1
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Moran J, Feltham L, Bagnall J, Goldrick M, Lord E, Nettleton C, Spiller DG, Roberts I, Paszek P. Live-cell imaging reveals single-cell and population-level infection strategies of Listeria monocytogenes in macrophages. Front Immunol 2023; 14:1235675. [PMID: 37675103 PMCID: PMC10478088 DOI: 10.3389/fimmu.2023.1235675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/01/2023] [Indexed: 09/08/2023] Open
Abstract
Pathogens have developed intricate strategies to overcome the host's innate immune responses. In this paper we use live-cell microscopy with a single bacterium resolution to follow in real time interactions between the food-borne pathogen L. monocytogenes and host macrophages, a key event controlling the infection in vivo. We demonstrate that infection results in heterogeneous outcomes, with only a subset of bacteria able to establish a replicative invasion of macrophages. The fate of individual bacteria in the same host cell was independent from the host cell and non-cooperative, being independent from co-infecting bacteria. A higher multiplicity of infection resulted in a reduced probability of replication of the overall bacterial population. By use of internalisation assays and conditional probabilities to mathematically describe the two-stage invasion process, we demonstrate that the higher MOI compromises the ability of macrophages to phagocytose bacteria. We found that the rate of phagocytosis is mediated via the secreted Listeriolysin toxin (LLO), while the probability of replication of intracellular bacteria remained constant. Using strains expressing fluorescent reporters to follow transcription of either the LLO-encoding hly or actA genes, we show that replicative bacteria exhibited higher PrfA regulon expression in comparison to those bacteria that did not replicate, however elevated PrfA expression per se was not sufficient to increase the probability of replication. Overall, this demonstrates a new role for the population-level, but not single cell, PrfA-mediated activity to regulate outcomes of host pathogen interactions.
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Affiliation(s)
| | | | | | | | | | | | | | - Ian Roberts
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Pawel Paszek
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
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2
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Downton P, Bagnall JS, England H, Spiller DG, Humphreys NE, Jackson DA, Paszek P, White MRH, Adamson AD. Overexpression of IκB⍺ modulates NF-κB activation of inflammatory target gene expression. Front Mol Biosci 2023; 10:1187187. [PMID: 37228587 PMCID: PMC10203502 DOI: 10.3389/fmolb.2023.1187187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Cells respond to inflammatory stimuli such as cytokines by activation of the nuclear factor-κB (NF-κB) signalling pathway, resulting in oscillatory translocation of the transcription factor p65 between nucleus and cytoplasm in some cell types. We investigate the relationship between p65 and inhibitor-κB⍺ (IκBα) protein levels and dynamic properties of the system, and how this interaction impacts on the expression of key inflammatory genes. Using bacterial artificial chromosomes, we developed new cell models of IκB⍺-eGFP protein overexpression in a pseudo-native genomic context. We find that cells with high levels of the negative regulator IκBα remain responsive to inflammatory stimuli and maintain dynamics for both p65 and IκBα. In contrast, canonical target gene expression is dramatically reduced by overexpression of IκBα, but can be partially rescued by overexpression of p65. Treatment with leptomycin B to promote nuclear accumulation of IκB⍺ also suppresses canonical target gene expression, suggesting a mechanism in which nuclear IκB⍺ accumulation prevents productive p65 interaction with promoter binding sites. This causes reduced target promoter binding and gene transcription, which we validate by chromatin immunoprecipitation and in primary cells. Overall, we show how inflammatory gene transcription is modulated by the expression levels of both IκB⍺ and p65. This results in an anti-inflammatory effect on transcription, demonstrating a broad mechanism to modulate the strength of inflammatory response.
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Affiliation(s)
- Polly Downton
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James S. Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Hazel England
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David G. Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Neil E. Humphreys
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Dean A. Jackson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Pawel Paszek
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michael R. H. White
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antony D. Adamson
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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3
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Kalliara E, Kardynska M, Bagnall J, Spiller DG, Müller W, Ruckerl D, Śmieja J, Biswas SK, Paszek P. Post-transcriptional regulatory feedback encodes JAK-STAT signal memory of interferon stimulation. Front Immunol 2022; 13:947213. [PMID: 36238296 PMCID: PMC9552616 DOI: 10.3389/fimmu.2022.947213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Immune cells fine tune their responses to infection and inflammatory cues. Here, using live-cell confocal microscopy and mathematical modelling, we investigate interferon-induced JAK-STAT signalling in innate immune macrophages. We demonstrate that transient exposure to IFN-γ stimulation induces a long-term desensitisation of STAT1 signalling and gene expression responses, revealing a dose- and time-dependent regulatory feedback that controls JAK-STAT responses upon re-exposure to stimulus. We show that IFN-α/β1 elicit different level of desensitisation from IFN-γ, where cells refractory to IFN-α/β1 are sensitive to IFN-γ, but not vice versa. We experimentally demonstrate that the underlying feedback mechanism involves regulation of STAT1 phosphorylation but is independent of new mRNA synthesis and cognate receptor expression. A new feedback model of the protein tyrosine phosphatase activity recapitulates experimental data and demonstrates JAK-STAT network’s ability to decode relative changes of dose, timing, and type of temporal interferon stimulation. These findings reveal that STAT desensitisation renders cells with signalling memory of type I and II interferon stimulation, which in the future may improve administration of interferon therapy.
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Affiliation(s)
- Eirini Kalliara
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Malgorzata Kardynska
- Department of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Zabrze, Poland
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - James Bagnall
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - David G. Spiller
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Werner Müller
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Dominik Ruckerl
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jarosław Śmieja
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Subhra K. Biswas
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pawel Paszek
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- *Correspondence: Pawel Paszek,
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4
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Downton P, Sanna F, Maidstone R, Poolman TM, Hayter EA, Dickson SH, Ciccone NA, Early JO, Adamson A, Spiller DG, Simpkins DA, Baxter M, Fischer R, Rattray M, Loudon ASI, Gibbs JE, Bechtold DA, Ray DW. Chronic inflammatory arthritis drives systemic changes in circadian energy metabolism. Proc Natl Acad Sci U S A 2022; 119:e2112781119. [PMID: 35482925 PMCID: PMC9170023 DOI: 10.1073/pnas.2112781119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 03/01/2022] [Indexed: 11/22/2022] Open
Abstract
Chronic inflammation underpins many human diseases. Morbidity and mortality associated with chronic inflammation are often mediated through metabolic dysfunction. Inflammatory and metabolic processes vary through circadian time, suggesting an important temporal crosstalk between these systems. Using an established mouse model of rheumatoid arthritis, we show that chronic inflammatory arthritis results in rhythmic joint inflammation and drives major changes in muscle and liver energy metabolism and rhythmic gene expression. Transcriptional and phosphoproteomic analyses revealed alterations in lipid metabolism and mitochondrial function associated with increased EGFR-JAK-STAT3 signaling. Metabolomic analyses confirmed rhythmic metabolic rewiring with impaired β-oxidation and lipid handling and revealed a pronounced shunt toward sphingolipid and ceramide accumulation. The arthritis-related production of ceramides was most pronounced during the day, which is the time of peak inflammation and increased reliance on fatty acid oxidation. Thus, our data demonstrate that localized joint inflammation drives a time-of-day–dependent build-up of bioactive lipid species driven by rhythmic inflammation and altered EGFR-STAT signaling.
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Affiliation(s)
- Polly Downton
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Fabio Sanna
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Robert Maidstone
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Toryn M. Poolman
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Edward A. Hayter
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Suzanna H. Dickson
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Nick A. Ciccone
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - James O. Early
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Antony Adamson
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - David G. Spiller
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Devin A. Simpkins
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Matthew Baxter
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, United Kingdom
| | - Magnus Rattray
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Andrew S. I. Loudon
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Julie E. Gibbs
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - David A. Bechtold
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - David W. Ray
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 9DU, United Kingdom
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5
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Cao K, Riley JS, Heilig R, Montes-Gómez AE, Vringer E, Berthenet K, Cloix C, Elmasry Y, Spiller DG, Ichim G, Campbell KJ, Gilmore AP, Tait SWG. Mitochondrial dynamics regulate genome stability via control of caspase-dependent DNA damage. Dev Cell 2022; 57:1211-1225.e6. [PMID: 35447090 PMCID: PMC9616799 DOI: 10.1016/j.devcel.2022.03.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 05/12/2021] [Revised: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 12/21/2022]
Abstract
Mitochondrial dysfunction is interconnected with cancer. Nevertheless, how defective mitochondria promote cancer is poorly understood. We find that mitochondrial dysfunction promotes DNA damage under conditions of increased apoptotic priming. Underlying this process, we reveal a key role for mitochondrial dynamics in the regulation of DNA damage and genome instability. The ability of mitochondrial dynamics to regulate oncogenic DNA damage centers upon the control of minority mitochondrial outer membrane permeabilization (MOMP), a process that enables non-lethal caspase activation leading to DNA damage. Mitochondrial fusion suppresses minority MOMP and its associated DNA damage by enabling homogeneous mitochondrial expression of anti-apoptotic BCL-2 proteins. Finally, we find that mitochondrial dysfunction inhibits pro-apoptotic BAX retrotranslocation, causing BAX mitochondrial localization and thereby promoting minority MOMP. Unexpectedly, these data reveal oncogenic effects of mitochondrial dysfunction that are mediated via mitochondrial dynamics and caspase-dependent DNA damage. Mitochondrial fission caused by mitochondrial dysfunction promotes DNA damage Minority MOMP occurs on dysfunctional, fragmented mitochondria Inter-mitochondrial heterogeneity in apoptotic priming underpins minority MOMP BAX accumulates on dysfunctional, fragmented mitochondria, sensitizing them to MOMP
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Affiliation(s)
- Kai Cao
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK; Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, People's Republic of China
| | - Joel S Riley
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK; Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Rosalie Heilig
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Alfredo E Montes-Gómez
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Esmee Vringer
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Kevin Berthenet
- Cancer Research Centre of Lyon (CRCL), INSERM 1052, CNRS 5286, Lyon, France; Cancer Cell Death Laboratory, Part of LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Catherine Cloix
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Yassmin Elmasry
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - David G Spiller
- Systems Microscopy, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Gabriel Ichim
- Cancer Research Centre of Lyon (CRCL), INSERM 1052, CNRS 5286, Lyon, France; Cancer Cell Death Laboratory, Part of LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Kirsteen J Campbell
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Andrew P Gilmore
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Stephen W G Tait
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK.
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6
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Koch AA, Bagnall JS, Smyllie NJ, Begley N, Adamson AD, Fribourgh JL, Spiller DG, Meng QJ, Partch CL, Strimmer K, House TA, Hastings MH, Loudon ASI. Quantification of protein abundance and interaction defines a mechanism for operation of the circadian clock. eLife 2022; 11:73976. [PMID: 35285799 PMCID: PMC8983044 DOI: 10.7554/elife.73976] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 09/16/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The mammalian circadian clock exerts control of daily gene expression through cycles of DNA binding. Here, we develop a quantitative model of how a finite pool of BMAL1 protein can regulate thousands of target sites over daily time scales. We used quantitative imaging to track dynamic changes in endogenous labelled proteins across peripheral tissues and the SCN. We determine the contribution of multiple rhythmic processes coordinating BMAL1 DNA binding, including cycling molecular abundance, binding affinities, and repression. We find nuclear BMAL1 concentration determines corresponding CLOCK through heterodimerisation and define a DNA residence time of this complex. Repression of CLOCK:BMAL1 is achieved through rhythmic changes to BMAL1:CRY1 association and high-affinity interactions between PER2:CRY1 which mediates CLOCK:BMAL1 displacement from DNA. Finally, stochastic modelling reveals a dual role for PER:CRY complexes in which increasing concentrations of PER2:CRY1 promotes removal of BMAL1:CLOCK from genes consequently enhancing ability to move to new target sites.
