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Seasons GM, Pellow C, Kuipers HF, Pike GB. Ultrasound and neuroinflammation: immune modulation via the heat shock response. Theranostics 2024; 14:3150-3177. [PMID: 38855178 PMCID: PMC11155413 DOI: 10.7150/thno.96270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Current pharmacological therapeutic approaches targeting chronic inflammation exhibit transient efficacy, often with adverse effects, limiting their widespread use - especially in the context of neuroinflammation. Effective interventions require the consideration of homeostatic function, pathway dysregulation, and pleiotropic effects when evaluating therapeutic targets. Signalling molecules have multiple functions dependent on the immune context, and this complexity results in therapeutics targeting a single signalling molecule often failing in clinical translation. Additionally, the administration of non-physiologic levels of neurotrophic or anti-inflammatory factors can alter endogenous signalling, resulting in unanticipated effects. Exacerbating these challenges, the central nervous system (CNS) is isolated by the blood brain barrier (BBB), restricting the infiltration of many pharmaceutical compounds into the brain tissue. Consequently, there has been marked interest in therapeutic techniques capable of modulating the immune response in a pleiotropic manner; ultrasound remains on this frontier. While ultrasound has been used therapeutically in peripheral tissues - accelerating healing in wounds, bone fractures, and reducing inflammation - it is only recently that it has been applied to the CNS. The transcranial application of low intensity pulsed ultrasound (LIPUS) has successfully mitigated neuroinflammation in vivo, in models of neurodegenerative disease across a broad spectrum of ultrasound parameters. To date, the underlying biological effects and signalling pathways modulated by ultrasound are poorly understood, with a diverse array of reported molecules implicated. The distributed nature of the beneficial response to LIPUS implies the involvement of an, as yet, undetermined upstream signalling pathway, homologous to the protective effect of febrile range hyperthermia in chronic inflammation. As such, we review the heat shock response (HSR), a protective signalling pathway activated by thermal and mechanical stress, as the possible upstream regulator of the anti-inflammatory effects of ultrasound.
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Affiliation(s)
- Graham M. Seasons
- Hotchkiss Brain Institute, University of Calgary, Alberta, T2N 4N1, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
| | - Carly Pellow
- Hotchkiss Brain Institute, University of Calgary, Alberta, T2N 4N1, Canada
- Department of Radiology, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
| | - Hedwich F. Kuipers
- Hotchkiss Brain Institute, University of Calgary, Alberta, T2N 4N1, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
- Department of Cell Biology & Anatomy, Hotchkiss Brain Institute and Snyder Institute for Chronic Diseases, University of Calgary, Alberta, T2N 1N4, Canada
| | - G. Bruce Pike
- Hotchkiss Brain Institute, University of Calgary, Alberta, T2N 4N1, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
- Department of Radiology, Cumming School of Medicine, University of Calgary, Alberta, T2N 1N4, Canada
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Amstein LK, Ackermann J, Hannig J, Đikić I, Fulda S, Koch I. Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis. PLoS Comput Biol 2022; 18:e1010383. [PMID: 35994517 PMCID: PMC9467317 DOI: 10.1371/journal.pcbi.1010383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 09/12/2022] [Accepted: 07/13/2022] [Indexed: 11/19/2022] Open
Abstract
The paper describes a mathematical model of the molecular switches of cell survival, apoptosis, and necroptosis in cellular signaling pathways initiated by tumor necrosis factor 1. Based on experimental findings in the literature, we constructed a Petri net model based on detailed molecular reactions of the molecular players, protein complexes, post-translational modifications, and cross talk. The model comprises 118 biochemical entities, 130 reactions, and 299 edges. We verified the model by evaluating invariant properties of the system at steady state and by in silico knockout analysis. Applying Petri net analysis techniques, we found 279 pathways, which describe signal flows from receptor activation to cellular response, representing the combinatorial diversity of functional pathways.120 pathways steered the cell to survival, whereas 58 and 35 pathways led to apoptosis and necroptosis, respectively. For 65 pathways, the triggered response was not deterministic and led to multiple possible outcomes. We investigated the in silico knockout behavior and identified important checkpoints of the TNFR1 signaling pathway in terms of ubiquitination within complex I and the gene expression dependent on NF-κB, which controls the caspase activity in complex II and apoptosis induction. Despite not knowing enough kinetic data of sufficient quality, we estimated system’s dynamics using a discrete, semi-quantitative Petri net model. It is still a challenge to develop mechanistic models for big molecular systems without the knowledge of enough kinetic parameters of sufficient quality. At the same time, more qualitative and semi-quantitative data have been produced in increasing numbers, e.g., by new high-throughput technologies. This has generated demands for new concepts at appropriate abstraction levels. The Petri net formalism enables the integration of qualitative as well as quantitative data and provides algorithms and methods for model verification and model simulation. Moreover, Petri nets exhibit a clear and coherent visualization. Here, we modeled the molecular switches between cell survival, apoptosis, and necroptosis induced by tumor necrosis factor 1. We were interested not only in an exhaustive exploration of all possible signaling pathways, but also in finding the system’s checkpoints. Our Petri net model comprises 118 biochemical entities, 130 reactions, and 299 edges. We found 279 pathways that describe signal flows from receptor activation to cellular response.120 pathways steered the cell to survival, whereas 58 and 35 pathways led to apoptosis and necroptosis, respectively. For 65 pathways, the triggered response was not deterministic, leading to multiple possible outcomes. We applied in silico knockout analyses to the Petri net model and could identify important checkpoints of the tumor necrosis factor 1 signaling pathway.
