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McColl TJ, Clarke DC. Kinetic modeling of leucine-mediated signaling and protein metabolism in human skeletal muscle. iScience 2024; 27:108634. [PMID: 38188514 PMCID: PMC10767222 DOI: 10.1016/j.isci.2023.108634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/09/2024] Open
Abstract
Skeletal muscle protein levels are governed by the relative rates of muscle protein synthesis (MPS) and breakdown (MPB). The mechanisms controlling these rates are complex, and their integrated behaviors are challenging to study through experiments alone. The purpose of this study was to develop and analyze a kinetic model of leucine-mediated mTOR signaling and protein metabolism in the skeletal muscle of young adults. Our model amalgamates published cellular-level models of the IRS1-PI3K-Akt-mTORC1 signaling system and of skeletal-muscle leucine kinetics with physiological-level models of leucine digestion and transport and insulin dynamics. The model satisfactorily predicts experimental data from diverse leucine feeding protocols. Model analysis revealed that total levels of p70S6K are a primary determinant of MPS, insulin signaling substantially affects muscle net protein balance via its effects on MPB, and p70S6K-mediated feedback of mTORC1 signaling reduces MPS in a dose-dependent manner.
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Affiliation(s)
- Taylor J. McColl
- Department of Biomedical Physiology and KinesiologySimon Fraser University, Burnaby, BC V5A 1S6, Canada
- Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - David C. Clarke
- Department of Biomedical Physiology and KinesiologySimon Fraser University, Burnaby, BC V5A 1S6, Canada
- Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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2
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Jalihal AP, Kraikivski P, Murali TM, Tyson JJ. Modeling and analysis of the macronutrient signaling network in budding yeast. Mol Biol Cell 2021; 32:ar20. [PMID: 34495680 PMCID: PMC8693975 DOI: 10.1091/mbc.e20-02-0117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Adaptive modulation of the global cellular growth state of unicellular organisms is crucial for their survival in fluctuating nutrient environments. Because these organisms must be able to respond reliably to ever varying and unpredictable nutritional conditions, their nutrient signaling networks must have a certain inbuilt robustness. In eukaryotes, such as the budding yeast Saccharomyces cerevisiae, distinct nutrient signals are relayed by specific plasma membrane receptors to signal transduction pathways that are interconnected in complex information-processing networks, which have been well characterized. However, the complexity of the signaling network confounds the interpretation of the overall regulatory "logic" of the control system. Here, we propose a literature-curated molecular mechanism of the integrated nutrient signaling network in budding yeast, focusing on early temporal responses to carbon and nitrogen signaling. We build a computational model of this network to reconcile literature-curated quantitative experimental data with our proposed molecular mechanism. We evaluate the robustness of our estimates of the model's kinetic parameter values. We test the model by comparing predictions made in mutant strains with qualitative experimental observations made in the same strains. Finally, we use the model to predict nutrient-responsive transcription factor activities in a number of mutant strains undergoing complex nutrient shifts.
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Affiliation(s)
- Amogh P Jalihal
- Genetics, Bioinformatics, and Computational Biology PhD Program
| | - Pavel Kraikivski
- Division of Systems Biology, Academy of Integrated Science, Virginia Tech, Blacksburg, VA 24061
| | - T M Murali
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061
| | - John J Tyson
- Division of Systems Biology, Academy of Integrated Science, Virginia Tech, Blacksburg, VA 24061.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061
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3
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Somvanshi PR, Mellon SH, Flory JD, Abu-Amara D, Wolkowitz OM, Yehuda R, Jett M, Hood L, Marmar C, Doyle FJ. Mechanistic inferences on metabolic dysfunction in posttraumatic stress disorder from an integrated model and multiomic analysis: role of glucocorticoid receptor sensitivity. Am J Physiol Endocrinol Metab 2019; 317:E879-E898. [PMID: 31322414 PMCID: PMC6879860 DOI: 10.1152/ajpendo.00065.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/28/2019] [Accepted: 07/17/2019] [Indexed: 02/08/2023]
Abstract
Posttraumatic stress disorder (PTSD) is associated with neuroendocrine alterations and metabolic abnormalities; however, how metabolism is affected by neuroendocrine disturbances is unclear. The data from combat-exposed veterans with PTSD show increased glycolysis to lactate flux, reduced TCA cycle flux, impaired amino acid and lipid metabolism, insulin resistance, inflammation, and hypersensitive hypothalamic-pituitary-adrenal (HPA) axis. To analyze whether the co-occurrence of multiple metabolic abnormalities is independent or arises from an underlying regulatory defect, we employed a systems biological approach using an integrated mathematical model and multiomic analysis. The models for hepatic metabolism, HPA axis, inflammation, and regulatory signaling were integrated to perform metabolic control analysis (MCA) with respect to the observations from our clinical data. We combined the metabolomics, neuroendocrine, clinical laboratory, and cytokine data from combat-exposed veterans with and without PTSD to characterize the differences in regulatory effects. MCA revealed mechanistic association of the HPA axis and inflammation with metabolic dysfunction consistent with PTSD. This was supported by the data using correlational and causal analysis that revealed significant associations between cortisol suppression, high-sensitivity C-reactive protein, homeostatic model assessment of insulin resistance, γ-glutamyltransferase, hypoxanthine, and several metabolites. Causal mediation analysis indicates that the effects of enhanced glucocorticoid receptor sensitivity (GRS) on glycolytic pathway, gluconeogenic and branched-chain amino acids, triglycerides, and hepatic function are jointly mediated by inflammation, insulin resistance, oxidative stress, and energy deficit. Our analysis suggests that the interventions to normalize GRS and inflammation may help to manage features of metabolic dysfunction in PTSD.