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Affiliation(s)
- Alex Ashton Koch
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James S Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Nicola J Smyllie
- Laboratory of Molecular Biology, Medical Research Council, Cambridge, United Kingdom
| | - Nicola Begley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antony D Adamson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jennifer L Fribourgh
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, United States
| | - David G Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Qing-Jun Meng
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, United States
| | - Korbinian Strimmer
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
| | - Thomas A House
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
| | - Michael H Hastings
- Laboratory of Molecular Biology, Medical Research Council, Cambridge, United Kingdom
| | - Andrew S I Loudon
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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7
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McNamara AV, Awais R, Momiji H, Dunham L, Featherstone K, Harper CV, Adamson AA, Semprini S, Jones NA, Spiller DG, Mullins JJ, Finkenstädt BF, Rand D, White MRH, Davis JRE. Transcription Factor Pit-1 Affects Transcriptional Timing in the Dual-Promoter Human Prolactin Gene. Endocrinology 2021; 162:6060060. [PMID: 33388754 PMCID: PMC7871365 DOI: 10.1210/endocr/bqaa249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Indexed: 12/31/2022]
Abstract
Gene transcription occurs in short bursts interspersed with silent periods, and these kinetics can be altered by promoter structure. The effect of alternate promoter architecture on transcription bursting is not known. We studied the human prolactin (hPRL) gene that contains 2 promoters, a pituitary-specific promoter that requires the transcription factor Pit-1 and displays dramatic transcriptional bursting activity and an alternate upstream promoter that is active in nonpituitary tissues. We studied large hPRL genomic fragments with luciferase reporters, and used bacterial artificial chromosome recombineering to manipulate critical promoter regions. Stochastic switch mathematical modelling of single-cell time-lapse luminescence image data revealed that the Pit-1-dependent promoter showed longer, higher-amplitude transcriptional bursts. Knockdown studies confirmed that the presence of Pit-1 stabilized and prolonged periods of active transcription. Pit-1 therefore plays an active role in establishing the timing of transcription cycles, in addition to its cell-specific functions.
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Affiliation(s)
- Anne V McNamara
- Systems Microscopy Centre, Division of Molecular and Cellular Function, School of Biological Sciences, Faculty Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Raheela Awais
- School of Life Sciences, University of Liverpool, Liverpool, UK
| | - Hiroshi Momiji
- Mathematics Institute & Zeeman Institute for Systems Biology, and Infectious Epidemiology Research, University of Warwick, Senate House Coventry, UK
| | - Lee Dunham
- Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Karen Featherstone
- Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Claire V Harper
- Department of Biology, Edge Hill University, Ormskirk, Lancashire, UK
| | - Antony A Adamson
- Genome Editing Unit, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Sabrina Semprini
- University/BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Nicholas A Jones
- Systems Microscopy Centre, Division of Molecular and Cellular Function, School of Biological Sciences, Faculty Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - David G Spiller
- Systems Microscopy Centre, Division of Molecular and Cellular Function, School of Biological Sciences, Faculty Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - John J Mullins
- University/BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Bärbel F Finkenstädt
- Mathematics Institute & Zeeman Institute for Systems Biology, and Infectious Epidemiology Research, University of Warwick, Senate House Coventry, UK
| | - David Rand
- Mathematics Institute & Zeeman Institute for Systems Biology, and Infectious Epidemiology Research, University of Warwick, Senate House Coventry, UK
| | - Michael R H White
- Systems Microscopy Centre, Division of Molecular and Cellular Function, School of Biological Sciences, Faculty Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Correspondence: Professor Michael R. H. White, Systems Microscopy Centre, Division of Molecular and Cellular Function, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PT, UK. E-mail: ; or Professor Julian R. E. Davis, Division of Diabetes, Endocrinology & Gastroenterology, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, M13 9PT, UK. E-mail:
| | - Julian R E Davis
- Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Correspondence: Professor Michael R. H. White, Systems Microscopy Centre, Division of Molecular and Cellular Function, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PT, UK. E-mail: ; or Professor Julian R. E. Davis, Division of Diabetes, Endocrinology & Gastroenterology, Faculty of Biology, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, M13 9PT, UK. E-mail:
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8
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Harper CV, McNamara AV, Spiller DG, Charnock JC, White MRH, Davis JRE. Calcium dynamics and chromatin remodelling underlie heterogeneity in prolactin transcription. J Mol Endocrinol 2021; 66:59-69. [PMID: 33112804 PMCID: PMC7774774 DOI: 10.1530/jme-20-0223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/20/2020] [Indexed: 12/01/2022]
Abstract
Pituitary cells have been reported to show spontaneous calcium oscillations and dynamic transcription cycles. To study both processes in the same living cell in real time, we used rat pituitary GH3 cells stably expressing human prolactin-luciferase or prolactin-EGFP reporter gene constructs loaded with a fluorescent calcium indicator and measured activity using single-cell time-lapse microscopy. We observed heterogeneity between clonal cells in the calcium activity and prolactin transcription in unstimulated conditions. There was a significant correlation between cells displaying spontaneous calcium spikes and cells showing spontaneous bursts in prolactin expression. Notably, cells showing no basal calcium activity showed low prolactin expression but elicited a significantly greater transcriptional response to BayK8644 compared to cells showing basal calcium activity. This suggested the presence of two subsets of cells within the population at any one time. Fluorescence-activated cell sorting was used to sort cells into two populations based on the expression level of prolactin-EGFP however, the bimodal pattern of expression was restored within 26 h. Chromatin immunoprecipitation showed that these sorted populations were distinct due to the extent of histone acetylation. We suggest that maintenance of a heterogeneous bimodal population is a fundamental characteristic of this cell type and that calcium activation and histone acetylation, at least in part, drive prolactin transcriptional competence.
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Affiliation(s)
- Claire V Harper
- Department of Biology, Edge Hill University, Ormskirk, Lancashire, UK
- Correspondence should be addressed to C V Harper:
| | - Anne V McNamara
- Systems Microscopy Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - David G Spiller
- Systems Microscopy Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jayne C Charnock
- Department of Biology, Edge Hill University, Ormskirk, Lancashire, UK
| | - Michael R H White
- Systems Microscopy Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Julian R E Davis
- Endocrine Sciences Research Group, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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9
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Kershaw S, Morgan DJ, Boyd J, Spiller DG, Kitchen G, Zindy E, Iqbal M, Rattray M, Sanderson CM, Brass A, Jorgensen C, Hussell T, Matthews LC, Ray DW. Glucocorticoids rapidly inhibit cell migration through a novel, non-transcriptional HDAC6 pathway. J Cell Sci 2020; 133:jcs242842. [PMID: 32381682 PMCID: PMC7295589 DOI: 10.1242/jcs.242842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 12/13/2019] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Glucocorticoids (GCs) act through the glucocorticoid receptor (GR, also known as NR3C1) to regulate immunity, energy metabolism and tissue repair. Upon ligand binding, activated GR mediates cellular effects by regulating gene expression, but some GR effects can occur rapidly without new transcription. Here, we show that GCs rapidly inhibit cell migration, in response to both GR agonist and antagonist ligand binding. The inhibitory effect on migration is prevented by GR knockdown with siRNA, confirming GR specificity, but not by actinomycin D treatment, suggesting a non-transcriptional mechanism. We identified a rapid onset increase in microtubule polymerisation following GC treatment, identifying cytoskeletal stabilisation as the likely mechanism of action. HDAC6 overexpression, but not knockdown of αTAT1, rescued the GC effect, implicating HDAC6 as the GR effector. Consistent with this hypothesis, ligand-dependent cytoplasmic interaction between GR and HDAC6 was demonstrated by quantitative imaging. Taken together, we propose that activated GR inhibits HDAC6 function, and thereby increases the stability of the microtubule network to reduce cell motility. We therefore report a novel, non-transcriptional mechanism whereby GCs impair cell motility through inhibition of HDAC6 and rapid reorganization of the cell architecture.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Stephen Kershaw
- Systems Oncology, Cancer Research UK Manchester Institute, Manchester, SK10 4TG, UK
| | - David J Morgan
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology and Inflammation University of Manchester, Manchester, M13 9PT, UK
| | - James Boyd
- Division of Cellular and Molecular Physiology, University of Liverpool, Liverpool, L69 3BX, UK
| | - David G Spiller
- Platform Sciences, Enabling Technologies, and Infrastructure, University of Manchester, Manchester, M13 9PT, UK
| | - Gareth Kitchen
- Division of Diabetes, Endocrinology, and Gastroenterology, University of Manchester, Manchester, M13 9PT, UK
| | - Egor Zindy
- Division of Informatics, Imaging, and Data Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Mudassar Iqbal
- Division of Informatics, Imaging, and Data Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Magnus Rattray
- Division of Informatics, Imaging, and Data Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Christopher M Sanderson
- Division of Cellular and Molecular Physiology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Andrew Brass
- Division of Informatics, Imaging, and Data Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Claus Jorgensen
- Systems Oncology, Cancer Research UK Manchester Institute, Manchester, SK10 4TG, UK
| | - Tracy Hussell
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology and Inflammation University of Manchester, Manchester, M13 9PT, UK
| | - Laura C Matthews
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - David W Ray
- Division of Diabetes, Endocrinology, and Gastroenterology, University of Manchester, Manchester, M13 9PT, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, OX3 7LE, and NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK
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10
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Paszek A, Kardyńska M, Bagnall J, Śmieja J, Spiller DG, Widłak P, Kimmel M, Widlak W, Paszek P. Heat shock response regulates stimulus-specificity and sensitivity of the pro-inflammatory NF-κB signalling. Cell Commun Signal 2020; 18:77. [PMID: 32448393 PMCID: PMC7245923 DOI: 10.1186/s12964-020-00583-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/16/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Ability to adapt to temperature changes trough the Heat Shock Response (HSR) pathways is one of the most fundamental and clinically relevant cellular response systems. Heat Shock (HS) affects the signalling and gene expression responses of the Nuclear Factor κB (NF-κB) transcription factor, a critical regulator of proliferation and inflammation, however, our quantitative understanding of how cells sense and adapt to temperature changes is limited. METHODS We used live-cell time-lapse microscopy and mathematical modelling to understand the signalling of the NF-κB system in the human MCF7 breast adenocarcinoma cells in response to pro-inflammatory Interleukin 1β (IL1β) and Tumour Necrosis Factor α (TNFα) cytokines, following exposure to a 37-43 °C range of physiological and clinical temperatures. RESULTS We show that exposure to 43 °C 1 h HS inhibits the immediate NF-κB signalling response to TNFα and IL1β stimulation although uptake of cytokines is not impaired. Within 4 h after HS treatment IL1β-induced NF-κB responses return to normal levels, but the recovery of the TNFα-induced responses is still affected. Using siRNA knock-down of Heat Shock Factor 1 (HSF1) we show that this stimulus-specificity is conferred via the Inhibitory κB kinase (IKK) signalosome where HSF1-dependent feedback regulates TNFα, but not IL1β-mediated IKK recovery post HS. Furthermore, we demonstrate that through the temperature-dependent denaturation and recovery of IKK, TNFα and IL1β-mediated signalling exhibit different temperature sensitivity and adaptation to repeated HS when exposed to a 37-43 °C temperature range. Specifically, IL1β-mediated NF-κB responses are more robust to temperature changes in comparison to those induced by TNFα treatment. CONCLUSIONS We demonstrate that the kinetics of the NF-κB system following temperature stress is cytokine specific and exhibit differential adaptation to temperature changes. We propose that this differential temperature sensitivity is mediated via the IKK signalosome, which acts as a bona fide temperature sensor trough the HSR cross-talk. This novel quantitative understanding of NF-κB and HSR interactions is fundamentally important for the potential optimization of therapeutic hyperthermia protocols. Video Abstract.
