151
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Rangarajan N, Fox Z, Singh A, Kulkarni P, Rangarajan G. Disorder, oscillatory dynamics and state switching: the role of c-Myc. J Theor Biol 2015; 386:105-14. [PMID: 26408335 DOI: 10.1016/j.jtbi.2015.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 09/12/2015] [Accepted: 09/15/2015] [Indexed: 12/15/2022]
Abstract
In this paper, using the intrinsically disordered oncoprotein Myc as an example, we present a mathematical model to help explain how protein oscillatory dynamics can influence state switching. Earlier studies have demonstrated that, while Myc overexpression can facilitate state switching and transform a normal cell into a cancer phenotype, its downregulation can reverse state-switching. A fundamental aspect of the model is that a Myc threshold determines cell fate in cells expressing p53. We demonstrate that a non-cooperative positive feedback loop coupled with Myc sequestration at multiple binding sites can generate bistable Myc levels. Normal quiescent cells with Myc levels below the threshold can respond to mitogenic signals to activate the cyclin/cdk oscillator for limited cell divisions but the p53/Mdm2 oscillator remains nonfunctional. In response to stress, the p53/Mdm2 oscillator is activated in pulses that are critical to DNA repair. But if stress causes Myc levels to cross the threshold, Myc inactivates the p53/Mdm2 oscillator, abrogates p53 pulses, and pushes the cyclin/cdk oscillator into overdrive sustaining unchecked proliferation seen in cancer. However, if Myc is downregulated, the cyclin/cdk oscillator is inactivated and the p53/Mdm2 oscillator is reset and the cancer phenotype is reversed.
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Affiliation(s)
| | - Zach Fox
- Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Abhyudai Singh
- Biomedical Engineering, University of Delaware, Newark, DE, USA; Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
| | - Prakash Kulkarni
- Department of Urology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore, India; Centre for Neuroscience, Indian Institute of Science, Bangalore, India.
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152
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de Oliveira LR, Mombach JCM, Castellani G. A simple stochastic model for the feedback circuit between p16INK4a and p53 mediated by p38MAPK: implications for senescence and apoptosis. MOLECULAR BIOSYSTEMS 2015; 11:2955-63. [PMID: 26281034 DOI: 10.1039/c5mb00230c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The mechanisms leading to the cell fate decision between apoptosis and senescence upon DNA damage are still unclear and have stochastic features. Cellular oxidative stress can generate DNA damage and activate the important mitogen-activated protein kinase 14 (p38MAPK) that is involved in pathologies like Alzheimer's disease. Based on experimental evidence we propose a simple network that might operate at the core of the cell control machinery for the choice between apoptosis and senescence involving the cross-talk between p38MAPK, the tumor suppressor protein p53 and the cyclin-dependent kinase inhibitor (p16INK4a). We have performed two types of analyses, deterministic and stochastic, exploring the system's parameter space, in the first, we calculated the fixed points of the deterministic model and, in the second, we numerically integrated the master equation for the stochastic version. The model shows a variety of behaviors dependent on the parameters including states of high expression levels of p53 or p16INK4a that can be associated with an apoptotic or senescent phenotype, respectively, in agreement with experimental data. In addition, we observe both monostable and bistable behavior (where bistability is a phenomenon in which two stable steady states coexist for a fixed set of control parameter values) which here we suggest to be involved in the cell fate decision problem.
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Affiliation(s)
- L R de Oliveira
- Physics Department, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil.
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153
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Castillo-Hair SM, Villota ER, Coronado AM. Design principles for robust oscillatory behavior. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:125-33. [PMID: 26279706 DOI: 10.1007/s11693-015-9178-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 07/29/2015] [Accepted: 07/31/2015] [Indexed: 11/29/2022]
Abstract
Oscillatory responses are ubiquitous in regulatory networks of living organisms, a fact that has led to extensive efforts to study and replicate the circuits involved. However, to date, design principles that underlie the robustness of natural oscillators are not completely known. Here we study a three-component enzymatic network model in order to determine the topological requirements for robust oscillation. First, by simulating every possible topological arrangement and varying their parameter values, we demonstrate that robust oscillators can be obtained by augmenting the number of both negative feedback loops and positive autoregulations while maintaining an appropriate balance of positive and negative interactions. We then identify network motifs, whose presence in more complex topologies is a necessary condition for obtaining oscillatory responses. Finally, we pinpoint a series of simple architectural patterns that progressively render more robust oscillators. Together, these findings can help in the design of more reliable synthetic biomolecular networks and may also have implications in the understanding of other oscillatory systems.
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Affiliation(s)
- Sebastian M Castillo-Hair
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, 25 Lima, Peru
| | - Elizabeth R Villota
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, 25 Lima, Peru
| | - Alberto M Coronado
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, 25 Lima, Peru
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154
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Yi W, Hu X, Chen Z, Liu L, Tian Y, Chen H, Cong YS, Yang F, Zhang L, Rudolph KL, Zhang Z, Zhao Y, Ju Z. Phosphatase Wip1 controls antigen-independent B-cell development in a p53-dependent manner. Blood 2015; 126:620-8. [PMID: 26012568 PMCID: PMC4520877 DOI: 10.1182/blood-2015-02-624114] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/06/2015] [Indexed: 01/08/2023] Open
Abstract
Wild-type p53-induced phosphatase 1 (Wip1), a phosphatase previously considered as an oncogene, has been implicated in the regulation of thymus homeostasis and neutrophil maturation. However, the role of Wip1 in B-cell development is unknown. We show that Wip1-deficient mice exhibit a significant reduction of B-cell numbers in the bone marrow, peripheral blood, and spleen. A reciprocal transplantation approach revealed a cell-intrinsic defect in early B-cell precursors caused by Wip1 deficiency. Further experiments revealed that Wip1 deficiency led to a sustained activation of p53 in B cells, which led to increased level of apoptosis in the pre-B-cell compartment. Notably, the impairment of B-cell development in Wip1-deficient mice was completely rescued by genetic ablation of p53, but not p21. Therefore, loss of Wip1 phosphatase induces a p53-dependent, but p21-independent, mechanism that impairs B-cell development by enhancing apoptosis in early B-cell precursors. Moreover, Wip1 deficiency exacerbated a decline in B-cell development caused by aging as evidenced in mice with aging and mouse models with serial competitive bone marrow transplantation, respectively. Our present data indicate that Wip1 plays a critical role in maintaining antigen-independent B-cell development in the bone marrow and preventing an aging-related decline in B-cell development.
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Affiliation(s)
- Weiwei Yi
- Institute of Aging Research, Hangzhou Normal University School of Medicine, Hangzhou, China
| | - Xuelian Hu
- Transplantation Biology Research Division, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhiyang Chen
- Institute of Aging Research, Hangzhou Normal University School of Medicine, Hangzhou, China; Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany
| | - Leiming Liu
- Institute of Aging Research, Hangzhou Normal University School of Medicine, Hangzhou, China; Sir Runrun Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuan Tian
- Transplantation Biology Research Division, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hui Chen
- Transplantation Biology Research Division, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Sheng Cong
- Institute of Aging Research, Hangzhou Normal University School of Medicine, Hangzhou, China
| | - Fan Yang
- Transplantation Biology Research Division, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lianfeng Zhang
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health; Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; and
| | | | - Zhixin Zhang
- Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Ministry of Education Key Laboratory of Birth Defects, Sichuan University, Chengdu, China
| | - Yong Zhao
- Transplantation Biology Research Division, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhenyu Ju
- Institute of Aging Research, Hangzhou Normal University School of Medicine, Hangzhou, China
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155
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Cuba CE, Valle AR, Ayala-Charca G, Villota ER, Coronado AM. Influence of parameter values on the oscillation sensitivities of two p53-Mdm2 models. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:77-84. [PMID: 26279702 DOI: 10.1007/s11693-015-9173-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/16/2015] [Accepted: 05/30/2015] [Indexed: 10/23/2022]
Abstract
Biomolecular networks that present oscillatory behavior are ubiquitous in nature. While some design principles for robust oscillations have been identified, it is not well understood how these oscillations are affected when the kinetic parameters are constantly changing or are not precisely known, as often occurs in cellular environments. Many models of diverse complexity level, for systems such as circadian rhythms, cell cycle or the p53 network, have been proposed. Here we assess the influence of hundreds of different parameter sets on the sensitivities of two configurations of a well-known oscillatory system, the p53 core network. We show that, for both models and all parameter sets, the parameter related to the p53 positive feedback, i.e. self-promotion, is the only one that presents sizeable sensitivities on extrema, periods and delay. Moreover, varying the parameter set values to change the dynamical characteristics of the response is more restricted in the simple model, whereas the complex model shows greater tunability. These results highlight the importance of the presence of specific network patterns, in addition to the role of parameter values, when we want to characterize oscillatory biochemical systems.
