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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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2
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Harper CV, Woodcock DJ, Lam C, Garcia-Albornoz M, Adamson A, Ashall L, Rowe W, Downton P, Schmidt L, West S, Spiller DG, Rand DA, White MRH. Temperature regulates NF-κB dynamics and function through timing of A20 transcription. Proc Natl Acad Sci U S A 2018; 115:E5243-9. [PMID: 29760065 DOI: 10.1073/pnas.1803609115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
NF-κB signaling plays a pivotal role in control of the inflammatory response. We investigated how the dynamics and function of NF-κB were affected by temperature within the mammalian physiological range (34 °C to 40 °C). An increase in temperature led to an increase in NF-κB nuclear/cytoplasmic oscillation frequency following Tumor Necrosis Factor alpha (TNFα) stimulation. Mathematical modeling suggested that this temperature sensitivity might be due to an A20-dependent mechanism, and A20 silencing removed the sensitivity to increased temperature. The timing of the early response of a key set of NF-κB target genes showed strong temperature dependence. The cytokine-induced expression of many (but not all) later genes was insensitive to temperature change (suggesting that they might be functionally temperature-compensated). Moreover, a set of temperature- and TNFα-regulated genes were implicated in NF-κB cross-talk with key cell-fate-controlling pathways. In conclusion, NF-κB dynamics and target gene expression are modulated by temperature and can accurately transmit multidimensional information to control inflammation.
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Versari C, Stoma S, Batmanov K, Llamosi A, Mroz F, Kaczmarek A, Deyell M, Lhoussaine C, Hersen P, Batt G. Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform. J R Soc Interface 2017; 14:20160705. [PMID: 28179544 PMCID: PMC5332563 DOI: 10.1098/rsif.2016.0705] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 09/01/2016] [Accepted: 12/15/2016] [Indexed: 11/23/2022] Open
Abstract
With the continuous expansion of single cell biology, the observation of the behaviour of individual cells over extended durations and with high accuracy has become a problem of central importance. Surprisingly, even for yeast cells that have relatively regular shapes, no solution has been proposed that reaches the high quality required for long-term experiments for segmentation and tracking (S&T) based on brightfield images. Here, we present CellStar, a tool chain designed to achieve good performance in long-term experiments. The key features are the use of a new variant of parametrized active rays for segmentation, a neighbourhood-preserving criterion for tracking, and the use of an iterative approach that incrementally improves S&T quality. A graphical user interface enables manual corrections of S&T errors and their use for the automated correction of other, related errors and for parameter learning. We created a benchmark dataset with manually analysed images and compared CellStar with six other tools, showing its high performance, notably in long-term tracking. As a community effort, we set up a website, the Yeast Image Toolkit, with the benchmark and the Evaluation Platform to gather this and additional information provided by others.
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Affiliation(s)
| | - Szymon Stoma
- Scientific Center for Optical and Electron Microscopy (ScopeM), ETH Zurich, Zurich, Switzerland
| | | | - Artémis Llamosi
- Laboratoire Matières et Systèmes Complexes, UMR7057, CNRS and Université Paris Diderot, Paris, France
- Inria and Université Paris-Saclay, Palaiseau, France
| | - Filip Mroz
- Institute of Computer Science, University of Wroclaw, Wroclaw, Poland
| | - Adam Kaczmarek
- Institute of Computer Science, University of Wroclaw, Wroclaw, Poland
| | - Matt Deyell
- Laboratoire Matières et Systèmes Complexes, UMR7057, CNRS and Université Paris Diderot, Paris, France
| | | | - Pascal Hersen
- Laboratoire Matières et Systèmes Complexes, UMR7057, CNRS and Université Paris Diderot, Paris, France
| | - Gregory Batt
- Inria and Université Paris-Saclay, Palaiseau, France
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Caballero I, Boyd J, Almiñana C, Sánchez-López JA, Basatvat S, Montazeri M, Maslehat Lay N, Elliott S, Spiller DG, White MR, Fazeli A. Understanding the dynamics of Toll-like Receptor 5 response to flagellin and its regulation by estradiol. Sci Rep 2017; 7:40981. [PMID: 28112187 DOI: 10.1038/srep40981] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/13/2016] [Indexed: 12/24/2022] Open
Abstract
Toll-like receptors (TLRs) are major players of the innate immune system. Once activated, they trigger a signalling cascade that leads to NF-κB translocation from the cytoplasm to the nucleus. Single cell analysis shows that NF-κB signalling dynamics are a critical determinant of transcriptional regulation. Moreover, the outcome of innate immune response is also affected by the cross-talk between TLRs and estrogen signalling. Here, we characterized the dynamics of TLR5 signalling, responsible for the recognition of flagellated bacteria, and those changes induced by estradiol in its signalling at the single cell level. TLR5 activation in MCF7 cells induced a single and sustained NF-κB translocation into the nucleus that resulted in high NF-κB transcription activity. The overall magnitude of NF-κB transcription activity was not influenced by the duration of the stimulus. No significant changes are observed in the dynamics of NF-κB translocation to the nucleus when MCF7 cells are incubated with estradiol. However, estradiol significantly decreased NF-κB transcriptional activity while increasing TLR5-mediated AP-1 transcription. The effect of estradiol on transcriptional activity was dependent on the estrogen receptor activated. This fine tuning seems to occur mainly in the nucleus at the transcription level rather than affecting the translocation of the NF-κB transcription factor.