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Affiliation(s)
- Anna Paszek
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
- System Microscopy Centre, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - Małgorzata Kardyńska
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - James Bagnall
- System Microscopy Centre, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Jarosław Śmieja
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - David G. Spiller
- System Microscopy Centre, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Piotr Widłak
- Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - Marek Kimmel
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
- Departments of Statistics and Bioengineering, Rice University, Houston, TX USA
| | - Wieslawa Widlak
- Maria Skłodowska-Curie National Research Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - Pawel Paszek
- System Microscopy Centre, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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11
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Yang N, Smyllie NJ, Morris H, Gonçalves CF, Dudek M, Pathiranage DRJ, Chesham JE, Adamson A, Spiller DG, Zindy E, Bagnall J, Humphreys N, Hoyland J, Loudon ASI, Hastings MH, Meng QJ. Quantitative live imaging of Venus::BMAL1 in a mouse model reveals complex dynamics of the master circadian clock regulator. PLoS Genet 2020; 16:e1008729. [PMID: 32352975 PMCID: PMC7217492 DOI: 10.1371/journal.pgen.1008729] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/12/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022] Open
Abstract
Evolutionarily conserved circadian clocks generate 24-hour rhythms in physiology and behaviour that adapt organisms to their daily and seasonal environments. In mammals, the suprachiasmatic nucleus (SCN) of the hypothalamus is the principal co-ordinator of the cell-autonomous clocks distributed across all major tissues. The importance of robust daily rhythms is highlighted by experimental and epidemiological associations between circadian disruption and human diseases. BMAL1 (a bHLH-PAS domain-containing transcription factor) is the master positive regulator within the transcriptional-translational feedback loops (TTFLs) that cell-autonomously define circadian time. It drives transcription of the negative regulators Period and Cryptochrome alongside numerous clock output genes, and thereby powers circadian time-keeping. Because deletion of Bmal1 alone is sufficient to eliminate circadian rhythms in cells and the whole animal it has been widely used as a model for molecular disruption of circadian rhythms, revealing essential, tissue-specific roles of BMAL1 in, for example, the brain, liver and the musculoskeletal system. Moreover, BMAL1 has clock-independent functions that influence ageing and protein translation. Despite the essential role of BMAL1 in circadian time-keeping, direct measures of its intra-cellular behaviour are still lacking. To fill this knowledge-gap, we used CRISPR Cas9 to generate a mouse expressing a knock-in fluorescent fusion of endogenous BMAL1 protein (Venus::BMAL1) for quantitative live imaging in physiological settings. The Bmal1Venus mouse model enabled us to visualise and quantify the daily behaviour of this core clock factor in central (SCN) and peripheral clocks, with single-cell resolution that revealed its circadian expression, anti-phasic to negative regulators, nuclear-cytoplasmic mobility and molecular abundance.
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Affiliation(s)
- Nan Yang
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, United Kingdom
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Nicola J. Smyllie
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Honor Morris
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, United Kingdom
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Cátia F. Gonçalves
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, United Kingdom
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michal Dudek
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, United Kingdom
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Dharshika R. J. Pathiranage
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, United Kingdom
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Johanna E. Chesham
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Antony Adamson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David G. Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Egor Zindy
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Neil Humphreys
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Judith Hoyland
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- NIHR Manchester Musculoskeletal Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Andrew S. I. Loudon
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michael H. Hastings
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Qing-Jun Meng
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, United Kingdom
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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12
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Papoutsopoulou S, Burkitt MD, Bergey F, England H, Hough R, Schmidt L, Spiller DG, White MHR, Paszek P, Jackson DA, Martins Dos Santos VAP, Sellge G, Pritchard DM, Campbell BJ, Müller W, Probert CS. Macrophage-Specific NF-κB Activation Dynamics Can Segregate Inflammatory Bowel Disease Patients. Front Immunol 2019; 10:2168. [PMID: 31572379 PMCID: PMC6749845 DOI: 10.3389/fimmu.2019.02168] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/28/2019] [Indexed: 01/14/2023] Open
Abstract
The heterogeneous nature of inflammatory bowel disease (IBD) presents challenges, particularly when choosing therapy. Activation of the NF-κB transcription factor is a highly regulated, dynamic event in IBD pathogenesis. Using a lentivirus approach, NF-κB-regulated luciferase was expressed in patient macrophages, isolated from frozen peripheral blood mononuclear cell samples. Following activation, samples could be segregated into three clusters based on the NF-κB-regulated luciferase response. The ulcerative colitis (UC) samples appeared only in the hypo-responsive Cluster 1, and in Cluster 2. Conversely, Crohn's disease (CD) patients appeared in all Clusters with their percentage being higher in the hyper-responsive Cluster 3. A positive correlation was seen between NF-κB-induced luciferase activity and the concentrations of cytokines released into medium from stimulated macrophages, but not with serum or biopsy cytokine levels. Confocal imaging of lentivirally-expressed p65 activation revealed that a higher proportion of macrophages from CD patients responded to endotoxin lipid A compared to controls. In contrast, cells from UC patients exhibited a shorter duration of NF-κB p65 subunit nuclear localization compared to healthy controls, and CD donors. Analysis of macrophage cytokine responses and patient metadata revealed a strong correlation between CD patients who smoked and hyper-activation of p65. These in vitro dynamic assays of NF-κB activation in blood-derived macrophages have the potential to segregate IBD patients into groups with different phenotypes and may therefore help determine response to therapy.
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Affiliation(s)
- Stamatia Papoutsopoulou
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.,Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Michael D Burkitt
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | | | - Hazel England
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Rachael Hough
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Lorraine Schmidt
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - David G Spiller
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Michael H R White
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Pawel Paszek
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Dean A Jackson
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Vitor A P Martins Dos Santos
- LifeGlimmer GmbH, Berlin, Germany.,Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, Netherlands
| | | | - D Mark Pritchard
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Barry J Campbell
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Werner Müller
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Chris S Probert
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
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13
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McDonnell SJ, Spiller DG, White MRH, Prior IA, Paraoan L. ER stress-linked autophagy stabilizes apoptosis effector PERP and triggers its co-localization with SERCA2b at ER-plasma membrane junctions. Cell Death Discov 2019; 5:132. [PMID: 31508245 PMCID: PMC6718399 DOI: 10.1038/s41420-019-0212-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 06/19/2019] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 01/01/2023] Open
Abstract
Specific molecular interactions that underpin the switch between ER stress-triggered autophagy-mediated cellular repair and cellular death by apoptosis are not characterized. This study reports the unexpected interaction elicited by ER stress between the plasma membrane (PM)-localized apoptosis effector PERP and the ER Ca2+ pump SERCA2b. We show that the p53 effector PERP, which specifically induces apoptosis when expressed above a threshold level, has a heterogeneous distribution across the PM of un-stressed cells and is actively turned over by the lysosome. PERP is upregulated following sustained starvation-induced autophagy, which precedes the onset of apoptosis indicating that PERP protein levels are controlled by a lysosomal pathway that is sensitive to cellular physiological state. Furthermore, ER stress stabilizes PERP at the PM and induces its increasing co-localization with SERCA2b at ER–PM junctions. The findings highlight a novel crosstalk between pro-survival autophagy and pro-death apoptosis pathways and identify, for the first time, accumulation of an apoptosis effector to ER–PM junctions in response to ER stress.
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Affiliation(s)
- Samantha J McDonnell
- 1Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX UK
| | - David G Spiller
- 2Systems Microscopy Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT UK
| | - Michael R H White
- 3School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT UK
| | - Ian A Prior
- 4Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX UK
| | - Luminita Paraoan
- 1Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX UK
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14
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Manning CS, Biga V, Boyd J, Kursawe J, Ymisson B, Spiller DG, Sanderson CM, Galla T, Rattray M, Papalopulu N. Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis. Nat Commun 2019; 10:2835. [PMID: 31249377 PMCID: PMC6597611 DOI: 10.1038/s41467-019-10734-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 08/15/2018] [Accepted: 05/17/2019] [Indexed: 12/17/2022] Open
Abstract
During embryogenesis cells make fate decisions within complex tissue environments. The levels and dynamics of transcription factor expression regulate these decisions. Here, we use single cell live imaging of an endogenous HES5 reporter and absolute protein quantification to gain a dynamic view of neurogenesis in the embryonic mammalian spinal cord. We report that dividing neural progenitors show both aperiodic and periodic HES5 protein fluctuations. Mathematical modelling suggests that in progenitor cells the HES5 oscillator operates close to its bifurcation boundary where stochastic conversions between dynamics are possible. HES5 expression becomes more frequently periodic as cells transition to differentiation which, coupled with an overall decline in HES5 expression, creates a transient period of oscillations with higher fold expression change. This increases the decoding capacity of HES5 oscillations and correlates with interneuron versus motor neuron cell fate. Thus, HES5 undergoes complex changes in gene expression dynamics as cells differentiate.
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Affiliation(s)
- Cerys S. Manning
- School of Medical Sciences, Division of Developmental Biology and Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | - Veronica Biga
- School of Medical Sciences, Division of Developmental Biology and Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | - James Boyd
- Department of Cellular and Molecular Physiology, University of Liverpool, Crown Street, Liverpool, L69 3BX UK
| | - Jochen Kursawe
- School of Medical Sciences, Division of Developmental Biology and Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | - Bodvar Ymisson
- School of Medical Sciences, Division of Developmental Biology and Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | - David G. Spiller
- School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | - Christopher M. Sanderson
- Department of Cellular and Molecular Physiology, University of Liverpool, Crown Street, Liverpool, L69 3BX UK
| | - Tobias Galla
- Theoretical Physics Division, School of Physics and Astronomy, University of Manchester, Manchester, M13 9PL UK
| | - Magnus Rattray
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | - Nancy Papalopulu
- School of Medical Sciences, Division of Developmental Biology and Medicine, Faculty of Biology Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT UK
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15
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Momiji H, Hassall KL, Featherstone K, McNamara AV, Patist AL, Spiller DG, Christian HC, White MRH, Davis JRE, Finkenstädt BF, Rand DA. Disentangling juxtacrine from paracrine signalling in dynamic tissue. PLoS Comput Biol 2019; 15:e1007030. [PMID: 31194728 PMCID: PMC6592563 DOI: 10.1371/journal.pcbi.1007030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/25/2019] [Accepted: 04/15/2019] [Indexed: 11/18/2022] Open
Abstract
Prolactin is a major hormone product of the pituitary gland, the central endocrine regulator. Despite its physiological importance, the cell-level mechanisms of prolactin production are not well understood. Having significantly improved the resolution of real-time-single-cell-GFP-imaging, the authors recently revealed that prolactin gene transcription is highly dynamic and stochastic yet shows space-time coordination in an intact tissue slice. However, it still remains an open question as to what kind of cellular communication mediates the observed space-time organization. To determine the type of interaction between cells we developed a statistical model. The degree of similarity between two expression time series was studied in terms of two distance measures, Euclidean and geodesic, the latter being a network-theoretic distance defined to be the minimal number of edges between nodes, and this was used to discriminate between juxtacrine from paracrine signalling. The analysis presented here suggests that juxtacrine signalling dominates. To further determine whether the coupling is coordinating transcription or post-transcriptional activities we used stochastic switch modelling to infer the transcriptional profiles of cells and estimated their similarity measures to deduce that their spatial cellular coordination involves coupling of transcription via juxtacrine signalling. We developed a computational model that involves an inter-cell juxtacrine coupling, yielding simulation results that show space-time coordination in the transcription level that is in agreement with the above analysis. The developed model is expected to serve as the prototype for the further study of tissue-level organised gene expression for epigenetically regulated genes, such as prolactin.