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Affiliation(s)
- Christian E Cuba
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
| | - Alexander R Valle
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
| | - Giancarlo Ayala-Charca
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
| | - Elizabeth R Villota
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
| | - Alberto M Coronado
- Faculty of Mechanical Engineering, Universidad Nacional de Ingeniería, Av. Túpac Amaru s/n - Puerta 3, Pabellón A, Lima 25, Peru
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156
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Zhang L, Liu L, He Z, Li G, Liu J, Song Z, Jin H, Rudolph KL, Yang H, Mao Y, Zhang L, Zhang H, Xiao Z, Ju Z. Inhibition of wild-type p53-induced phosphatase 1 promotes liver regeneration in mice by direct activation of mammalian target of rapamycin. Hepatology 2015; 61:2030-41. [PMID: 25704606 DOI: 10.1002/hep.27755] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/14/2015] [Indexed: 12/21/2022]
Abstract
UNLABELLED The liver possesses extraordinary regenerative capacity in response to injury. However, liver regeneration (LR) is often impaired in disease conditions. Wild-type p53-induced phosphatase 1 (Wip1) is known as a tumor promoter and enhances cell proliferation, mainly by deactivating antioncogenes. However, in this work, we identified an unexpected role of Wip1 in LR. In contrast to its known role in promoting cell proliferation in extrahepatic tissue, we found that Wip1 suppressed hepatocyte proliferation after partial hepatectomy (PHx). Deletion of Wip1 increased the rate of LR after PHx. Enhanced LR in Wip1-deficient mice was a result of the activation of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1) pathway. Furthermore, we showed that Wip1 physically interacted with and dephosphorylated mTOR. Interestingly, inhibition of Wip1 also activated the p53 pathway during LR. Disruption of the p53 pathway further enhanced LR in Wip1-deficient mice. Therefore, inhibition of Wip1 has a dual role in LR, i.e., promoting hepatocyte proliferation through activation of the mTORC1 pathway, meanwhile suppressing LR through activation of the p53 pathway. However, the proregenerative role of mTORC1 overwhelms the antiproliferative role of p53. Furthermore, CCT007093, a Wip1 inhibitor, enhanced LR and increased the survival rate of mice after major hepatectomy. CONCLUSION mTOR is a new direct target of Wip1. Wip1 inhibition can activate the mTORC1 pathway and enhance hepatocyte proliferation after hepatectomy. These findings have clinical applications in cases where LR is critical, including acute liver failure, cirrhosis, or small-for-size liver transplantations.
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Affiliation(s)
- Lingling Zhang
- Institute of Aging Research, Leibniz Link Partner Group on Stem Cell Aging, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Leiming Liu
- Sir Runrun Shaw Hospital, Medical School, Zhejiang University, Hangzhou, China
| | - Zhiyong He
- The Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China
| | - Guangbing Li
- Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Junping Liu
- Institute of Aging Research, Leibniz Link Partner Group on Stem Cell Aging, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Zhangfa Song
- Sir Runrun Shaw Hospital, Medical School, Zhejiang University, Hangzhou, China
| | - Hongchuan Jin
- Sir Runrun Shaw Hospital, Medical School, Zhejiang University, Hangzhou, China
| | | | - Huayu Yang
- Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yilei Mao
- Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Lianfeng Zhang
- Institute of Laboratory Animal Sciences, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Hongbing Zhang
- Institute of Basic Medical Sciences and School of Basic Medicine, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhicheng Xiao
- The Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China
| | - Zhenyu Ju
- Institute of Aging Research, Leibniz Link Partner Group on Stem Cell Aging, School of Medicine, Hangzhou Normal University, Hangzhou, China
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157
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Mirzayans R, Andrais B, Scott A, Wang YW, Weiss RH, Murray D. Spontaneous γH2AX Foci in Human Solid Tumor-Derived Cell Lines in Relation to p21WAF1 and WIP1 Expression. Int J Mol Sci 2015; 16:11609-28. [PMID: 26006237 PMCID: PMC4463719 DOI: 10.3390/ijms160511609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/12/2015] [Accepted: 05/15/2015] [Indexed: 12/26/2022] Open
Abstract
Phosphorylation of H2AX on Ser139 (γH2AX) after exposure to ionizing radiation produces nuclear foci that are detectable by immunofluorescence microscopy. These so-called γH2AX foci have been adopted as quantitative markers for DNA double-strand breaks. High numbers of spontaneous γH2AX foci have also been reported for some human solid tumor-derived cell lines, but the molecular mechanism(s) for this response remains elusive. Here we show that cancer cells (e.g., HCT116; MCF7) that constitutively express detectable levels of p21WAF1 (p21) exhibit low numbers of γH2AX foci (<3/nucleus), whereas p21 knockout cells (HCT116p21−/−) and constitutively low p21-expressing cells (e.g., MDA-MB-231) exhibit high numbers of foci (e.g., >50/nucleus), and that these foci are not associated with apoptosis. The majority (>95%) of cells within HCT116p21−/− and MDA-MB-231 cultures contain high levels of phosphorylated p53, which is localized in the nucleus. We further show an inverse relationship between γH2AX foci and nuclear accumulation of WIP1, an oncogenic phosphatase. Our studies suggest that: (i) p21 deficiency might provide a selective pressure for the emergence of apoptosis-resistant progeny exhibiting genomic instability, manifested as spontaneous γH2AX foci coupled with phosphorylation and nuclear accumulation of p53; and (ii) p21 might contribute to positive regulation of WIP1, resulting in dephosphorylation of γH2AX.
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Affiliation(s)
- Razmik Mirzayans
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada.
| | - Bonnie Andrais
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada.
| | - April Scott
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada.
| | - Ying W Wang
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada.
| | - Robert H Weiss
- Division of Nephrology, Department of Internal Medicine, University of California, Davis, CA 95616, USA.
- Department of Medicine, Mather VA Medical Center, Sacramento, CA 95655, USA.
| | - David Murray
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada.
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158
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Zhao B, Zhang WD, Duan YL, Lu YQ, Cun YX, Li CH, Guo K, Nie WH, Li L, Zhang R, Zheng P. Filia Is an ESC-Specific Regulator of DNA Damage Response and Safeguards Genomic Stability. Cell Stem Cell 2015; 16:684-98. [PMID: 25936915 DOI: 10.1016/j.stem.2015.03.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 02/16/2015] [Accepted: 03/22/2015] [Indexed: 12/20/2022]
Abstract
Pluripotent stem cells (PSCs) hold great promise in cell-based therapy, but the genomic instability seen in culture hampers their full application. A greater understanding of the factors that regulate genomic stability in PSCs could help address this issue. Here we describe the identification of Filia as a specific regulator of genomic stability in mouse embryonic stem cells (ESCs). Filia expression is induced by genotoxic stress. Filia promotes centrosome integrity and regulates the DNA damage response (DDR) through multiple pathways, including DDR signaling, cell-cycle checkpoints and damage repair, ESC differentiation, and apoptosis. Filia depletion causes ESC genomic instability, induces resistance to apoptosis, and promotes malignant transformation. As part of its role in DDR, Filia interacts with PARP1 and stimulates its enzymatic activity. Filia also constitutively resides on centrosomes and translocates to DNA damage sites and mitochondria, consistent with its multifaceted roles in regulating centrosome integrity, damage repair, and apoptosis.
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Affiliation(s)
- Bo Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei-Dao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ying-Liang Duan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yong-Qing Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yi-Xian Cun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Chao-Hui Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Kun Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Wen-Hui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Lei Li
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute Cancer Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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159
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Resendis-Antonio O, González-Torres C, Jaime-Muñoz G, Hernandez-Patiño CE, Salgado-Muñoz CF. Modeling metabolism: A window toward a comprehensive interpretation of networks in cancer. Semin Cancer Biol 2015; 30:79-87. [DOI: 10.1016/j.semcancer.2014.04.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/01/2014] [Accepted: 04/04/2014] [Indexed: 12/01/2022]
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160
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Mothes J, Busse D, Kofahl B, Wolf J. Sources of dynamic variability in NF-κB signal transduction: a mechanistic model. Bioessays 2015; 37:452-62. [PMID: 25640005 PMCID: PMC4409097 DOI: 10.1002/bies.201400113] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The transcription factor NF-κB (p65/p50) plays a central role in the coordination of cellular responses by activating the transcription of numerous target genes. The precise role of the dynamics of NF-κB signalling in regulating gene expression is still an open question. Here, we show that besides external stimulation intracellular parameters can influence the dynamics of NF-κB. By applying mathematical modelling and bifurcation analyses, we show that NF-κB is capable of exhibiting different types of dynamics in response to the same stimulus. We identified the total NF-κB concentration and the IκBα transcription rate constant as two critical parameters that modulate the dynamics and the fold change of NF-κB. Both parameters might vary as a result of cell-to-cell variability. The regulation of the IκBα transcription rate constant, e.g. by co-factors, provides the possibility of regulating the NF-κB dynamics by crosstalk.