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Affiliation(s)
- Pramod R Somvanshi
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts
| | - Synthia H Mellon
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, California
| | - Janine D Flory
- Department of Psychiatry, James J. Peters Veterans Affairs Medical Center, Bronx, New York
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Duna Abu-Amara
- Department of Psychiatry, New York Langone Medical School, New York, New York
| | - Owen M Wolkowitz
- Department of Psychiatry, University of California, San Francisco, California
| | - Rachel Yehuda
- Department of Psychiatry, James J. Peters Veterans Affairs Medical Center, Bronx, New York
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marti Jett
- Integrative Systems Biology, US Army Medical Research and Materiel Command, US Army Center for Environmental Health Research, Fort Detrick, Frederick, Maryland
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington
| | - Charles Marmar
- Department of Psychiatry, New York Langone Medical School, New York, New York
| | - Francis J Doyle
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts
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4
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Dorvash M, Farahmandnia M, Mosaddeghi P, Farahmandnejad M, Saber H, Khorraminejad-Shirazi M, Azadi A, Tavassoly I. Dynamic modeling of signal transduction by mTOR complexes in cancer. J Theor Biol 2019; 483:109992. [PMID: 31493485 DOI: 10.1016/j.jtbi.2019.109992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/05/2019] [Accepted: 09/02/2019] [Indexed: 02/07/2023]
Abstract
Signal integration has a crucial role in the cell fate decision and dysregulation of the cellular signaling pathways is a primary characteristic of cancer. As a signal integrator, mTOR shows a complex dynamical behavior which determines the cell fate at different cellular processes levels, including cell cycle progression, cell survival, cell death, metabolic reprogramming, and aging. The dynamics of the complex responses to rapamycin in cancer cells have been attributed to its differential time-dependent inhibitory effects on mTORC1 and mTORC2, the two main complexes of mTOR. Two explanations were previously provided for this phenomenon: 1-Rapamycin does not inhibit mTORC2 directly, whereas it prevents mTORC2 formation by sequestering free mTOR protein (Le Chatelier's principle). 2-Components like Phosphatidic Acid (PA) further stabilize mTORC2 compared with mTORC1. To understand the mechanism by which rapamycin differentially inhibits the mTOR complexes in the cancer cells, we present a mathematical model of rapamycin mode of action based on the first explanation, i.e., Le Chatelier's principle. Translating the interactions among components of mTORC1 and mTORC2 into a mathematical model revealed the dynamics of rapamycin action in different doses and time-intervals of rapamycin treatment. This model shows that rapamycin has stronger effects on mTORC1 compared with mTORC2, simply due to its direct interaction with free mTOR and mTORC1, but not mTORC2, without the need to consider other components that might further stabilize mTORC2. Based on our results, even when mTORC2 is less stable compared with mTORC1, it can be less inhibited by rapamycin.
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Affiliation(s)
- Mohammadreza Dorvash
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Cell and Molecular Medicine Student Research Group, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Farahmandnia
- Cell and Molecular Medicine Student Research Group, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pouria Mosaddeghi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Cell and Molecular Medicine Student Research Group, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mitra Farahmandnejad
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Cell and Molecular Medicine Student Research Group, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hosein Saber
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammadhossein Khorraminejad-Shirazi
- Cell and Molecular Medicine Student Research Group, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Azadi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutics, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Tavassoly
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029, USA.