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Affiliation(s)
- Hiroshi Momiji
- Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom, Mathematics Institute, University of Warwick, Coventry, United Kingdom
- * E-mail: (HM); (MRHW); (JRED); (BFF); (DAR)
| | - Kirsty L. Hassall
- Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Karen Featherstone
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
| | - Anne V. McNamara
- Systems Microscopy Centre, University of Manchester, Manchester, United Kingdom
| | - Amanda L. Patist
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
| | - David G. Spiller
- Systems Microscopy Centre, University of Manchester, Manchester, United Kingdom
| | - Helen C. Christian
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Michael R. H. White
- Systems Microscopy Centre, University of Manchester, Manchester, United Kingdom
- * E-mail: (HM); (MRHW); (JRED); (BFF); (DAR)
| | - Julian R. E. Davis
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
- * E-mail: (HM); (MRHW); (JRED); (BFF); (DAR)
| | - Bärbel F. Finkenstädt
- Department of Statistics, University of Warwick, Coventry, United Kingdom
- * E-mail: (HM); (MRHW); (JRED); (BFF); (DAR)
| | - David A. Rand
- Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom, Mathematics Institute, University of Warwick, Coventry, United Kingdom
- * E-mail: (HM); (MRHW); (JRED); (BFF); (DAR)
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16
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Bagnall J, Boddington C, England H, Brignall R, Downton P, Alsoufi Z, Boyd J, Rowe W, Bennett A, Walker C, Adamson A, Patel NMX, O’Cualain R, Schmidt L, Spiller DG, Jackson DA, Müller W, Muldoon M, White MRH, Paszek P. Quantitative analysis of competitive cytokine signaling predicts tissue thresholds for the propagation of macrophage activation. Sci Signal 2018; 11:11/540/eaaf3998. [DOI: 10.1126/scisignal.aaf3998] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Vranic S, Rodrigues AF, Buggio M, Newman L, White MRH, Spiller DG, Bussy C, Kostarelos K. Live Imaging of Label-Free Graphene Oxide Reveals Critical Factors Causing Oxidative-Stress-Mediated Cellular Responses. ACS Nano 2018; 12:1373-1389. [PMID: 29286639 DOI: 10.1021/acsnano.7b07734] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The interest in graphene and its translation into commercial products has been expanding at a high pace. Based on previously described pulmonary safety concerns for carbon nanomaterials, there is a great need to define parameters guiding interactions between graphene-based materials and the pulmonary system. The aim of the present study was to determine the importance of two critical parameters: lateral dimensions of the material and coating with proteins in relation to each other and their pulmonary impact. Endotoxin-free materials with distinct lateral dimensions, s-GO (50-200 nm) and l-GO (5-15 μm), were produced and thoroughly characterized. Exploiting intrinsic fluorescence of graphene oxide (GO) and using confocal live-cell imaging, the behavior of the cells in response to the material was visualized in real time. Although BEAS-2B cells internalized GO efficiently, l-GO was linked to higher plasma membrane interactions correlated with elevated reactive oxygen species (ROS) levels, pro-inflammatory response, and greater cytotoxicity, in agreement with the oxidative stress paradigm. For both GO types, the presence of serum alleviated lipid peroxidation of plasma membrane and decreased intracellular ROS levels. However, protein coating was not enough to entirely mitigate toxicity and inflammatory response induced by l-GO. In vitro results were validated in vivo, as l-GO was more prone to induce pulmonary granulomatous response in mice compared to s-GO. In conclusion, the lateral dimension of GO played a more important role than serum protein coating in determining biological responses to the material. It was also demonstrated that time-lapse imaging of live cells interacting with label-free GO sheets can be used as a tool to assess GO-induced cytotoxicity.
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Affiliation(s)
- Sandra Vranic
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, The University of Manchester , AV Hill Building, Manchester M13 9PT, U.K
- National Graphene Institute, The University of Manchester , Booth Street East, Manchester M13 9PL, U.K
| | - Artur Filipe Rodrigues
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, The University of Manchester , AV Hill Building, Manchester M13 9PT, U.K
- National Graphene Institute, The University of Manchester , Booth Street East, Manchester M13 9PL, U.K
| | - Maurizio Buggio
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, The University of Manchester , AV Hill Building, Manchester M13 9PT, U.K
- National Graphene Institute, The University of Manchester , Booth Street East, Manchester M13 9PL, U.K
| | - Leon Newman
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, The University of Manchester , AV Hill Building, Manchester M13 9PT, U.K
- National Graphene Institute, The University of Manchester , Booth Street East, Manchester M13 9PL, U.K
| | - Michael R H White
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester , Michael Smith Building, Manchester M13 9PT, U.K
| | - David G Spiller
- FBMH Platform Sciences, Enabling Technologies & Infrastructure, FBMH Research & Innovation, Faculty of Biology, Medicine and Health, The University of Manchester , Michael Smith Building, Manchester M13 9PT, U.K
| | - Cyrill Bussy
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, The University of Manchester , AV Hill Building, Manchester M13 9PT, U.K
- National Graphene Institute, The University of Manchester , Booth Street East, Manchester M13 9PL, U.K
| | - Kostas Kostarelos
- Nanomedicine Lab, Faculty of Biology, Medicine and Health, The University of Manchester , AV Hill Building, Manchester M13 9PT, U.K
- National Graphene Institute, The University of Manchester , Booth Street East, Manchester M13 9PL, U.K
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18
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Dunham LSS, Momiji H, Harper CV, Downton PJ, Hey K, McNamara A, Featherstone K, Spiller DG, Rand DA, Finkenstädt B, White MRH, Davis JRE. Asymmetry between Activation and Deactivation during a Transcriptional Pulse. Cell Syst 2017; 5:646-653.e5. [PMID: 29153839 PMCID: PMC5747351 DOI: 10.1016/j.cels.2017.10.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 08/04/2017] [Accepted: 10/18/2017] [Indexed: 11/23/2022]
Abstract
Transcription in eukaryotic cells occurs in gene-specific bursts or pulses of activity. Recent studies identified a spectrum of transcriptionally active “on-states,” interspersed with periods of inactivity, but these “off-states” and the process of transcriptional deactivation are poorly understood. To examine what occurs during deactivation, we investigate the dynamics of switching between variable rates. We measured live single-cell expression of luciferase reporters from human growth hormone or human prolactin promoters in a pituitary cell line. Subsequently, we applied a statistical variable-rate model of transcription, validated by single-molecule FISH, to estimate switching between transcriptional rates. Under the assumption that transcription can switch to any rate at any time, we found that transcriptional activation occurs predominantly as a single switch, whereas deactivation occurs with graded, stepwise decreases in transcription rate. Experimentally altering cAMP signalling with forskolin or chromatin remodelling with histone deacetylase inhibitor modifies the duration of defined transcriptional states. Our findings reveal transcriptional activation and deactivation as mechanistically independent, asymmetrical processes. Gene transcription switches between variable rates Single-cell microscopy and mathematical modeling quantifies switch dynamics We observe an asymmetry in the activation/deactivation of transcriptional bursts
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Affiliation(s)
- Lee S S Dunham
- Division of Endocrinology, Diabetes and Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Manchester M13 9PT, UK
| | - Hiroshi Momiji
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4, 7AL, UK
| | - Claire V Harper
- Division of Cellular and Molecular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Polly J Downton
- Division of Cellular and Molecular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Kirsty Hey
- Department of Statistics, University of Warwick, Coventry CV4 7AL, UK
| | - Anne McNamara
- Division of Cellular and Molecular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Karen Featherstone
- Division of Endocrinology, Diabetes and Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Manchester M13 9PT, UK
| | - David G Spiller
- Division of Cellular and Molecular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - David A Rand
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4, 7AL, UK
| | | | - Michael R H White
- Division of Cellular and Molecular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK.
| | - Julian R E Davis
- Division of Endocrinology, Diabetes and Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Manchester M13 9PT, UK.
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19
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Abstract
The mammalian NUDT13 protein possesses a sequence motif characteristic of the NADH pyrophosphohydrolase subfamily of Nudix hydrolases. Due to the persistent insolubility of the recombinant product expressed in Escherichia coli, active mouse Nudt13 was expressed in insect cells from a baculovirus vector as a histidine-tagged recombinant protein. In vitro, it efficiently hydrolysed NADH to NMNH and AMP and NADPH to NMNH and 2',5'-ADP and had a marked preference for the reduced pyridine nucleotides. Much lower activity was obtained with other nucleotide substrates tested. K m and k cat values for NADH were 0.34 mM and 7 s-1 respectively. Expression of Nudt13 as an N-terminal fusion to green fluorescent protein revealed that it was targeted exclusively to mitochondria by the N-terminal targeting peptide, suggesting that Nudt13 may act to regulate the concentration of mitochondrial reduced pyridine nucleotide cofactors and the NAD(P)+/NAD(P)H ratio in this organelle and elsewhere. Future studies of the enzymology of pyridine nucleotide metabolism in relation to energy homeostasis, redox control, free radical production and cellular integrity should consider the possible regulatory role of Nudt13.
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Affiliation(s)
- Salama R Abdelraheim
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Department of Biochemistry, Faculty of Medicine, Minia University, Minia, 61519, Egypt
| | - David G Spiller
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Faculty of Biology, Medicine and Health, Systems Microscopy Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Alexander G McLennan
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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20
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Awais R, Spiller DG, White MRH, Paraoan L. p63 is required beside p53 for PERP-mediated apoptosis in uveal melanoma. Br J Cancer 2016; 115:983-992. [PMID: 27584665 PMCID: PMC5061904 DOI: 10.1038/bjc.2016.269] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 06/05/2016] [Revised: 07/31/2016] [Accepted: 08/02/2016] [Indexed: 12/23/2022] Open
Abstract
Background: PERP (p53 apoptosis effector related to PMP-22), a transcriptional target of p53, is downregulated and contributes to the impairment of apoptosis in uveal melanoma (UM). Intriguingly, PERP is not induced in UM despite functional p53. p63, located on chromosome 3, which is characteristically altered in high-risk UM, can transactivate PERP. Here, we determine the functional role of p63 expression in the initiation of p53/PERP-mediated apoptosis in UM. Methods: PERP expression was monitored by quantitative PCR (qPCR) and immunoblotting in UM cell lines treated with DNA-damaging agents. The functional role of p63 was assessed by transient expression of p63-turbo GFP (p63-tGFP) in the apoptosis- resistant, 3q-deficient OCM-1 cells. Expression and localisation of p63, PERP and p53, and induction of apoptosis were characterised by qPCR, immunoblotting and live cell confocal microscopy. Results: PERP expression was significantly downregulated in all UM cell lines. DNA-damaging treatments failed to induce apoptosis and activate PERP in OCM-1 cells, which displayed non-functional levels of p63. Expression of p63-tGFP induced apoptosis with marked increase in PERP expression and associated p53 accumulation. Conclusions: Lack of p63 contributes to reduced PERP levels and impaired p53-mediated apoptosis in UM. p63 expression is required for PERP-mediated apoptosis in UM.
