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1
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Tran NN, Nguyen A, Rahman TW, Baetica AA. Fundamental Trade-Offs in the Robustness of Biological Systems with Feedback Regulation. ACS Synth Biol 2025; 14:1099-1111. [PMID: 40198741 PMCID: PMC12012877 DOI: 10.1021/acssynbio.4c00704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 03/11/2025] [Accepted: 03/13/2025] [Indexed: 04/10/2025]
Abstract
Natural biological systems use feedback regulation to effectively respond and adapt to their changing environment. Even though in engineered systems we understand how accurate feedback can be depending on the electronic or mechanical parts that it is implemented with, we largely lack a similar theoretical framework to study feedback regulation in biological systems. Specifically, it is not fully understood or quantified how accurate or robust the implementation of biological feedback actually is. In this paper, we study the sensitivity of biological feedback to variations in biochemical parameters using five example circuits: positive autoregulation, negative autoregulation, double-positive feedback, positive-negative feedback, and double-negative feedback (the toggle switch). We find that some of these examples of biological feedback are subjected to fundamental performance trade-offs, and we propose multi-objective optimization as a framework to study their properties. The impact of this work is to improve robust circuit design for synthetic biology and to improve our understanding of feedback for systems biology.
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Affiliation(s)
- Nguyen
Hoai Nam Tran
- Department
of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - An Nguyen
- School
of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Tasfia Wasima Rahman
- Department
of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Ania-Ariadna Baetica
- Department
of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104, United States
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2
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Li CM, Sun T, Yang MJ, Yang Z, Li Q, Shi JL, Zhang C, Jin JF. Complement activation targeted inhibitor C2-FH ameliorates acetaminophen-induced liver injury in mice. World J Hepatol 2024; 16:1188-1198. [PMID: 39474574 PMCID: PMC11514617 DOI: 10.4254/wjh.v16.i10.1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 09/12/2024] [Accepted: 09/19/2024] [Indexed: 10/21/2024] Open
Abstract
BACKGROUND Complement activation is recognized as an important factor in the progression of liver damage caused by acetaminophen (APAP). However, the role of the complement inhibitor C2-FH in APAP-induced liver injury remains unclear.
AIM To explore C2-FH in protecting against APAP-induced liver injury by inhibiting complement activation.
METHODS A model of APAP-induced liver injury was used to study the protective effect of C2-FH on liver injury. C2-FH was administered through intraperitoneal injection 30 minutes after APAP treatment. We detected the effects of C2-FH on liver function, inflammatory response and complement activation. Additionally, RNA-sequencing (RNA-Seq) analysis was conducted to understand the mechanism through which C2-FH provides protection against APAP-induced liver injury.
RESULTS C2-FH inhibited the increase in serum alanine aminotransferase activity, aspartate aminotransferase activity and lactate dehydrogenase, and reduced liver tissue necrosis caused by APAP. Moreover, it attenuated the inflammatory response and inhibited complement activation in APAP-induced liver injury. RNA-Seq analysis provided additional explanations for the protective role of C2-FH against APAP-induced liver injury.
CONCLUSION C2-FH attenuates APAP-induced liver injury by inhibiting complement activation.
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Affiliation(s)
- Chun-Mei Li
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Tian Sun
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Mou-Jie Yang
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Zhi Yang
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Qing Li
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Jia-Lin Shi
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Chong Zhang
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Jun-Fei Jin
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
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3
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Li CM, Sun T, Yang MJ, Yang Z, Li Q, Shi JL, Zhang C, Jin JF. Complement activation targeted inhibitor C2-FH ameliorates acetaminophen-induced liver injury in mice. World J Hepatol 2024; 16:1368-1378. [DOI: 10.4254/wjh.v16.i10.1368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 09/12/2024] [Accepted: 09/19/2024] [Indexed: 11/22/2024] Open
Abstract
BACKGROUND Complement activation is recognized as an important factor in the progression of liver damage caused by acetaminophen (APAP). However, the role of the complement inhibitor C2-FH in APAP-induced liver injury remains unclear.
AIM To explore C2-FH in protecting against APAP-induced liver injury by inhibiting complement activation.
METHODS A model of APAP-induced liver injury was used to study the protective effect of C2-FH on liver injury. C2-FH was administered through intraperitoneal injection 30 minutes after APAP treatment. We detected the effects of C2-FH on liver function, inflammatory response and complement activation. Additionally, RNA-sequencing (RNA-Seq) analysis was conducted to understand the mechanism through which C2-FH provides protection against APAP-induced liver injury.
RESULTS C2-FH inhibited the increase in serum alanine aminotransferase activity, aspartate aminotransferase activity and lactate dehydrogenase, and reduced liver tissue necrosis caused by APAP. Moreover, it attenuated the inflammatory response and inhibited complement activation in APAP-induced liver injury. RNA-Seq analysis provided additional explanations for the protective role of C2-FH against APAP-induced liver injury.
CONCLUSION C2-FH attenuates APAP-induced liver injury by inhibiting complement activation.
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Affiliation(s)
- Chun-Mei Li
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Tian Sun
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Mou-Jie Yang
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Zhi Yang
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Qing Li
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Jia-Lin Shi
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Chong Zhang
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
| | - Jun-Fei Jin
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- China-United States Lipids in Health and Disease Research Center, Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, the Affiliated Hospital of Guilin Medical University, Guilin 541001, Guangxi Zhuang Autonomous Region, China
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Singh V, Naldi A, Soliman S, Niarakis A. A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint. NPJ Syst Biol Appl 2023; 9:33. [PMID: 37454172 DOI: 10.1038/s41540-023-00294-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Rheumatoid arthritis (RA) is a complex autoimmune disease with an unknown aetiology. However, rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS) play a significant role in initiating and perpetuating destructive joint inflammation by expressing immuno-modulating cytokines, adhesion molecules, and matrix remodelling enzymes. In addition, RA-FLS are primary drivers of inflammation, displaying high proliferative rates and an apoptosis-resistant phenotype. Thus, RA-FLS-directed therapies could become a complementary approach to immune-directed therapies by predicting the optimal conditions that would favour RA-FLS apoptosis, limit inflammation, slow the proliferation rate and minimise bone erosion and cartilage destruction. In this paper, we present a large-scale Boolean model for RA-FLS that consists of five submodels focusing on apoptosis, cell proliferation, matrix degradation, bone erosion and inflammation. The five-phenotype-specific submodels can be simulated independently or as a global model. In silico simulations and perturbations reproduced the expected biological behaviour of the system under defined initial conditions and input values. The model was then used to mimic the effect of mono or combined therapeutic treatments and predict novel targets and drug candidates through drug repurposing analysis.
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Affiliation(s)
- Vidisha Singh
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde-Genhotel, Univ Evry, Evry, France
| | - Aurelien Naldi
- Lifeware Group, Inria, Saclay-île de France, 91120, Palaiseau, France
| | - Sylvain Soliman
- Lifeware Group, Inria, Saclay-île de France, 91120, Palaiseau, France
| | - Anna Niarakis
- Université Paris-Saclay, Laboratoire Européen de Recherche pour la Polyarthrite rhumatoïde-Genhotel, Univ Evry, Evry, France.
- Lifeware Group, Inria, Saclay-île de France, 91120, Palaiseau, France.
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5
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Vainshelbaum NM, Salmina K, Gerashchenko BI, Lazovska M, Zayakin P, Cragg MS, Pjanova D, Erenpreisa J. Role of the Circadian Clock "Death-Loop" in the DNA Damage Response Underpinning Cancer Treatment Resistance. Cells 2022; 11:880. [PMID: 35269502 PMCID: PMC8909334 DOI: 10.3390/cells11050880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 12/11/2022] Open
Abstract
Here, we review the role of the circadian clock (CC) in the resistance of cancer cells to genotoxic treatments in relation to whole-genome duplication (WGD) and telomere-length regulation. The CC drives the normal cell cycle, tissue differentiation, and reciprocally regulates telomere elongation. However, it is deregulated in embryonic stem cells (ESCs), the early embryo, and cancer. Here, we review the DNA damage response of cancer cells and a similar impact on the cell cycle to that found in ESCs—overcoming G1/S, adapting DNA damage checkpoints, tolerating DNA damage, coupling telomere erosion to accelerated cell senescence, and favouring transition by mitotic slippage into the ploidy cycle (reversible polyploidy). Polyploidy decelerates the CC. We report an intriguing positive correlation between cancer WGD and the deregulation of the CC assessed by bioinformatics on 11 primary cancer datasets (rho = 0.83; p < 0.01). As previously shown, the cancer cells undergoing mitotic slippage cast off telomere fragments with TERT, restore the telomeres by ALT-recombination, and return their depolyploidised offspring to telomerase-dependent regulation. By reversing this polyploidy and the CC “death loop”, the mitotic cycle and Hayflick limit count are thus again renewed. Our review and proposed mechanism support a life-cycle concept of cancer and highlight the perspective of cancer treatment by differentiation.
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Affiliation(s)
- Ninel Miriam Vainshelbaum
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (N.M.V.); Latvia; (K.S.); (M.L.); (P.Z.); (D.P.)
- Faculty of Biology, University of Latvia, LV-1050 Riga, Latvia
| | - Kristine Salmina
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (N.M.V.); Latvia; (K.S.); (M.L.); (P.Z.); (D.P.)
| | - Bogdan I. Gerashchenko
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine;
| | - Marija Lazovska
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (N.M.V.); Latvia; (K.S.); (M.L.); (P.Z.); (D.P.)
| | - Pawel Zayakin
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (N.M.V.); Latvia; (K.S.); (M.L.); (P.Z.); (D.P.)
| | - Mark Steven Cragg
- Centre for Cancer Immunology, School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | - Dace Pjanova
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (N.M.V.); Latvia; (K.S.); (M.L.); (P.Z.); (D.P.)
| | - Jekaterina Erenpreisa
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (N.M.V.); Latvia; (K.S.); (M.L.); (P.Z.); (D.P.)