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Affiliation(s)
- Leonie K. Amstein
- Goethe University Frankfurt, Institute of Computer Science, Department of Molecular Bioinformatics, Frankfurt am Main, Germany
| | - Jörg Ackermann
- Goethe University Frankfurt, Institute of Computer Science, Department of Molecular Bioinformatics, Frankfurt am Main, Germany
| | - Jennifer Hannig
- Cognitive Information Systems, Kompetenzzentrum für Informationstechnologie, Technische Hochschule Mittelhessen, Friedberg, Germany
| | - Ivan Đikić
- Goethe University Frankfurt, Institute of Biochemistry II, Medical Faculty, Frankfurt am Main, Germany
| | - Simone Fulda
- Goethe University Frankfurt, Institute of Biochemistry II, Medical Faculty, Frankfurt am Main, Germany
| | - Ina Koch
- Goethe University Frankfurt, Institute of Computer Science, Department of Molecular Bioinformatics, Frankfurt am Main, Germany
- * E-mail:
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Mostafizar M, Cortes-Pérez C, Snow W, Djordjevic J, Adlimoghaddam A, Albensi BC. Challenges with Methods for Detecting and Studying the Transcription Factor Nuclear Factor Kappa B (NF-κB) in the Central Nervous System. Cells 2021; 10:1335. [PMID: 34071243 PMCID: PMC8228352 DOI: 10.3390/cells10061335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 01/01/2023] Open
Abstract
The transcription factor nuclear factor kappa B (NF-κB) is highly expressed in almost all types of cells. NF-κB is involved in many complex biological processes, in particular in immunity. The activation of the NF-κB signaling pathways is also associated with cancer, diabetes, neurological disorders and even memory. Hence, NF-κB is a central factor for understanding not only fundamental biological presence but also pathogenesis, and has been the subject of intense study in these contexts. Under healthy physiological conditions, the NF-κB pathway promotes synapse growth and synaptic plasticity in neurons, while in glia, NF-κB signaling can promote pro-inflammatory responses to injury. In addition, NF-κB promotes the maintenance and maturation of B cells regulating gene expression in a majority of diverse signaling pathways. Given this, the protein plays a predominant role in activating the mammalian immune system, where NF-κB-regulated gene expression targets processes of inflammation and host defense. Thus, an understanding of the methodological issues around its detection for localization, quantification, and mechanistic insights should have a broad interest across the molecular neuroscience community. In this review, we summarize the available methods for the proper detection and analysis of NF-κB among various brain tissues, cell types, and subcellular compartments, using both qualitative and quantitative methods. We also summarize the flexibility and performance of these experimental methods for the detection of the protein, accurate quantification in different samples, and the experimental challenges in this regard, as well as suggestions to overcome common challenges.
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Affiliation(s)
- Marina Mostafizar
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Claudia Cortes-Pérez
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Wanda Snow
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Jelena Djordjevic
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Aida Adlimoghaddam
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
| | - Benedict C. Albensi
- Division of Neurodegenerative Disorders, St. Boniface Hospital Research, Winnipeg, MB R2H 2A6, Canada; (M.M.); (C.C.-P.); (W.S.); (J.D.); (A.A.)