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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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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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Delibaltov DL, Gaur U, Kim J, Kourakis M, Newman-Smith E, Smith W, Belteton SA, Szymanski DB, Manjunath BS. CellECT: cell evolution capturing tool. BMC Bioinformatics 2016; 17:88. [PMID: 26887436 PMCID: PMC4756481 DOI: 10.1186/s12859-016-0927-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 04/19/2015] [Accepted: 02/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Robust methods for the segmentation and analysis of cells in 3D time sequences (3D+t) are critical for quantitative cell biology. While many automated methods for segmentation perform very well, few generalize reliably to diverse datasets. Such automated methods could significantly benefit from at least minimal user guidance. Identification and correction of segmentation errors in time-series data is of prime importance for proper validation of the subsequent analysis. The primary contribution of this work is a novel method for interactive segmentation and analysis of microscopy data, which learns from and guides user interactions to improve overall segmentation. RESULTS We introduce an interactive cell analysis application, called CellECT, for 3D+t microscopy datasets. The core segmentation tool is watershed-based and allows the user to add, remove or modify existing segments by means of manipulating guidance markers. A confidence metric learns from the user interaction and highlights regions of uncertainty in the segmentation for the user's attention. User corrected segmentations are then propagated to neighboring time points. The analysis tool computes local and global statistics for various cell measurements over the time sequence. Detailed results on two large datasets containing membrane and nuclei data are presented: a 3D+t confocal microscopy dataset of the ascidian Phallusia mammillata consisting of 18 time points, and a 3D+t single plane illumination microscopy (SPIM) dataset consisting of 192 time points. Additionally, CellECT was used to segment a large population of jigsaw-puzzle shaped epidermal cells from Arabidopsis thaliana leaves. The cell coordinates obtained using CellECT are compared to those of manually segmented cells. CONCLUSIONS CellECT provides tools for convenient segmentation and analysis of 3D+t membrane datasets by incorporating human interaction into automated algorithms. Users can modify segmentation results through the help of guidance markers, and an adaptive confidence metric highlights problematic regions. Segmentations can be propagated to multiple time points, and once a segmentation is available for a time sequence cells can be analyzed to observe trends. The segmentation and analysis tools presented here generalize well to membrane or cell wall volumetric time series datasets.
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Affiliation(s)
- Diana L Delibaltov
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Utkarsh Gaur
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Jennifer Kim
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Matthew Kourakis
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Erin Newman-Smith
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - William Smith
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Samuel A Belteton
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Daniel B Szymanski
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA.,Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - B S Manjunath
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
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Xue M, Momiji H, Rabbani N, Barker G, Bretschneider T, Shmygol A, Rand DA, Thornalley PJ. Frequency Modulated Translocational Oscillations of Nrf2 Mediate the Antioxidant Response Element Cytoprotective Transcriptional Response. Antioxid Redox Signal 2015; 23:613-29. [PMID: 25178584 PMCID: PMC4556091 DOI: 10.1089/ars.2014.5962] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 08/14/2014] [Accepted: 08/31/2014] [Indexed: 12/20/2022]
Abstract
AIMS Stress responsive signaling coordinated by nuclear factor erythroid 2-related factor 2 (Nrf2) provides an adaptive response for protection of cells against toxic insults, oxidative stress and metabolic dysfunction. Nrf2 regulates a battery of protective genes by binding to regulatory antioxidant response elements (AREs). The aim of this study was to examine how Nrf2 signals cell stress status and regulates transcription to maintain homeostasis. RESULTS In live cell microscopy we observed that Nrf2 undergoes autonomous translocational frequency-modulated oscillations between cytoplasm and nucleus. Oscillations occurred in quiescence and when cells were stimulated at physiological levels of activators, they decrease in period and amplitude and then evoke a cytoprotective transcriptional response. We propose a mechanism whereby oscillations are produced by negative feedback involving successive de-phosphorylation and phosphorylation steps. Nrf2 was inactivated in the nucleus and reactivated on return to the cytoplasm. Increased frequency of Nrf2 on return to the cytoplasm with increased reactivation or refresh-rate under stress conditions activated the transcriptional response mediating cytoprotective effects. The serine/threonine-protein phosphatase PGAM5, member of the Nrf2 interactome, was a key regulatory component. INNOVATION We found that Nrf2 is activated in cells without change in total cellular Nrf2 protein concentration. Regulation of ARE-linked protective gene transcription occurs rather through translocational oscillations of Nrf2. We discovered cytoplasmic refresh rate of Nrf2 is important in maintaining and regulating the transcriptional response and links stress challenge to increased cytoplasmic surveillance. We found silencing and inhibition of PGAM5 provides potent activation of Nrf2. CONCLUSION Frequency modulated translocational oscillations of Nrf2 mediate the ARE-linked cytoprotective transcriptional response.