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Kuganesan N, Dlamini S, Tillekeratne LV, Taylor WR. Tumor suppressor p53 promotes ferroptosis in oxidative stress conditions independent of modulation of ferroptosis by p21, CDKs, Rb and E2F. J Biol Chem 2021; 297:101365. [PMID: 34728216 DOI: 10.1016/j.jbc.2021.101365] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 01/11/2023] Open
Abstract
p53 is a well-established critical cell cycle regulator. By inducing transcription of the gene encoding p21, p53 inhibits cyclin-dependent kinase (CDK)-mediated phosphorylation of cell cycle inhibitor RB proteins. Phosphorylation of RB releases E2F transcription factor proteins that transactivate cell cycle-promoting genes. Here we sought to uncover the contribution of p53, p21, CDK, RB, and E2F to the regulation of ferroptosis, an oxidative form of cell death. Our studies have uncovered unexpected complexity in this regulation. First, we showed that elevated levels of p53 enhance ferroptosis in multiple inducible and isogenic systems. On the other hand, we found that p21 suppresses ferroptosis. Elevation of CDK activity also suppressed ferroptosis under conditions where p21 suppressed ferroptosis, suggesting that the impact of p21 must extend beyond CDK inhibition. Furthermore, we showed that overexpression of E2F suppresses ferroptosis in part via a p21-dependent mechanism, consistent with reports that this transcription factor can induce transcription of p21. Finally, deletion of RB genes enhanced ferroptosis. Taken together, these results show that signals affecting ferroptotic sensitivity emanate from multiple points within the p53 tumor suppressor pathway.
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Affiliation(s)
- Nishanth Kuganesan
- Department of Biological Sciences, University of Toledo, 2801 W. Bancroft Street, MS 601, Toledo, OH 43606
| | - Samkeliso Dlamini
- Department of Medicinal and Biological Chemistry, University of Toledo, 2801 W. Bancroft Street, MS 601, Toledo, OH 43606
| | - Lm Viranga Tillekeratne
- Department of Medicinal and Biological Chemistry, University of Toledo, 2801 W. Bancroft Street, MS 601, Toledo, OH 43606.
| | - William R Taylor
- Department of Biological Sciences, University of Toledo, 2801 W. Bancroft Street, MS 601, Toledo, OH 43606.
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De S, Campbell C, Venkitaraman AR, Esposito A. Pulsatile MAPK Signaling Modulates p53 Activity to Control Cell Fate Decisions at the G2 Checkpoint for DNA Damage. Cell Rep 2021; 30:2083-2093.e5. [PMID: 32075732 PMCID: PMC7029415 DOI: 10.1016/j.celrep.2020.01.074] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 12/04/2019] [Accepted: 01/22/2020] [Indexed: 01/01/2023] Open
Abstract
Cell-autonomous changes in p53 expression govern the duration and outcome of cell-cycle arrest at the G2 checkpoint for DNA damage. Here, we report that mitogen-activated protein kinase (MAPK) signaling integrates extracellular cues with p53 dynamics to determine cell fate at the G2 checkpoint. Optogenetic tools and quantitative cell biochemistry reveal transient oscillations in MAPK activity dependent on ataxia-telangiectasia-mutated kinase after DNA damage. MAPK inhibition alters p53 dynamics and p53-dependent gene expression after checkpoint enforcement, prolonging G2 arrest. In contrast, sustained MAPK signaling induces the phosphorylation of CDC25C, and consequently, the accumulation of pro-mitotic kinases, thereby relaxing checkpoint stringency and permitting cells to evade prolonged G2 arrest and senescence induction. We propose a model in which this MAPK-mediated mechanism integrates extracellular cues with cell-autonomous p53-mediated signals, to safeguard genomic integrity during tissue proliferation. Early steps in oncogene-driven carcinogenesis may imbalance this tumor-suppressive mechanism to trigger genome instability.
DNA damage elicits opposing pro-survival and pro-arrest responses via MAPK and p53 MAPK pulsations modulate p53-dependent transcription to determine cell fate MAPK/p53 signal dynamics control the stringency of the G2 DNA damage checkpoint MAPK/p53 integrate extracellular and intracellular cues to protect genome integrity
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Affiliation(s)
- Siddharth De
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Callum Campbell
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
| | - Alessandro Esposito
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
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8
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Erenpreisa J, Salmina K, Anatskaya O, Cragg MS. Paradoxes of cancer: Survival at the brink. Semin Cancer Biol 2020; 81:119-131. [PMID: 33340646 DOI: 10.1016/j.semcancer.2020.12.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/17/2022]
Abstract
The fundamental understanding of how Cancer initiates, persists and then progresses is evolving. High-resolution technologies, including single-cell mutation and gene expression measurements, are now attainable, providing an ever-increasing insight into the molecular details. However, this higher resolution has shown that somatic mutation theory itself cannot explain the extraordinary resistance of cancer to extinction. There is a need for a more Systems-based framework of understanding cancer complexity, which in particular explains the regulation of gene expression during cell-fate decisions. Cancer displays a series of paradoxes. Here we attempt to approach them from the view-point of adaptive exploration of gene regulatory networks at the edge of order and chaos, where cell-fate is changed by oscillations between alternative regulators of cellular senescence and reprogramming operating through self-organisation. On this background, the role of polyploidy in accessing the phylogenetically pre-programmed "oncofetal attractor" state, related to unicellularity, and the de-selection of unsuitable variants at the brink of cell survival is highlighted. The concepts of the embryological and atavistic theory of cancer, cancer cell "life-cycle", and cancer aneuploidy paradox are dissected under this lense. Finally, we challenge researchers to consider that cancer "defects" are mostly the adaptation tools of survival programs that have arisen during evolution and are intrinsic of cancer. Recognition of these features should help in the development of more successful anti-cancer treatments.
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Affiliation(s)
| | - Kristine Salmina
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | | | - Mark S Cragg
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
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Dynamic Behavior of p53 Driven by Delay and a Microrna-34a-Mediated Feedback Loop. Int J Mol Sci 2020; 21:ijms21041271. [PMID: 32070036 PMCID: PMC7072921 DOI: 10.3390/ijms21041271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/30/2020] [Accepted: 02/09/2020] [Indexed: 01/02/2023] Open
Abstract
The tumor suppressor protein p53 is a critical hub in the comprehensive transcriptional network that inhibits the growth of cells after acute stress stimulation. In this paper, an integrated model of the p53 signaling pathway in response to DNA damage is proposed and the p53 stability and oscillatory dynamics are analyzed. Through theoretical analysis and numerical simulation, we find that the delay as a bifurcation parameter can drive the p53-Mdm2 module to undergo a supercritical Hopf bifurcation, thereby producing oscillation behavior. Moreover, we demonstrate how the positive feedback loop formed by p53* and microRNA-34a (miR-34a) with the feature of double-negative regulation produces limit-cycle oscillations. Further, we find that miR-34a can affect the critical value of Hopf bifurcation in delay-induced p53 networks. In addition, we show that ATM, once activated by DNA damage, makes p53* undergo two Hopf bifurcations. These results revealed that both time delay and miR-34a can have tumor suppressing roles by promoting p53 oscillation or high level expression, which will provide a perspective for promoting the development of anti-cancer drugs by targeting miR-34a and time delay.
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10
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Higgins CE, Tang J, Mian BM, Higgins SP, Gifford CC, Conti DJ, Meldrum KK, Samarakoon R, Higgins PJ. TGF-β1-p53 cooperativity regulates a profibrotic genomic program in the kidney: molecular mechanisms and clinical implications. FASEB J 2019; 33:10596-10606. [PMID: 31284746 PMCID: PMC6766640 DOI: 10.1096/fj.201900943r] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/10/2019] [Indexed: 12/11/2022]
Abstract
Chronic kidney disease affects >15% of the U.S. population and >850 million individuals worldwide. Fibrosis is the common outcome of many chronic renal disorders and, although the etiology varies (i.e., diabetes, hypertension, ischemia, acute injury, and urologic obstructive disorders), persistently elevated renal TGF-β1 levels result in the relentless progression of fibrotic disease. TGF-β1 orchestrates the multifaceted program of renal fibrogenesis involving proximal tubular dysfunction, failed epithelial recovery and redifferentiation, and subsequent tubulointerstitial fibrosis, eventually leading to chronic renal disease. Recent findings implicate p53 as a cofactor in the TGF-β1-induced signaling pathway and a transcriptional coregulator of several TGF-β1 profibrotic response genes by complexing with receptor-activated SMADs, which are homologous to the small worms (SMA) and Drosophilia mothers against decapentaplegic (MAD) gene families. The cooperative p53-TGF-β1 genomic cluster includes genes involved in cell growth control and extracellular matrix remodeling [e.g., plasminogen activator inhibitor-1 (PAI-1; serine protease inhibitor, clade E, member 1), connective tissue growth factor, and collagen I]. Although the molecular basis for this codependency is unclear, many TGF-β1-responsive genes possess p53 binding motifs. p53 up-regulation and increased p53 phosphorylation; moreover, they are evident in nephrotoxin- and ischemia/reperfusion-induced injury, diabetic nephropathy, ureteral obstructive disease, and kidney allograft rejection. Pharmacologic and genetic approaches that target p53 attenuate expression of the involved genes and mitigate the fibrotic response, confirming a key role for p53 in renal disorders. This review focuses on mechanisms whereby p53 functions as a transcriptional regulator within the TGF-β1 cluster with an emphasis on the potent fibrosis-promoting PAI-1 gene.-Higgins, C. E., Tang, J., Mian, B. M., Higgins, S. P., Gifford, C. C., Conti, D. J., Meldrum, K. K., Samarakoon, R., Higgins, P. J. TGF-β1-p53 cooperativity regulates a profibrotic genomic program in the kidney: molecular mechanisms and clinical implications.