- Department of Pharmacology and Therapeutics, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R2H 2A6, Canada
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Hobbs S, Reynoso M, Geddis AV, Mitrophanov AY, Matheny RW. LPS-stimulated NF-κB p65 dynamic response marks the initiation of TNF expression and transition to IL-10 expression in RAW 264.7 macrophages. Physiol Rep 2018; 6:e13914. [PMID: 30426723 PMCID: PMC6234144 DOI: 10.14814/phy2.13914] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
During injury and infection, inflammation is a response by macrophages to effect healing and repair. The kinetics of the responses of proinflammatory TNFα, anti-inflammatory IL-10, and inflammatory master regulator NF-κB elicited by lipopolysaccharide (LPS) may be critical determinants of the inflammatory response by macrophages; however, there is a lack of homogeneous kinetic data in this pathway. To address this gap, we used the RAW 264.7 macrophage cell line to define intracellular signaling kinetics and cytokine expression in cells treated with LPS for 15 min to 72 h. The abundance of IκBα was maximally reduced 45-min following LPS treatment, but expression increased at 10-h, reaching a maximum at 16 h. NF-κB phosphorylation was significantly increased 45-min following LPS treatment, maximal at 2-h, and decreased to basal levels by 6-h. Nuclear NF-κB expression was elevated 30-min following LPS treatment, maximal by 45-min, and returned to basal levels by 24-h. Binding of nuclear NF-κB to consensus oligonucleotide sequences followed a similar pattern to that observed for p-NF-κB, but lasted slightly longer. Following LPS treatment, TNFα mRNA expression began at 1-h, was maximal at 6-h, and decreased starting at 10-h. TNFα protein secretion in conditioned growth medium began at 4-h and was maximal by 16-h. IL-10 mRNA expression was induced by LPS at 10-h, and was maximal at 16-h. IL-10 protein secretion was induced at 16-h and was maximal at 24-h. Our data reveal the temporal kinetics of pro- and anti-inflammatory signaling events that may be important therapeutic targets for inflammatory diseases.
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Affiliation(s)
- Stuart Hobbs
- Military Performance Division U.S. Army Research Institute of Environmental MedicineNatickMassachusetts
| | - Marinaliz Reynoso
- Military Performance Division U.S. Army Research Institute of Environmental MedicineNatickMassachusetts
| | - Alyssa V. Geddis
- Military Performance Division U.S. Army Research Institute of Environmental MedicineNatickMassachusetts
| | - Alexander Y. Mitrophanov
- DoD Biotechnology High Performance Computing Software Applications InstituteTelemedicine and Advanced Technology Research CenterU.S. Army Medical Research and Materiel CommandFt. DetrickMaryland
| | - Ronald W. Matheny
- Military Performance Division U.S. Army Research Institute of Environmental MedicineNatickMassachusetts
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5
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Xiang B, Xiao C, Shen T, Li X. Anti-inflammatory effects of anisalcohol on lipopolysaccharide-stimulated BV2 microglia via selective modulation of microglia polarization and down-regulation of NF-κB p65 and JNK activation. Mol Immunol 2018; 95:39-46. [DOI: 10.1016/j.molimm.2018.01.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 01/05/2023]
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Anderson WD, Makadia HK, Greenhalgh AD, Schwaber JS, David S, Vadigepalli R. Computational modeling of cytokine signaling in microglia. MOLECULAR BIOSYSTEMS 2016; 11:3332-46. [PMID: 26440115 DOI: 10.1039/c5mb00488h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Neuroinflammation due to glial activation has been linked to many CNS diseases. We developed a computational model of a microglial cytokine interaction network to study the regulatory mechanisms of microglia-mediated neuroinflammation. We established a literature-based cytokine network, including TNFα, TGFβ, and IL-10, and fitted a mathematical model to published data from LPS-treated microglia. The addition of a previously unreported TGFβ autoregulation loop to our model was required to account for experimental data. Global sensitivity analysis revealed that TGFβ- and IL-10-mediated inhibition of TNFα was critical for regulating network behavior. We assessed the sensitivity of the LPS-induced TNFα response profile to the initial TGFβ and IL-10 levels. The analysis showed two relatively shifted TNFα response profiles within separate domains of initial condition space. Further analysis revealed that TNFα exhibited adaptation to sustained LPS stimulation. We simulated the effects of functionally inhibiting TGFβ and IL-10 on TNFα adaptation. Our analysis showed that TGFβ and IL-10 knockouts (TGFβ KO and IL-10 KO) exert divergent effects on adaptation. TFGβ KO attenuated TNFα adaptation whereas IL-10 KO enhanced TNFα adaptation. We experimentally tested the hypothesis that IL-10 KO enhances TNFα adaptation in murine macrophages and found supporting evidence. These opposing effects could be explained by differential kinetics of negative feedback. Inhibition of IL-10 reduced early negative feedback that results in enhanced TNFα-mediated TGFβ expression. We propose that differential kinetics in parallel negative feedback loops constitute a novel mechanism underlying the complex and non-intuitive pro- versus anti-inflammatory effects of individual cytokine perturbations.