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Spinosa PC, Humphries BA, Lewin Mejia D, Buschhaus JM, Linderman JJ, Luker GD, Luker KE. Short-term cellular memory tunes the signaling responses of the chemokine receptor CXCR4. Sci Signal 2019; 12:eaaw4204. [PMID: 31289212 PMCID: PMC7059217 DOI: 10.1126/scisignal.aaw4204] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The chemokine receptor CXCR4 regulates fundamental processes in development, normal physiology, and diseases, including cancer. Small subpopulations of CXCR4-positive cells drive the local invasion and dissemination of malignant cells during metastasis, emphasizing the need to understand the mechanisms controlling responses at the single-cell level to receptor activation by the chemokine ligand CXCL12. Using single-cell imaging, we discovered that short-term cellular memory of changes in environmental conditions tuned CXCR4 signaling to Akt and ERK, two kinases activated by this receptor. Conditioning cells with growth stimuli before CXCL12 exposure increased the number of cells that initiated CXCR4 signaling and the amplitude of Akt and ERK activation. Data-driven, single-cell computational modeling revealed that growth factor conditioning modulated CXCR4-dependent activation of Akt and ERK by decreasing extrinsic noise (preexisting cell-to-cell differences in kinase activity) in PI3K and mTORC1. Modeling established mTORC1 as critical for tuning single-cell responses to CXCL12-CXCR4 signaling. Our single-cell model predicted how combinations of extrinsic noise in PI3K, Ras, and mTORC1 superimposed on different driver mutations in the ERK and/or Akt pathways to bias CXCR4 signaling. Computational experiments correctly predicted that selected kinase inhibitors used for cancer therapy shifted subsets of cells to states that were more permissive to CXCR4 activation, suggesting that such drugs may inadvertently potentiate pro-metastatic CXCR4 signaling. Our work establishes how changing environmental inputs modulate CXCR4 signaling in single cells and provides a framework to optimize the development and use of drugs targeting this signaling pathway.
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Affiliation(s)
- Phillip C Spinosa
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brock A Humphries
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Daniela Lewin Mejia
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Johanna M Buschhaus
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jennifer J Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gary D Luker
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Department of Biomedical Engineering, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kathryn E Luker
- Department of Radiology Center for Molecular Imaging, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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6
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Charidemou E, Ashmore T, Li X, McNally BD, West JA, Liggi S, Harvey M, Orford E, Griffin JL. A randomized 3-way crossover study indicates that high-protein feeding induces de novo lipogenesis in healthy humans. JCI Insight 2019; 4:124819. [PMID: 31145699 PMCID: PMC6629161 DOI: 10.1172/jci.insight.124819] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 05/08/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Dietary changes have led to the growing prevalence of type 2 diabetes and nonalcoholic fatty liver disease. A hallmark of both disorders is hepatic lipid accumulation, derived in part from increased de novo lipogenesis. Despite the popularity of high-protein diets for weight loss, the effect of dietary protein on de novo lipogenesis is poorly studied. We aimed to characterize the effect of dietary protein on de novo lipid synthesis. METHODS We use a 3-way crossover interventional study in healthy males to determine the effect of high-protein feeding on de novo lipogenesis, combined with in vitro models to determine the lipogenic effects of specific amino acids. The primary outcome was a change in de novo lipogenesis–associated triglycerides in response to protein feeding. RESULTS We demonstrate that high-protein feeding, rich in glutamate, increases de novo lipogenesis–associated triglycerides in plasma (1.5-fold compared with control; P < 0.0001) and liver-derived very low-density lipoprotein particles (1.8-fold; P < 0.0001) in samples from human subjects (n = 9 per group). In hepatocytes, we show that glutamate-derived carbon is incorporated into triglycerides via palmitate. In addition, supplementation with glutamate, glutamine, and leucine, but not lysine, increased triglyceride synthesis and decreased glucose uptake. Glutamate, glutamine, and leucine increased activation of protein kinase B, suggesting that induction of de novo lipogenesis occurs via the insulin signaling cascade. CONCLUSION These findings provide mechanistic insight into how select amino acids induce de novo lipogenesis and insulin resistance, suggesting that high-protein feeding to tackle diabetes and obesity requires greater consideration. FUNDING The research was supported by UK Medical Research Council grants MR/P011705/1, MC_UP_A090_1006 and MR/P01836X/1. JLG is supported by the Imperial Biomedical Research Centre, National Institute for Health Research (NIHR). A subset of amino acids may induce de novo lipogenesis in humans, suggesting that use of high-protein diets to tackle diabetes requires greater consideration.