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Affiliation(s)
- Craig E. Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - Jiaqi Tang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - Badar M. Mian
- The Urological Institute of Northeastern New York, Albany, New York, USA
- Division of Urology, Department of Surgery, Albany Medical College, Albany, New York, USA
| | - Stephen P. Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - Cody C. Gifford
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - David J. Conti
- Division of Transplantation Surgery, Department of Surgery, Albany Medical College, Albany, New York, USA
| | - Kirstan K. Meldrum
- Division of Pediatric Urology, Central Michigan University, Mount Pleasant, Michigan, USA
| | - Rohan Samarakoon
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - Paul J. Higgins
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
- The Urological Institute of Northeastern New York, Albany, New York, USA
- Division of Urology, Department of Surgery, Albany Medical College, Albany, New York, USA
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11
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Ivanov D. Notch Signaling-Induced Oscillatory Gene Expression May Drive Neurogenesis in the Developing Retina. Front Mol Neurosci 2019; 12:226. [PMID: 31607861 PMCID: PMC6761228 DOI: 10.3389/fnmol.2019.00226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/04/2019] [Indexed: 12/21/2022] Open
Abstract
After integrating classic and cutting-edge research, we proposed a unified model that attempts to explain the key steps of mammalian retinal neurogenesis. We proposed that the Notch signaling-induced lateral inhibition mechanism promotes oscillatory expression of Hes1. Oscillating Hes1 inhibitory activity as a result leads to oscillatory expression of Notch signaling inhibitors, activators/inhibitors of retinal neuronal phenotypes, and cell cycle-promoting genes all within a retinal progenitor cell (RPC). We provided a mechanism explaining not only how oscillatory expression prevents the progenitor-to-precursor transition, but also how this transition happens. Our proposal of the mechanism posits that the levels of the above factors not only oscillate but also rise (with the exception of Hes1) as the factors accumulate within a progenitor. Depending on which factors accumulate fastest and reach the required supra-threshold levels (cell cycle activators or Notch signaling inhibitors), the progenitor either proliferates or begins to differentiate without any further proliferation when Notch signaling ceases. Thus, oscillatory gene expression may regulate an RPC's decision to proliferate or differentiate. Meanwhile, a post-mitotic precursor's selection of one retinal neuronal phenotype over many others depends on the expression level of key transcription factors (activators) required for each of these retinal neuronal phenotypes. Because the events described above are stochastic due to oscillatory gene expression and gene product inheritance from a mother RPC after its division, an RPC or precursor's decision requires the assignment of probabilities to specific outcomes in the selection process. While low and sustained (non-oscillatory) Notch signaling activity is required to promote the transition of retinal progenitors into various retinal neuronal phenotypes, we propose that the lateral inhibition mechanism, combined with high expression of the BMP signaling-induced Inhibitor of Differentiation (ID) protein family, promotes high and sustained (non-oscillatory) Hes1 and Hes5 expression. These events facilitate the transition of an RPC into the Müller glia (MG) phenotype at the late stage of retinal development.
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Affiliation(s)
- Dmitry Ivanov
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States.,Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
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12
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Guha A, Ahuja D, Das Mandal S, Parasar B, Deyasi K, Roy D, Sharma V, Willard B, Ghosh A, Ray PS. Integrated Regulation of HuR by Translation Repression and Protein Degradation Determines Pulsatile Expression of p53 Under DNA Damage. iScience 2019; 15:342-359. [PMID: 31103853 PMCID: PMC6548907 DOI: 10.1016/j.isci.2019.05.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/20/2018] [Accepted: 05/01/2019] [Indexed: 12/21/2022] Open
Abstract
Expression of tumor suppressor p53 is regulated at multiple levels, disruption of which often leads to cancer. We have adopted an approach combining computational systems modeling with experimental validation to elucidate the translation regulatory network that controls p53 expression post DNA damage. The RNA-binding protein HuR activates p53 mRNA translation in response to UVC-induced DNA damage in breast carcinoma cells. p53 and HuR levels show pulsatile change post UV irradiation. The computed model fitted with the observed pulse of p53 and HuR only when hypothetical regulators of synthesis and degradation of HuR were incorporated. miR-125b, a UV-responsive microRNA, was found to represses the translation of HuR mRNA. Furthermore, UV irradiation triggered proteasomal degradation of HuR mediated by an E3-ubiquitin ligase tripartite motif-containing 21 (TRIM21). The integrated action of miR-125b and TRIM21 constitutes an intricate control system that regulates pulsatile expression of HuR and p53 and determines cell viability in response to DNA damage.
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Affiliation(s)
- Abhishek Guha
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Deepika Ahuja
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Sukhen Das Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Bibudha Parasar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Krishanu Deyasi
- Department of Mathematics and Statistics, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Debadrita Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Vasundhara Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Belinda Willard
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Anandamohan Ghosh
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India.
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13
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Sun T, Mu D, Cui J. Mathematical model identifies effective P53 accumulation with target gene binding affinity in DNA damage response for cell fate decision. Cell Cycle 2018; 17:2716-2730. [PMID: 30488759 DOI: 10.1080/15384101.2018.1553342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Functional p53 signaling is essential for appropriate responses to diverse stimuli. P53 dynamics employs the information from the stimulus leading to selective gene expression and cell fate decision. However, the decoding mechanism of p53 dynamics under DNA damage challenge remains poorly understood. Here we mathematically modeled the recently dual-phase p53 dynamics under doxorubicin treatment. We found that p53 could perform sequential pulses followed by a high-amplitude terminal pulse at relatively low doxorubicin treatment, whereas p53 became steadily accumulated when damage level was high. The effective p53 integral above a threshold but not the absolute accumulation of p53 precisely discriminated survival and death. Silencing negative regulators in p53 network might promote the occurrence of terminal pulse. Furthermore, lower binding affinity and degradation rate of p53 target genes could favorably discriminate high and low dose doxorubicin treatment. Grouping by temporal profiles suggested that the p53 dynamics rather than the doxorubicin doses could better discriminate cellular outcomes and confer less variation for effective p53 integral reemphasizing the importance of p53 level regulation. Our model has established a theoretical framework that p53 dynamics can work cooperatively with its binding affinity to target genes leading to cell fate choice, providing new clues of optimized clinical design by manipulating p53 dynamics.
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Affiliation(s)
- Tingzhe Sun
- a School of Life Sciences , Anqing Normal University , Anqing , Anhui , China
| | - Dan Mu
- a School of Life Sciences , Anqing Normal University , Anqing , Anhui , China
| | - Jun Cui
- b MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences , Sun Yat-sen University , Guangzhou , Guangdong , China
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14
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The MDM2-p53 pathway is involved in preconditioning-induced neuronal tolerance to ischemia. Sci Rep 2018; 8:1610. [PMID: 29371613 PMCID: PMC5785500 DOI: 10.1038/s41598-018-19921-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 01/10/2018] [Indexed: 01/01/2023] Open
Abstract
Brain preconditioning (PC) refers to a state of transient tolerance against a lethal insult that can be evoked by a prior mild event. It is thought that PC may induce different pathways responsible for neuroprotection, which may involve the attenuation of cell damage pathways, including the apoptotic cell death. In this context, p53 is a stress sensor that accumulates during brain ischemia leading to neuronal death. The murine double minute 2 gene (MDM2), a p53-specific E3 ubiquitin ligase, is the main cellular antagonist of p53, mediating its degradation by the proteasome. Here, we study the role of MDM2-p53 pathway on PC-induced neuroprotection both in cultured neurons (in vitro) and rat brain (in vivo). Our results show that PC increased neuronal MDM2 protein levels, which prevented ischemia-induced p53 stabilization and neuronal death. Indeed, PC attenuated ischemia-induced activation of the p53/PUMA/caspase-3 signaling pathway. Pharmacological inhibition of MDM2-p53 interaction in neurons abrogated PC-induced neuroprotection against ischemia. Finally, the relevance of the MDM2-p53 pathway was confirmed in rat brain using a PC model in vivo. These findings demonstrate the key role of the MDM2-p53 pathway in PC-induced neuroprotection against a subsequent ischemic insult and poses MDM2 as an essential target in ischemic tolerance.
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15
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Abstract
Crucial, natural protection against tumour onset in humans is orchestrated by the dynamic protein p53. The best-characterised functions of p53 relate to its cellular stress responses. In this review, we explore emerging insights into p53 activities and their functional consequences. We compare p53 in humans and elephants, in search of salient features of cancer protection.
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Affiliation(s)
- Sue Haupt
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia.,Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Ygal Haupt
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia.,Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Department of Pathology, University of Melbourne, Parkville, Australia
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16
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Sun T, Li X, Shen P. Modeling amplified p53 responses under DNA-PK inhibition in DNA damage response. Oncotarget 2017; 8:17105-17114. [PMID: 28177883 PMCID: PMC5370026 DOI: 10.18632/oncotarget.15062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/10/2017] [Indexed: 12/13/2022] Open
Abstract
During DNA double strand breaks (DSBs) repair, coordinated activation of phosphatidylinositol 3-kinase (PI3K)-like kinases can activate p53 signaling pathway. Recent findings have identified novel interplays among these kinases demonstrating amplified first p53 pulses under DNA-PK inhibition. However, no theoretical model has been developed to characterize such dynamics. In current work, we modeled the prolonged p53 pulses with DNA-PK inhibitor. We could identify a dose-dependent increase in the first pulse amplitude and width. Meanwhile, weakened DNA-PK mediated ATM inhibition was insufficient to reproduce such dynamic behavior. Moreover, the information flow was shifted predominantly to the first pulse under DNA-PK inhibition. Furthermore, the amplified p53 responses were relatively robust. Taken together, our model can faithfully replicate amplified p53 responses under DNA-PK inhibition and provide insights into cell fate decision by manipulating p53 dynamics.