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Affiliation(s)
- Janina Mothes
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
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161
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Salehi-Reyhani A, Gesellchen F, Mampallil D, Wilson R, Reboud J, Ces O, Willison KR, Cooper JM, Klug DR. Chemical-Free Lysis and Fractionation of Cells by Use of Surface Acoustic Waves for Sensitive Protein Assays. Anal Chem 2015; 87:2161-9. [DOI: 10.1021/ac5033758] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Frank Gesellchen
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
| | - Dileep Mampallil
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
| | - Rab Wilson
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
| | - Julien Reboud
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
| | | | | | - Jonathan M. Cooper
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
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162
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Shaltiel IA, Krenning L, Bruinsma W, Medema RH. The same, only different - DNA damage checkpoints and their reversal throughout the cell cycle. J Cell Sci 2015; 128:607-20. [PMID: 25609713 DOI: 10.1242/jcs.163766] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cell cycle checkpoints activated by DNA double-strand breaks (DSBs) are essential for the maintenance of the genomic integrity of proliferating cells. Following DNA damage, cells must detect the break and either transiently block cell cycle progression, to allow time for repair, or exit the cell cycle. Reversal of a DNA-damage-induced checkpoint not only requires the repair of these lesions, but a cell must also prevent permanent exit from the cell cycle and actively terminate checkpoint signalling to allow cell cycle progression to resume. It is becoming increasingly clear that despite the shared mechanisms of DNA damage detection throughout the cell cycle, the checkpoint and its reversal are precisely tuned to each cell cycle phase. Furthermore, recent findings challenge the dogmatic view that complete repair is a precondition for cell cycle resumption. In this Commentary, we highlight cell-cycle-dependent differences in checkpoint signalling and recovery after a DNA DSB, and summarise the molecular mechanisms that underlie the reversal of DNA damage checkpoints, before discussing when and how cell fate decisions after a DSB are made.
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Affiliation(s)
- Indra A Shaltiel
- The Netherlands Cancer Institute, Division of Cell Biology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lenno Krenning
- The Netherlands Cancer Institute, Division of Cell Biology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Wytse Bruinsma
- The Netherlands Cancer Institute, Division of Cell Biology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - René H Medema
- The Netherlands Cancer Institute, Division of Cell Biology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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163
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Abstract
The ataxia-telangiectasia mutated (ATM) protein kinase is a master regulator of the DNA damage response, and it coordinates checkpoint activation, DNA repair, and metabolic changes in eukaryotic cells in response to DNA double-strand breaks and oxidative stress. Loss of ATM activity in humans results in the pleiotropic neurodegeneration disorder ataxia-telangiectasia. ATM exists in an inactive state in resting cells but can be activated by the Mre11-Rad50-Nbs1 (MRN) complex and other factors at sites of DNA breaks. In addition, oxidation of ATM activates the kinase independently of the MRN complex. This review discusses these mechanisms of activation, as well as the posttranslational modifications that affect this process and the cellular factors that affect the efficiency and specificity of ATM activation and substrate phosphorylation. I highlight functional similarities between the activation mechanisms of ATM, phosphatidylinositol 3-kinases (PI3Ks), and the other PI3K-like kinases, as well as recent structural insights into their regulation.
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Affiliation(s)
- Tanya T Paull
- Howard Hughes Medical Institute, Department of Molecular Biosciences, and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712;
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164
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Zhang XW, Wang XF, Ni SJ, Qin W, Zhao LQ, Hua RX, Lu YW, Li J, Dimri GP, Guo WJ. UBTD1 induces cellular senescence through an UBTD1-Mdm2/p53 positive feedback loop. J Pathol 2015; 235:656-67. [PMID: 25382750 DOI: 10.1002/path.4478] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 09/22/2014] [Accepted: 11/04/2014] [Indexed: 01/13/2023]
Abstract
The tumour suppressor p53 plays an important role in tumourigenesis. Besides inducing apoptosis, it regulates cellular senescence, which constitutes an important barrier to tumourigenesis. The mechanism of regulation of cellular senescence by p53 and its downstream pathway are poorly understood. Here, we report that the ubiquitin domain-containing 1 (UBTD1) gene, a new downstream target of p53, induces cellular senescence and acts as a novel tumour suppressor by a mechanism that depends on p53. Expression of UBTD1 increased upon cellular senescence induced by serial passageing of cultures, as well as by exposure to DNA-damageing drugs that induce premature senescence. Over-expression of UBTD1 induces senescence in human fibroblasts and cancer cells and attenuation of the transformed phenotype in cancer cells. UBTD1 is down-regulated in gastric and colorectal cancer tissues, and its lower expression correlates with a more aggressive phenotype and worse prognosis. Multivariate analysis revealed that UBTD1 expression was an independent prognostic factor for gastric cancer patients. Furthermore, UBTD1 increased the stability of p53 protein, by promoting the degradation of Mdm2 protein. Importantly, UBTD1 and p53 function mutually depend on each other in regulating cellular senescence and proliferation. Thus, our data suggest that, upon DNA damage, p53 induction by UBTD1 creates a positive feedback mechanism to further increase p53 expression. Our results establish UBTD1 as a regulator of cellular senescence that mediates p53 function, and provide insights into the mechanism of Mdm2 inhibition that impacts p53 dynamics during cellular senescence and tumourigenesis.
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Affiliation(s)
- Xiao-Wei Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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165
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Chong KH, Samarasinghe S, Kulasiri D. Mathematical modelling of p53 basal dynamics and DNA damage response. Math Biosci 2015; 259:27-42. [DOI: 10.1016/j.mbs.2014.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 10/23/2014] [Accepted: 10/31/2014] [Indexed: 02/06/2023]
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166
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Zhou CH, Zhang XP, Liu F, Wang W. Involvement of miR-605 and miR-34a in the DNA damage response promotes apoptosis induction. Biophys J 2014; 106:1792-800. [PMID: 24739178 DOI: 10.1016/j.bpj.2014.02.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 02/20/2014] [Accepted: 02/26/2014] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs are key regulators of gene expression at the posttranscriptional level. In this study, we focus on miR-605 and miR-34a, which are direct transcriptional targets of p53 and in turn enhance its tumor suppressor function by acting upstream and downstream of it, respectively. miR-605 promotes p53 activation by repressing the expression of mdm2, whereas miR-34a promotes p53-dependent apoptosis by suppressing the expression of antiapoptotic genes such as bcl-2. What roles they play in the p53-mediated DNA damage response is less well understood. Here, we develop a four-module model of the p53 network to investigate the effect of miR-605 and miR-34a on the cell-fate decision after ionizing radiation. Results of numerical simulation indicate that the cell fate is closely associated with network dynamics. The concentration of p53 undergoes few pulses in response to repairable DNA damage, or it first oscillates and then switches to high plateau levels after irreparable damage. The amplitude of p53 pulses rises to various extents depending on miR-605 expression, and miR-605 accelerates the switching behavior of p53 levels to induce apoptosis. In parallel, miR-34a promotes apoptosis by enhancing the accumulation of free p53AIP1, a key proapoptotic protein. Thus, both miR-605 and miR-34a can mediate cellular outcomes and the timing of apoptosis. Moreover, miR-605 and PTEN complement each other in elevating p53 levels to trigger apoptosis. Taken together, miR-605 and miR-34a cooperate to endow the network with a fail-safe mechanism for apoptosis induction. This computational study also enriches our understanding of the action modes of p53-targeted microRNAs.
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Affiliation(s)
- Chun-Hong Zhou
- National Laboratory of Solid State Microstructures, and Department of Physics, Nanjing University, Nanjing, China; School of Physics and Electronic Engineering, Jiangsu Normal University, Xuzhou, China
| | - Xiao-Peng Zhang
- National Laboratory of Solid State Microstructures, and Department of Physics, Nanjing University, Nanjing, China
| | - Feng Liu
- National Laboratory of Solid State Microstructures, and Department of Physics, Nanjing University, Nanjing, China.
| | - Wei Wang
- National Laboratory of Solid State Microstructures, and Department of Physics, Nanjing University, Nanjing, China.
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167
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Sammons MA, Zhu J, Drake AM, Berger SL. TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity. Genome Res 2014; 25:179-88. [PMID: 25391375 PMCID: PMC4315292 DOI: 10.1101/gr.181883.114] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Despite overwhelming evidence that transcriptional activation by TP53 is critical for its tumor suppressive activity, the mechanisms by which TP53 engages the genome in the context of chromatin to activate transcription are not well understood. Using a compendium of novel and existing genome-wide data sets, we examined the relationship between TP53 binding and the dynamics of the local chromatin environment. Our analysis revealed three distinct categories of TP53 binding events that differ based on the dynamics of the local chromatin environment. The first class of TP53 binding events occurs near transcriptional start sites (TSS) and is defined by previously characterized promoter-associated chromatin modifications. The second class comprises a large cohort of preestablished, promoter-distal enhancer elements that demonstrates dynamic histone acetylation and transcription upon TP53 binding. The third class of TP53 binding sites is devoid of classic chromatin modifications and, remarkably, fall within regions of inaccessible chromatin, suggesting that TP53 has intrinsic pioneer factor activity and binds within structurally inaccessible regions of chromatin. Intriguingly, these inaccessible TP53 binding sites feature several enhancer-like properties in cell types within the epithelial lineage, indicating that TP53 binding events include a group of “proto-enhancers” that become active enhancers given the appropriate cellular context. These data indicate that TP53, along with TP63, may act as pioneer factors to specify epithelial enhancers. Further, these findings suggest that rather than following a global cell-type invariant stress response program, TP53 may tune its response based on the lineage-specific epigenomic landscape.
