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Xu M, Fang L, Xue Q, Zhang X, He Y. The Nrf2 Pathway Alleviates Overloading Force-Induced TMJ Degeneration by Downregulating Oxidative Stress Reactions. J Inflamm Res 2023; 16:5601-5612. [PMID: 38046402 PMCID: PMC10691432 DOI: 10.2147/jir.s434799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/10/2023] [Indexed: 12/05/2023] Open
Abstract
Objective Oxidative stress is involved in the mechanisms associated with temporomandibular joint (TMJ) diseases. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a crucial oxidative stress marker, but the specific mechanisms of its regulation in the early stages of mandibular condylar cartilage (MCC) degeneration remain unclear. This study aimed to explore the regulatory role of Nrf2 and its related oxidative stress signaling pathway in the early stage of MCC degeneration. Materials and Methods Overloading force-induced MCC degeneration was performed in wild-type and Nrf2 knockout mice, as well as in mice after treatment with the Nrf2 activator cardamonin. Changes in MCC degeneration and the expression of oxidative stress markers in the corresponding situations were observed. Results Nrf2 and NADPH oxidase 2 (NOX2) expression were elevated during early MCC degeneration induced by an overloading force. MCC degeneration was aggravated when Nrf2 was knocked out, accompanied by increased NOX2 and superoxide dismutase 2 (SOD2) expression. The MCC degeneration process was alleviated after cardamonin treatment, with activation of the Nrf2 pathway and decreased NOX2 and SOD2 expression. Conclusion Early MCC degeneration is accompanied by mild oxidative stress progression. Activated Nrf2 and related pathways could alleviate the degeneration of MCC.
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Affiliation(s)
- Minglu Xu
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Lingli Fang
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Qin Xue
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Xuyang Zhang
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Yao He
- Department of Orthodontics, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
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2
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Wang YL, Jin LL, Cheng X, Yan WF, Deng H, Shen QK, Quan ZS, Jin CM, Zhang CH. Synthesis and evaluation of in vitro and in vivo anti -Toxoplasma gondii activity of tetraoxane-substituted ursolic acid derivatives. Nat Prod Res 2023; 37:3654-3662. [PMID: 35834719 DOI: 10.1080/14786419.2022.2098497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/29/2022] [Accepted: 06/25/2022] [Indexed: 10/17/2022]
Abstract
A series of derivatives of ursolic acid (UA) were synthesised, the anti-Toxoplasma gondii activity was tested, and the selectivity index (SI) of these compounds was calculated to determine the derivative with the best anti-Toxoplasma gondii activity. Compound A7 showed the best activity against the Toxoplasma gondii (IC50 in T. gondii infected GES-1 cells: 9.1 ± 7.2 μM), better than the lead compound UA and the positive control drug Spiramycin. Compound A7 was selected for further in vivo research: A7 was tested for its effect on the inhibition rate of tachyzoites in mice and its biochemical parameters, such as alanine aminotransferase, aspartate aminotransferase, glutathione, and malondialdehyde were determined. Compound A7 was evaluated for its anti-Toxoplasma activity and partial damage to the liver. Therefore, the results show that compound A7 could be a potential lead compound for developing a novel anti-Toxoplasma gondii molecule.
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Affiliation(s)
- Ya-Lan Wang
- Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Li-Li Jin
- Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Xu Cheng
- Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Wei-Feng Yan
- Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Hao Deng
- Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Qing-Kun Shen
- Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Zhe-Shan Quan
- Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Chun-Mei Jin
- Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Chang-Hao Zhang
- Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affifiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
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3
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Manna S, Ruano CSM, Hegenbarth JC, Vaiman D, Gupta S, McCarthy FP, Méhats C, McCarthy C, Apicella C, Scheel J. Computational Models on Pathological Redox Signalling Driven by Pregnancy: A Review. Antioxidants (Basel) 2022; 11:antiox11030585. [PMID: 35326235 PMCID: PMC8945226 DOI: 10.3390/antiox11030585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 02/04/2023] Open
Abstract
Oxidative stress is associated with a myriad of diseases including pregnancy pathologies with long-term cardiovascular repercussions for both the mother and baby. Aberrant redox signalling coupled with deficient antioxidant defence leads to chronic molecular impairment. Abnormal placentation has been considered the primary source for reactive species; however, placental dysfunction has been deemed secondary to maternal cardiovascular maladaptation in pregnancy. While various therapeutic interventions, aimed at combating deregulated oxidative stress during pregnancy have shown promise in experimental models, they often result as inconclusive or detrimental in clinical trials, warranting the need for further research to identify candidates. The strengths and limitations of current experimental methods in redox research are discussed. Assessment of redox status and oxidative stress in experimental models and in clinical practice remains challenging; the state-of-the-art of computational models in this field is presented in this review, comparing static and dynamic models which provide functional information such as protein-protein interactions, as well as the impact of changes in molecular species on the redox-status of the system, respectively. Enhanced knowledge of redox biology in during pregnancy through computational modelling such as generation of Systems Biology Markup Language model which integrates existing models to a larger network in the context of placenta physiology.