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Affiliation(s)
- Evelina Charidemou
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Tom Ashmore
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Xuefei Li
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ben D McNally
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - James A West
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Sonia Liggi
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Harvey
- Medical Research Council - Elsie Widdowson Laboratory, Cambridge, United Kingdom
| | - Elise Orford
- Medical Research Council - Elsie Widdowson Laboratory, Cambridge, United Kingdom
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.,Computational and Systems Medicine, Surgery and Cancer, Imperial College London, London, United Kingdom
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7
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Jacquier M, Kuriakose S, Bhardwaj A, Zhang Y, Shrivastav A, Portet S, Varma Shrivastav S. Investigation of Novel Regulation of N-myristoyltransferase by Mammalian Target of Rapamycin in Breast Cancer Cells. Sci Rep 2018; 8:12969. [PMID: 30154572 PMCID: PMC6113272 DOI: 10.1038/s41598-018-30447-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/16/2018] [Indexed: 01/02/2023] Open
Abstract
Breast cancer is the most common cancer in women worldwide. Hormone receptor breast cancers are the most common ones and, about 2 out of every 3 cases of breast cancer are estrogen receptor (ER) positive. Selective ER modulators, such as tamoxifen, are the first line of endocrine treatment of breast cancer. Despite the expression of hormone receptors some patients develop tamoxifen resistance and 50% present de novo tamoxifen resistance. Recently, we have demonstrated that activated mammalian target of rapamycin (mTOR) is positively associated with overall survival and recurrence free survival in ER positive breast cancer patients who were later treated with tamoxifen. Since altered expression of protein kinase B (PKB)/Akt in breast cancer cells affect N-myristoyltransferase 1 (NMT1) expression and activity, we investigated whether mTOR, a downstream target of PKB/Akt, regulates NMT1 in ER positive breast cancer cells (MCF7 cells). We inhibited mTOR by treating MCF7 cells with rapamycin and observed that the expression of NMT1 increased with rapamycin treatment over the period of time with a concomitant decrease in mTOR phosphorylation. We further employed mathematical modelling to investigate hitherto not known relationship of mTOR with NMT1. We report here for the first time a collection of models and data validating regulation of NMT1 by mTOR.
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Affiliation(s)
- Marine Jacquier
- Department of Mathematics, University of Manitoba, Winnipeg, Canada
| | - Shiby Kuriakose
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba, Canada
| | - Apurva Bhardwaj
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba, Canada
| | - Yang Zhang
- Department of Mathematics, University of Manitoba, Winnipeg, Canada
| | - Anuraag Shrivastav
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada.,Research Institute of Hematology and Oncology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Stéphanie Portet
- Department of Mathematics, University of Manitoba, Winnipeg, Canada
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8
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Varusai TM, Nguyen LK. Dynamic modelling of the mTOR signalling network reveals complex emergent behaviours conferred by DEPTOR. Sci Rep 2018; 8:643. [PMID: 29330362 PMCID: PMC5766521 DOI: 10.1038/s41598-017-18400-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/01/2017] [Indexed: 01/10/2023] Open
Abstract
The mechanistic Target of Rapamycin (mTOR) signalling network is an evolutionarily conserved network that controls key cellular processes, including cell growth and metabolism. Consisting of the major kinase complexes mTOR Complex 1 and 2 (mTORC1/2), the mTOR network harbours complex interactions and feedback loops. The DEP domain-containing mTOR-interacting protein (DEPTOR) was recently identified as an endogenous inhibitor of both mTORC1 and 2 through direct interactions, and is in turn degraded by mTORC1/2, adding an extra layer of complexity to the mTOR network. Yet, the dynamic properties of the DEPTOR-mTOR network and the roles of DEPTOR in coordinating mTORC1/2 activation dynamics have not been characterised. Using computational modelling, systems analysis and dynamic simulations we show that DEPTOR confers remarkably rich and complex dynamic behaviours to mTOR signalling, including abrupt, bistable switches, oscillations and co-existing bistable/oscillatory responses. Transitions between these distinct modes of behaviour are enabled by modulating DEPTOR expression alone. We characterise the governing conditions for the observed dynamics by elucidating the network in its vast multi-dimensional parameter space, and develop strategies to identify core network design motifs underlying these dynamics. Our findings provide new systems-level insights into the complexity of mTOR signalling contributed by DEPTOR.