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Affiliation(s)
- Morgan A Sammons
- Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jiajun Zhu
- Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Adam M Drake
- Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Shelley L Berger
- Departments of Cell and Developmental Biology, Genetics, and Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Penn Epigenetics Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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168
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Borcherds W, Theillet FX, Katzer A, Finzel A, Mishall KM, Powell AT, Wu H, Manieri W, Dieterich C, Selenko P, Loewer A, Daughdrill GW. Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells. Nat Chem Biol 2014; 10:1000-2. [PMID: 25362358 DOI: 10.1038/nchembio.1668] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 09/05/2014] [Indexed: 12/23/2022]
Abstract
Levels of residual structure in disordered interaction domains determine in vitro binding affinities, but whether they exert similar roles in cells is not known. Here, we show that increasing residual p53 helicity results in stronger Mdm2 binding, altered p53 dynamics, impaired target gene expression and failure to induce cell cycle arrest upon DNA damage. These results establish that residual structure is an important determinant of signaling fidelity in cells.
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Affiliation(s)
- Wade Borcherds
- 1] Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA. [2] Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, USA
| | - François-Xavier Theillet
- In-cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany
| | - Andrea Katzer
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Ana Finzel
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Katie M Mishall
- 1] Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA. [2] Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, USA
| | - Anne T Powell
- 1] Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA. [2] Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, USA
| | - Hongwei Wu
- 1] Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA. [2] Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, USA
| | - Wanda Manieri
- Drug Discovery Department, Moffitt Cancer Center, University of South Florida, Tampa, Florida, USA
| | | | - Philipp Selenko
- In-cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany
| | - Alexander Loewer
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Gary W Daughdrill
- 1] Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA. [2] Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, USA
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169
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Gaglia G, Lahav G. Constant rate of p53 tetramerization in response to DNA damage controls the p53 response. Mol Syst Biol 2014; 10:753. [PMID: 25344068 PMCID: PMC4299375 DOI: 10.15252/msb.20145168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The dynamics of the tumor suppressor protein p53 have been previously investigated in single
cells using fluorescently tagged p53. Such approach reports on the total abundance of p53 but does
not provide a measure for functional p53. We used fluorescent protein-fragment complementation assay
(PCA) to quantify in single cells the dynamics of p53 tetramers, the functional units of p53. We
found that while total p53 increases proportionally to the input strength, p53 tetramers are formed
in cells at a constant rate. This breaks the linear input–output relation and dampens the p53
response. Disruption of the p53-binding protein ARC led to a dose-dependent rate of tetramers
formation, resulting in enhanced tetramerization and induction of p53 target genes. Our work
suggests that constraining the p53 response in face of variable inputs may protect cells from
committing to terminal outcomes and highlights the importance of quantifying the active form of
signaling molecules in single cells. Quantification of the dynamics of p53 tetramers in single cells using a fluorescent
protein-fragment complementation assay reveals that, while total p53 increases proportionally to the
DNA damage strength, p53 tetramers are formed at a constant rate.
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Affiliation(s)
- Giorgio Gaglia
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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170
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Davis DM, Purvis JE. Computational analysis of signaling patterns in single cells. Semin Cell Dev Biol 2014; 37:35-43. [PMID: 25263011 DOI: 10.1016/j.semcdb.2014.09.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/11/2014] [Accepted: 09/13/2014] [Indexed: 01/19/2023]
Abstract
Signaling proteins are flexible in both form and function. They can bind to multiple molecular partners and integrate diverse types of cellular information. When imaged by time-lapse microscopy, many signaling proteins show complex patterns of activity or localization that vary from cell to cell. This heterogeneity is so prevalent that it has spurred the development of new computational strategies to analyze single-cell signaling patterns. A collective observation from these analyses is that cells appear less heterogeneous when their responses are normalized to, or synchronized with, other single-cell measurements. In many cases, these transformed signaling patterns show distinct dynamical trends that correspond with predictable phenotypic outcomes. When signaling mechanisms are unclear, computational models can suggest putative molecular interactions that are experimentally testable. Thus, computational analysis of single-cell signaling has not only provided new ways to quantify the responses of individual cells, but has helped resolve longstanding questions surrounding many well-studied human signaling proteins including NF-κB, p53, ERK1/2, and CDK2. A number of specific challenges lie ahead for single-cell analysis such as quantifying the contribution of non-cell autonomous signaling as well as the characterization of protein signaling dynamics in vivo.
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Affiliation(s)
- Denise M Davis
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, United States
| | - Jeremy E Purvis
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264, United States.
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171
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Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar I. Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies. Sci Rep 2014; 4:6245. [PMID: 25175563 PMCID: PMC4150106 DOI: 10.1038/srep06245] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/11/2014] [Indexed: 01/22/2023] Open
Abstract
Developing pharmacological strategies for controlling ionizing radiation (IR)-induced cell death is important for both mitigating radiation damage and alleviating the side effects of anti-cancer radiotherapy manifested in surrounding tissue morbidity. Exposure to IR often triggers the onset of p53-dependent apoptotic pathways. Here we build a stochastic model of p53 induced apoptosis comprised of coupled modules of nuclear p53 activation, mitochondrial cytochrome c release and cytosolic caspase activation that also takes into account cellular heterogeneity. Our simulations show that the strength of p53 transcriptional activity and its coupling (or timing with respect) to mitochondrial pore opening are major determinants of cell fate: for systems where apoptosis is elicited via a p53-transcription-independent mechanism, direct activation of Bax by p53 becomes critical to IR-induced-damage initiation. We further show that immediate administration of PUMA inhibitors following IR exposure effectively suppresses excessive cell death, provided that there is a strong caspase/Bid feedback loop; however, the efficacy of the treatment diminishes with increasing delay in treatment implementation. In contrast, the combined inhibition of Bid and Bax elicits an anti-apoptotic response that is effective over a range of time delays.
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Affiliation(s)
- Bing Liu
- 1] Department of Computational &Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA [2]
| | - Divesh Bhatt
- 1] Department of Computational &Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA [2]
| | - Zoltán N Oltvai
- 1] Department of Computational &Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA [2] Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joel S Greenberger
- Department of Radiation Oncology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department of Computational &Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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172
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Eliaš J, Dimitrio L, Clairambault J, Natalini R. The dynamics of p53 in single cells: physiologically based ODE and reaction-diffusion PDE models. Phys Biol 2014; 11:045001. [PMID: 25075792 DOI: 10.1088/1478-3975/11/4/045001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The intracellular signalling network of the p53 protein plays important roles in genome protection and the control of cell cycle phase transitions. Recently observed oscillatory behaviour in single cells under stress conditions has inspired several research groups to simulate and study the dynamics of the protein with the aim of gaining a proper understanding of the physiological meanings of the oscillations. We propose compartmental ODE and PDE models of p53 activation and regulation in single cells following DNA damage and we show that the p53 oscillations can be retrieved by plainly involving p53-Mdm2 and ATM-p53-Wip1 negative feedbacks, which are sufficient for oscillations experimentally, with no further need to introduce any delays into the protein responses and without considering additional positive feedback.
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Affiliation(s)
- Ján Eliaš
- UPMC, Laboratoire Jacques-Louis Lions, 4 Place Jussieu, F-75005 Paris, France & INRIA Paris-Rocquencourt, MAMBA project-team, Paris and Rocquencourt, France
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173
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Investigation of oscillation accumulation triggered genetic switch in gene regulatory networks. J Theor Biol 2014; 353:61-6. [PMID: 24650938 DOI: 10.1016/j.jtbi.2014.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/09/2014] [Accepted: 03/10/2014] [Indexed: 11/22/2022]
Abstract
Genetic oscillator motifs and genetic switch motifs are blocks of biochemical reaction networks, which are involved in the regulation of rhythms, cell cycle progression, signal processing and cell fate decision. These motifs often interact to constitute complex signal processing systems. There widely exists the oscillation accumulation triggered mechanism in gene regulatory networks, i.e., an oscillator promotes the accumulation of a signaling protein over a threshold value, and activates a switch. The structure can be fund in some important biological function switches, such as apoptosis and DNA repair. We propose the structure as an oscillation accumulation triggered genetic switch (OATGS). Through mathematical modeling and analysis, results show the OATGS with features of robustness to noise and triggered mode. In addition, we show the existence of OATGS features and triggered manner in p53 gene regulatory networks, and explain some of the p53 regulation process, such as counting mechanism and pulse shape. We speculate that OATGS with oscillation accumulation triggered manner is a new important biological function switch.
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174
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Iwamoto K, Hamada H, Eguchi Y, Okamoto M. Stochasticity of intranuclear biochemical reaction processes controls the final decision of cell fate associated with DNA damage. PLoS One 2014; 9:e101333. [PMID: 25003668 PMCID: PMC4086823 DOI: 10.1371/journal.pone.0101333] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/01/2014] [Indexed: 01/08/2023] Open
Abstract
A massive integrative mathematical model of DNA double-strand break (DSB) generation, DSB repair system, p53 signaling network, and apoptosis induction pathway was constructed to explore the dominant factors of unknown criteria of cell fate decision. In the proposed model, intranuclear reactions were modeled as stochastic processes and cytoplasmic reactions as deterministic processes, and both reaction sets were simulated simultaneously. The simulated results at the single-cell level showed that the model generated several sustained oscillations (pulses) of p53, Mdm2, ATM, and Wip1, and cell-to-cell variability in the number of p53 pulses depended on IR intensity. In cell populations, the model generated damped p53 oscillations, and IR intensity affected the amplitude of the first p53 oscillation. Cells were then subjected to the same IR dose exhibiting apoptosis induction variability. These simulated results are in quantitative agreement with major biological findings observed in human breast cancer epithelial MCF7, NIH3T3, and fibrosarcoma cells, demonstrating that the proposed model was concededly biologically appropriate. Statistical analysis of the simulated results shows that the generation of multiple p53 pulses is a prerequisite for apoptosis induction. Furthermore, cells exhibited considerable individual variability in p53 dynamics, which correlated with intrinsic apoptosis induction. The simulated results based on the proposed model demonstrated that the stochasticity of intranuclear biochemical reaction processes controls the final decision of cell fate associated with DNA damage. Applying stochastic simulation to an exploration of intranuclear biochemical reaction processes is indispensable in enhancing the understanding of the dynamic characteristics of biological multi-layered systems of higher organisms.