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Affiliation(s)
- Tingzhe Sun
- School of Life Sciences, AnQing Normal University, AnQing, Anhui, 246011, China
| | - Xinda Li
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, 210023, China
| | - Pingping Shen
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, 210023, China
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17
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Lazo PA. Reverting p53 activation after recovery of cellular stress to resume with cell cycle progression. Cell Signal 2017; 33:49-58. [PMID: 28189587 DOI: 10.1016/j.cellsig.2017.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/23/2017] [Accepted: 02/06/2017] [Indexed: 11/17/2022]
Abstract
The activation of p53 in response to different types of cellular stress induces several protective reactions including cell cycle arrest, senescence or cell death. These protective effects are a consequence of the activation of p53 by specific phosphorylation performed by several kinases. The reversion of the cell cycle arrest, induced by p53, is a consequence of the phosphorylated and activated p53, which triggers its own downregulation and that of its positive regulators. The different down-regulatory processes have a sequential and temporal order of events. The mechanisms implicated in p53 down-regulation include phosphatases, deacetylases, and protein degradation by the proteasome or autophagy, which also affect different p53 protein targets and functions. The necessary first step is the dephosphorylation of p53 to make it available for interaction with mdm2 ubiquitin-ligase, which requires the activation of phosphatases targeting both p53 and p53-activating kinases. In addition, deacetylation of p53 is required to make lysine residues accessible to ubiquitin ligases. The combined action of these downregulatory mechanisms brings p53 protein back to its basal levels, and cell cycle progression can resume if cells have overcome the stress or damage situation. The specific targeting of these down-regulatory mechanisms can be exploited for therapeutic purposes in cancers harbouring wild-type p53.
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Affiliation(s)
- Pedro A Lazo
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Salamanca, Spain.
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18
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Saeed MT, Ahmad J, Kanwal S, Holowatyj AN, Sheikh IA, Zafar Paracha R, Shafi A, Siddiqa A, Bibi Z, Khan M, Ali A. Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression. PeerJ 2016; 4:e2348. [PMID: 27703839 PMCID: PMC5047222 DOI: 10.7717/peerj.2348] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022] Open
Abstract
The alteration of glucose metabolism, through increased uptake of glucose and glutamine addiction, is essential to cancer cell growth and invasion. Increased flux of glucose through the Hexosamine Biosynthetic Pathway (HBP) drives increased cellular O-GlcNAcylation (hyper-O-GlcNAcylation) and contributes to cancer progression by regulating key oncogenes. However, the association between hyper-O-GlcNAcylation and activation of these oncogenes remains poorly characterized. Here, we implement a qualitative modeling framework to analyze the role of the Biological Regulatory Network in HBP activation and its potential effects on key oncogenes. Experimental observations are encoded in a temporal language format and model checking is applied to infer the model parameters and qualitative model construction. Using this model, we discover step-wise genetic alterations that promote cancer development and invasion due to an increase in glycolytic flux, and reveal critical trajectories involved in cancer progression. We compute delay constraints to reveal important associations between the production and degradation rates of proteins. O-linked N-acetylglucosamine transferase (OGT), an enzyme used for addition of O-GlcNAc during O-GlcNAcylation, is identified as a key regulator to promote oncogenesis in a feedback mechanism through the stabilization of c-Myc. Silencing of the OGT and c-Myc loop decreases glycolytic flux and leads to programmed cell death. Results of network analyses also identify a significant cycle that highlights the role of p53-Mdm2 circuit oscillations in cancer recovery and homeostasis. Together, our findings suggest that the OGT and c-Myc feedback loop is critical in tumor progression, and targeting these mediators may provide a mechanism-based therapeutic approach to regulate hyper-O-GlcNAcylation in human cancer.
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Affiliation(s)
- Muhammad Tariq Saeed
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Jamil Ahmad
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan; School of Computer Science and IT, Stratford University, VA, United States
| | - Shahzina Kanwal
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou , China
| | - Andreana N Holowatyj
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute , Detroit , MI , United States
| | - Iftikhar A Sheikh
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Rehan Zafar Paracha
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Aamir Shafi
- School of Electrical Engineering and Computer Science (SEECS), National University of Sciences and Technology (NUST), Islamabad, Pakistan; College of Computer Science and Information Technology, University of Dammam, Al Khobar, Kingdom of Saudi Arabia
| | - Amnah Siddiqa
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Zurah Bibi
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Mukaram Khan
- Research Centre for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
| | - Amjad Ali
- Atta-ur-Rehman School of Applied Bio-science (ASAB), National University of Sciences and Technology (NUST) , Islamabad , Pakistan
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19
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Jackson RA, Chen ES. Synthetic lethal approaches for assessing combinatorial efficacy of chemotherapeutic drugs. Pharmacol Ther 2016; 162:69-85. [DOI: 10.1016/j.pharmthera.2016.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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20
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Chen SH, Forrester W, Lahav G. Schedule-dependent interaction between anticancer treatments. Science 2016; 351:1204-8. [PMID: 26965628 DOI: 10.1126/science.aac5610] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 01/28/2016] [Indexed: 12/16/2022]
Abstract
The oncogene MDMX is overexpressed in many cancers, leading to suppression of the tumor suppressor p53. Inhibitors of the oncogene product MDMX therefore might help reactivate p53 and enhance the efficacy of DNA-damaging drugs. However, we currently lack a quantitative understanding of how MDMX inhibition affects the p53 signaling pathway and cell sensitivity to DNA damage. Live cell imaging showed that MDMX depletion triggered two distinct phases of p53 accumulation in single cells: an initial postmitotic pulse, followed by low-amplitude oscillations. The response to DNA damage was sharply different in these two phases; in the first phase, MDMX depletion was synergistic with DNA damage in causing cell death, whereas in the second phase, depletion of MDMX inhibited cell death. Thus a quantitative understanding of signal dynamics and cellular states is important for designing an optimal schedule of dual-drug administration.
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Affiliation(s)
- Sheng-Hong Chen
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - William Forrester
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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21
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Wu W, Sun W, Sun T. Modeling the heterogeneity of p53 dynamics in DNA damage response. J Bioinform Comput Biol 2016; 14:1650001. [PMID: 26493683 DOI: 10.1142/s0219720016500013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The tumor suppressor p53 can be activated by DNA damage and exhibits undamped pulses. Recent reports have demonstrated a non-threshold mechanism for p53 dynamics. However, no related theoretical studies have been proposed. Here, we constructed a refined DNA damage repair model that incorporated both intrinsic and extrinsic DNA lesions. We proposed that the basal DNA damage may trigger significant fractions of p53 pulses. We also reproduced the heterogeneity of p53 dynamics in experiments. The number of p53 pulses showed no correlations with DNA damage. We also replicated the linear correlation between DNA damage and the probability of igniting a pulse. Our model has unraveled the heterogeneous p53 responses.
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Affiliation(s)
- Wenlei Wu
- Institute and Hospital of Stomatology, Nanjing University Medical School, Nanjing, Jiangsu 210008, P. R. China
| | - Weibin Sun
- Institute and Hospital of Stomatology, Nanjing University Medical School, Nanjing, Jiangsu 210008, P. R. China
| | - Tingzhe Sun
- School of Life Sciences, AnQing Normal University, AnQing, Anhui 246011, P. R. China
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22
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Moore R, Ooi HK, Kang T, Bleris L, Ma L. MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells. PLoS Comput Biol 2015; 11:e1004653. [PMID: 26642352 PMCID: PMC4671655 DOI: 10.1371/journal.pcbi.1004653] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
The p53 tumor suppressor protein plays a critical role in cellular stress and cancer prevention. A number of post-transcriptional regulators, termed microRNAs, are closely connected with the p53-mediated cellular networks. While the molecular interactions among p53 and microRNAs have emerged, a systems-level understanding of the regulatory mechanism and the role of microRNAs-forming feedback loops with the p53 core remains elusive. Here we have identified from literature that there exist three classes of microRNA-mediated feedback loops revolving around p53, all with the nature of positive feedback coincidentally. To explore the relationship between the cellular performance of p53 with the microRNA feedback pathways, we developed a mathematical model of the core p53-MDM2 module coupled with three microRNA-mediated positive feedback loops involving miR-192, miR-34a, and miR-29a. Simulations and bifurcation analysis in relationship to extrinsic noise reproduce the oscillatory behavior of p53 under DNA damage in single cells, and notably show that specific microRNA abrogation can disrupt the wild-type cellular phenotype when the ubiquitous cell-to-cell variability is taken into account. To assess these in silico results we conducted microRNA-perturbation experiments in MCF7 breast cancer cells. Time-lapse microscopy of cell-population behavior in response to DNA double-strand breaks, together with image classification of single-cell phenotypes across a population, confirmed that the cellular p53 oscillations are compromised after miR-192 perturbations, matching well with the model predictions. Our study via modeling in combination with quantitative experiments provides new evidence on the role of microRNA-mediated positive feedback loops in conferring robustness to the system performance of stress-induced response of p53. DNA damage triggered activities of the tumor suppressor protein p53 could be significantly dynamical. The functional role of p53 oscillations in cellular decision making during cancer development has been appreciated. A set of recent studies have revealed extensive crosstalk between the p53 network and microRNAs, but the specifics of the participation of microRNAs in the regulation of the p53 signaling pathway remains largely elusive. Here we investigated microRNAs that form feedback regulation with p53. We enumerated the molecular interactions among these microRNAs and the p53 core and developed a mathematical model to reproduce the DNA damage induced p53 oscillations in single cells. We performed computer simulations and system analysis in combination with experimental assessment to probe the behavior of p53 under microRNA-inhibited conditions. We show that the robust cellular performance of the stress response of p53 in a breast cancer cell line is controlled by miR-192, which forms positive feedback loops with p53.
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Affiliation(s)
- Richard Moore
- Bioengineering Department, University of Texas at Dallas, Richardson, Texas, United States of America
- Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Hsu Kiang Ooi
- Bioengineering Department, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Taek Kang
- Bioengineering Department, University of Texas at Dallas, Richardson, Texas, United States of America
- Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, Richardson, Texas, United States of America
- Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
- Electrical Engineering Department, University of Texas at Dallas, Richardson, Texas, United States of America
- * E-mail: (LB); (LM)
| | - Lan Ma
- Bioengineering Department, University of Texas at Dallas, Richardson, Texas, United States of America
- * E-mail: (LB); (LM)
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23
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Bradbury R, Jiang WG, Cui YX. The clinical and therapeutic uses of MDM2 and PSMA and their potential interaction in aggressive cancers. Biomark Med 2015; 9:1353-70. [PMID: 26581688 DOI: 10.2217/bmm.15.94] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Prostate-specific membrane antigen (PSMA) overexpression is observed in the neovasculature of solid tumors, but not in the vasculature of normal tissues. Increased PSMA expression is positively associated with tumor stage and grade, although its function in cancer remains unclear. Mouse double minute 2 (MDM2) is a negative regulator of the p53 tumor suppressor and is reported to regulate VEGF expression and angiogenesis. Both proteins have been considered as biomarkers and therapeutic targets for advanced solid tumors. Our work and a recent microarray-based gene profiling study suggest there could be signaling interplay between MDM2 and PSMA. We herein review the mechanisms underlining the outgrowth of tumors associated with PSMA and MDM2, their potential interaction and how this may be applied to anticancer therapeutics.