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Affiliation(s)
- Samprikta Manna
- Department of Obstetrics and Gynaecology, Cork University Maternity Hospital, University College Cork, T12 YE02 Cork, Ireland;
- Correspondence:
| | - Camino S. M. Ruano
- Institut Cochin, Inserm U1016, UMR8104 CNRS, Université de Paris, 75014 Paris, France; (C.S.M.R.); (D.V.); (C.M.); (C.A.)
| | - Jana-Charlotte Hegenbarth
- Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, 6211 KH Maastricht, The Netherlands;
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Daniel Vaiman
- Institut Cochin, Inserm U1016, UMR8104 CNRS, Université de Paris, 75014 Paris, France; (C.S.M.R.); (D.V.); (C.M.); (C.A.)
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, Rostock University, 18051 Rostock, Germany; (S.G.); (J.S.)
| | - Fergus P. McCarthy
- Department of Obstetrics and Gynaecology, Cork University Maternity Hospital, University College Cork, T12 YE02 Cork, Ireland;
| | - Céline Méhats
- Institut Cochin, Inserm U1016, UMR8104 CNRS, Université de Paris, 75014 Paris, France; (C.S.M.R.); (D.V.); (C.M.); (C.A.)
| | - Cathal McCarthy
- Department of Pharmacology and Therapeutics, Western Gateway Building, University College Cork, T12 K8AF Cork, Ireland;
| | - Clara Apicella
- Institut Cochin, Inserm U1016, UMR8104 CNRS, Université de Paris, 75014 Paris, France; (C.S.M.R.); (D.V.); (C.M.); (C.A.)
| | - Julia Scheel
- Department of Systems Biology and Bioinformatics, Rostock University, 18051 Rostock, Germany; (S.G.); (J.S.)
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Tice RR, Bassan A, Amberg A, Anger LT, Beal MA, Bellion P, Benigni R, Birmingham J, Brigo A, Bringezu F, Ceriani L, Crooks I, Cross K, Elespuru R, Faulkner DM, Fortin MC, Fowler P, Frericks M, Gerets HHJ, Jahnke GD, Jones DR, Kruhlak NL, Lo Piparo E, Lopez-Belmonte J, Luniwal A, Luu A, Madia F, Manganelli S, Manickam B, Mestres J, Mihalchik-Burhans AL, Neilson L, Pandiri A, Pavan M, Rider CV, Rooney JP, Trejo-Martin A, Watanabe-Sailor KH, White AT, Woolley D, Myatt GJ. In Silico Approaches In Carcinogenicity Hazard Assessment: Current Status and Future Needs. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 20. [PMID: 35368437 DOI: 10.1016/j.comtox.2021.100191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Historically, identifying carcinogens has relied primarily on tumor studies in rodents, which require enormous resources in both money and time. In silico models have been developed for predicting rodent carcinogens but have not yet found general regulatory acceptance, in part due to the lack of a generally accepted protocol for performing such an assessment as well as limitations in predictive performance and scope. There remains a need for additional, improved in silico carcinogenicity models, especially ones that are more human-relevant, for use in research and regulatory decision-making. As part of an international effort to develop in silico toxicological protocols, a consortium of toxicologists, computational scientists, and regulatory scientists across several industries and governmental agencies evaluated the extent to which in silico models exist for each of the recently defined 10 key characteristics (KCs) of carcinogens. This position paper summarizes the current status of in silico tools for the assessment of each KC and identifies the data gaps that need to be addressed before a comprehensive in silico carcinogenicity protocol can be developed for regulatory use.