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Affiliation(s)
- Raheela Awais
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - David G Spiller
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Michael R H White
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Luminita Paraoan
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
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21
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Adamson A, Boddington C, Downton P, Rowe W, Bagnall J, Lam C, Maya-Mendoza A, Schmidt L, Harper CV, Spiller DG, Rand DA, Jackson DA, White MRH, Paszek P. Signal transduction controls heterogeneous NF-κB dynamics and target gene expression through cytokine-specific refractory states. Nat Commun 2016; 7:12057. [PMID: 27381163 PMCID: PMC4935804 DOI: 10.1038/ncomms12057] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 05/25/2016] [Indexed: 02/03/2023] Open
Abstract
Cells respond dynamically to pulsatile cytokine stimulation. Here we report that single, or well-spaced pulses of TNFα (>100 min apart) give a high probability of NF-κB activation. However, fewer cells respond to shorter pulse intervals (<100 min) suggesting a heterogeneous refractory state. This refractory state is established in the signal transduction network downstream of TNFR and upstream of IKK, and depends on the level of the NF-κB system negative feedback protein A20. If a second pulse within the refractory phase is IL-1β instead of TNFα, all of the cells respond. This suggests a mechanism by which two cytokines can synergistically activate an inflammatory response. Gene expression analyses show strong correlation between the cellular dynamic response and NF-κB-dependent target gene activation. These data suggest that refractory states in the NF-κB system constitute an inherent design motif of the inflammatory response and we suggest that this may avoid harmful homogenous cellular activation.
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Affiliation(s)
- Antony Adamson
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Christopher Boddington
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Polly Downton
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - William Rowe
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - James Bagnall
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Connie Lam
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Apolinar Maya-Mendoza
- The Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Lorraine Schmidt
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Claire V. Harper
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David G. Spiller
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David A. Rand
- Warwick Systems Biology and Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
| | - Dean A. Jackson
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Michael R. H. White
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Pawel Paszek
- Systems Microscopy Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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22
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Smyllie NJ, Pilorz V, Boyd J, Meng QJ, Saer B, Chesham JE, Maywood ES, Krogager TP, Spiller DG, Boot-Handford R, White MRH, Hastings MH, Loudon ASI. Visualizing and Quantifying Intracellular Behavior and Abundance of the Core Circadian Clock Protein PERIOD2. Curr Biol 2016; 26:1880-6. [PMID: 27374340 PMCID: PMC4963210 DOI: 10.1016/j.cub.2016.05.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/03/2016] [Accepted: 05/05/2016] [Indexed: 11/24/2022]
Abstract
Transcriptional-translational feedback loops (TTFLs) are a conserved molecular motif of circadian clocks. The principal clock in mammals is the suprachiasmatic nucleus (SCN) of the hypothalamus. In SCN neurons, auto-regulatory feedback on core clock genes Period (Per) and Cryptochrome (Cry) following nuclear entry of their protein products is the basis of circadian oscillation [1, 2]. In Drosophila clock neurons, the movement of dPer into the nucleus is subject to a circadian gate that generates a delay in the TTFL, and this delay is thought to be critical for oscillation [3, 4]. Analysis of the Drosophila clock has strongly influenced models of the mammalian clock, and such models typically infer complex spatiotemporal, intracellular behaviors of mammalian clock proteins. There are, however, no direct measures of the intracellular behavior of endogenous circadian proteins to support this: dynamic analyses have been limited and often have no circadian dimension [5, 6, 7]. We therefore generated a knockin mouse expressing a fluorescent fusion of native PER2 protein (PER2::VENUS) for live imaging. PER2::VENUS recapitulates the circadian functions of wild-type PER2 and, importantly, the behavior of PER2::VENUS runs counter to the Drosophila model: it does not exhibit circadian gating of nuclear entry. Using fluorescent imaging of PER2::VENUS, we acquired the first measures of mobility, molecular concentration, and localization of an endogenous circadian protein in individual mammalian cells, and we showed how the mobility and nuclear translocation of PER2 are regulated by casein kinase. These results provide new qualitative and quantitative insights into the cellular mechanism of the mammalian circadian clock. Reporter mouse is used for real-time fluorescent imaging of mammalian clock protein PER2 In contrast to Drosophila, localization of PER2 is not subject to circadian gating Circadian abundance, mobility, and intracellular dynamics of native PER2 are quantified Casein kinase1 controls nucleocytoplasmic mobility of PER2 alongside circadian period
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Affiliation(s)
- Nicola J Smyllie
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Violetta Pilorz
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - James Boyd
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Qing-Jun Meng
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Ben Saer
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Johanna E Chesham
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Elizabeth S Maywood
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Toke P Krogager
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David G Spiller
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Raymond Boot-Handford
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Michael R H White
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Michael H Hastings
- Neurobiology Division, Medical Research Council (MRC) Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Andrew S I Loudon
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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23
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Ankers JM, Awais R, Jones NA, Boyd J, Ryan S, Adamson AD, Harper CV, Bridge L, Spiller DG, Jackson DA, Paszek P, Sée V, White MR. Dynamic NF-κB and E2F interactions control the priority and timing of inflammatory signalling and cell proliferation. eLife 2016; 5. [PMID: 27185527 PMCID: PMC4869934 DOI: 10.7554/elife.10473] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [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: 07/30/2015] [Accepted: 04/13/2016] [Indexed: 01/07/2023] Open
Abstract
Dynamic cellular systems reprogram gene expression to ensure appropriate cellular fate responses to specific extracellular cues. Here we demonstrate that the dynamics of Nuclear Factor kappa B (NF-κB) signalling and the cell cycle are prioritised differently depending on the timing of an inflammatory signal. Using iterative experimental and computational analyses, we show physical and functional interactions between NF-κB and the E2 Factor 1 (E2F-1) and E2 Factor 4 (E2F-4) cell cycle regulators. These interactions modulate the NF-κB response. In S-phase, the NF-κB response was delayed or repressed, while cell cycle progression was unimpeded. By contrast, activation of NF-κB at the G1/S boundary resulted in a longer cell cycle and more synchronous initial NF-κB responses between cells. These data identify new mechanisms by which the cellular response to stress is differentially controlled at different stages of the cell cycle. DOI:http://dx.doi.org/10.7554/eLife.10473.001 Investigating how cells adapt to the constantly changing environment inside the body is vitally important for understanding how the body responds to an injury or infection. One of the ways in which human cells adapt is by dividing to produce new cells. This takes place in a repeating pattern of events, known as the cell cycle, through which a cell copies its DNA (in a stage known as S-phase) and then divides to make two daughter cells. Each stage of the cell cycle is tightly controlled; for example, a family of proteins called E2 factors control the entry of the cell into S phase. “Inflammatory” signals produced by a wound or during an infection can activate a protein called Nuclear Factor-kappaB (NF-κB), which controls the activity of genes that allow cells to adapt to the situation. Research shows that the activity of NF-κB is also regulated by the cell cycle, but it has not been clear how this works. Here, Ankers et al. investigated whether the stage of the cell cycle might affect how NF-κB responds to inflammatory signals. The experiments show that the NF-κB response was stronger in cells that were just about to enter S-phase than in cells that were already copying their DNA. An E2 factor called E2F-1 –which accumulates in the run up to S-phase – interacts with NF-κB and can alter the activity of certain genes. However, during S-phase, another E2 factor family member called E2F-4 binds to NF-κB and represses its activation. Next, Ankers et al. used a mathematical model to understand how these protein interactions can affect the response of cells to inflammatory signals. These findings suggest that direct interactions between E2 factor proteins and NF-κB enable cells to decide whether to divide or react in different ways to inflammatory signals. The research tools developed in this study, combined with other new experimental techniques, will allow researchers to accurately predict how cells will respond to inflammatory signals at different points in the cell cycle. DOI:http://dx.doi.org/10.7554/eLife.10473.002
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Affiliation(s)
- John M Ankers
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom
| | - Raheela Awais
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom.,Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Nicholas A Jones
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - James Boyd
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Sheila Ryan
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom.,Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Antony D Adamson
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Claire V Harper
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Lloyd Bridge
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom.,Department of Mathematics, University of Swansea, Swansea, United Kingdom
| | - David G Spiller
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Dean A Jackson
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Pawel Paszek
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Violaine Sée
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom
| | - Michael Rh White
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
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24
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Featherstone K, Hey K, Momiji H, McNamara AV, Patist AL, Woodburn J, Spiller DG, Christian HC, McNeilly AS, Mullins JJ, Finkenstädt BF, Rand DA, White MRH, Davis JRE. Spatially coordinated dynamic gene transcription in living pituitary tissue. eLife 2016; 5:e08494. [PMID: 26828110 PMCID: PMC4749562 DOI: 10.7554/elife.08494] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 12/13/2015] [Indexed: 12/22/2022] Open
Abstract
Transcription at individual genes in single cells is often pulsatile and stochastic. A key question emerges regarding how this behaviour contributes to tissue phenotype, but it has been a challenge to quantitatively analyse this in living cells over time, as opposed to studying snap-shots of gene expression state. We have used imaging of reporter gene expression to track transcription in living pituitary tissue. We integrated live-cell imaging data with statistical modelling for quantitative real-time estimation of the timing of switching between transcriptional states across a whole tissue. Multiple levels of transcription rate were identified, indicating that gene expression is not a simple binary 'on-off' process. Immature tissue displayed shorter durations of high-expressing states than the adult. In adult pituitary tissue, direct cell contacts involving gap junctions allowed local spatial coordination of prolactin gene expression. Our findings identify how heterogeneous transcriptional dynamics of single cells may contribute to overall tissue behaviour.
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Affiliation(s)
- Karen Featherstone
- Centre for Endocrinology and Diabetes, University of Manchester, Manchester, United Kingdom
| | - Kirsty Hey
- Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Hiroshi Momiji
- Warwick Systems Biology, University of Warwick, Coventry, United Kingdom
| | - Anne V McNamara
- Systems Biology Centre, University of Manchester, Manchester, United Kingdom
| | - Amanda L Patist
- Centre for Endocrinology and Diabetes, University of Manchester, Manchester, United Kingdom
| | - Joanna Woodburn
- Centre for Endocrinology and Diabetes, University of Manchester, Manchester, United Kingdom
| | - David G Spiller
- Systems Biology Centre, University of Manchester, Manchester, United Kingdom
| | - Helen C Christian
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Alan S McNeilly
- MRC Centre for Reproductive Health, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - John J Mullins
- The Molecular Physiology Group, Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - David A Rand
- Warwick Systems Biology, University of Warwick, Coventry, United Kingdom
| | - Michael RH White
- Systems Biology Centre, University of Manchester, Manchester, United Kingdom
| | - Julian RE Davis
- Centre for Endocrinology and Diabetes, University of Manchester, Manchester, United Kingdom
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25
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Phillips NE, Manning CS, Pettini T, Biga V, Marinopoulou E, Stanley P, Boyd J, Bagnall J, Paszek P, Spiller DG, White MRH, Goodfellow M, Galla T, Rattray M, Papalopulu N. Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation. eLife 2016; 5:e16118. [PMID: 27700985 PMCID: PMC5050025 DOI: 10.7554/elife.16118] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 03/17/2016] [Accepted: 08/24/2016] [Indexed: 01/27/2023] Open
Abstract
Recent studies suggest that cells make stochastic choices with respect to differentiation or division. However, the molecular mechanism underlying such stochasticity is unknown. We previously proposed that the timing of vertebrate neuronal differentiation is regulated by molecular oscillations of a transcriptional repressor, HES1, tuned by a post-transcriptional repressor, miR-9. Here, we computationally model the effects of intrinsic noise on the Hes1/miR-9 oscillator as a consequence of low molecular numbers of interacting species, determined experimentally. We report that increased stochasticity spreads the timing of differentiation in a population, such that initially equivalent cells differentiate over a period of time. Surprisingly, inherent stochasticity also increases the robustness of the progenitor state and lessens the impact of unequal, random distribution of molecules at cell division on the temporal spread of differentiation at the population level. This advantageous use of biological noise contrasts with the view that noise needs to be counteracted.