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Affiliation(s)
- Kazunari Iwamoto
- Graduate school of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Hiroyuki Hamada
- Department of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Synthetic Systems Biology Research Center, Kyushu University, Fukuoka, Japan
- * E-mail:
| | - Yukihiro Eguchi
- Kyushu University Bio-Architecture Center, Kyushu University, Fukuoka, Japan
| | - Masahiro Okamoto
- Department of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Synthetic Systems Biology Research Center, Kyushu University, Fukuoka, Japan
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175
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Dynamic signal encoding--from cells to organisms. Semin Cell Dev Biol 2014; 34:91-8. [PMID: 25008461 DOI: 10.1016/j.semcdb.2014.06.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/15/2014] [Accepted: 06/30/2014] [Indexed: 02/01/2023]
Abstract
Encoding information at the level of signal dynamics is characterized by distinct features, such as robustness to noise and high information content. Currently, a growing number of studies are unravelling the functional importance of signalling dynamics at the single cell level. In addition, first insights are emerging into how the principles of dynamic signal encoding apply to a multicellular context, such as development. In this review, we will first discuss general concepts of information transmission via signalling dynamics and recent experimental examples focusing on underlying principles, including the role of intracellular network topologies. How multicellular organisms use temporal modulation of specific signalling pathways, such as signalling gradients or oscillations, to faithfully control cell fate decisions and pattern formation will also be addressed. Finally, we will consider how technical advancements in the detection and perturbation of signalling dynamics contribute to reshaping our understanding of dynamic signalling in developing organisms.
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176
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Cremona CA, Behrens A. ATM signalling and cancer. Oncogene 2014; 33:3351-60. [PMID: 23851492 DOI: 10.1038/onc.2013.275] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/17/2013] [Accepted: 05/20/2013] [Indexed: 12/12/2022]
Abstract
ATM, the protein kinase mutated in the rare human disease ataxia telangiectasia (A-T), has been the focus of intense scrutiny over the past two decades. Initially this was because of the unusual radiosensitive phenotype of cells from A-T patients, and latterly because investigating ATM signalling has yielded valuable insights into the DNA damage response, redox signalling and cancer. With the recent explosion in genomic data, ATM alterations have been revealed both in the germline as a predisposing factor for cancer and as somatic changes in tumours themselves. Here we review these findings, as well as advances in the understanding of ATM signalling mechanisms in cancer and ATM inhibition as a strategy for cancer treatment.
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Affiliation(s)
- C A Cremona
- Mammalian Genetics Lab, Cancer Research UK London Research Institute, London, UK
| | - A Behrens
- Mammalian Genetics Lab, Cancer Research UK London Research Institute, London, UK
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177
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Eliaš J, Clairambault J. Reaction-diffusion systems for spatio-temporal intracellular protein networks: A beginner's guide with two examples. Comput Struct Biotechnol J 2014; 10:12-22. [PMID: 25210594 PMCID: PMC4151873 DOI: 10.1016/j.csbj.2014.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Spatio-temporal dynamics of a variety of proteins is, among other things, regulated by post-translational modifications of these proteins. Such modifications can thus influence stability and biochemical activities of the proteins, activity and stability of their upstream targets within specific signalling pathways. Commonly used mathematical tools for such protein–protein (and/or protein-mRNA) interactions in single cells, namely, Michaelis–Menten and Hill kinetics, yielding a system of ordinary differential equations, are extended here into (non-linear) partial differential equations by taking into account a more realistic spatial representation of the environment where these reactions occur. In the modelling framework under consideration, all interactions occur in a cell divided into two compartments, the nucleus and the cytoplasm, connected by the semipermeable nuclear membrane and bounded by the impermeable cell membrane. Passive transport mechanism, modelled by the so-called Kedem–Katchalsky boundary conditions, is used here to represent migration of species throughout the nuclear membrane. Nonlinear systems of partial differential equations are solved by the semi-implicit Rothe method. Examples of two spatial oscillators are shown. Namely, these are the circadian rhythm for concentration of the FRQ protein in Neurospora crassa and oscillatory dynamics observed in the activation and regulation of the p53 protein following DNA damage in mammalian cells.
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Affiliation(s)
- Ján Eliaš
- Université Pierre et Marie Curie Paris 06, Sorbonne Universités, Laboratoire Jacques-Louis Lions, boîte courrier 187, F75253 Cedex 05, Paris, France
| | - Jean Clairambault
- Université Pierre et Marie Curie Paris 06, Sorbonne Universités, Laboratoire Jacques-Louis Lions, boîte courrier 187, F75253 Cedex 05, Paris, France
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178
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Dynamics of posttranslational modifications of p53. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2014; 2014:245610. [PMID: 24899917 PMCID: PMC4037116 DOI: 10.1155/2014/245610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/06/2014] [Indexed: 11/25/2022]
Abstract
The latest experimental evidence indicates that acetylation of p53 at K164 (lysine 164) and K120 may induce directly cell apoptosis under severe DNA damage. However, previous cell apoptosis models only studied the effects of active and/or inactive p53, that is, phosphorylation/dephosphorylation of p53. In the present paper, based partly on Geva-Zatorsky et al. (2006) and Batchelor et al. (2008), we propose a new cell apoptosis network, in which p53 has three statuses, that is, unphosphorylated p53, phosphorylated p53, and acetylated p53. The time delay differential equations (DDEs) are formulated based on our network to investigate the dynamical insights of p53-induced cell apoptosis. In agreement with experiments (Loewer et al. (2010)), our simulations indicate that acetylated p53 accumulates gradually and then induces the proapoptotic protein Bax under enough DNA damage. Moreover, phosphorylated p53 oscillates and initiates cell repair during DNA damage.
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179
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Sun T, Cui J. A plausible model for bimodal p53 switch in DNA damage response. FEBS Lett 2014; 588:815-21. [PMID: 24486906 DOI: 10.1016/j.febslet.2014.01.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 12/26/2013] [Accepted: 01/13/2014] [Indexed: 01/10/2023]
Abstract
p53 is a tumor suppressor and the p53 dynamics displays stimulus dependent patterns. Recent evidence suggests a bimodal p53 switch in cell fate decision. However, no theoretical studies have been proposed to investigate bimodal p53 induction. Here we constructed a model and showed that MDM2-p53 mRNA binding might contribute to bimodal p53 switch through an intrinsic positive feedback loop. Lower damage favored pulsing while monotonic increasing was generated with higher damage. Bimodal p53 dynamics was largely influenced by cellular MDM2 and elevated p53/MDM2 ratios with increasing etoposide favor mono-ubiquitination. Our model replicated recent experiments and provided potential insights into dynamic mechanisms of bimodal switch.
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Affiliation(s)
- Tingzhe Sun
- School of Life Sciences, AnQing Normal University, AnQing 246011, Anhui, PR China.
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, PR China.
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180
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Correlation between oncogenic mutations and parameter sensitivity of the apoptosis pathway model. PLoS Comput Biol 2014; 10:e1003451. [PMID: 24465201 PMCID: PMC3900373 DOI: 10.1371/journal.pcbi.1003451] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 12/08/2013] [Indexed: 11/24/2022] Open
Abstract
One of the major breakthroughs in oncogenesis research in recent years is the discovery that, in most patients, oncogenic mutations are concentrated in a few core biological functional pathways. This discovery indicates that oncogenic mechanisms are highly related to the dynamics of biologic regulatory networks, which govern the behaviour of functional pathways. Here, we propose that oncogenic mutations found in different biological functional pathways are closely related to parameter sensitivity of the corresponding networks. To test this hypothesis, we focus on the DNA damage-induced apoptotic pathway—the most important safeguard against oncogenesis. We first built the regulatory network that governs the apoptosis pathway, and then translated the network into dynamics equations. Using sensitivity analysis of the network parameters and comparing the results with cancer gene mutation spectra, we found that parameters that significantly affect the bifurcation point correspond to high-frequency oncogenic mutations. This result shows that the position of the bifurcation point is a better measure of the functionality of a biological network than gene expression levels of certain key proteins. It further demonstrates the suitability of applying systems-level analysis to biological networks as opposed to studying genes or proteins in isolation. Among complex genetic diseases affecting humans, cancer is a major cause of death. In 2008, a genome-wide analysis of hundreds of tumour samples showed that oncogenic mutations are concentrated in a few core functional pathways, revealing a new conceptual framework for cancer biology research, where the role of oncogenic mutations and oncogenic mechanisms are addressed from a network perspective. We therefore propose a new way of identifying high-frequency gene mutations in cancer: gene mutations may affect their corresponding proteins' activity in the biological regulatory network and can be considered as perturbations of the dynamical system. Therefore, mutations that induce qualitative changes in biological networks should correspond to high-frequency mutations in cancer. This concept can help us identify and understand the function of genes that play an important role in oncogenesis, thereby allowing targeted and effective design of gene-based therapy in cancer.