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Affiliation(s)
- Raymond R Tice
- RTice Consulting, Hillsborough, North Carolina, 27278, USA
| | | | - Alexander Amberg
- Sanofi Preclinical Safety, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Lennart T Anger
- Genentech, Inc., South San Francisco, California, 94080, USA
| | - Marc A Beal
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | | | | | - Jeffrey Birmingham
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
| | - Alessandro Brigo
- Roche Pharmaceutical Research & Early Development, Pharmaceutical Sciences, Roche Innovation, Center Basel, F. Hoffmann-La Roche Ltd, CH-4070, Basel, Switzerland
| | | | - Lidia Ceriani
- Humane Society International, 1000 Brussels, Belgium
| | - Ian Crooks
- British American Tobacco (Investments) Ltd, GR&D Centre, Southampton, SO15 8TL, United Kingdom
| | | | - Rosalie Elespuru
- Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, Maryland, 20993, USA
| | - David M Faulkner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marie C Fortin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey, 08855, USA
| | - Paul Fowler
- FSTox Consulting (Genetic Toxicology), Northamptonshire, United Kingdom
| | | | | | - Gloria D Jahnke
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Naomi L Kruhlak
- Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, Maryland, 20993, USA
| | - Elena Lo Piparo
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Juan Lopez-Belmonte
- Cuts Ice Ltd Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Amarjit Luniwal
- North American Science Associates (NAMSA) Inc., Minneapolis, Minnesota, 55426, USA
| | - Alice Luu
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | - Federica Madia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Serena Manganelli
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | | | - Jordi Mestres
- IMIM Institut Hospital Del Mar d'Investigacions Mèdiques and Universitat Pompeu Fabra, Doctor Aiguader 88, Parc de Recerca Biomèdica, 08003 Barcelona, Spain; and Chemotargets SL, Baldiri Reixac 4, Parc Científic de Barcelona, 08028, Barcelona, Spain
| | | | - Louise Neilson
- Broughton Nicotine Services, Oak Tree House, Earby, Lancashire, BB18 6JZ United Kingdom
| | - Arun Pandiri
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Cynthia V Rider
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | - John P Rooney
- Integrated Laboratory Systems, LLC., Morrisville, North Carolina, 27560, USA
| | | | - Karen H Watanabe-Sailor
- School of Mathematical and Natural Sciences, Arizona State University, West Campus, Glendale, Arizona, 85306, USA
| | - Angela T White
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
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5
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Shang FF, Wang MY, Ai JP, Shen QK, Guo HY, Jin CM, Chen FE, Quan ZS, Jin L, Zhang C. Synthesis and evaluation of mycophenolic acid derivatives as potential anti-Toxoplasma gondii agents. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02803-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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6
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Finding new edges: systems approaches to MTOR signaling. Biochem Soc Trans 2021; 49:41-54. [PMID: 33544134 PMCID: PMC7924996 DOI: 10.1042/bst20190730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/23/2020] [Accepted: 01/05/2021] [Indexed: 11/17/2022]
Abstract
Cells have evolved highly intertwined kinase networks to finely tune cellular homeostasis to the environment. The network converging on the mechanistic target of rapamycin (MTOR) kinase constitutes a central hub that integrates metabolic signals and adapts cellular metabolism and functions to nutritional changes and stress. Feedforward and feedback loops, crosstalks and a plethora of modulators finely balance MTOR-driven anabolic and catabolic processes. This complexity renders it difficult — if not impossible — to intuitively decipher signaling dynamics and network topology. Over the last two decades, systems approaches have emerged as powerful tools to simulate signaling network dynamics and responses. In this review, we discuss the contribution of systems studies to the discovery of novel edges and modulators in the MTOR network in healthy cells and in disease.
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7
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Abstract
This book chapter is drafted for biologists with experimental experiences in ROS biology but being newcomers in the field of modeling. We start with a general introduction about computational modeling in biology and an overview of software tools suitable for beginners. This chapter encompasses an introduction to computational models with special focus on simulation of ROS dynamics. A step-by-step tutorial follows providing guidance for all relevant model development processes. This course of action gives a comprehensible way to understand the benefits of computational models and to gain the necessary knowledge to build own small equation-based models. Small models can be created without any special programming expertise or in-depth technical and mathematical knowledge. Afterward in the final section, a short overview of pitfalls, challenges, and limitations is provided, combined with suggestions for further reading to improve and expand modeling skills of biologists.
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Affiliation(s)
- Jana Schleicher
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, University Hospital Jena, Jena, Germany.
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8
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Bhowmick R, Sarkar RR. Differential suitability of reactive oxygen species and the role of glutathione in regulating paradoxical behavior in gliomas: A mathematical perspective. PLoS One 2020; 15:e0235204. [PMID: 32584884 PMCID: PMC7316271 DOI: 10.1371/journal.pone.0235204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 06/10/2020] [Indexed: 12/18/2022] Open
Abstract
Manipulative strategies of ROS in cancer are often exhibited as changes in the redox and thiol ratio of the cells. Cellular responses to oxidative insults are generated in response to these changes which are triggered due to the rerouting of the metabolic framework to maintain survival under stress. However, mechanisms of these metabolic re-routing are not clearly understood and remained debatable. In the present work, we have designed a context-based dynamic metabolic model to establish that the coordinated functioning of glutathione peroxidase (GTHP), glutathione oxidoreductase (GTHO) and NADPH oxidase (NOX) is crucial in determining cancerous transformation, specifically in gliomas. Further, we propose that the puzzling duality of ROS (represented by changes in h2o2 in the present model) in exhibiting varying cellular fates can be determined by considering simultaneous changes in nadph/nadp+ and gsh/gssg that occur during the reprogramming of metabolic reactions. This will be helpful in determining the pro-apoptotic or anti-apoptotic fate of gliomas and can be useful in designing effective pro-oxidant and/or anti-oxidant therapeutic approaches against gliomas.