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Affiliation(s)
- Nick E Phillips
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Cerys S Manning
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Tom Pettini
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Veronica Biga
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Elli Marinopoulou
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Peter Stanley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James Boyd
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Pawel Paszek
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David G Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michael RH White
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Marc Goodfellow
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom,Centre for Biomedical Modelling and Analysis, University of Exeter, Exeter, United Kingdom,EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Tobias Galla
- Theoretical Physics, School of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Nancy Papalopulu
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom,
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26
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McNamara AV, Adamson AD, Dunham LSS, Semprini S, Spiller DG, McNeilly AS, Mullins JJ, Davis JRE, White MRH. Role of Estrogen Response Element in the Human Prolactin Gene: Transcriptional Response and Timing. Mol Endocrinol 2015; 30:189-200. [PMID: 26691151 PMCID: PMC4792233 DOI: 10.1210/me.2015-1186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The use of bacterial artificial chromosome (BAC) reporter constructs in molecular physiology enables the inclusion of large sections of flanking DNA, likely to contain regulatory elements and enhancers regions that contribute to the transcriptional output of a gene. Using BAC recombineering, we have manipulated a 160-kb human prolactin luciferase (hPRL-Luc) BAC construct and mutated the previously defined proximal estrogen response element (ERE) located -1189 bp relative to the transcription start site, to assess its involvement in the estrogen responsiveness of the entire hPRL locus. We found that GH3 cell lines stably expressing Luc under control of the ERE-mutated hPRL promoter (ERE-Mut) displayed a dramatically reduced transcriptional response to 17β-estradiol (E2) treatment compared with cells expressing Luc from the wild-type (WT) ERE hPRL-Luc promoter (ERE-WT). The -1189 ERE controls not only the response to E2 treatment but also the acute transcriptional response to TNFα, which was abolished in ERE-Mut cells. ERE-WT cells displayed a biphasic transcriptional response after TNFα treatment, the acute phase of which was blocked after treatment with the estrogen receptor antagonist 4-hydroxy-tamoxifen. Unexpectedly, we show the oscillatory characteristics of hPRL promoter activity in individual living cells were unaffected by disruption of this crucial response element, real-time bioluminescence imaging showed that transcription cycles were maintained, with similar cycle lengths, in ERE-WT and ERE-Mut cells. These data suggest the -1189 ERE is the dominant response element involved in the hPRL transcriptional response to both E2 and TNFα and, crucially, that cycles of hPRL promoter activity are independent of estrogen receptor binding.
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Affiliation(s)
- Anne V McNamara
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Antony D Adamson
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Lee S S Dunham
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Sabrina Semprini
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - David G Spiller
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Alan S McNeilly
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - John J Mullins
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Julian R E Davis
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Michael R H White
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
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Rand U, Spiller DG, Adamson A, Cicin-Sain L, White MR. ID: 183. Cytokine 2015. [DOI: 10.1016/j.cyto.2015.08.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bagnall J, Leedale J, Taylor SE, Spiller DG, White MRH, Sharkey KJ, Bearon RN, Sée V. Tight control of hypoxia-inducible factor-α transient dynamics is essential for cell survival in hypoxia. J Biol Chem 2014; 289:5549-64. [PMID: 24394419 PMCID: PMC3937633 DOI: 10.1074/jbc.m113.500405] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [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] [Indexed: 01/02/2023] Open
Abstract
Intracellular signaling involving hypoxia-inducible factor (HIF) controls the adaptive responses to hypoxia. There is a growing body of evidence demonstrating that intracellular signals encode temporal information. Thus, the dynamics of protein levels, as well as protein quantity and/or localization, impacts on cell fate. We hypothesized that such temporal encoding has a role in HIF signaling and cell fate decisions triggered by hypoxic conditions. Using live cell imaging in a controlled oxygen environment, we observed transient 3-h pulses of HIF-1α and -2α expression under continuous hypoxia. We postulated that the well described prolyl hydroxylase (PHD) oxygen sensors and HIF negative feedback regulators could be the origin of the pulsatile HIF dynamics. We used iterative mathematical modeling and experimental analysis to scrutinize which parameter of the PHD feedback could control HIF timing and we probed for the functional redundancy between the three main PHD proteins. We identified PHD2 as the main PHD responsible for HIF peak duration. We then demonstrated that this has important consequences, because the transient nature of the HIF pulse prevents cell death by avoiding transcription of p53-dependent pro-apoptotic genes. We have further shown the importance of considering HIF dynamics for coupling mathematical models by using a described HIF-p53 mathematical model. Our results indicate that the tight control of HIF transient dynamics has important functional consequences on the cross-talk with key signaling pathways controlling cell survival, which is likely to impact on HIF targeting strategies for hypoxia-associated diseases such as tumor progression and ischemia.
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Affiliation(s)
- James Bagnall
- From the Centre for Cell Imaging, Institute of Integrative Biology, and
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Thomas LW, Lam C, Clark RE, White MRH, Spiller DG, Moots RJ, Edwards SW. Serine 162, an essential residue for the mitochondrial localization, stability and anti-apoptotic function of Mcl-1. PLoS One 2012; 7:e45088. [PMID: 23024798 PMCID: PMC3443205 DOI: 10.1371/journal.pone.0045088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 08/17/2012] [Indexed: 11/19/2022] Open
Abstract
Mcl-1 is an anti-apoptotic member of the Bcl-2 family that plays a key role in normal development, but also in pathologies such as cancer. It has some unusual properties compared to other anti-apoptotic members of the Bcl-2 family, and its expression and function are dynamically regulated by a variety of post-transcriptional and post-translational processes. Of note, Mcl-1 protein has a very short half life, and its stability and function may be regulated by reversible phosphorylation. There is also evidence to suggest that it may be localized to different subcellular compartments. The aim of this work was to determine whether residues within the PEST region of Mcl-1 that may undergo reversible phosphorylation, also regulate its subcellular distribution. We show that EGFP:Mcl-1 localizes mainly to the mitochondria of HeLa cells, with some additional cytoplasmic and nuclear localization. The mutations, S64A, S64E, S121A, S159A, T163A and T163E did not significantly affect the localization of Mcl-1. However, mutation of Ser162 to the phospho-null residue, Alanine resulted in an essentially nuclear localization, with some cytoplasmic but no mitochondrial localization. This mutant Mcl-1 protein, S162A, showed significantly decreased stability and it decreased the ability to protect against Bak-induced apoptosis. These data identify a new molecular determinant of Mcl-1 function, localization and stability that may be important for understanding the role of this protein in disease.
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Affiliation(s)
- Luke W. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Connie Lam
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard E. Clark
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael R. H. White
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - David G. Spiller
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Robert J. Moots
- Institute of Aging and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Steven W. Edwards
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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Smith KD, Vaughan-Thomas A, Spiller DG, Clegg PD, Innes JF, Comerford EJ. Variations in cell morphology in the canine cruciate ligament complex. Vet J 2012; 193:561-6. [PMID: 22465617 DOI: 10.1016/j.tvjl.2012.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 02/20/2012] [Accepted: 02/22/2012] [Indexed: 11/29/2022]
Abstract
Cell morphology may reflect the mechanical environment of tissues and influence tissue physiology and response to injury. Normal cruciate ligaments (CLs) from disease-free stifle joints were harvested from dog breeds with a high (Labrador retriever) and low (Greyhound) risk of cranial cruciate ligament (CCL) rupture. Antibodies against the cytoskeletal components vimentin and alpha tubulin were used to analyse cell morphology; nuclei were stained with 4',6-diamidino-2-phenylindole, and images were collected using conventional and confocal microscopy. Both cranial and caudal CLs contained cells of heterogenous morphologies. Cells were arranged between collagen bundles and frequently had cytoplasmic processes. Some of these processes were long (type A cells), others were shorter, thicker and more branched (type B cells), and some had no processes (type C cells). Processes were frequently shown to contact other cells, extending longitudinally and transversely through the CLs. Cells with longer processes had fusiform nuclei, and those with no processes had rounded nuclei and were more frequent in the mid-substance of both CLs. Cells with long processes were more commonly noted in the CLs of the Greyhound. As contact between cells may facilitate direct communication, variances in cell morphology between breeds at a differing risk of CCL rupture may reflect differences in CL physiology.
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Affiliation(s)
- K D Smith
- Faculty of Veterinary Medicine, Small Animal Hospital, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK.
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Bakstad D, Adamson A, Spiller DG, White MRH. Quantitative measurement of single cell dynamics. Curr Opin Biotechnol 2012; 23:103-9. [PMID: 22137453 DOI: 10.1016/j.copbio.2011.11.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/04/2011] [Accepted: 11/07/2011] [Indexed: 01/24/2023]
Abstract
Over the past 20 years luminescent and fluorescent imaging assays have been developed to report on the dynamics of transcription and protein translocation in single cells. The combination of these measurements with mathematical analysis is having an increasingly significant impact on cell biology. There is an urgent need to translate these assays to the study of cells and tissues in vivo, which requires new tools and technologies. Emergence of these new tools and techniques will further the understanding of the role of signalling and transcriptional dynamics in the generation of cellular heterogeneity and the control of cell fate.
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Featherstone K, Harper CV, McNamara A, Semprini S, Spiller DG, McNeilly J, McNeilly AS, Mullins JJ, White MRH, Davis JRE. Pulsatile patterns of pituitary hormone gene expression change during development. Development 2011. [DOI: 10.1242/dev.076216] [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: 11/20/2022]
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Featherstone K, Harper CV, McNamara A, Semprini S, Spiller DG, McNeilly J, McNeilly AS, Mullins JJ, White MRH, Davis JRE. Pulsatile patterns of pituitary hormone gene expression change during development. J Cell Sci 2011; 124:3484-91. [PMID: 21984812 DOI: 10.1242/jcs.088500] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Important questions in biology have emerged recently concerning the timing of transcription in living cells. Studies on clonal cell lines have shown that transcription is often pulsatile and stochastic, with implications for cellular differentiation. Currently, information regarding transcriptional activity at cellular resolution within a physiological context remains limited. To investigate single-cell transcriptional activity in real-time in living tissue we used bioluminescence imaging of pituitary tissue from transgenic rats in which luciferase gene expression is driven by a pituitary hormone gene promoter. We studied fetal and neonatal pituitary tissue to assess whether dynamic patterns of transcription change during tissue development. We show that gene expression in single cells is highly pulsatile at the time endocrine cells first appear but becomes stabilised as the tissue develops in early neonatal life. This stabilised transcription pattern might depend upon tissue architecture or paracrine signalling, as isolated cells, generated from enzymatic dispersion of the tissue, display pulsatile luminescence. Nascent cells in embryonic tissue also showed coordinated transcription activity over short distances further indicating that cellular context is important for transcription activity. Overall, our data show that cells alter their patterns of gene expression according to their context and developmental stage, with important implications for cellular differentiation.