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181
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Burgin E, Salehi-Reyhani A, Barclay M, Brown A, Kaplinsky J, Novakova M, Neil MAA, Ces O, Willison KR, Klug DR. Absolute quantification of protein copy number using a single-molecule-sensitive microarray. Analyst 2014; 139:3235-44. [DOI: 10.1039/c4an00091a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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182
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Abstract
Ataxia-telangiectasia mutated (ATM) kinase, the mutation of which causes the autosomal recessive disease ataxia-telangiectasia, plays an essential role in the maintenance of genome stability. Extensive studies have revealed that activated ATM signals to a massive list of proteins to facilitate cell cycle checkpoints, DNA repair, and many other aspects of physiological responses in the event of DNA double-strand breaks. ATM also plays functional roles beyond the well-characterized DNA damage response (DDR). In this review article, we discuss the recent findings on the molecular mechanisms of ATM in DDR, the mitotic spindle checkpoint, as well as hyperactive ATM signaling in cancer invasion and metastasis.
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Affiliation(s)
- Rebecca J. Boohaker
- Department of Oncology, Drug Discovery Division, Southern Research Institute, Birmingham, AL, USA
| | - Bo Xu
- Department of Oncology, Drug Discovery Division, Southern Research Institute, Birmingham, AL, USA
- Cancer Cell Biology Program, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
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183
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Abstract
A fundamental problem in biology is to understand how genetic circuits implement core cellular functions. Time-lapse microscopy techniques are beginning to provide a direct view of circuit dynamics in individual living cells. Unexpectedly, we are discovering that key transcription and regulatory factors pulse on and off repeatedly, and often stochastically, even when cells are maintained in constant conditions. This type of spontaneous dynamic behavior is pervasive, appearing in diverse cell types from microbes to mammalian cells. Here, we review recent work showing how pulsing is generated and controlled by underlying regulatory circuits and how it provides critical capabilities to cells in stress response, signaling, and development. A major theme is the ability of pulsing to enable time-based regulation analogous to strategies used in engineered systems. Thus, pulsatile dynamics is emerging as a central, and still largely unexplored, layer of temporal organization in the cell.
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Affiliation(s)
- Joe H Levine
- Howard Hughes Medical Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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184
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Schaber J, Lapytsko A, Flockerzi D. Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. J R Soc Interface 2013; 11:20130971. [PMID: 24307567 PMCID: PMC3869172 DOI: 10.1098/rsif.2013.0971] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Negative feedback control is a ubiquitous feature of biochemical systems, as is time delay between a signal and its response. Negative feedback in conjunction with time delay can lead to oscillations. In a cellular context, it might be beneficial to mitigate oscillatory behaviour to avoid recurring stress situations. This can be achieved by increasing the distance between the parameters of the system and certain thresholds, beyond which oscillations occur. This distance has been termed resistance. Here, we prove that in a generic three-dimensional negative feedback system the resistance of the system is modified by nested autoinhibitory feedbacks. Our system features negative feedbacks through both input-inhibition as well as output-activation, a signalling component with mass conservation and perfect adaptation. We show that these features render the system applicable to biological data, exemplified by the high osmolarity glycerol system in yeast and the mammalian p53 system. Output-activation is better supported by data than input-inhibition and also shows distinguished properties with respect to the system's stimulus. Our general approach might be useful in designing synthetic systems in which oscillations can be tuned by synthetic autoinhibitory feedbacks.
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Affiliation(s)
- Jörg Schaber
- Institute for Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, , Magdeburg, Germany
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185
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Novel recurrent neural network for modelling biological networks: Oscillatory p53 interaction dynamics. Biosystems 2013; 114:191-205. [DOI: 10.1016/j.biosystems.2013.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 08/07/2013] [Accepted: 08/28/2013] [Indexed: 12/12/2022]
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186
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Loewer A, Karanam K, Mock C, Lahav G. The p53 response in single cells is linearly correlated to the number of DNA breaks without a distinct threshold. BMC Biol 2013; 11:114. [PMID: 24252182 PMCID: PMC3906995 DOI: 10.1186/1741-7007-11-114] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/13/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The tumor suppressor protein p53 is activated by cellular stress. DNA double strand breaks (DSBs) induce the activation of the kinase ATM, which stabilizes p53 and activates its transcriptional activity. Single cell analysis revealed that DSBs induced by gamma irradiation trigger p53 accumulation in a series of pulses that vary in number from cell to cell. Higher levels of irradiation increase the number of p53 pulses suggesting that they arise from periodic examination of the damage by ATM. If damage persists, additional pulses of p53 are triggered. The threshold of damage required for activating a p53 pulse is unclear. Previous studies that averaged the response across cell populations suggested that one or two DNA breaks are sufficient for activating ATM and p53. However, it is possible that by averaging over a population of cells important features of the dependency between DNA breaks and p53 dynamics are missed. RESULTS Using fluorescent reporters we developed a system for following in individual cells the number of DSBs, the kinetics of repair and the p53 response. We found a large variation in the initial number of DSBs and the rate of repair between individual cells. Cells with higher number of DSBs had higher probability of showing a p53 pulse. However, there was no distinct threshold number of breaks for inducing a p53 pulse. We present evidence that the decision to activate p53 given a specific number of breaks is not entirely stochastic, but instead is influenced by both cell-intrinsic factors and previous exposure to DNA damage. We also show that the natural variations in the initial amount of p53, rate of DSB repair and cell cycle phase do not affect the probability of activating p53 in response to DNA damage. CONCLUSIONS The use of fluorescent reporters to quantify DNA damage and p53 levels in live cells provided a quantitative analysis of the complex interrelationships between both processes. Our study shows that p53 activation differs even between cells that have a similar number of DNA breaks. Understanding the origin and consequences of such variability in normal and cancerous cells is crucial for developing efficient and selective therapeutic interventions.
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Affiliation(s)
- Alexander Loewer
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, 13125 Berlin-Buch, Germany
| | - Ketki Karanam
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline Mock
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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187
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Li Z, Sun B, Clewell RA, Adeleye Y, Andersen ME, Zhang Q. Dose-Response Modeling of Etoposide-Induced DNA Damage Response. Toxicol Sci 2013; 137:371-84. [DOI: 10.1093/toxsci/kft259] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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188
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Mirzayans R, Andrais B, Scott A, Wang YW, Murray D. Ionizing radiation-induced responses in human cells with differing TP53 status. Int J Mol Sci 2013; 14:22409-35. [PMID: 24232458 PMCID: PMC3856071 DOI: 10.3390/ijms141122409] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/29/2013] [Accepted: 11/04/2013] [Indexed: 12/20/2022] Open
Abstract
Ionizing radiation triggers diverse responses in human cells encompassing apoptosis, necrosis, stress-induced premature senescence (SIPS), autophagy, and endopolyploidy (e.g., multinucleation). Most of these responses result in loss of colony-forming ability in the clonogenic survival assay. However, not all modes of so-called clonogenic cell "death" are necessarily advantageous for therapeutic outcome in cancer radiotherapy. For example, the crosstalk between SIPS and autophagy is considered to influence the capacity of the tumor cells to maintain a prolonged state of growth inhibition that unfortunately can be succeeded by tumor regrowth and disease recurrence. Likewise, endopolyploid giant cells are able to segregate into near diploid descendants that continue mitotic activities. Herein we review the current knowledge on the roles that the p53 and p21(WAF1) tumor suppressors play in determining the fate of human fibroblasts (normal and Li-Fraumeni syndrome) and solid tumor-derived cells after exposure to ionizing radiation. In addition, we discuss the important role of WIP1, a p53-regulated oncogene, in the temporal regulation of the DNA damage response and its contribution to p53 dynamics post-irradiation. This article highlights the complexity of the DNA damage response and provides an impetus for rethinking the nature of cancer cell resistance to therapeutic agents.
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Affiliation(s)
- Razmik Mirzayans
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada; E-Mails: (B.A.); (A.S.); (Y.W.W.); (D.M.)
| | - Bonnie Andrais
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada; E-Mails: (B.A.); (A.S.); (Y.W.W.); (D.M.)
| | - April Scott
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada; E-Mails: (B.A.); (A.S.); (Y.W.W.); (D.M.)
| | - Ying W. Wang
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada; E-Mails: (B.A.); (A.S.); (Y.W.W.); (D.M.)
| | - David Murray
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada; E-Mails: (B.A.); (A.S.); (Y.W.W.); (D.M.)