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Affiliation(s)
- Rupa Bhowmick
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Ram Rup Sarkar
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
- * E-mail:
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9
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Xu L, Yu Y, Sang R, Ge B, Wang M, Zhou H, Zhang X. Inonotus obliquus polysaccharide protects against adverse pregnancy caused by Toxoplasma gondii infection through regulating Th17/Treg balance via TLR4/NF-κB pathway. Int J Biol Macromol 2020; 146:832-840. [DOI: 10.1016/j.ijbiomac.2019.10.051] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/25/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
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10
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Villaverde AF, Fröhlich F, Weindl D, Hasenauer J, Banga JR. Benchmarking optimization methods for parameter estimation in large kinetic models. Bioinformatics 2019; 35:830-838. [PMID: 30816929 PMCID: PMC6394396 DOI: 10.1093/bioinformatics/bty736] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/04/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022] Open
Abstract
Motivation Kinetic models contain unknown parameters that are estimated by optimizing the fit to experimental data. This task can be computationally challenging due to the presence of local optima and ill-conditioning. While a variety of optimization methods have been suggested to surmount these issues, it is difficult to choose the best one for a given problem a priori. A systematic comparison of parameter estimation methods for problems with tens to hundreds of optimization variables is currently missing, and smaller studies provided contradictory findings. Results We use a collection of benchmarks to evaluate the performance of two families of optimization methods: (i) multi-starts of deterministic local searches and (ii) stochastic global optimization metaheuristics; the latter may be combined with deterministic local searches, leading to hybrid methods. A fair comparison is ensured through a collaborative evaluation and a consideration of multiple performance metrics. We discuss possible evaluation criteria to assess the trade-off between computational efficiency and robustness. Our results show that, thanks to recent advances in the calculation of parametric sensitivities, a multi-start of gradient-based local methods is often a successful strategy, but a better performance can be obtained with a hybrid metaheuristic. The best performer combines a global scatter search metaheuristic with an interior point local method, provided with gradients estimated with adjoint-based sensitivities. We provide an implementation of this method to render it available to the scientific community. Availability and implementation The code to reproduce the results is provided as Supplementary Material and is available at Zenodo https://doi.org/10.5281/zenodo.1304034. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Fabian Fröhlich
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Mathematical Modeling of Biological Systems, Center for Mathematics, Technische Universität München, Garching, Germany
| | - Daniel Weindl
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Mathematical Modeling of Biological Systems, Center for Mathematics, Technische Universität München, Garching, Germany
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11
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Guimera AM, Shanley DP, Proctor CJ. Modelling the role of redox-related mechanisms in musculoskeletal ageing. Free Radic Biol Med 2019; 132:11-18. [PMID: 30219703 DOI: 10.1016/j.freeradbiomed.2018.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023]
Abstract
The decline in the musculoskeletal system with age is driven at the cellular level by random molecular damage. Cells possess mechanisms to repair or remove damage and many of the pathways involved in this response are regulated by redox signals. However, with ageing there is an increase in oxidative stress which can lead to chronic inflammation and disruption of redox signalling pathways. The complexity of the processes involved has led to the use of computational modelling to help increase our understanding of the system, test hypotheses and make testable predictions. This paper will give a brief background of the biological systems that have been modelled, an introduction to computational modelling, a review of models that involve redox-related mechanisms that are applicable to musculoskeletal ageing, and finally a discussion of the future potential for modelling in this field.
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Affiliation(s)
- Alvaro Martinez Guimera
- Institute for Cell and Molecular Biosciences, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
| | - Daryl P Shanley
- Institute for Cell and Molecular Biosciences, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
| | - Carole J Proctor
- Institute of Cellular Medicine, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK.