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Affiliation(s)
- Thawfeek M Varusai
- European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.,Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia. .,Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, 3800, Australia. .,Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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9
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Sulaimanov N, Klose M, Busch H, Boerries M. Understanding the mTOR signaling pathway via mathematical modeling. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2017; 9:e1379. [PMID: 28186392 PMCID: PMC5573916 DOI: 10.1002/wsbm.1379] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/09/2016] [Accepted: 12/07/2016] [Indexed: 12/12/2022]
Abstract
The mechanistic target of rapamycin (mTOR) is a central regulatory pathway that integrates a variety of environmental cues to control cellular growth and homeostasis by intricate molecular feedbacks. In spite of extensive knowledge about its components, the molecular understanding of how these function together in space and time remains poor and there is a need for Systems Biology approaches to perform systematic analyses. In this work, we review the recent progress how the combined efforts of mathematical models and quantitative experiments shed new light on our understanding of the mTOR signaling pathway. In particular, we discuss the modeling concepts applied in mTOR signaling, the role of multiple feedbacks and the crosstalk mechanisms of mTOR with other signaling pathways. We also discuss the contribution of principles from information and network theory that have been successfully applied in dissecting design principles of the mTOR signaling network. We finally propose to classify the mTOR models in terms of the time scale and network complexity, and outline the importance of the classification toward the development of highly comprehensive and predictive models. WIREs Syst Biol Med 2017, 9:e1379. doi: 10.1002/wsbm.1379 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Nurgazy Sulaimanov
- Department of Electrical Engineering and Information TechnologyTechnische Universität DarmstadtDarmstadtGermany
- Department of BiologyTechnische Universitat DarmstadtDarmstadtGermany
| | - Martin Klose
- Systems Biology of the Cellular Microenvironment at the DKFZ Partner Site Freiburg ‐ Member of the German Cancer Consortium, Institute of Molecular Medicine and Cell ResearchAlbert‐Ludwigs‐University FreiburgFreiburgGermany and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment at the DKFZ Partner Site Freiburg ‐ Member of the German Cancer Consortium, Institute of Molecular Medicine and Cell ResearchAlbert‐Ludwigs‐University FreiburgFreiburgGermany and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment at the DKFZ Partner Site Freiburg ‐ Member of the German Cancer Consortium, Institute of Molecular Medicine and Cell ResearchAlbert‐Ludwigs‐University FreiburgFreiburgGermany and German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Vanhaelen Q, Aliper AM, Zhavoronkov A. A comparative review of computational methods for pathway perturbation analysis: dynamical and topological perspectives. MOLECULAR BIOSYSTEMS 2017; 13:1692-1704. [DOI: 10.1039/c7mb00170c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Stem cells offer great promise within the field of regenerative medicine but despite encouraging results, the large scale use of stem cells for therapeutic applications still faces challenges when it comes to controlling signaling pathway responses with respect to environmental perturbations.
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Affiliation(s)
- Q. Vanhaelen
- Insilico Medicine Inc
- Johns Hopkins University
- ETC
- USA
| | - A. M. Aliper
- Insilico Medicine Inc
- Johns Hopkins University
- ETC
- USA
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11
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A systems study reveals concurrent activation of AMPK and mTOR by amino acids. Nat Commun 2016; 7:13254. [PMID: 27869123 PMCID: PMC5121333 DOI: 10.1038/ncomms13254] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 09/13/2016] [Indexed: 12/17/2022] Open
Abstract
Amino acids (aa) are not only building blocks for proteins, but also signalling molecules, with the mammalian target of rapamycin complex 1 (mTORC1) acting as a key mediator. However, little is known about whether aa, independently of mTORC1, activate other kinases of the mTOR signalling network. To delineate aa-stimulated mTOR network dynamics, we here combine a computational–experimental approach with text mining-enhanced quantitative proteomics. We report that AMP-activated protein kinase (AMPK), phosphatidylinositide 3-kinase (PI3K) and mTOR complex 2 (mTORC2) are acutely activated by aa-readdition in an mTORC1-independent manner. AMPK activation by aa is mediated by Ca2+/calmodulin-dependent protein kinase kinase β (CaMKKβ). In response, AMPK impinges on the autophagy regulators Unc-51-like kinase-1 (ULK1) and c-Jun. AMPK is widely recognized as an mTORC1 antagonist that is activated by starvation. We find that aa acutely activate AMPK concurrently with mTOR. We show that AMPK under aa sufficiency acts to sustain autophagy. This may be required to maintain protein homoeostasis and deliver metabolite intermediates for biosynthetic processes. mTORC1 is known to mediate the signalling activity of amino acids. Here, the authors combine modelling with experiments and find that amino acids acutely stimulate mTORC2, IRS/PI3K and AMPK, independently of mTORC1. AMPK activation through CaMKKβ sustains autophagy under non-starvation conditions.