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Affiliation(s)
- Robyn Bradbury
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, UK
| | - Wen G Jiang
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, UK
| | - Yu-Xin Cui
- Cardiff China Medical Research Collaborative, School of Medicine, Cardiff University, UK
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Li H, Liu Q, Wang Z, Fang R, Shen Y, Cai X, Gao Y, Li Y, Zhang X, Ye L. The oncoprotein HBXIP modulates the feedback loop of MDM2/p53 to enhance the growth of breast cancer. J Biol Chem 2015; 290:22649-61. [PMID: 26229107 DOI: 10.1074/jbc.m115.658468] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 12/26/2022] Open
Abstract
MDM2 and p53 form a negative feedback loop, in which p53 as a transcription factor positively regulates MDM2 and MDM2 negatively regulates tumor suppressor p53 through promoting its degradation. However, the mechanism of the feedback loop is poorly understood in cancers. We had reported previously that the oncoprotein hepatitis B X-interacting protein (HBXIP) is a key oncoprotein in the development of cancer. Thus, we supposed that HBXIP might be involved in the event. Here, we observed that the expression levels of HBXIP were positively correlated to those of MDM2 in clinical breast cancer tissues. Interestingly, HBXIP was able to up-regulate MDM2 at the levels of mRNA and protein in MCF-7 breast cancer cells. Mechanically, HBXIP increased the promoter activities of MDM2 through directly binding to p53 in the P2 promoter of MDM2. Strikingly, we identified that the acetyltransferase p300 was recruited by HBXIP to p53 in the promoter of MDM2. Moreover, we validated that HBXIP enhanced the p53 degradation mediated by MDM2. Functionally, the knockdown of HBXIP or/and p300 inhibited the proliferation of breast cancer cells in vitro, and the depletion of MDM2 or overexpression of p53 significantly blocked the HBXIP-promoted growth of breast cancer in vitro and in vivo. Thus, we concluded that highly expressed HBXIP accelerates the MDM2-mediated degradation of p53 in breast cancer through modulating the feedback loop of MDM2/p53, resulting in the fast growth of breast cancer cells. Our findings provide new insights into the mechanism of the acceleration of the MDM2/p53 feedback loop in the development of cancer.
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Affiliation(s)
- Hang Li
- From the Department of Biochemistry and
| | - Qian Liu
- From the Department of Biochemistry and
| | - Zhen Wang
- From the Department of Biochemistry and
| | | | - Yu Shen
- From the Department of Biochemistry and
| | | | - Yuen Gao
- the Department of Cancer Research, State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | | | - Xiaodong Zhang
- the Department of Cancer Research, State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lihong Ye
- From the Department of Biochemistry and
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Singh VK, Romaine PL, Seed TM. Medical Countermeasures for Radiation Exposure and Related Injuries: Characterization of Medicines, FDA-Approval Status and Inclusion into the Strategic National Stockpile. HEALTH PHYSICS 2015; 108:607-630. [PMID: 25905522 PMCID: PMC4418776 DOI: 10.1097/hp.0000000000000279] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/05/2015] [Indexed: 05/28/2023]
Abstract
World events over the past decade have highlighted the threat of nuclear terrorism as well as an urgent need to develop radiation countermeasures for acute radiation exposures and subsequent bodily injuries. An increased probability of radiological or nuclear incidents due to detonation of nuclear weapons by terrorists, sabotage of nuclear facilities, dispersal and exposure to radioactive materials, and accidents provides the basis for such enhanced radiation exposure risks for civilian populations. Although the search for suitable radiation countermeasures for radiation-associated injuries was initiated more than half a century ago, no safe and effective radiation countermeasure for the most severe of these injuries, namely acute radiation syndrome (ARS), has been approved by the United States Food and Drug Administration (FDA). The dearth of FDA-approved radiation countermeasures has prompted intensified research for a new generation of radiation countermeasures. In this communication, the authors have listed and reviewed the status of radiation countermeasures that are currently available for use, or those that might be used for exceptional nuclear/radiological contingencies, plus a limited few medicines that show early promise but still remain experimental in nature and unauthorized for human use by the FDA.
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Affiliation(s)
- Vijay K. Singh
- *Radiation Countermeasures Program, Armed Forces Radiobiology Research Institute, Bethesda, MD; †Department of Radiation Biology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD; ‡Tech Micro Services, Bethesda, MD
| | - Patricia L.P. Romaine
- *Radiation Countermeasures Program, Armed Forces Radiobiology Research Institute, Bethesda, MD; †Department of Radiation Biology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD; ‡Tech Micro Services, Bethesda, MD
| | - Thomas M. Seed
- *Radiation Countermeasures Program, Armed Forces Radiobiology Research Institute, Bethesda, MD; †Department of Radiation Biology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD; ‡Tech Micro Services, Bethesda, MD
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Hormoz S, Bhanot G, Biehl M, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Dayarian A. Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets. Bioinformatics 2014; 31:492-500. [PMID: 25152231 PMCID: PMC4325538 DOI: 10.1093/bioinformatics/btu569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Motivation: Translating findings in rodent models to human models has been a cornerstone of modern biology and drug development. However, in many cases, a naive ‘extrapolation’ between the two species has not succeeded. As a result, clinical trials of new drugs sometimes fail even after considerable success in the mouse or rat stage of development. In addition to in vitro studies, inter-species translation requires analytical tools that can predict the enriched gene sets in human cells under various stimuli from corresponding measurements in animals. Such tools can improve our understanding of the underlying biology and optimize the allocation of resources for drug development. Results: We developed an algorithm to predict differential gene set enrichment as part of the sbv IMPROVER (systems biology verification in Industrial Methodology for Process Verification in Research) Species Translation Challenge, which focused on phosphoproteomic and transcriptomic measurements of normal human bronchial epithelial (NHBE) primary cells under various stimuli and corresponding measurements in rat (NRBE) primary cells. We find that gene sets exhibit a higher inter-species correlation compared with individual genes, and are potentially more suited for direct prediction. Furthermore, in contrast to a similar cross-species response in protein phosphorylation states 5 and 25 min after exposure to stimuli, gene set enrichment 6 h after exposure is significantly different in NHBE cells compared with NRBE cells. In spite of this difference, we were able to develop a robust algorithm to predict gene set activation in NHBE with high accuracy using simple analytical methods. Availability and implementation: Implementation of all algorithms is available as source code (in Matlab) at http://bhanot.biomaps.rutgers.edu/wiki/codes_SC3_Predicting_GeneSets.zip, along with the relevant data used in the analysis. Gene sets, gene expression and protein phosphorylation data are available on request. Contact:hormoz@kitp.ucsb.edu
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Affiliation(s)
- Sahand Hormoz
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA
| | - Gyan Bhanot
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA
| | - Michael Biehl
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA
| | - Erhan Bilal
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA
| | - Pablo Meyer
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA
| | - Raquel Norel
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA
| | - Kahn Rhrissorrakrai
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA
| | - Adel Dayarian
- Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA
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Zhang P, Brusic V. Mathematical modeling for novel cancer drug discovery and development. Expert Opin Drug Discov 2014; 9:1133-50. [PMID: 25062617 DOI: 10.1517/17460441.2014.941351] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Mathematical modeling enables: the in silico classification of cancers, the prediction of disease outcomes, optimization of therapy, identification of promising drug targets and prediction of resistance to anticancer drugs. In silico pre-screened drug targets can be validated by a small number of carefully selected experiments. AREAS COVERED This review discusses the basics of mathematical modeling in cancer drug discovery and development. The topics include in silico discovery of novel molecular drug targets, optimization of immunotherapies, personalized medicine and guiding preclinical and clinical trials. Breast cancer has been used to demonstrate the applications of mathematical modeling in cancer diagnostics, the identification of high-risk population, cancer screening strategies, prediction of tumor growth and guiding cancer treatment. EXPERT OPINION Mathematical models are the key components of the toolkit used in the fight against cancer. The combinatorial complexity of new drugs discovery is enormous, making systematic drug discovery, by experimentation, alone difficult if not impossible. The biggest challenges include seamless integration of growing data, information and knowledge, and making them available for a multiplicity of analyses. Mathematical models are essential for bringing cancer drug discovery into the era of Omics, Big Data and personalized medicine.
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Affiliation(s)
- Ping Zhang
- CSIRO Computational Informatics , Marsfield, NSW , Australia
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He Y, Tollini L, Kim TH, Itahana Y, Zhang Y. The anaphase-promoting complex/cyclosome is an E3 ubiquitin ligase for Mdm2. Cell Cycle 2014; 13:2101-9. [PMID: 24804778 DOI: 10.4161/cc.29106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Mdm2 proto-oncoprotein is the primary negative regulator for p53. While it is believed that Mdm2 degradation is regulated via its own E3 ubiquitin ligase activity, recent development of knock-in mouse models demonstrates that Mdm2 E3 ligase function is dispensable for self-degradation in vivo. Here, we show that the anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase for Mdm2 degradation. We demonstrate that APC2, a scaffold subunit of APC/C, binds to Mdm2 and is required for Mdm2 polyubiquitination and proteasomal degradation. Downregulation of APC2 by RNAi results in transcription-independent accumulation of Mdm2 and attenuation of stress-induced p53 stabilization, leading to decreased senescence and increased cell survival. Furthermore, APC2 expression is frequently downregulated in human cancers; in tumor cell lines, APC2 downregulation correlates with Mdm2 overexpression. Our study shows the regulation of Mdm2 by the E3 ubiquitin ligase APC/C and has important therapeutic implications for tumors with Mdm2 overexpression.