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12
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Xu L, Sang R, Yu Y, Li J, Ge B, Zhang X. The polysaccharide from Inonotus obliquus protects mice from Toxoplasma gondii-induced liver injury. Int J Biol Macromol 2018; 125:1-8. [PMID: 30445083 DOI: 10.1016/j.ijbiomac.2018.11.114] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 10/23/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
Abstract
The study aimed to explore the protective effects and mechanism of Inonotus obliquus polysaccharide (IOP) on liver injury caused by Toxoplasma gondii (T. gondii) infection in mice. The results showed that treatment with IOP significantly decreased the liver coefficient, the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), malondialdehyde (MDA) and nitric oxide (NO), and increased the contents of antioxidant enzyme superoxide dismutase (SOD) and glutathione (GSH). IOP effectively decreased the expression of serum tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), interferon-γ (IFN-γ) and interluekin-4 (IL-4) in T. gondii-infected mice. In agreement with these observations, IOP also alleviated hepatic pathological damages caused by T. gondii. Furthermore, we found that IOP down-regulated the levels of toll-like receptor 2 (TLR2) and toll-like receptor 4 (TLR4), phosphorylations of nuclear factor-κappaB (NF-κB) p65 and inhibitor kappaBα (IκBα), whereas up-regulated the expressions of nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1). These findings suggest that IOP possesses hepatoprotective effects against T. gondii-induced liver injury in mice, and such protection is at least in part due to its anti-inflammatory effects through inhibiting the TLRs/NF-κB signaling axis and the activation of an antioxidant response by inducing the Nrf2/HO-1 signaling.
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Affiliation(s)
- Lu Xu
- Department of Animal Medicine, Agricultural College, Yanbian University, Gongyuan Street, Yanji, Jilin 133002, PR China
| | - Rui Sang
- Department of Animal Medicine, Agricultural College, Yanbian University, Gongyuan Street, Yanji, Jilin 133002, PR China
| | - Yifan Yu
- Department of Animal Medicine, Agricultural College, Yanbian University, Gongyuan Street, Yanji, Jilin 133002, PR China
| | - Jinxia Li
- Department of Animal Medicine, Agricultural College, Yanbian University, Gongyuan Street, Yanji, Jilin 133002, PR China
| | - Bingjie Ge
- Department of Animal Medicine, Agricultural College, Yanbian University, Gongyuan Street, Yanji, Jilin 133002, PR China
| | - Xuemei Zhang
- Department of Animal Medicine, Agricultural College, Yanbian University, Gongyuan Street, Yanji, Jilin 133002, PR China.
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13
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Golubev A, Hanson AD, Gladyshev VN. A Tale of Two Concepts: Harmonizing the Free Radical and Antagonistic Pleiotropy Theories of Aging. Antioxid Redox Signal 2018; 29:1003-1017. [PMID: 28874059 PMCID: PMC6104246 DOI: 10.1089/ars.2017.7105] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/09/2017] [Accepted: 08/31/2017] [Indexed: 12/18/2022]
Abstract
SIGNIFICANCE The two foremost concepts of aging are the mechanistic free radical theory (FRT) of how we age and the evolutionary antagonistic pleiotropy theory (APT) of why we age. Both date from the late 1950s. The FRT holds that reactive oxygen species (ROS) are the principal contributors to the lifelong cumulative damage suffered by cells, whereas the APT is generally understood as positing that genes that are good for young organisms can take over a population even if they are bad for the old organisms. Recent Advances: Here, we provide a common ground for the two theories by showing how aging can result from the inherent chemical reactivity of many biomolecules, not just ROS, which imposes a fundamental constraint on biological evolution. Chemically reactive metabolites spontaneously modify slowly renewable macromolecules in a continuous way over time; the resulting buildup of damage wrought by the genes coding for enzymes that generate such small molecules eventually masquerades as late-acting pleiotropic effects. In aerobic organisms, ROS are major agents of this damage but they are far from alone. CRITICAL ISSUES Being related to two sides of the same phenomenon, these theories should be compatible. However, the interface between them is obscured by the FRT mistaking a subset of damaging processes for the whole, and the APT mistaking a cumulative quantitative process for a qualitative switch. FUTURE DIRECTIONS The manifestations of ROS-mediated cumulative chemical damage at the population level may include the often-observed negative correlation between fitness and the rate of its decline with increasing age, further linking FRT and APT. Antioxid. Redox Signal. 29, 1003-1017.