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12
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Di Camillo B, Carlon A, Eduati F, Toffolo GM. A rule-based model of insulin signalling pathway. BMC SYSTEMS BIOLOGY 2016; 10:38. [PMID: 27245161 PMCID: PMC4888568 DOI: 10.1186/s12918-016-0281-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 05/12/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND The insulin signalling pathway (ISP) is an important biochemical pathway, which regulates some fundamental biological functions such as glucose and lipid metabolism, protein synthesis, cell proliferation, cell differentiation and apoptosis. In the last years, different mathematical models based on ordinary differential equations have been proposed in the literature to describe specific features of the ISP, thus providing a description of the behaviour of the system and its emerging properties. However, protein-protein interactions potentially generate a multiplicity of distinct chemical species, an issue referred to as "combinatorial complexity", which results in defining a high number of state variables equal to the number of possible protein modifications. This often leads to complex, error prone and difficult to handle model definitions. RESULTS In this work, we present a comprehensive model of the ISP, which integrates three models previously available in the literature by using the rule-based modelling (RBM) approach. RBM allows for a simple description of a number of signalling pathway characteristics, such as the phosphorylation of signalling proteins at multiple sites with different effects, the simultaneous interaction of many molecules of the signalling pathways with several binding partners, and the information about subcellular localization where reactions take place. Thanks to its modularity, it also allows an easy integration of different pathways. After RBM specification, we simulated the dynamic behaviour of the ISP model and validated it using experimental data. We the examined the predicted profiles of all the active species and clustered them in four clusters according to their dynamic behaviour. Finally, we used parametric sensitivity analysis to show the role of negative feedback loops in controlling the robustness of the system. CONCLUSIONS The presented ISP model is a powerful tool for data simulation and can be used in combination with experimental approaches to guide the experimental design. The model is available at http://sysbiobig.dei.unipd.it/ was submitted to Biomodels Database ( https://www.ebi.ac.uk/biomodels-main/ # MODEL 1604100005).
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Affiliation(s)
- Barbara Di Camillo
- Department of Information Engineering, University of Padova, Via Gradenigo 6A, Padova, 35131, Italy
| | - Azzurra Carlon
- Department of Information Engineering, University of Padova, Via Gradenigo 6A, Padova, 35131, Italy.,Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Federica Eduati
- Department of Information Engineering, University of Padova, Via Gradenigo 6A, Padova, 35131, Italy.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Gianna Maria Toffolo
- Department of Information Engineering, University of Padova, Via Gradenigo 6A, Padova, 35131, Italy.
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Somvanshi PR, Patel AK, Bhartiya S, Venkatesh KV. Influence of plasma macronutrient levels on hepatic metabolism: role of regulatory networks in homeostasis and disease states. RSC Adv 2016. [DOI: 10.1039/c5ra18128c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multilevel regulations by metabolic, signaling and transcription pathways form a complex network that works to provide robust metabolic regulation in the liver. This analysis indicates that dietary perturbations in these networks can lead to insulin resistance.