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189
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Eliaš J, Dimitrio L, Clairambault J, Natalini R. The p53 protein and its molecular network: modelling a missing link between DNA damage and cell fate. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:232-47. [PMID: 24113167 DOI: 10.1016/j.bbapap.2013.09.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 09/23/2013] [Accepted: 09/25/2013] [Indexed: 12/29/2022]
Abstract
Various molecular pharmacokinetic-pharmacodynamic (PK-PD) models have been proposed in the last decades to represent and predict drug effects in anticancer chemotherapies. Most of these models are cell population based since clearly measurable effects of drugs can be seen much more easily on populations of cells, healthy and tumour, than in individual cells. The actual targets of drugs are, however, cells themselves. The drugs in use either disrupt genome integrity by causing DNA strand breaks, and consequently initiate programmed cell death, or block cell proliferation mainly by inhibiting factors that enable cells to proceed from one cell cycle phase to the next through checkpoints in the cell division cycle. DNA damage caused by cytotoxic drugs (and also cytostatic drugs at high concentrations) activates, among others, the p53 protein-modulated signalling pathways that directly or indirectly force the cell to make a decision between survival and death. The paper aims to become the first-step in a larger scale enterprise that should bridge the gap between intracellular and population PK-PD models, providing oncologists with a rationale to predict and optimise the effects of anticancer drugs in the clinic. So far, it only sticks at describing p53 activation and regulation in single cells following their exposure to DNA damaging stress agents. We show that p53 oscillations that have been observed in individual cells can be reconstructed and predicted by compartmentalising cellular events occurring after DNA damage, either in the nucleus or in the cytoplasm, and by describing network interactions, using ordinary differential equations (ODEs), between the ATM, p53, Mdm2 and Wip1 proteins, in each compartment, nucleus or cytoplasm, and between the two compartments. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications.
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Affiliation(s)
- Ján Eliaš
- UPMC, Laboratoire Jacques-Louis Lions, 4 Place Jussieu, F-75005 Paris, France; INRIA Paris-Rocquencourt, Bang project-team, Paris and Rocquencourt, France.
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190
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Programming biological models in Python using PySB. Mol Syst Biol 2013; 9:646. [PMID: 23423320 PMCID: PMC3588907 DOI: 10.1038/msb.2013.1] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 01/07/2013] [Indexed: 12/19/2022] Open
Abstract
PySB is a framework for creating biological models as Python programs using a
high-level, action-oriented vocabulary that promotes transparency, extensibility and
reusability. PySB interoperates with many existing modeling tools and supports
distributed model development. ![]()
PySB models are programs and leverage existing programming tools for documentation, testing, and collaborative development. Reusable functions can encode common low-level biochemical processes as well as high-level modules, making models transparent and concise. Modeling workflow is accelerated through close integration with Python numerical tools and interoperability with existing modeling software. We demonstrate the use of PySB to encode 15 alternative hypotheses for the mitochondrial regulation of apoptosis, including a new ‘Embedded Together' model based on recent biochemical findings.
Mathematical equations are fundamental to modeling biological networks, but as
networks get large and revisions frequent, it becomes difficult to manage equations
directly or to combine previously developed models. Multiple simultaneous efforts to
create graphical standards, rule-based languages, and integrated software
workbenches aim to simplify biological modeling but none fully meets the need for
transparent, extensible, and reusable models. In this paper we describe PySB, an
approach in which models are not only created using programs, they are programs.
PySB draws on programmatic modeling concepts from little b and ProMot, the
rule-based languages BioNetGen and Kappa and the growing library of Python numerical
tools. Central to PySB is a library of macros encoding familiar biochemical actions
such as binding, catalysis, and polymerization, making it possible to use a
high-level, action-oriented vocabulary to construct detailed models. As Python
programs, PySB models leverage tools and practices from the open-source software
community, substantially advancing our ability to distribute and manage the work of
testing biochemical hypotheses. We illustrate these ideas using new and previously
published models of apoptosis.
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191
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Activation and control of p53 tetramerization in individual living cells. Proc Natl Acad Sci U S A 2013; 110:15497-501. [PMID: 24006363 DOI: 10.1073/pnas.1311126110] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Homo-oligomerization is found in many biological systems and has been extensively studied in vitro. However, our ability to quantify and understand oligomerization processes in cells is still limited. We used fluorescence correlation spectroscopy and mathematical modeling to measure the dynamics of the tetramers formed by the tumor suppressor protein p53 in single living cells. Previous in vitro studies suggested that in basal conditions all p53 molecules are bound in dimers. We found that in resting cells p53 is present in a mix of oligomeric states with a large cell-to-cell variation. After DNA damage, p53 molecules in all cells rapidly assemble into tetramers before p53 protein levels increase. We developed a model to understand the connection between p53 accumulation and tetramerization. We found that the rapid increase in p53 tetramers requires a combination of active tetramerization and protein stabilization, however tetramerization alone is sufficient to activate p53 transcriptional targets. This suggests triggering tetramerization as a mechanism for activating the p53 pathway in cancer cells. Many other transcription factors homo-oligomerize, and our approach provides a unique way for probing the dynamics and functional consequences of oligomerization.
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192
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De Zio D, Cianfanelli V, Cecconi F. New insights into the link between DNA damage and apoptosis. Antioxid Redox Signal 2013; 19:559-71. [PMID: 23025416 PMCID: PMC3717195 DOI: 10.1089/ars.2012.4938] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE When lesions are unrepaired or there are defects in the DNA repair system, DNA damage is often correlated to apoptosis. However, different kinds of lesions and different degrees of lesion severity can trigger numerous signaling responses. RECENT ADVANCES DNA repair proteins involved in specific DNA repair pathways can modulate the function or activity of some apoptotic factors, further emphasizing the crosstalk between DNA damage and cell death. CRITICAL ISSUES Here, we discuss the signaling networks that link DNA damage to apoptosis, and we focus on post-translational modifications, leading to crucial changes in protein behavior, following various kinds of DNA damage. Moreover, we analyze the existence of apoptosis-related functions of typical repair proteins, leading to diverse, often-overlapping, DNA damage responses. FUTURE DIRECTIONS The better understanding of the regulation and the functionality of key DNA repair proteins, also involved in apoptosis regulation, has the potential of modulating the cell outcomes on DNA damage, particularly in the context of cancer treatment.
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Affiliation(s)
- Daniela De Zio
- Dulbecco Telethon Institute at the Department of Biology, University of Rome Tor Vergata, Rome, Italy.
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193
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Wip1 suppresses apoptotic cell death through direct dephosphorylation of BAX in response to γ-radiation. Cell Death Dis 2013; 4:e744. [PMID: 23907458 PMCID: PMC3763429 DOI: 10.1038/cddis.2013.252] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/01/2013] [Accepted: 06/06/2013] [Indexed: 12/13/2022]
Abstract
Wild-type p53-induced phosphatase 1 (Wip1) is a p53-inducible serine/threonine phosphatase that switches off DNA damage checkpoint responses by the dephosphorylation of certain proteins (i.e. p38 mitogen-activated protein kinase, p53, checkpoint kinase 1, checkpoint kinase 2, and uracil DNA glycosylase) involved in DNA repair and the cell cycle checkpoint. Emerging data indicate that Wip1 is amplified or overexpressed in various human tumors, and its detection implies a poor prognosis. In this study, we show that Wip1 interacts with and dephosphorylates BAX to suppress BAX-mediated apoptosis in response to γ-irradiation in prostate cancer cells. Radiation-resistant LNCaP cells showed dramatic increases in Wip1 levels and impaired BAX movement to the mitochondria after γ-irradiation, and these effects were reverted by a Wip1 inhibitor. These results show that Wip1 directly interacts with and dephosphorylates BAX. Dephosphorylation occurs at threonines 172, 174 and 186, and BAX proteins with mutations at these sites fail to translocate efficiently to the mitochondria following cellular γ-irradiation. Overexpression of Wip1 and BAX, but not phosphatase-dead Wip1, in BAX-deficient cells strongly reduces apoptosis. Our results suggest that BAX dephosphorylation of Wip1 phosphatase is an important regulator of resistance to anticancer therapy. This study is the first to report the downregulation of BAX activity by a protein phosphatase.
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194
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Abstract
Cell populations rarely exhibit gene-expression profiles that are homogeneous in time and space. In the temporal domain, dynamical behaviors such as oscillations and pulses of protein production pervade cell biology, underlying phenomena as diverse as circadian rhythmicity, cell cycle control, stress and damage responses, and stem-cell pluripotency. In multicellular populations, spatial heterogeneities are crucial for decision making and development, among many other functions. Cells need to exquisitely coordinate this temporal and spatial variation to survive. Although the spatiotemporal character of gene expression is challenging to quantify experimentally at the level of individual cells, it is beneficial from the modeling viewpoint, because it provides strong constraints that can be probed by theoretically analyzing mathematical models of candidate gene and protein circuits. Here, we review recent examples of temporal dynamics and spatial patterning in gene expression to show how modeling such phenomenology can help us unravel the molecular mechanisms of cellular function.