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Affiliation(s)
- Karen Featherstone
- Developmental Biomedicine Research Group, Faculty of Medical and Human Sciences, AV Hill Building, University of Manchester, Manchester M13 9PT, UK
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Powell GF, Ward DA, Prescott MC, Spiller DG, White MRH, Turner PC, Earley FGP, Phillips J, Rees HH. The molecular action of the novel insecticide, Pyridalyl. Insect Biochem Mol Biol 2011; 41:459-469. [PMID: 21497652 DOI: 10.1016/j.ibmb.2011.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 03/02/2011] [Accepted: 03/20/2011] [Indexed: 05/30/2023]
Abstract
Pyridalyl is a recently discovered insecticide that exhibits high insecticidal activity against Lepidoptera and Thysanoptera. Pyridalyl action requires cytochrome P450 activity, possibly for production of a bioactive derivative, Pyridalyl metabolism being prevented by general P450 inhibitors. Apoptosis is apparently not involved in the cytotoxicity. Continuous culture of Spodoptera frugiperda Sf21 cells in sub-lethal doses of Pyridalyl, results in a Pyridalyl-resistant cell line. Probing the molecular action of Pyridalyl by comparison of the proteomes of Pyridalyl-resistant and -susceptible cell lines, revealed differential expression of a number of proteins, including the up-regulation of thiol peroxiredoxin (TPx), in the resistant cells. Treatment of Bombyx mori larvae with Pyridalyl, followed by comparison of the midgut microsomal sub-proteome, revealed the up-regulation of three proteasome subunits. Such subunits, together with Hsp70 stress proteins, glyceraldehyde 3-phosphate dehydrogenases (GAPDHs) and thiol peroxiredoxin (TPx) were also up-regulated in the whole proteome of B. mori BM36 cells following treatment with the insecticide. The foregoing results lead to the hypothesis that cytochrome P450 action leads to an active Pyridalyl metabolite, which results in production of reactive oxygen species (ROS), that leads to damage to cellular macromolecules (e.g., proteins) and enhanced proteasome activity leads to increased protein degradation and necrotic cell death.
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Affiliation(s)
- Gerard F Powell
- School of Biological Sciences, The University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
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Harper CV, Finkenstädt B, Woodcock DJ, Friedrichsen S, Semprini S, Ashall L, Spiller DG, Mullins JJ, Rand DA, Davis JRE, White MRH. Dynamic analysis of stochastic transcription cycles. PLoS Biol 2011; 9:e1000607. [PMID: 21532732 PMCID: PMC3075210 DOI: 10.1371/journal.pbio.1000607] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 02/24/2011] [Indexed: 01/13/2023] Open
Abstract
In individual mammalian cells the expression of some genes such as prolactin is highly variable over time and has been suggested to occur in stochastic pulses. To investigate the origins of this behavior and to understand its functional relevance, we quantitatively analyzed this variability using new mathematical tools that allowed us to reconstruct dynamic transcription rates of different reporter genes controlled by identical promoters in the same living cell. Quantitative microscopic analysis of two reporter genes, firefly luciferase and destabilized EGFP, was used to analyze the dynamics of prolactin promoter-directed gene expression in living individual clonal and primary pituitary cells over periods of up to 25 h. We quantified the time-dependence and cyclicity of the transcription pulses and estimated the length and variation of active and inactive transcription phases. We showed an average cycle period of approximately 11 h and demonstrated that while the measured time distribution of active phases agreed with commonly accepted models of transcription, the inactive phases were differently distributed and showed strong memory, with a refractory period of transcriptional inactivation close to 3 h. Cycles in transcription occurred at two distinct prolactin-promoter controlled reporter genes in the same individual clonal or primary cells. However, the timing of the cycles was independent and out-of-phase. For the first time, we have analyzed transcription dynamics from two equivalent loci in real-time in single cells. In unstimulated conditions, cells showed independent transcription dynamics at each locus. A key result from these analyses was the evidence for a minimum refractory period in the inactive-phase of transcription. The response to acute signals and the result of manipulation of histone acetylation was consistent with the hypothesis that this refractory period corresponded to a phase of chromatin remodeling which significantly increased the cyclicity. Stochastically timed bursts of transcription in an apparently random subset of cells in a tissue may thus produce an overall coordinated but heterogeneous phenotype capable of acute responses to stimuli.
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Affiliation(s)
- Claire V. Harper
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Bärbel Finkenstädt
- Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Dan J. Woodcock
- Warwick Systems Biology Centre, University of Warwick, United Kingdom
| | - Sönke Friedrichsen
- Endocrinology Group, School of Biomedicine, University of Manchester, Manchester, United Kingdom
| | - Sabrina Semprini
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Louise Ashall
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - David G. Spiller
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - John J. Mullins
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - David A. Rand
- Warwick Systems Biology Centre, University of Warwick, United Kingdom
- * E-mail: (DAR); (JRED); (MRHW)
| | - Julian R. E. Davis
- Endocrinology Group, School of Biomedicine, University of Manchester, Manchester, United Kingdom
- * E-mail: (DAR); (JRED); (MRHW)
| | - Michael R. H. White
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom
- * E-mail: (DAR); (JRED); (MRHW)
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Smith KD, Vaughan-Thomas A, Spiller DG, Innes JF, Clegg PD, Comerford EJ. The organisation of elastin and fibrillins 1 and 2 in the cruciate ligament complex. J Anat 2011; 218:600-7. [PMID: 21466551 DOI: 10.1111/j.1469-7580.2011.01374.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Although elastin fibres and oxytalan fibres (bundles of microfibrils) have important mechanical, biochemical and cell regulatory functions, neither their distribution nor their function in cruciate ligaments has been investigated. Twelve pairs of cruciate ligaments (CLs) were obtained from 10 adult dogs with no evidence of knee osteoarthritis. Elastic fibres were identified using Verhoeff's and Miller's staining. Fibrillins 1 and 2 were immunolocalised and imaged using confocal laser scanning microscopy. Hydrated, unfixed tissue was analysed using Nomarski differential interference microscopy (NDIC), allowing structural and mechanical analysis. Microfibrils and elastin fibres were widespread in both CLs, predominantly within ligament fascicles, parallel to collagen bundles. Although elastin fibres were sparse, microfibrils were abundant. We described abundant fibres composed of both fibrillin 1 and fibrillin 2, which had a similar pattern of distribution to oxytalan fibres. NDIC demonstrated complex interfascicular and interbundle anatomy in the CL complex. The distribution of elastin fibres is suggestive of a mechanical role in bundle reorganisation following ligament deformation. The presence and location of fibrillin 2 in oxytalan fibres in ligament differs from the solely fibrillin 1-containing oxytalan fibres previously described in tendon and may demonstrate a fundamental difference between ligament and tendon.
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Affiliation(s)
- Kinley D Smith
- Department of Musculoskeletal Biology, Institute of Aging and Chronic disease and School of Veterinary Science, Leahurst Campus, University of Liverpool, Liverpool, UK.
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Du CJ, Marcello M, Spiller DG, White MRH, Bretschneider T. Interactive segmentation of clustered cells via geodesic commute distance and constrained density weighted Nyström method. Cytometry A 2011; 77:1137-47. [PMID: 21069796 DOI: 10.1002/cyto.a.20993] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An interactive method is proposed for complex cell segmentation, in particular of clustered cells. This article has two main contributions: First, we explore a hybrid combination of the random walk and the geodesic graph based methods for image segmentation and propose the novel concept of geodesic commute distance to classify pixels. The computation of geodesic commute distance requires an eigenvector decomposition of the weighted Laplacian matrix of a graph constructed from the image to be segmented. Second, by incorporating pairwise constraints from seeds into the algorithm, we present a novel method for eigenvector decomposition, namely a constrained density weighted Nyström method. Both visual and quantitative comparison with other semiautomatic algorithms including Voronoi-based segmentation, grow cut, graph cuts, random walk, and geodesic method are given to evaluate the performance of the proposed method, which is a powerful tool for quantitative analysis of clustered cell images in live cell imaging.
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Affiliation(s)
- Cheng-Jin Du
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom.
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Carter BO, Weaver JVM, Wang W, Spiller DG, Adams DJ, Cooper AI. Microencapsulation using an oil-in-water-in-air ‘dry water emulsion’. Chem Commun (Camb) 2011; 47:8253-5. [DOI: 10.1039/c1cc12698a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Barnes TC, Spiller DG, Anderson ME, Edwards SW, Moots RJ. Endothelial activation and apoptosis mediated by neutrophil-dependent interleukin 6 trans-signalling: a novel target for systemic sclerosis? Ann Rheum Dis 2010; 70:366-72. [PMID: 21068092 PMCID: PMC3015068 DOI: 10.1136/ard.2010.133587] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Objectives Systemic sclerosis (SSc) is a connective tissue disease associated with significant morbidity and mortality and generally inadequate treatment. Endothelial cell activation and apoptosis are thought to be pivotal in the pathogenesis of this disease, but the mechanisms that mediate this remain unknown. Methods Human dermal microvascular endothelial cells were cultured with healthy control neutrophils in the presence of 25% healthy control or SSc serum for 24 h. Apoptosis was measured by annexin V-FITC binding and endothelial cell activation was measured using an allophycocyanin-conjugated E-selectin antibody. Fluorescence was quantified and localised using confocal microscopy. Results SSc serum resulted in significantly increased apoptosis (p=0.006) and E-selectin expression (p=0.00004) in endothelial cells compared with control serum, effects that were critically dependent on the presence of neutrophils. Recombinant interleukin 6 (IL-6) reproduced these findings. Immunodepletion of IL-6 and the use of an IL-6 neutralising antibody decreased the effect of SSc serum on E-selectin expression. Soluble gp130, which specifically blocks IL-6 trans-signalling, negated the effect of SSc serum on both E-selectin expression and apoptosis. Conclusions SSc serum induces endothelial cell activation and apoptosis in endothelial cell-neutrophil co-cultures, mediated largely by IL-6 and dependent on the presence of neutrophils. Together with other pathologically relevant effects of IL-6, these data justify further exploration of IL-6 as a therapeutic target in SSc.
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Affiliation(s)
- Theresa C Barnes
- School of Clinical Sciences, University of Liverpool, Liverpool, UK
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Turner DA, Paszek P, Woodcock DJ, Nelson DE, Horton CA, Wang Y, Spiller DG, Rand DA, White MRH, Harper CV. Physiological levels of TNFalpha stimulation induce stochastic dynamics of NF-kappaB responses in single living cells. J Cell Sci 2010; 123:2834-43. [PMID: 20663918 DOI: 10.1242/jcs.069641] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nuclear factor kappa B (NF-kappaB) signalling is activated by cellular stress and inflammation and regulates cytokine expression. We applied single-cell imaging to investigate dynamic responses to different doses of tumour necrosis factor alpha (TNFalpha). Lower doses activated fewer cells and those responding showed an increasingly variable delay in the initial NF-kappaB nuclear translocation and associated IkappaBalpha degradation. Robust 100 minute nuclear:cytoplasmic NF-kappaB oscillations were observed over a wide range of TNFalpha concentrations. The result is supported by computational analyses, which identified a limit cycle in the system with a stable 100 minute period over a range of stimuli, and indicated no co-operativity in the pathway activation. These results suggest that a stochastic threshold controls functional all-or-nothing responses in individual cells. Deterministic and stochastic models simulated the experimentally observed activation threshold and gave rise to new predictions about the structure of the system and open the way for better mechanistic understanding of physiological TNFalpha activation of inflammatory responses in cells and tissues.