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Affiliation(s)
- Pramod R. Somvanshi
- Biosystems Engineering Lab
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai
- India 400076
| | - Anilkumar K. Patel
- Biosystems Engineering Lab
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai
- India 400076
| | - Sharad Bhartiya
- Control Systems Engineering Lab
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai
- India 400076
| | - K. V. Venkatesh
- Biosystems Engineering Lab
- Department of Chemical Engineering
- Indian Institute of Technology Bombay
- Mumbai
- India 400076
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14
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Cantalapiedra-Hijar G, Ortigues-Marty I, Lemosquet S. Diets rich in starch improve the efficiency of amino acids use by the mammary gland in lactating Jersey cows. J Dairy Sci 2015. [DOI: 10.3168/jds.2015-9518] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Arriola Apelo S, Knapp J, Hanigan M. Invited review: Current representation and future trends of predicting amino acid utilization in the lactating dairy cow. J Dairy Sci 2014; 97:4000-17. [DOI: 10.3168/jds.2013-7392] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 03/06/2014] [Indexed: 12/20/2022]
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16
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Kariya Y, Honma M, Suzuki H. Systems-based understanding of pharmacological responses with combinations of multidisciplinary methodologies. Biopharm Drug Dispos 2013; 34:489-507. [DOI: 10.1002/bdd.1865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 10/06/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Yoshiaki Kariya
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine; The University of Tokyo; 113-8655 Tokyo Japan
| | - Masashi Honma
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine; The University of Tokyo; 113-8655 Tokyo Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine; The University of Tokyo; 113-8655 Tokyo Japan
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Nijhout HF, Callier V. A new mathematical approach for qualitative modeling of the insulin-TOR-MAPK network. Front Physiol 2013; 4:245. [PMID: 24062690 PMCID: PMC3771213 DOI: 10.3389/fphys.2013.00245] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/20/2013] [Indexed: 12/20/2022] Open
Abstract
In this paper we develop a novel mathematical model of the insulin-TOR-MAPK signaling network that controls growth. Most data on the properties of the insulin and MAPK signaling networks are static and the responses to experimental interventions, such as knockouts, overexpression, and hormonal input are typically reported as scaled quantities. The modeling paradigm we develop here uses scaled variables and is ideally suited to simulate systems in which much of the available data are scaled. Our mathematical representation of signaling networks provides a way to reconcile theory and experiments, thus leading to a better understanding of the properties and function of these signaling networks. We test the performance of the model against a broad diversity of experimental data. The model correctly reproduces experimental insulin dose-response relationships. We study the interaction between insulin and MAPK signaling in the control of protein synthesis, and the interactions between amino acids, insulin and TOR signaling. We study the effects of variation in FOXO expression on protein synthesis and glucose transport capacity, and show that a FOXO knockout can partially rescue protein synthesis capacity of an insulin receptor (INR) knockout. We conclude that the modeling paradigm we develop provides a simple tool to investigate the qualitative properties of signaling networks.
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Smith GR, Shanley DP. Computational modelling of the regulation of Insulin signalling by oxidative stress. BMC SYSTEMS BIOLOGY 2013; 7:41. [PMID: 23705851 PMCID: PMC3668293 DOI: 10.1186/1752-0509-7-41] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 04/19/2013] [Indexed: 12/20/2022]
Abstract
Background Existing models of insulin signalling focus on short term dynamics, rather than the longer term dynamics necessary to understand many physiologically relevant behaviours. We have developed a model of insulin signalling in rodent adipocytes that includes both transcriptional feedback through the Forkhead box type O (FOXO) transcription factor, and interaction with oxidative stress, in addition to the core pathway. In the model Reactive Oxygen Species are both generated endogenously and can be applied externally. They regulate signalling though inhibition of phosphatases and induction of the activity of Stress Activated Protein Kinases, which themselves modulate feedbacks to insulin signalling and FOXO. Results Insulin and oxidative stress combined produce a lower degree of activation of insulin signalling than insulin alone. Fasting (nutrient withdrawal) and weak oxidative stress upregulate antioxidant defences while stronger oxidative stress leads to a short term activation of insulin signalling but if prolonged can have other effects including degradation of the insulin receptor substrate (IRS1) and FOXO. At high insulin the protective effect of moderate oxidative stress may disappear. Conclusion Our model is consistent with a wide range of experimental data, some of which is difficult to explain. Oxidative stress can have effects that are both up- and down-regulatory on insulin signalling. Our model therefore shows the complexity of the interaction between the two pathways and highlights the need for such integrated computational models to give insight into the dysregulation of insulin signalling along with more data at the individual level. A complete SBML model file can be downloaded from BIOMODELS (https://www.ebi.ac.uk/biomodels-main) with unique identifier MODEL1212210000. Other files and scripts are available as additional files with this journal article and can be downloaded from https://github.com/graham1034/Smith2012_insulin_signalling.