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Affiliation(s)
- Alexey Golubev
- Department of Carcinogenesis and Oncogerontology, Petrov Research Institute of Oncology, Saint Petersburg, Russia
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow Russia
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Christ B, Dahmen U, Herrmann KH, König M, Reichenbach JR, Ricken T, Schleicher J, Ole Schwen L, Vlaic S, Waschinsky N. Computational Modeling in Liver Surgery. Front Physiol 2017; 8:906. [PMID: 29249974 PMCID: PMC5715340 DOI: 10.3389/fphys.2017.00906] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/25/2017] [Indexed: 12/13/2022] Open
Abstract
The need for extended liver resection is increasing due to the growing incidence of liver tumors in aging societies. Individualized surgical planning is the key for identifying the optimal resection strategy and to minimize the risk of postoperative liver failure and tumor recurrence. Current computational tools provide virtual planning of liver resection by taking into account the spatial relationship between the tumor and the hepatic vascular trees, as well as the size of the future liver remnant. However, size and function of the liver are not necessarily equivalent. Hence, determining the future liver volume might misestimate the future liver function, especially in cases of hepatic comorbidities such as hepatic steatosis. A systems medicine approach could be applied, including biological, medical, and surgical aspects, by integrating all available anatomical and functional information of the individual patient. Such an approach holds promise for better prediction of postoperative liver function and hence improved risk assessment. This review provides an overview of mathematical models related to the liver and its function and explores their potential relevance for computational liver surgery. We first summarize key facts of hepatic anatomy, physiology, and pathology relevant for hepatic surgery, followed by a description of the computational tools currently used in liver surgical planning. Then we present selected state-of-the-art computational liver models potentially useful to support liver surgery. Finally, we discuss the main challenges that will need to be addressed when developing advanced computational planning tools in the context of liver surgery.
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Affiliation(s)
- Bruno Christ
- Molecular Hepatology Lab, Clinics of Visceral, Transplantation, Thoracic and Vascular Surgery, University Hospital Leipzig, University of Leipzig, Leipzig, Germany
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, University Hospital Jena, Jena, Germany
| | - Karl-Heinz Herrmann
- Medical Physics Group, Institute for Diagnostic and Interventional Radiology, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Matthias König
- Department of Biology, Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
| | - Jürgen R Reichenbach
- Medical Physics Group, Institute for Diagnostic and Interventional Radiology, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Tim Ricken
- Mechanics, Structural Analysis, and Dynamics, TU Dortmund University, Dortmund, Germany
| | - Jana Schleicher
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, University Hospital Jena, Jena, Germany.,Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany
| | | | - Sebastian Vlaic
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Navina Waschinsky
- Mechanics, Structural Analysis, and Dynamics, TU Dortmund University, Dortmund, Germany
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Systems modelling ageing: from single senescent cells to simple multi-cellular models. Essays Biochem 2017; 61:369-377. [PMID: 28698310 PMCID: PMC5869859 DOI: 10.1042/ebc20160087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/25/2017] [Accepted: 05/25/2017] [Indexed: 01/10/2023]
Abstract
Systems modelling has been successfully used to investigate several key molecular mechanisms of ageing. Modelling frameworks to allow integration of models and methods to enhance confidence in models are now well established. In this article, we discuss these issues and work through the process of building an integrated model for cellular senescence as a single cell and in a simple tissue context.
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Mc Auley MT, Guimera AM, Hodgson D, Mcdonald N, Mooney KM, Morgan AE, Proctor CJ. Modelling the molecular mechanisms of aging. Biosci Rep 2017; 37:BSR20160177. [PMID: 28096317 PMCID: PMC5322748 DOI: 10.1042/bsr20160177] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/15/2016] [Accepted: 01/16/2017] [Indexed: 01/09/2023] Open
Abstract
The aging process is driven at the cellular level by random molecular damage that slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the aging process. The complexity of the aging process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards and discusses many specific examples of models that have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field.
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Affiliation(s)
- Mark T Mc Auley
- Faculty of Science and Engineering, University of Chester, Chester, U.K
| | - Alvaro Martinez Guimera
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, U.K
| | - David Hodgson
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
| | - Neil Mcdonald
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, U.K
| | | | - Amy E Morgan
- Faculty of Science and Engineering, University of Chester, Chester, U.K
| | - Carole J Proctor
- MRC/Arthritis Research UK Centre for Musculoskeletal Ageing (CIMA), Newcastle University, Newcastle upon Tyne, Ormskirk, U.K.
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, U.K
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Fröhlich F, Kaltenbacher B, Theis FJ, Hasenauer J. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLoS Comput Biol 2017; 13:e1005331. [PMID: 28114351 PMCID: PMC5256869 DOI: 10.1371/journal.pcbi.1005331] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 12/20/2016] [Indexed: 01/06/2023] Open
Abstract
Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large- and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics. In this manuscript, we introduce a scalable method for parameter estimation for genome-scale biochemical reaction networks. Mechanistic models for genome-scale biochemical reaction networks describe the behavior of thousands of chemical species using thousands of parameters. Standard methods for parameter estimation are usually computationally intractable at these scales. Adjoint sensitivity based approaches have been suggested to have superior scalability but any rigorous evaluation is lacking. We implement a toolbox for adjoint sensitivity analysis for biochemical reaction network which also supports the import of SBML models. We show by means of a set of benchmark models that adjoint sensitivity based approaches unequivocally outperform standard approaches for large-scale models and that the achieved speedup increases with respect to both the number of parameters and the number of chemical species in the model. This demonstrates the applicability of adjoint sensitivity based approaches to parameter estimation for genome-scale mechanistic model. The MATLAB toolbox implementing the developed methods is available from http://ICB-DCM.github.io/AMICI/.