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Affiliation(s)
- Yizhou He
- Department of Radiation Oncology; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA; Lineberger Comprehensive Cancer Center; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA; Curriculum in Genetics and Molecular Biology; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Laura Tollini
- Department of Radiation Oncology; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA; Lineberger Comprehensive Cancer Center; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA; Curriculum in Genetics and Molecular Biology; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Tae-Hyung Kim
- Department of Radiation Oncology; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA; Lineberger Comprehensive Cancer Center; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Yoko Itahana
- Department of Radiation Oncology; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA; Lineberger Comprehensive Cancer Center; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA
| | - Yanping Zhang
- Department of Radiation Oncology; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA; Lineberger Comprehensive Cancer Center; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA; Department of Pharmacology; School of Medicine; University of North Carolina at Chapel Hill; Chapel Hill, NC USA; Laboratory of Biological Cancer Therapy; Xuzhou Medical College; Xuzhou, China
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Wink S, Hiemstra S, Huppelschoten S, Danen E, Niemeijer M, Hendriks G, Vrieling H, Herpers B, van de Water B. Quantitative high content imaging of cellular adaptive stress response pathways in toxicity for chemical safety assessment. Chem Res Toxicol 2014; 27:338-55. [PMID: 24450961 DOI: 10.1021/tx4004038] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the past decade, major leaps forward have been made on the mechanistic understanding and identification of adaptive stress response landscapes underlying toxic insult using transcriptomics approaches. However, for predictive purposes of adverse outcome several major limitations in these approaches exist. First, the limited number of samples that can be analyzed reduces the in depth analysis of concentration-time course relationships for toxic stress responses. Second these transcriptomics analysis have been based on the whole cell population, thereby inevitably preventing single cell analysis. Third, transcriptomics is based on the transcript level, totally ignoring (post)translational regulation. We believe these limitations are circumvented with the application of high content analysis of relevant toxicant-induced adaptive stress signaling pathways using bacterial artificial chromosome (BAC) green fluorescent protein (GFP) reporter cell-based assays. The goal is to establish a platform that incorporates all adaptive stress pathways that are relevant for toxicity, with a focus on drug-induced liver injury. In addition, cellular stress responses typically follow cell perturbations at the subcellular organelle level. Therefore, we complement our reporter line panel with reporters for specific organelle morphometry and function. Here, we review the approaches of high content imaging of cellular adaptive stress responses to chemicals and the application in the mechanistic understanding and prediction of chemical toxicity at a systems toxicology level.
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Affiliation(s)
- Steven Wink
- Division of Toxicology, Leiden Academic Centre for Drug Research (LACDR), Leiden University , The Netherlands
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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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Abstract
Mdm2 is best known as the primary negative regulator of p53, but a growing body of evidence suggests that Mdm2 also has a number of functions independent of its role in regulating p53. Although these functions are not yet well-characterized, they have been implicated in regulating of a number of cellular processes, including cell-cycle control, apoptosis, differentiation, genome stability, and transcription, among others. It appears that Mdm2 exerts these functions through a surprisingly wide variety of mechanisms. For example, it has been shown that Mdm2 can ubiquitinate alternative targets, can stimulate the activity of transcription factors, and can directly bind to mRNA to regulate its stability. Dysregulation of p53-independent functions could be responsible for the oncogenic properties of Mdm2 seen even in the absence of p53, and may explain why approximately 10 % of human tumors overexpress Mdm2 instead of inactivating p53 through other mechanisms. As the p53-independent functions of Mdm2 present novel targets for potential therapeutic interventions, fully characterizing these cellular and pathogenic roles of Mdm2 will be important in the study of tumor biology and the treatment of cancer.
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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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Kell DB. Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it. FEBS J 2013; 280:5957-80. [PMID: 23552054 DOI: 10.1111/febs.12268] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/20/2013] [Accepted: 03/26/2013] [Indexed: 12/16/2022]
Abstract
Despite the sequencing of the human genome, the rate of innovative and successful drug discovery in the pharmaceutical industry has continued to decrease. Leaving aside regulatory matters, the fundamental and interlinked intellectual issues proposed to be largely responsible for this are: (a) the move from 'function-first' to 'target-first' methods of screening and drug discovery; (b) the belief that successful drugs should and do interact solely with single, individual targets, despite natural evolution's selection for biochemical networks that are robust to individual parameter changes; (c) an over-reliance on the rule-of-5 to constrain biophysical and chemical properties of drug libraries; (d) the general abandoning of natural products that do not obey the rule-of-5; (e) an incorrect belief that drugs diffuse passively into (and presumably out of) cells across the bilayers portions of membranes, according to their lipophilicity; (f) a widespread failure to recognize the overwhelmingly important role of proteinaceous transporters, as well as their expression profiles, in determining drug distribution in and between different tissues and individual patients; and (g) the general failure to use engineering principles to model biology in parallel with performing 'wet' experiments, such that 'what if?' experiments can be performed in silico to assess the likely success of any strategy. These facts/ideas are illustrated with a reasonably extensive literature review. Success in turning round drug discovery consequently requires: (a) decent systems biology models of human biochemical networks; (b) the use of these (iteratively with experiments) to model how drugs need to interact with multiple targets to have substantive effects on the phenotype; (c) the adoption of polypharmacology and/or cocktails of drugs as a desirable goal in itself; (d) the incorporation of drug transporters into systems biology models, en route to full and multiscale systems biology models that incorporate drug absorption, distribution, metabolism and excretion; (e) a return to 'function-first' or phenotypic screening; and (f) novel methods for inferring modes of action by measuring the properties on system variables at all levels of the 'omes. Such a strategy offers the opportunity of achieving a state where we can hope to predict biological processes and the effect of pharmaceutical agents upon them. Consequently, this should both lower attrition rates and raise the rates of discovery of effective drugs substantially.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester, UK; Manchester Institute of Biotechnology, The University of Manchester, UK
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Abstract
PURPOSE We evaluated in vitro the role of CO(2)-induced oxidative stress on the expression of proteins involved in cell-cycle regulation of neuroblastoma cells. METHODS SH-SY5Y cells were exposed to CO(2) at 15 mmHg pressure (100 %) for 4 h and then moved to normal condition for 24 h. Control cells were maintained in 5 % CO(2) for the same time. ROS production was determined by fluorescent staining with H2DCF-DA. DNA damage was measured by COMET assay. p53 protein expression was analyzed by western blot and confocal laser scanning microscopy was used to evaluate its sub-cellular localization. Cyclin expression was quantified by real-time PCR and western blot. Cell-cycle analysis was performed by FACS. RESULTS CO(2) incubation was associated with an increase in ROS production (p < 0.01), cell DNA damage mainly after 24 h (12 % increase of tail DNA content and 4-fold increase of tail length) and a significant up-regulation in p53 expression at 24 h with an intense nuclear staining. In CO(2)-treated cells, we observed an S-phase arrest in correlation with a reduction of cyclin B1 expression. CONCLUSIONS In vitro-simulated pneumoperitoneum environment with CO(2) induces oxidative stress and cell DNA damage, leading to p53 up-regulation involved in cell-cycle arrest of neuroblastoma cells.
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Choi M, Shi J, Jung SH, Chen X, Cho KH. Attractor landscape analysis reveals feedback loops in the p53 network that control the cellular response to DNA damage. Sci Signal 2012; 5:ra83. [PMID: 23169817 DOI: 10.1126/scisignal.2003363] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The protein p53 functions as a tumor suppressor and can trigger either cell cycle arrest or apoptosis in response to DNA damage. We used Boolean network modeling and attractor landscape analysis to analyze the state transition dynamics of a simplified p53 network for which particular combinations of activation states of the molecules corresponded to specific cellular outcomes. Our results identified five critical interactions in the network that determined the cellular response to DNA damage, and simulations lacking any of these interactions produced states associated with sustained p53 activity, which corresponded to a cell death response. Attractor landscape analysis of the cellular response to DNA damage of the breast cancer cell line MCF7 and the effect of the Mdm2 (murine double minute 2) inhibitor nutlin-3 indicated that nutlin-3 would exhibit limited efficacy in triggering cell death, because the cell death state was not induced to a large extent by simulations with nutlin-3 and instead produced a state consistent with oscillatory p53 dynamics and cell cycle arrest. Attractor landscape analysis also suggested that combining nutlin-3 with inhibition of Wip1 would synergize to stimulate a sustained increase in p53 activity and promote p53-mediated cell death. We validated this synergistic effect in stimulating p53 activity and triggering cell death with single-cell imaging of a fluorescent p53 reporter in MCF7 cells. Thus, attractor landscape analysis of p53 network dynamics and its regulation can identify potential therapeutic strategies for treating cancer.
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Affiliation(s)
- Minsoo Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
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Goldbeter A, Gérard C, Gonze D, Leloup JC, Dupont G. Systems biology of cellular rhythms. FEBS Lett 2012; 586:2955-65. [PMID: 22841722 DOI: 10.1016/j.febslet.2012.07.041] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 07/17/2012] [Accepted: 07/17/2012] [Indexed: 12/22/2022]
Abstract
Rhythms abound in biological systems, particularly at the cellular level where they originate from the feedback loops present in regulatory networks. Cellular rhythms can be investigated both by experimental and modeling approaches, and thus represent a prototypic field of research for systems biology. They have also become a major topic in synthetic biology. We review advances in the study of cellular rhythms of biochemical rather than electrical origin by considering a variety of oscillatory processes such as Ca++ oscillations, circadian rhythms, the segmentation clock, oscillations in p53 and NF-κB, synthetic oscillators, and the oscillatory dynamics of cyclin-dependent kinases driving the cell cycle. Finally we discuss the coupling between cellular rhythms and their robustness with respect to molecular noise.
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Affiliation(s)
- A Goldbeter
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, B-1050 Brussels, Belgium.