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Affiliation(s)
- Graham R Smith
- Centre for Integrated Systems Biology of Ageing & Nutrition (CISBAN), Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
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Somvanshi PR, Patel AK, Bhartiya S, Venkatesh K. Analysis of Integrated Insulin-mTOR Signalling Network -Diabetes Perspective. ACTA ACUST UNITED AC 2013. [DOI: 10.3182/20131216-3-in-2044.00039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Sonntag AG, Dalle Pezze P, Shanley DP, Thedieck K. A modelling-experimental approach reveals insulin receptor substrate (IRS)-dependent regulation of adenosine monosphosphate-dependent kinase (AMPK) by insulin. FEBS J 2012; 279:3314-28. [PMID: 22452783 DOI: 10.1111/j.1742-4658.2012.08582.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mammalian target of rapamycin (mTOR) kinase responds to growth factors, nutrients and cellular energy status and is a central controller of cellular growth. mTOR exists in two multiprotein complexes that are embedded into a complex signalling network. Adenosine monophosphate-dependent kinase (AMPK) is activated by energy deprivation and shuts off adenosine 5'-triphosphate (ATP)-consuming anabolic processes, in part via the inactivation of mTORC1. Surprisingly, we observed that AMPK not only responds to energy deprivation but can also be activated by insulin, and is further induced in mTORC1-deficient cells. We have recently modelled the mTOR network, covering both mTOR complexes and their insulin and nutrient inputs. In the present study we extended the network by an AMPK module to generate the to date most comprehensive data-driven dynamic AMPK-mTOR network model. In order to define the intersection via which AMPK is activated by the insulin network, we compared simulations for six different hypothetical model structures to our observed AMPK dynamics. Hypotheses ranking suggested that the most probable intersection between insulin and AMPK was the insulin receptor substrate (IRS) and that the effects of canonical IRS downstream cues on AMPK would be mediated via an mTORC1-driven negative-feedback loop. We tested these predictions experimentally in multiple set-ups, where we inhibited or induced players along the insulin-mTORC1 signalling axis and observed AMPK induction or inhibition. We confirmed the identified model and therefore report a novel connection within the insulin-mTOR-AMPK network: we conclude that AMPK is positively regulated by IRS and can be inhibited via the negative-feedback loop.
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Affiliation(s)
- Annika G Sonntag
- Bioinformatics and Molecular Genetics (Faculty of Biology), Institute for Biology 3, Albert-Ludwigs-Universität Freiburg, Germany
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Dalle Pezze P, Sonntag AG, Thien A, Prentzell MT, Gödel M, Fischer S, Neumann-Haefelin E, Huber TB, Baumeister R, Shanley DP, Thedieck K. A dynamic network model of mTOR signaling reveals TSC-independent mTORC2 regulation. Sci Signal 2012; 5:ra25. [PMID: 22457331 DOI: 10.1126/scisignal.2002469] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The kinase mammalian target of rapamycin (mTOR) exists in two multiprotein complexes (mTORC1 and mTORC2) and is a central regulator of growth and metabolism. Insulin activation of mTORC1, mediated by phosphoinositide 3-kinase (PI3K), Akt, and the inhibitory tuberous sclerosis complex 1/2 (TSC1-TSC2), initiates a negative feedback loop that ultimately inhibits PI3K. We present a data-driven dynamic insulin-mTOR network model that integrates the entire core network and used this model to investigate the less well understood mechanisms by which insulin regulates mTORC2. By analyzing the effects of perturbations targeting several levels within the network in silico and experimentally, we found that, in contrast to current hypotheses, the TSC1-TSC2 complex was not a direct or indirect (acting through the negative feedback loop) regulator of mTORC2. Although mTORC2 activation required active PI3K, this was not affected by the negative feedback loop. Therefore, we propose an mTORC2 activation pathway through a PI3K variant that is insensitive to the negative feedback loop that regulates mTORC1. This putative pathway predicts that mTORC2 would be refractory to Akt, which inhibits TSC1-TSC2, and, indeed, we found that mTORC2 was insensitive to constitutive Akt activation in several cell types. Our results suggest that a previously unknown network structure connects mTORC2 to its upstream cues and clarifies which molecular connectors contribute to mTORC2 activation.
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Affiliation(s)
- Piero Dalle Pezze
- Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, UK
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Nyman E, Cedersund G, Strålfors P. Insulin signaling - mathematical modeling comes of age. Trends Endocrinol Metab 2012; 23:107-15. [PMID: 22285743 DOI: 10.1016/j.tem.2011.12.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 01/08/2023]
Abstract
Signaling pathways that only a few years ago appeared simple and understandable, albeit far from complete, have evolved into very complex multi-layered networks of cellular control mechanisms, which in turn are integrated in a similarly complex whole-body level of control mechanisms. This complexity sets limits for classical biochemical reasoning, such that a correct and complete analysis of experimental data while taking the full complexity into account is not possible. In this Opinion we propose that mathematical modeling can be used as a tool in insulin signaling research, and we demonstrate how recent developments in modeling - and the integration of modeling in the experimental process - provide new possibilities to approach and decipher complex biological systems more efficiently.
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Affiliation(s)
- Elin Nyman
- Department of Clinical and Experimental Medicine, University of Linköping, SE58185 Linköping, Sweden
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