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Affiliation(s)
- Fabian Fröhlich
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching, Germany
| | | | - Fabian J. Theis
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching, Germany
| | - Jan Hasenauer
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching, Germany
- * E-mail:
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18
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Pereira EJ, Smolko CM, Janes KA. Computational Models of Reactive Oxygen Species as Metabolic Byproducts and Signal-Transduction Modulators. Front Pharmacol 2016; 7:457. [PMID: 27965578 PMCID: PMC5126069 DOI: 10.3389/fphar.2016.00457] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/14/2016] [Indexed: 12/30/2022] Open
Abstract
Reactive oxygen species (ROS) are widely involved in intracellular signaling and human pathologies, but their precise roles have been difficult to enumerate and integrate holistically. The context- and dose-dependent intracellular effects of ROS can lead to contradictory experimental results and confounded interpretations. For example, lower levels of ROS promote cell signaling and proliferation, whereas abundant ROS cause overwhelming damage to biomolecules and cellular apoptosis or senescence. These complexities raise the question of whether the many facets of ROS biology can be joined under a common mechanistic framework using computational modeling. Here, we take inventory of some current models for ROS production or ROS regulation of signaling pathways. Several models captured non-intuitive observations or made predictions that were later verified by experiment. There remains a need for systems-level analyses that jointly incorporate ROS production, handling, and modulation of multiple signal-transduction cascades.
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Affiliation(s)
- Elizabeth J Pereira
- Department of Biomedical Engineering, University of Virginia, Charlottesville VA, USA
| | - Christian M Smolko
- Department of Biomedical Engineering, University of Virginia, Charlottesville VA, USA
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville VA, USA
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Yu B, Tan L, Zheng R, Tan H, Zheng L. Targeted delivery and controlled release of Paclitaxel for the treatment of lung cancer using single-walled carbon nanotubes. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 68:579-584. [DOI: 10.1016/j.msec.2016.06.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/19/2016] [Accepted: 06/07/2016] [Indexed: 10/21/2022]
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20
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Zheng L, Wu S, Tan L, Tan H, Yu B. Chitosan-functionalised single-walled carbon nanotube-mediated drug delivery of SNX-2112 in cancer cells. J Biomater Appl 2016; 31:379-86. [PMID: 27231263 DOI: 10.1177/0885328216651183] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Delivery of amphiphobic drugs (insoluble in both water and oil) has been a great challenge in drug delivery. SNX-2112, a novel inhibitor of Hsp90, is a promising drug candidate for treating various types of cancers; however, the insolubility greatly limits its clinical application. This study aimed to build a new type of drug delivery system using single-walled carbon nanotubes (SWNTs) for controllable release of SNX-2112; chitosan (CHI) was non-covalently added to SWNTs to improve their biocompatibility. SWNTs-CHI demonstrated high drug-loading capability; the release of SNX-2112 was pH triggered and time related. The intracellular reactive oxygen species of SWNTs–CHI increased, compared with that of SWNTs, leading to higher mitogen-activated protein kinase and cell apoptosis. The results of western-blotting, lactate dehydrogenase (LDH) release assay, and cell viability assay analyses indicated that apoptosis-related proteins were abundantly expressed in K562 cells and that the drug delivery system significantly inhibited K562 cells. Thus, SWNT–CHI/SNX-2112 shows great potential as a drug delivery system for cancer therapy.
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Affiliation(s)
- Lixia Zheng
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shao Wu
- Department of Pharmacy, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huo Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Baodan Yu
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Mooney KM, Morgan AE, Mc Auley MT. Aging and computational systems biology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:123-39. [PMID: 26825379 DOI: 10.1002/wsbm.1328] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/15/2015] [Accepted: 12/29/2015] [Indexed: 12/11/2022]
Abstract
Aging research is undergoing a paradigm shift, which has led to new and innovative methods of exploring this complex phenomenon. The systems biology approach endeavors to understand biological systems in a holistic manner, by taking account of intrinsic interactions, while also attempting to account for the impact of external inputs, such as diet. A key technique employed in systems biology is computational modeling, which involves mathematically describing and simulating the dynamics of biological systems. Although a large number of computational models have been developed in recent years, these models have focused on various discrete components of the aging process, and to date no model has succeeded in completely representing the full scope of aging. Combining existing models or developing new models may help to address this need and in so doing could help achieve an improved understanding of the intrinsic mechanisms which underpin aging.