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Affiliation(s)
- Mingzhan Xue
- Clinical Sciences Research Laboratories, Warwick Medical School, University Hospital, University of Warwick, Coventry, United Kingdom
| | - Hiroshi Momiji
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Naila Rabbani
- Clinical Sciences Research Laboratories, Warwick Medical School, University Hospital, University of Warwick, Coventry, United Kingdom
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Guy Barker
- School of Life Sciences, University of Warwick, Wellesbourne, United Kingdom
| | - Till Bretschneider
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Anatoly Shmygol
- Clinical Sciences Research Laboratories, Warwick Medical School, University Hospital, University of Warwick, Coventry, United Kingdom
| | - David A. Rand
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Paul J. Thornalley
- Clinical Sciences Research Laboratories, Warwick Medical School, University Hospital, University of Warwick, Coventry, United Kingdom
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
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WIESMANN V, FRANZ D, HELD C, MÜNZENMAYER C, PALMISANO R, WITTENBERG T. Review of free software tools for image analysis of fluorescence cell micrographs. J Microsc 2014; 257:39-53. [DOI: 10.1111/jmi.12184] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/19/2014] [Indexed: 01/26/2023]
Affiliation(s)
- V. WIESMANN
- Fraunhofer Institute for Integrated Circuits IIS; Erlangen Germany
| | - D. FRANZ
- Fraunhofer Institute for Integrated Circuits IIS; Erlangen Germany
- University Erlangen Nuremberg; Erlangen Germany
| | - C. HELD
- Fraunhofer Institute for Integrated Circuits IIS; Erlangen Germany
| | - C. MÜNZENMAYER
- Fraunhofer Institute for Integrated Circuits IIS; Erlangen Germany
| | - R. PALMISANO
- Optical Imaging Center Erlangen; OICE; Erlangen Germany
- Max Planck Institute for the Science of Light; Erlangen Germany
| | - T. WITTENBERG
- Fraunhofer Institute for Integrated Circuits IIS; Erlangen Germany
- University Erlangen Nuremberg; Erlangen Germany
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10
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Bertolusso R, Tian B, Zhao Y, Vergara L, Sabree A, Iwanaszko M, Lipniacki T, Brasier AR, Kimmel M. Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise. PLoS One 2014; 9:e93396. [PMID: 24710104 PMCID: PMC3977818 DOI: 10.1371/journal.pone.0093396] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 11/27/2013] [Accepted: 03/04/2014] [Indexed: 01/01/2023] Open
Abstract
We present an integrated dynamical cross-talk model of the epithelial innate immune response (IIR) incorporating RIG-I and TLR3 as the two major pattern recognition receptors (PRR) converging on the RelA and IRF3 transcriptional effectors. bioPN simulations reproduce biologically relevant gene-and protein abundance measurements in response to time course, gene silencing and dose-response perturbations both at the population and single cell level. Our computational predictions suggest that RelA and IRF3 are under auto- and cross-regulation. We predict, and confirm experimentally, that RIG-I mRNA expression is controlled by IRF7. We also predict the existence of a TLR3-dependent, IRF3-independent transcription factor (or factors) that control(s) expression of MAVS, IRF3 and members of the IKK family. Our model confirms the observed dsRNA dose-dependence of oscillatory patterns in single cells, with periods of 1-3 hr. Model fitting to time series, matched by knockdown data suggests that the NF-κB module operates in a different regime (with different coefficient values) than in the TNFα-stimulation experiments. In future studies, this model will serve as a foundation for identification of virus-encoded IIR antagonists and examination of stochastic effects of viral replication. Our model generates simulated time series, which reproduce the noisy oscillatory patterns of activity (with 1-3 hour period) observed in individual cells. Our work supports the hypothesis that the IIR is a phenomenon that emerged by evolution despite highly variable responses at an individual cell level.
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Affiliation(s)
- Roberto Bertolusso
- Department of Statistics, Rice University, Houston, Texas, United States of America
| | - Bing Tian
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
| | - Leoncio Vergara
- Center for Biomedical Engineering, UTMB, Galveston, Texas, United States of America
| | - Aqeeb Sabree
- Department of Statistics, Rice University, Houston, Texas, United States of America
| | - Marta Iwanaszko
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Allan R. Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, Texas, United States of America
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland
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Affiliation(s)
- Kaustav Nandy
- Optical Microscopy and Analysis Laboratory, Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, 21702, USA.
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