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Affiliation(s)
- Pau Rué
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
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195
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Longo DM, Selimkhanov J, Kearns JD, Hasty J, Hoffmann A, Tsimring LS. Dual delayed feedback provides sensitivity and robustness to the NF-κB signaling module. PLoS Comput Biol 2013; 9:e1003112. [PMID: 23825938 PMCID: PMC3694842 DOI: 10.1371/journal.pcbi.1003112] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 04/26/2013] [Indexed: 01/22/2023] Open
Abstract
Many cellular stress-responsive signaling systems exhibit highly dynamic behavior with oscillatory features mediated by delayed negative feedback loops. What remains unclear is whether oscillatory behavior is the basis for a signaling code based on frequency modulation (FM) or whether the negative feedback control modules have evolved to fulfill other functional requirements. Here, we use experimentally calibrated computational models to interrogate the negative feedback loops that regulate the dynamic activity of the transcription factor NF-κB. Linear stability analysis of the model shows that oscillatory frequency is a hard-wired feature of the primary negative feedback loop and not a function of the stimulus, thus arguing against an FM signaling code. Instead, our modeling studies suggest that the two feedback loops may be tuned to provide for rapid activation and inactivation capabilities for transient input signals of a wide range of durations; by minimizing late phase oscillations response durations may be fine-tuned in a graded rather than quantized manner. Further, in the presence of molecular noise the dual delayed negative feedback system minimizes stochastic excursions of the output to produce a robust NF-κB response.
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Affiliation(s)
- Diane M. Longo
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Jangir Selimkhanov
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- San Diego Center for Systems Biology, La Jolla, California, United States of America
| | - Jeffrey D. Kearns
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- San Diego Center for Systems Biology, La Jolla, California, United States of America
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- BioCircuits Institute, University of California San Diego, La Jolla, California, United States of America
| | - Alexander Hoffmann
- San Diego Center for Systems Biology, La Jolla, California, United States of America
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- BioCircuits Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (AH); (LST)
| | - Lev S. Tsimring
- San Diego Center for Systems Biology, La Jolla, California, United States of America
- BioCircuits Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (AH); (LST)
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196
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Chen X, Chen J, Gan S, Guan H, Zhou Y, Ouyang Q, Shi J. DNA damage strength modulates a bimodal switch of p53 dynamics for cell-fate control. BMC Biol 2013; 11:73. [PMID: 23800173 PMCID: PMC3702437 DOI: 10.1186/1741-7007-11-73] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/05/2013] [Indexed: 01/22/2023] Open
Abstract
Background The p53 pathway is differentially activated in response to distinct DNA damage, leading to alternative phenotypic outcomes in mammalian cells. Recent evidence suggests that p53 expression dynamics play an important role in the differential regulation of cell fate, but questions remain as to how p53 dynamics and the subsequent cellular response are modulated by variable DNA damage. Results We identified a novel, bimodal switch of p53 dynamics modulated by DNA-damage strength that is crucial for cell-fate control. After low DNA damage, p53 underwent periodic pulsing and cells entered cell-cycle arrest. After high DNA damage, p53 underwent a strong monotonic increase and cells activated apoptosis. We found that the damage dose-dependent bimodal switch was due to differential Mdm2 upregulation, which controlled the alternative cell fates mainly by modulating the induction level and pro-apoptotic activities of p53. Conclusions Our findings not only uncover a new mode of regulation for p53 dynamics and cell fate, but also suggest that p53 oscillation may function as a suppressor, maintaining a low level of p53 induction and pro-apoptotic activities so as to render cell-cycle arrest that allows damage repair.
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Affiliation(s)
- Xi Chen
- Center for Quantitative Systems Biology and Department of Physics, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, China
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197
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Assessing dose-dependent differences in DNA-damage, p53 response and genotoxicity for quercetin and curcumin. Toxicol In Vitro 2013; 27:1877-87. [PMID: 23764886 DOI: 10.1016/j.tiv.2013.05.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/20/2013] [Accepted: 05/21/2013] [Indexed: 01/01/2023]
Abstract
As part of a longer-term goal to create a quantitative mechanistic model of the p53-Mdm2 DNA-damage pathway, we are studying cellular responses to compounds causing DNA-damage by various modes-of action, including two natural polyphenols: quercetin (QUE) and curcumin (CUR). QUE and CUR are weak mutagens in some in vitro assays and possess both anti- or pro-oxidant effects depending on dose. This study examines the dose-response of DNA-damage pathway to these compounds in HT1080 cells (a human cell line with wild-type p53) at doses relevant to human exposure. CUR was more potent in causing reactive oxygen species, DNA damage (measured as phospho-H2AX) and p53 induction, with lowest observed effect levels (LOELs; 3-8 μM) approximately three-fold lower than QUE (20-30 μM). CUR showed a strong G2/M arrest and apoptosis at ≈ 10 μM. QUE caused S phase arrest at low doses (8 μM) and apoptosis was only induced at much higher doses (60 μM). At concentrations with similar levels of p-H2AX and p53 biomarkers, CUR caused greater micronuclei frequency. CUR induced clear increases micronuclei at 3-6 μM, while QUE had a weaker micronuclei response even at the highest doses. Thus, even with two compounds sharing common chemistries, DNA-damage response patterns differed significantly in terms of dose and cell fate.
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198
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Network nonlinearities in drug treatment. Interdiscip Sci 2013; 5:85-94. [PMID: 23740389 DOI: 10.1007/s12539-013-0165-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 12/25/2012] [Accepted: 03/22/2013] [Indexed: 10/26/2022]
Abstract
Despite major achievements in the understanding of human disease, there is a general perception that the drug development industry has failed to meet the expectations that recent advances in biotechnology should drive. One of the potential sources of failure of many next generation drugs is that their targets are embedded in highly nonlinear signaling pathways and gene networks with multiple negative and positive feedback loops of regulation. There is increasing evidence that this complex network shapes the response to external perturbations in the form of drug treatment, originating bistability, hypersensitivity, robustness, complex dose-response curves or schedule dependent activity. This review focuses on the effect of nonlinearities on signaling and gene networks involved in human disease, using tools from Nonlinear Dynamics to discuss the implications and to overcome the effects of the nonlinearities on regulatory networks.
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199
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Kim JK, Jackson TL. Mechanisms that enhance sustainability of p53 pulses. PLoS One 2013; 8:e65242. [PMID: 23755198 PMCID: PMC3670918 DOI: 10.1371/journal.pone.0065242] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/26/2013] [Indexed: 02/07/2023] Open
Abstract
The tumor suppressor p53 protein shows various dynamic responses depending on the types and extent of cellular stresses. In particular, in response to DNA damage induced by γ-irradiation, cells generate a series of p53 pulses. Recent research has shown the importance of sustaining repeated p53 pulses for recovery from DNA damage. However, far too little attention has been paid to understanding how cells can sustain p53 pulses given the complexities of genetic heterogeneity and intrinsic noise. Here, we explore potential molecular mechanisms that enhance the sustainability of p53 pulses by developing a new mathematical model of the p53 regulatory system. This model can reproduce many experimental results that describe the dynamics of p53 pulses. By simulating the model both deterministically and stochastically, we found three potential mechanisms that improve the sustainability of p53 pulses: 1) the recently identified positive feedback loop between p53 and Rorα allows cells to sustain p53 pulses with high amplitude over a wide range of conditions, 2) intrinsic noise can often prevent the dampening of p53 pulses even after mutations, and 3) coupling of p53 pulses in neighboring cells via cytochrome-c significantly reduces the chance of failure in sustaining p53 pulses in the presence of heterogeneity among cells. Finally, in light of these results, we propose testable experiments that can reveal important mechanisms underlying p53 dynamics.
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Affiliation(s)
- Jae Kyoung Kim
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Trachette L. Jackson
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
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Scafoglio C, Smolka M, Zhou H, Perissi V, Rosenfeld MG. The co-repressor SMRT delays DNA damage-induced caspase activation by repressing pro-apoptotic genes and modulating the dynamics of checkpoint kinase 2 activation. PLoS One 2013; 8:e59986. [PMID: 23690919 PMCID: PMC3656868 DOI: 10.1371/journal.pone.0059986] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 02/23/2013] [Indexed: 12/31/2022] Open
Abstract
Checkpoint kinase 2 (Chk2) is a major regulator of DNA damage response and can induce alternative cellular responses: cell cycle arrest and DNA repair or programmed cell death. Here, we report the identification of a new role of Chk2 in transcriptional regulation that also contributes to modulating the balance between survival and apoptosis following DNA damage. We found that Chk2 interacts with members of the NCoR/SMRT transcriptional co-regulator complexes and serves as a functional component of the repressor complex, being required for recruitment of SMRT on the promoter of pro-apoptotic genes upon DNA damage. Thus, the co-repressor SMRT exerts a critical protective action against genotoxic stress-induced caspase activation, repressing a functionally important cohort of pro-apoptotic genes. Amongst them, SMRT is responsible for basal repression of Wip1, a phosphatase that de-phosphorylates and inactivates Chk2, thus affecting a feedback loop responsible for licensing the correct timing of Chk2 activation and the proper execution of the DNA repair process.
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Affiliation(s)
- Claudio Scafoglio
- Howard Hughes Medical Institute and School of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (CS); (MGR)
| | - Marcus Smolka
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
| | - Huilin Zhou
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Valentina Perissi
- Howard Hughes Medical Institute and School of Medicine, University of California San Diego, La Jolla, California, United States of America
- School of Medicine, Boston University, Boston, Massachusetts, United States of America
| | - Michael G. Rosenfeld
- Howard Hughes Medical Institute and School of Medicine, University of California San Diego, La Jolla, California, United States of America
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (CS); (MGR)
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