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Affiliation(s)
- David A Turner
- Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Liverpool, UK
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42
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Paszek P, Ryan S, Ashall L, Sillitoe K, Harper CV, Spiller DG, Rand DA, White MRH. Population robustness arising from cellular heterogeneity. Proc Natl Acad Sci U S A 2010; 107:11644-9. [PMID: 20534546 PMCID: PMC2895068 DOI: 10.1073/pnas.0913798107] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Heterogeneity between individual cells is a common feature of dynamic cellular processes, including signaling, transcription, and cell fate; yet the overall tissue level physiological phenotype needs to be carefully controlled to avoid fluctuations. Here we show that in the NF-kappaB signaling system, the precise timing of a dual-delayed negative feedback motif [involving stochastic transcription of inhibitor kappaB (IkappaB)-alpha and -epsilon] is optimized to induce heterogeneous timing of NF-kappaB oscillations between individual cells. We suggest that this dual-delayed negative feedback motif enables NF-kappaB signaling to generate robust single cell oscillations by reducing sensitivity to key parameter perturbations. Simultaneously, enhanced cell heterogeneity may represent a mechanism that controls the overall coordination and stability of cell population responses by decreasing temporal fluctuations of paracrine signaling. It has often been thought that dynamic biological systems may have evolved to maximize robustness through cell-to-cell coordination and homogeneity. Our analyses suggest in contrast, that this cellular variation might be advantageous and subject to evolutionary selection. Alternative types of therapy could perhaps be designed to modulate this cellular heterogeneity.
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Affiliation(s)
- Pawel Paszek
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - Sheila Ryan
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - Louise Ashall
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - Kate Sillitoe
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - Claire V. Harper
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - David G. Spiller
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
| | - David A. Rand
- Warwick Systems Biology and Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Michael R. H. White
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; and
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Abstract
Populations of cells are almost always heterogeneous in function and fate. To understand the plasticity of cells, it is vital to measure quantitatively and dynamically the molecular processes that underlie cell-fate decisions in single cells. Early events in cell signalling often occur within seconds of the stimulus, whereas intracellular signalling processes and transcriptional changes can take minutes or hours. By contrast, cell-fate decisions, such as whether a cell divides, differentiates or dies, can take many hours or days. Multiparameter experimental and computational methods that integrate quantitative measurement and mathematical simulation of these noisy and complex processes are required to understand the highly dynamic mechanisms that control cell plasticity and fate.
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Affiliation(s)
- David G Spiller
- Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Crown Street, Liverpool L69 7ZB, UK
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Meley D, Spiller DG, White MRH, McDowell H, Pizer B, Sée V. p53-mediated delayed NF-κB activity enhances etoposide-induced cell death in medulloblastoma. Cell Death Dis 2010; 1:e41. [PMID: 21364648 PMCID: PMC3032310 DOI: 10.1038/cddis.2010.16] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Medulloblastoma (MB) is an embryonic brain tumour that arises in the cerebellum. Using several MB cell lines, we have demonstrated that the chemotherapeutic drug etoposide induces a p53- and caspase-dependent cell death. We have observed an additional caspase-independent cell death mechanism involving delayed nuclear factor κB (NF-κB) activity. The delayed induction was controlled by a p53-dependent transcription step and the production of death receptors (especially CD95/Fas). We further demonstrated that in both MB and glioblastoma (GM) cell lines, in which the p53 pathway was not functional, no p65 activation could be detected upon etoposide treatment. MB cell lines that have mutations in p53 or NF-κB are either less sensitive (NF-κB mutant) or even completely resistant (p53 mutant) to chemotherapeutic intervention. The optimal cell death was only achieved when both p53 and NF-κB were switched on. Taken together, our results shed light on the mechanism of NF-κB activation by etoposide in brain tumours and show that the genetic background of MB and GM cells determines their sensitivity to chemotherapy and has to be taken into account for efficient therapeutic intervention.
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Affiliation(s)
- D Meley
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool, UK
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45
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Harper CV, Featherstone K, Semprini S, Friedrichsen S, McNeilly J, Paszek P, Spiller DG, McNeilly AS, Mullins JJ, Davis JRE, White MRH. Dynamic organisation of prolactin gene expression in living pituitary tissue. J Cell Sci 2010; 123:424-30. [PMID: 20130141 DOI: 10.1242/jcs.060434] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gene expression in living cells is highly dynamic, but temporal patterns of gene expression in intact tissues are largely unknown. The mammalian pituitary gland comprises several intermingled cell types, organised as interdigitated networks that interact functionally to generate co-ordinated hormone secretion. Live-cell imaging was used to quantify patterns of reporter gene expression in dispersed lactotrophic cells or intact pituitary tissue from bacterial artificial chromosome (BAC) transgenic rats in which a large prolactin genomic fragment directed expression of luciferase or destabilised enhanced green fluorescent protein (d2EGFP). Prolactin promoter activity in transgenic pituitaries varied with time across different regions of the gland. Although amplitude of transcriptional responses differed, all regions of the gland displayed similar overall patterns of reporter gene expression over a 50-hour period, implying overall co-ordination of cellular behaviour. By contrast, enzymatically dispersed pituitary cell cultures showed unsynchronised fluctuations of promoter activity amongst different cells, suggesting that transcriptional patterns were constrained by tissue architecture. Short-term, high resolution, single cell analyses in prolactin-d2EGFP transgenic pituitary slice preparations showed varying transcriptional patterns with little correlation between adjacent cells. Together, these data suggest that pituitary tissue comprises a series of cell ensembles, which individually display a variety of patterns of short-term stochastic behaviour, but together yield long-range and long-term coordinated behaviour.
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Affiliation(s)
- Claire V Harper
- Centre for Cell Imaging, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
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46
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Cesbron Y, Sée V, Free P, Nativo P, Shaheen U, Rigden DJ, Spiller DG, Fernig DG, White MR, Prior IA, Brust M, Lounis B, Lévy R. Intracellular Delivery and Fate of Peptide-Capped Gold Nanoparticles. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.1081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Chen L, Revel S, Morris K, Spiller DG, Serpell LC, Adams DJ. Low molecular weight gelator–dextran composites. Chem Commun (Camb) 2010; 46:6738-40. [DOI: 10.1039/c0cc01842b] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Sée V, Free P, Cesbron Y, Nativo P, Shaheen U, Rigden DJ, Spiller DG, Fernig DG, White MRH, Prior IA, Brust M, Lounis B, Lévy R. Cathepsin L digestion of nanobioconjugates upon endocytosis. ACS Nano 2009; 3:2461-8. [PMID: 19728690 DOI: 10.1021/nn9006994] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Understanding the dynamic fate and interactions of bioconjugated nanoparticles within living cells and organisms is a prerequisite for their use as in situ sensors or actuators. While recent research has provided indications on the effect of size, shape, and surface properties of nanoparticles on their internalization by living cells, the biochemical fate of the nanoparticles after internalization has been essentially unknown. Here we show that, upon internalization in a wide range of mammalian cells, biological molecules attached to the nanoparticles are degraded within the endosomal compartments through peptide cleavage by the protease cathepsin L. Importantly, using bioinformatics tools, we show that cathepsin L is able to cleave more than a third of the human proteome, indicating that this degradation process is likely to happen to most nanoparticles conjugated with peptides and proteins and cannot be ignored in the design of nanomaterials for intracellular applications. Preservation of the bioconjugates can be achieved by a combination of cathepsin inhibition and endosome disruption.
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Affiliation(s)
- Violaine Sée
- Centre for Cell Imaging, University of Liverpool, UK.
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49
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White MRH, Spiller DG. Is frequency-encoding of information a major theme in cellular processes? Cell Cycle 2009; 8:2677-2678. [PMID: 19690458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
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50
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Jameson D, Turner DA, Ankers J, Kennedy S, Ryan S, Swainston N, Griffiths T, Spiller DG, Oliver SG, White MRH, Kell DB, Paton NW. Information management for high content live cell imaging. BMC Bioinformatics 2009; 10:226. [PMID: 19622144 PMCID: PMC2723092 DOI: 10.1186/1471-2105-10-226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 07/21/2009] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND High content live cell imaging experiments are able to track the cellular localisation of labelled proteins in multiple live cells over a time course. Experiments using high content live cell imaging will generate multiple large datasets that are often stored in an ad-hoc manner. This hinders identification of previously gathered data that may be relevant to current analyses. Whilst solutions exist for managing image data, they are primarily concerned with storage and retrieval of the images themselves and not the data derived from the images. There is therefore a requirement for an information management solution that facilitates the indexing of experimental metadata and results of high content live cell imaging experiments. RESULTS We have designed and implemented a data model and information management solution for the data gathered through high content live cell imaging experiments. Many of the experiments to be stored measure the translocation of fluorescently labelled proteins from cytoplasm to nucleus in individual cells. The functionality of this database has been enhanced by the addition of an algorithm that automatically annotates results of these experiments with the timings of translocations and periods of any oscillatory translocations as they are uploaded to the repository. Testing has shown the algorithm to perform well with a variety of previously unseen data. CONCLUSION Our repository is a fully functional example of how high throughput imaging data may be effectively indexed and managed to address the requirements of end users. By implementing the automated analysis of experimental results, we have provided a clear impetus for individuals to ensure that their data forms part of that which is stored in the repository. Although focused on imaging, the solution provided is sufficiently generic to be applied to other functional proteomics and genomics experiments. The software is available from: fhttp://code.google.com/p/livecellim/
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Affiliation(s)
- Daniel Jameson
- Manchester Centre for Integrative Systems Biology, School of Chemistry, and Manchester Interdisciplinary Biocentre, University of Manchester, 131, Princess St, Manchester, M1 7DN, UK
| | - David A Turner
- Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Crown St., Liverpool, L69 7ZB, UK
| | - John Ankers
- Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Crown St., Liverpool, L69 7ZB, UK
| | - Stephnie Kennedy
- Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Crown St., Liverpool, L69 7ZB, UK
| | - Sheila Ryan
- Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Crown St., Liverpool, L69 7ZB, UK
| | - Neil Swainston
- Manchester Centre for Integrative Systems Biology, School of Chemistry, and Manchester Interdisciplinary Biocentre, University of Manchester, 131, Princess St, Manchester, M1 7DN, UK
| | - Tony Griffiths
- School of Computer Science, Kilburn Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - David G Spiller
- Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Crown St., Liverpool, L69 7ZB, UK
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Michael RH White
- Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Crown St., Liverpool, L69 7ZB, UK
| | - Douglas B Kell
- Manchester Centre for Integrative Systems Biology, School of Chemistry, and Manchester Interdisciplinary Biocentre, University of Manchester, 131, Princess St, Manchester, M1 7DN, UK
| | - Norman W Paton
- School of Computer Science, Kilburn Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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