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Moss BL, Elhammali A, Fowlkes T, Gross S, Vinjamoori A, Contag CH, Piwnica-Worms D. Interrogation of inhibitor of nuclear factor κB α/nuclear factor κB (IκBα/NF-κB) negative feedback loop dynamics: from single cells to live animals in vivo. J Biol Chem 2012; 287:31359-70. [PMID: 22807442 DOI: 10.1074/jbc.m112.364018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Full understanding of the biological significance of negative feedback processes requires interrogation at multiple scales as follows: in single cells, cell populations, and live animals in vivo. The transcriptionally coupled IκBα/NF-κB negative feedback loop, a pivotal regulatory node of innate immunity and inflammation, represents a model system for multiscalar reporters. Using a κB(5)→IκBα-FLuc bioluminescent reporter, we rigorously evaluated the dynamics of ΙκBα degradation and subsequent NF-κB transcriptional activity in response to diverse modes of TNFα stimulation. Modulating TNFα concentration or pulse duration yielded complex, reproducible, and differential ΙκBα dynamics in both cell populations and live single cells. Tremendous heterogeneity in the transcriptional amplitudes of individual responding cells was observed, which was greater than the heterogeneity in the transcriptional kinetics of responsive cells. Furthermore, administration of various TNFα doses in vivo generated ΙκBα dynamic profiles in the liver resembling those observed in single cells and populations of cells stimulated with TNFα pulses. This suggested that dose modulation of circulating TNFα was perceived by hepatocytes in vivo as pulses of increasing duration. Thus, a robust bioluminescent reporter strategy enabled rigorous quantitation of NF-κB/ΙκBα dynamics in both live single cells and cell populations and furthermore, revealed reproducible behaviors that informed interpretation of in vivo studies.
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Affiliation(s)
- Britney L Moss
- Molecular Imaging Center, Mallinckrodt Institute of Radiology, Department of Cell Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Jensen MH, Krishna S. Inducing phase-locking and chaos in cellular oscillators by modulating the driving stimuli. FEBS Lett 2012; 586:1664-8. [DOI: 10.1016/j.febslet.2012.04.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/23/2012] [Accepted: 04/23/2012] [Indexed: 01/18/2023]
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Abstract
BACKGROUND The tumor suppressor p53 has become one of most investigated genes. Once activated by stress, p53 leads to cellular responses such as cell cycle arrest and apoptosis. METHODOLOGY/PRINCIPAL FINDINGS Most previous models have ignored the basal dynamics of p53 under nonstressed conditions. To explore the basal dynamics of p53, we constructed a stochastic delay model by incorporating two negative feedback loops. We found that protein distribution of p53 under nonstressed condition is highly skewed with a fraction of cells showing high p53 levels comparable to those observed under stressed conditions. Under nonstressed conditions, asynchronous and spontaneous p53 pulses are triggered by basal DNA double strand breaks produced during normal cell cycle progression. The first peaking times show a predominant G1 distribution while the second ones are more widely distributed. The spontaneous pulses are triggered by an excitable mechanism. Once initiated, the amplitude and duration of pulses remain unchanged. Furthermore, the spontaneous pulses are filtered by ataxia telangiectasia mutated protein mediated posttranslational modifications and do not result in substantial p21 transcription. If challenged by externally severe DNA damage, cells generate synchronous p53 pulses and induce significantly high levels of p21. The high expression of p21 can also be partially induced by lowering the deacetylation rate. CONCLUSIONS Our results demonstrated that the dynamics of p53 under nonstressed conditions is initiated by an excitable mechanism and cells become fully responsive only when cells are confronted with severe damage. These findings advance our understanding of the mechanism of p53 pulses and unlock many opportunities to p53-based therapy.
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Tarocchi M, Hannivoort R, Hoshida Y, Lee UE, Vetter D, Narla G, Villanueva A, Oren M, Llovet JM, Friedman SL. Carcinogen-induced hepatic tumors in KLF6+/- mice recapitulate aggressive human hepatocellular carcinoma associated with p53 pathway deregulation. Hepatology 2011; 54:522-31. [PMID: 21563203 PMCID: PMC3144998 DOI: 10.1002/hep.24413] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 04/25/2011] [Indexed: 12/11/2022]
Abstract
UNLABELLED Inactivation of KLF6 is common in hepatocellular carcinoma (HCC) associated with hepatitis C virus (HCV) infection, thereby abrogating its normal antiproliferative activity in liver cells. The aim of the study was to evaluate the impact of KLF6 depletion on human HCC and experimental hepatocarcinogenesis in vivo. In patients with surgically resected HCC, reduced tumor expression of KLF6 was associated with decreased survival. Consistent with its role as a tumor suppressor, KLF6+/- mice developed significantly more tumors in response to the chemical carcinogen diethyl nitrosamine (DEN) than wild-type animals. Gene expression signatures in both surrounding tissue and tumors of KLF6+/- mice closely recapitulated those associated with aggressive human HCCs. Expression microarray profiling also revealed an increase in Mdm2 mRNA in tumors from KLF6+/- compared with KLF6+/+ mice, which was validated by way of quantitative real-time polymerase chain reaction and western blot analysis in both human HCC and DEN-induced murine tumors. Moreover, chromatin immunoprecipitation and cotransfection assays established the P2 intronic promoter of Mdm2 as a bona fide transcriptional target repressed by KLF6. Whereas KLF6 overexpression in HCC cell lines and primary hepatocytes led to reduced MDM2 levels and increased p53 protein and transcriptional activity, reduction in KLF6 by small interfering RNA led to increased MDM2 and reduced p53. CONCLUSION Our findings indicate that KLF6 deficiency contributes significantly to the carcinogenic milieu in human and murine HCC and uncover a novel tumor suppressor activity of KLF6 in HCC by linking its transcriptional repression of Mdm2 to stabilizing p53.
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Affiliation(s)
- Mirko Tarocchi
- Department of Medicine/Division of Liver Diseases, Mount Sinai School of Medicine, New York, NY,Department of Clinical Pathophysiology/Gastroenterology Unit, University of Florence, Florence, Italy
| | - Rebekka Hannivoort
- Department of Medicine/Division of Liver Diseases, Mount Sinai School of Medicine, New York, NY,Department of Gastroenterology and Hepatology, University of Groningen, Groningen, the Netherlands
| | - Yujin Hoshida
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge MA
| | - Ursula E. Lee
- Department of Medicine/Division of Liver Diseases, Mount Sinai School of Medicine, New York, NY
| | - Diana Vetter
- Department of Medicine/Division of Liver Diseases, Mount Sinai School of Medicine, New York, NY
| | - Goutham Narla
- Department of Medicine/Division of Hematology/Oncology, Mount Sinai School of Medicine, New York, NY,Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY
| | - Augusto Villanueva
- HCC Translational Research Laboratory, Barcelona-Clinic Liver Cancer Group, Liver Unit. Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS); Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clinic, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats
| | - Moshe Oren
- Department of Molecular Cell Biology, The Weizmann Institute, Rehovot, Israel
| | - Josep M. Llovet
- Department of Medicine/Division of Liver Diseases, Mount Sinai School of Medicine, New York, NY,HCC Translational Research Laboratory, Barcelona-Clinic Liver Cancer Group, Liver Unit. Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS); Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clinic, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats
| | - Scott L. Friedman
- Department of Medicine/Division of Liver Diseases, Mount Sinai School of Medicine, New York, NY
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Schisano B, Tripathi G, McGee K, McTernan PG, Ceriello A. Glucose oscillations, more than constant high glucose, induce p53 activation and a metabolic memory in human endothelial cells. Diabetologia 2011; 54:1219-26. [PMID: 21287141 DOI: 10.1007/s00125-011-2049-0] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 12/07/2010] [Indexed: 10/18/2022]
Abstract
AIMS/HYPOTHESIS Damage persists in HUVECs exposed to a constant high glucose concentration long after glucose normalisation, a phenomenon termed 'metabolic memory'. Evaluation of the effects of exposure of HUVECs to oscillating high glucose on the induction of markers of oxidative stress and DNA damage (phospho-γ-histone H2AX and PKCδ) and onset of metabolic memory, and the possible role of the tumour suppressor transcriptional factor p53 is of pivotal interest. METHODS HUVECs were incubated for 3 weeks in 5 or 25 mmol/l glucose or oscillating glucose (24 h in 5 mmol/l glucose followed by 24 h in 25 mmol/l glucose) or for 1 week in constant 5 mmol/l glucose after being exposed for 2 weeks to continuous 25 mmol/l high glucose or oscillating glucose. Transcriptional activity of p53 was also evaluated in the first 24 h after high glucose exposure. RESULTS High constant glucose upregulated phospho-γ-histone H2AX and protein kinase C (PKC)δ compared with control. Oscillating glucose was even more effective than both normal and constant high glucose. Both constant and oscillating glucose resulted in a memory effect, which was more pronounced in the oscillating condition. Transcriptional activity of p53 peaked 6 h after glucose exposure, showing a predicted oscillatory behaviour. CONCLUSIONS/INTERPRETATION Exposure to oscillating glucose was more deleterious than constant high glucose and induced a metabolic memory after glucose normalisation. Hyperactivation of p53 during glucose oscillation might be due to the absence of consistent feedback inhibition during each glucose spike and might account for the worse outcome of this condition.
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Affiliation(s)
- B Schisano
- Clinical Science Research Institute (CSRI), Warwick Medical School, University of Warwick, University Hospital-Walsgrave Campus, Coventry, CV2 2DX, UK
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Valbuena A, Sanz-García M, López-Sánchez I, Vega FM, Lazo PA. Roles of VRK1 as a new player in the control of biological processes required for cell division. Cell Signal 2011; 23:1267-72. [PMID: 21514377 DOI: 10.1016/j.cellsig.2011.04.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 04/04/2011] [Indexed: 11/28/2022]
Abstract
Cell division, in addition to an accurate transmission of genetic information to daughter cells, also requires the temporal and spatial coordination of several biological processes without which cell division would not be feasible. These processes include the temporal coordination of DNA replication and chromosome segregation, regulation of nuclear envelope disassembly and assembly, chromatin condensation and Golgi fragmentation for its redistribution into daughter cells, among others. However, little is known regarding regulatory proteins and signalling pathways that might participate in the coordination of all these different biological functions. Such regulatory players should directly have a role in the processes leading to cell division. VRK1 (Vaccinia-related kinase 1) is an early response gene required for cyclin D1 expression, regulates p53 by a specific Thr18 phosphorylation, controls chromatin condensation by histone phosphorylation, nuclear envelope assembly by phosphorylation of BANF1, and participates in signalling required for Golgi fragmentation late in the G2 phase. We propose that VRK1, a Ser-Thr kinase, might be a candidate to play an important coordinator role in these cell division processes as part of a novel signalling pathway.