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Affiliation(s)
- Kathleen M Mooney
- Faculty of Health and Social care, Edge Hill University, Lancashire, UK
| | - Amy E Morgan
- Faculty of Science and Engineering, University of Chester, Chester, UK
| | - Mark T Mc Auley
- Faculty of Science and Engineering, University of Chester, Chester, UK
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Quasi-Steady-State Analysis based on Structural Modules and Timed Petri Net Predict System's Dynamics: The Life Cycle of the Insulin Receptor. Metabolites 2015; 5:766-93. [PMID: 26694479 PMCID: PMC4693194 DOI: 10.3390/metabo5040766] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/23/2015] [Accepted: 12/09/2015] [Indexed: 02/01/2023] Open
Abstract
The insulin-dependent activation and recycling of the insulin receptor play an essential role in the regulation of the energy metabolism, leading to a special interest for pharmaceutical applications. Thus, the recycling of the insulin receptor has been intensively investigated, experimentally as well as theoretically. We developed a time-resolved, discrete model to describe stochastic dynamics and study the approximation of non-linear dynamics in the context of timed Petri nets. Additionally, using a graph-theoretical approach, we analyzed the structure of the regulatory system and demonstrated the close interrelation of structural network properties with the kinetic behavior. The transition invariants decomposed the model into overlapping subnetworks of various sizes, which represent basic functional modules. Moreover, we computed the quasi-steady states of these subnetworks and demonstrated that they are fundamental to understand the dynamic behavior of the system. The Petri net approach confirms the experimental results of insulin-stimulated degradation of the insulin receptor, which represents a common feature of insulin-resistant, hyperinsulinaemic states.
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Gray CW, Coster ACF. A receptor state space model of the insulin signalling system in glucose transport. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2015; 32:457-73. [PMID: 25673317 DOI: 10.1093/imammb/dqv003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/10/2015] [Indexed: 11/13/2022]
Abstract
Insulin is a potent peptide hormone that regulates glucose levels in the blood. Insulin-sensitive cells respond to insulin stimulation with the translocation of glucose transporter 4 (GLUT4) to the plasma membrane (PM), enabling the clearance of glucose from the blood. Defects in this process can give rise to insulin resistance and ultimately diabetes. One widely cited model of insulin signalling leading to glucose transport is that of Sedaghat et al. (2002) Am. J. Physiol. Endocrinol. Metab. 283, E1084-E1101. Consisting of 20 deterministic ordinary differential equations (ODEs), it is the most comprehensive model of insulin signalling to date. However, the model possesses some major limitations, including the non-conservation of key components. In the current work, we detail mathematical and sensitivity analyses of the Sedaghat model. Based on the results of these analyses, we propose a reduced state space model of the insulin receptor subsystem. This reduced model maintains the input-output relation of the original model but is computationally more efficient, analytically tractable and resolves some of the limitations of the Sedaghat model.
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Affiliation(s)
- Catheryn W Gray
- School of Mathematics and Statistics, UNSW Australia, Sydney, New South Wales, Australia
| | - Adelle C F Coster
- School of Mathematics and Statistics, UNSW Australia, Sydney, New South Wales, Australia
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Quantitative Analysis of Robustness of Dynamic Response and Signal Transfer in Insulin mediated PI3K/AKT Pathway. Comput Chem Eng 2014; 71:715-727. [PMID: 25506104 DOI: 10.1016/j.compchemeng.2014.07.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Robustness is a critical feature of signaling pathways ensuring signal propagation with high fidelity in the event of perturbations. Here we present a detailed quantitative analysis of robustness in insulin mediated PI3K/AKT pathway, a critical signaling pathway maintaining self-renewal in human embryonic stem cells. Using global sensitivity analysis, we identified robustness promoting mechanisms that ensure (1) maintenance of a first order or overshoot dynamics of self-renewal molecule, p-AKT and (2) robust transfer of signals from oscillatory insulin stimulus to p-AKT in the presence of noise. Our results indicate that negative feedback controls the robustness to most perturbations. Faithful transfer of signal from the stimulating ligand to p-AKT occurs even in the presence of noise, albeit with signal attenuation and high frequency cut-off. Negative feedback contributes to signal attenuation, while positive regulators upstream of PIP3 contribute to signal amplification. These results establish precise mechanisms to modulate self-renewal molecules like p-AKT.
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