Cultured ,Swiss 3T3 Cells ,Immunity, Cellular ,Gene Transfer Techniques ,virus diseases ,Cell Biology ,DNA ,Articles ,Molecular biology ,Cell Nucleus Structures ,COS Cells ,Histone deacetylase activity ,Erratum ,HeLa Cells ,Plasmids - 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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- 2006
16. Molecular analysis of the Chlamydomonas nuclear gene encoding PsbW and demonstration that PsbW is a subunit of photosystem II, but not photosystem I.
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Cleo L. Bishop, Saul Purton, and Jonathan H.A. Nugent
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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. [ABSTRACT FROM AUTHOR]
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- 2003
17. MCL-1 is modulated in Crohn’s disease fibrosis by miR-29b via IL-6 and IL-8
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Andrew Silver, Roger Feakins, Anke Nijhuis, Cleo L. Bishop, James O. Lindsay, Shameer Mehta, and Renata Curciarello
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0301 basic medicine ,Crohn’s disease ,Cell ,0302 clinical medicine ,Crohn Disease ,Fibrosis ,immune system diseases ,hemic and lymphatic diseases ,FIBROSIS ,Protein Isoforms ,3' Untranslated Regions ,medicine.diagnostic_test ,microRNA ,Regular Article ,purl.org/becyt/ford/3.1 [https] ,Transfection ,CROHN’S DISEASE ,Up-Regulation ,Intestines ,Medicina Básica ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,purl.org/becyt/ford/3 [https] ,CIENCIAS MÉDICAS Y DE LA SALUD ,Histology ,Inmunología ,Biology ,Immunofluorescence ,Models, Biological ,Proinflammatory cytokine ,Pathology and Forensic Medicine ,03 medical and health sciences ,medicine ,Humans ,Interleukin 8 ,RNA, Messenger ,Neurology & Neurosurgery ,Binding Sites ,Base Sequence ,Interleukin-6 ,MICRORNA ,miR-29b ,Interleukin-8 ,MIR-29B ,Cell Biology ,Fibroblasts ,medicine.disease ,Molecular biology ,Myeloid Cell Leukemia Sequence 1 Protein ,MicroRNAs ,030104 developmental biology ,Apoptosis ,1116 Medical Physiology ,MCL-1 - 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. Fil: Nijhuis, Anke. Queen Mary University of London; Reino Unido Fil: Curciarello, Renata. Queen Mary University of London; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Mehta, Shameer. Queen Mary University of London; Reino Unido Fil: Feakins, Roger. The Royal London Hospital; Reino Unido Fil: Bishop, Cleo L.. Queen Mary University of London; Reino Unido Fil: Lindsay, James O.. Queen Mary University of London; Reino Unido Fil: Silver, Andrew. Queen Mary University of London; Reino Unido
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18. The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans
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Martha R. Stampfer, Cleo L. Bishop, Sreeram V. Ramagopalan, James C. Garbe, David H. Beach, Marita G. Overhoff, Vardhman K. Rakyan, Robert Lowe, and James Koh
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Aging ,medicine.disease_cause ,Germline ,Epigenesis, Genetic ,0302 clinical medicine ,Neoplasms ,2.1 Biological and endogenous factors ,Aetiology ,Cellular Senescence ,Epigenesis ,Cancer ,Genetics ,0303 health sciences ,Single Nucleotide ,Biological Sciences ,Phenotype ,3. Good health ,Cell biology ,Cell Aging ,Generic Health Relevance ,030220 oncology & carcinogenesis ,DNA methylation ,Female ,Cell aging ,Adult ,Bioinformatics ,1.1 Normal biological development and functioning ,Biology ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Young Adult ,Genetic ,Clinical Research ,Information and Computing Sciences ,medicine ,Humans ,Polymorphism ,Cyclin-Dependent Kinase Inhibitor p16 ,030304 developmental biology ,Research ,Human Genome ,Genetic Variation ,DNA Methylation ,medicine.disease ,Human genetics ,Carcinogenesis ,Environmental Sciences - 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. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0748-4) contains supplementary material, which is available to authorized users.
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