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Affiliation(s)
- Alberto Valbuena
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
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Jang MS, Lee SJ, Kim CJ, Lee CW, Kim E. Phosphorylation by polo-like kinase 1 induces the tumor-suppressing activity of FADD. Oncogene 2011; 30:471-81. [PMID: 20890306 DOI: 10.1038/onc.2010.423] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 07/23/2010] [Accepted: 07/23/2010] [Indexed: 12/14/2022]
Abstract
Phosphorylation of the Fas-associated death domain (FADD) protein sensitizes cancer cells to various chemotherapeutics. However, the molecular mechanism underlying chemosensitization by phosphorylated FADD (P-FADD) is poorly understood. In this study, we describe the physical interactions and functional interplay between Polo-like kinase 1 (Plk1) and FADD. Plk1 phosphorylates FADD at Ser-194 in response to treatment with taxol. Overexpression of a phosphorylation-mimicking mutant, FADD S194D, caused degradation of Plk1 in an ubiquitin-independent manner, and delayed cytokinesis, consistent with the expected cellular phenotype of Plk1 deficiency. This demonstrates that Plk1 is regulated via a negative feedback loop by its substrate, FADD. Overexpression of FADD S194D sensitized HeLa cells to a low dose of taxol independently of caspase activation, whereas overexpression of FADD S194D resulted in caspase activation in response to a high dose of taxol. Therefore, we examined whether the death potential of P-FADD affected Plk1-mediated tumorigenesis. Transfection of FADD S194D inhibited colony formation by Plk1-overexpressing HeLa cells (HeLa-Plk1). Moreover, overexpression of FADD S194D suppressed tumorigenesis in nude mice xenografted with HeLa-Plk1. Therefore, this study reports the first in vivo validation of tumor-suppressing activity of P-FADD. Collectively, our data demonstrate that in response to taxol, Plk1 endows death-promoting and tumor-suppressor functions to its substrate, FADD.
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Affiliation(s)
- M-S Jang
- College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, Korea
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Manfredi JJ. The Mdm2-p53 relationship evolves: Mdm2 swings both ways as an oncogene and a tumor suppressor. Genes Dev 2010; 24:1580-9. [PMID: 20679392 DOI: 10.1101/gad.1941710] [Citation(s) in RCA: 270] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mdm2 has been well characterized as a negative regulator of the tumor suppressor p53. Recent studies have shown that Mdm2 is activated in response to a variety of oncogenic pathways independent of p53. Although its role as an oncogene via suppression of p53 function remains clear, growing evidence argues for p53-independent effects, as well as the remarkable possibility that Mdm2 has tumor suppressor functions in the appropriate context. Hence, Mdm2 is proving to be a key player in human cancer in its own right, and thus an important target for therapeutic intervention.
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Affiliation(s)
- James J Manfredi
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA.
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Azmi AS, Philip PA, Aboukameel A, Wang Z, Banerjee S, Zafar SF, Goustin AS, Almhanna K, Yang D, Sarkar FH, Mohammad RM. Reactivation of p53 by novel MDM2 inhibitors: implications for pancreatic cancer therapy. Curr Cancer Drug Targets 2010; 10:319-31. [PMID: 20370686 DOI: 10.2174/156800910791190229] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 01/09/2010] [Indexed: 01/22/2023]
Abstract
The present study is the first to show in pancreatic cancer (PC) the growth inhibition and apoptosis by novel MDM2 inhibitors (MI-319 & 219) through reactivation of p53 pathway. Our results highlight two new secondary targets of MDM2 inhibitor 'SIRT1' and Ku70. SIRT1 which has a role in ageing and cancer and is known to regulate p53 signaling through acetylation. Ku70 is a key component of non-homologous end joining machinery in the DNA damage pathway and is known to regulate apoptosis by blocking Bax entry into mitochondria. Growth inhibition and apoptosis by MI-219, MI-319 was accompanied by increase in levels of p53 along with p21(WAF1) and the proapoptotic Puma. SiRNA against p21(WAF1) abrogated the growth inhibition of PC cells confirming p21(WAF1) as a key player downstream of activated p53. Immunoprecipitation-western blot analysis revealed reduced association of MDM2-p53 interaction in drug exposed PC cells. In combination studies, the inhibitors synergistically augmented anti-tumor effects of therapeutic drug gemcitabine both in terms of cell growth inhibition as well as apoptosis. Surface plasmon resonance studies confirmed strong binding between MI-319 and Ku70 (K(D) 170 nM). Western blot revealed suppression of SIRT1 and Ku70 with simultaneous upregulation of acetyl-p53 (Lys379) and Bax. Co-Immunoprecipitation studies confirmed that MI-319 could disrupt Ku70-Bax and SIRT1-Bax interaction. Further, using wt-p53 xenograft of Capan-2, we found that oral administration of MI-319 at 300 mg/kg for 14 days resulted in significant tumor growth inhibition without any observed toxicity to the animals. No tumor inhibition was found in mut-p53 BxPC-3 xenografts. In light of our results, the inhibitors of MDM2 warrant clinical investigation as new agents for PC treatment.
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Affiliation(s)
- Asfar S Azmi
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Ouattara DA, Abou-Jaoudé W, Kaufman M. From structure to dynamics: Frequency tuning in the p53-Mdm2 network. II. J Theor Biol 2010; 264:1177-89. [DOI: 10.1016/j.jtbi.2010.03.031] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 03/16/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
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Xu H, Zhang Z, Li M, Zhang R. MDM2 promotes proteasomal degradation of p21Waf1 via a conformation change. J Biol Chem 2010; 285:18407-14. [PMID: 20308078 DOI: 10.1074/jbc.m109.059568] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MDM2 plays a major role in cancer development and progression via both p53-dependent and -independent functions. One of its p53-independent functions is the induction of the ubiquitin-independent proteasomal degradation of p21(Waf1). The present study was designed to characterize the mechanism(s) by which MDM2 induces p21(Waf1) degradation. We first determined the regions of MDM2 required for p21(Waf1) degradation using pulldown assays and Western blotting and then examined the mechanisms using limited proteolysis and fluorescence resonance energy transfer assays. We found that the MDM2-p21(Waf1) interaction depended on the central domain of MDM2 and that nuclear localization of both proteins was necessary for p21(Waf1) degradation. Specifically, amino acids 226-250 of MDM2 were required for p21(Waf1) binding and degradation, and amino acids 251-260 were necessary for p21(Waf1) degradation. The latter region induced a conformation change in p21(Waf1), increasing its interaction with the C8 subunit of the proteasome, leading to its degradation. When MDM2 lacked either segment (aa 226-250 or aa 251-260), its capacity to promote p21(Waf1) degradation and cell cycle progression was significantly reduced. In summary, the present study elucidated a previously unknown mechanism by which MDM2 promotes the degradation of an intact protein (p21(Waf1)) through an ubiquitin-independent proteasomal degradation pathway. Because MDM2 also increases the degradation of other proteins in a ubiquitin-independent manner, this mechanism may underlie part of its tumorigenic properties.
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Affiliation(s)
- Hongxia Xu
- Division of Clinical Pharmacology, Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Yadavilli S, Chen Z, Albrecht T, Muganda PM. Mechanism of diepoxybutane-induced p53 regulation in human cells. J Biochem Mol Toxicol 2010; 23:373-86. [PMID: 20024960 DOI: 10.1002/jbt.20300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Diepoxybutane (DEB) is the most potent active metabolite of the environmental chemical 1,3-butadiene (BD). BD is a known mutagen and human carcinogen and possesses multisystems organ toxicity. We previously reported the elevation of p53 in human TK6 lymphoblasts undergoing DEB-induced apoptosis. In this study, we have characterized the DEB-induced p53 accumulation and investigated the mechanisms by which DEB regulates this p53 accumulation. The elevation of p53 levels in DEB-exposed TK6 lymphoblasts and human embryonic lung (HEL) human fibroblasts was found to be largely due to the stabilization of the p53 protein. DEB increased the acetylation of p53 at lys-382, dramatically reduced complex formation between p53 and its regulator protein mdm2 and induced the phosphorylation of p53 at serines 15, 20, 37, 46, and 392 in human lymphoblasts. A dramatic increase in phosphorylation of p53 at serine 15 in correlation to total p53 levels was observed in DEB-exposed Ataxia Telangiectasia Mutated (ATM) proficient human lymphoblasts as compared to DEB-exposed ATM-deficient human lymphoblasts; this implicates the ATM kinase in the elevation of p53 levels in DEB-exposed cells. Collectively, these findings explain for the first time the mechanism by which p53 accumulates in DEB-exposed cells and contributes to the understanding of the molecular toxicity of DEB and BD.
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Affiliation(s)
- Sridevi Yadavilli
- Environmental Toxicology Ph.D. Program, Southern University, Baton Rouge, LA 70813, USA
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Abstract
The really interesting genes (RING)-finger-containing oncoprotein, Mdm2, is a promising drug target for cancer therapy. A key Mdm2 function is to promote ubiquitylation and proteasomal-dependent degradation of the tumor suppressor protein p53. Recent reports provide novel important insights into Mdm2-mediated regulation of p53 and how the physical and functional interactions between these two proteins are regulated. Moreover, a p53-independent role of Mdm2 has recently been confirmed by genetic data. These advances and their potential implications for the development of new cancer therapeutic strategies form the focus of this review.
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Affiliation(s)
- J-C Marine
- Laboratory For Molecular Cancer Biology, VIB-UGent, Ghent B-9052, Belgium.
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Numerical and Experimental Analysis of the p53-mdm2 Regulatory Pathway. LECTURE NOTES OF THE INSTITUTE FOR COMPUTER SCIENCES, SOCIAL INFORMATICS AND TELECOMMUNICATIONS ENGINEERING 2010. [DOI: 10.1007/978-3-642-14859-0_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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