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Affiliation(s)
- Warren D Anderson
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA. and Graduate Program in Neuroscience, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hirenkumar K Makadia
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA. and Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Andrew D Greenhalgh
- Center for Research in Neuroscience, The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - James S Schwaber
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA. and Graduate Program in Neuroscience, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - Samuel David
- Center for Research in Neuroscience, The Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA. and Graduate Program in Neuroscience, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, USA
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7
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Ouyang YB, Stary CM, White RE, Giffard RG. The use of microRNAs to modulate redox and immune response to stroke. Antioxid Redox Signal 2015; 22:187-202. [PMID: 24359188 PMCID: PMC4281877 DOI: 10.1089/ars.2013.5757] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE Cerebral ischemia is a major cause of death and disability throughout the world, yet therapeutic options remain limited. The interplay between the cellular redox state and the immune response plays a critical role in determining the extent of neural cell injury after ischemia and reperfusion. Excessive amounts of reactive oxygen species (ROS) generated by mitochondria and other sources act both as triggers and effectors of inflammation. This review will focus on the interplay between these two mechanisms. RECENT ADVANCES MicroRNAs (miRNAs) are important post-transcriptional regulators that interact with multiple target messenger RNAs coordinately regulating target genes, including those involved in controlling mitochondrial function, redox state, and inflammatory pathways. This review will focus on the regulation of mitochondria, ROS, and inflammation by miRNAs in the chain of deleterious intra- and intercellular events that lead to brain cell death after cerebral ischemia. CRITICAL ISSUES Although pretreatment using miRNAs was effective in cerebral ischemia in rodents, testing treatment after the onset of ischemia is an essential next step in the development of acute stroke treatment. In addition, miRNA formulation and delivery into the CNS remain a challenge in the clinical translation of miRNA therapy. FUTURE DIRECTIONS Future research should focus on post-treatment and potential clinical use of miRNAs.
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Affiliation(s)
- Yi-Bing Ouyang
- Department of Anesthesia, Stanford University School of Medicine , Stanford, California
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8
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Lian H, Yang L, Cole A, Sun L, Chiang ACA, Fowler SW, Shim DJ, Rodriguez-Rivera J, Taglialatela G, Jankowsky JL, Lu HC, Zheng H. NFκB-activated astroglial release of complement C3 compromises neuronal morphology and function associated with Alzheimer's disease. Neuron 2014; 85:101-115. [PMID: 25533482 DOI: 10.1016/j.neuron.2014.11.018] [Citation(s) in RCA: 423] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2014] [Indexed: 11/26/2022]
Abstract
Abnormal NFκB activation has been implicated in Alzheimer's disease (AD). However, the signaling pathways governing NFκB regulation and function in the brain are poorly understood. We identify complement protein C3 as an astroglial target of NFκB and show that C3 release acts through neuronal C3aR to disrupt dendritic morphology and network function. Exposure to Aβ activates astroglial NFκB and C3 release, consistent with the high levels of C3 expression in brain tissue from AD patients and APP transgenic mice, where C3aR antagonist treatment rescues cognitive impairment. Therefore, dysregulation of neuron-glia interaction through NFκB/C3/C3aR signaling may contribute to synaptic dysfunction in AD, and C3aR antagonists may be therapeutically beneficial.
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Affiliation(s)
- Hong Lian
- Huffington Center on Aging, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Li Yang
- Huffington Center on Aging, Houston, TX 77030, USA
| | - Allysa Cole
- Huffington Center on Aging, Houston, TX 77030, USA
| | - Lu Sun
- Huffington Center on Aging, Houston, TX 77030, USA
| | - Angie C-A Chiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephanie W Fowler
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - David J Shim
- Huffington Center on Aging, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Giulio Taglialatela
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Joanna L Jankowsky
- Huffington Center on Aging, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hui-Chen Lu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine and the Cain Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Hui Zheng
- Huffington Center on Aging, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
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DeGracia DJ, Tri Anggraini F, Taha DTM, Huang ZF. Inductive and Deductive Approaches to Acute Cell Injury. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:859341. [PMID: 27437490 PMCID: PMC4897055 DOI: 10.1155/2014/859341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/25/2014] [Indexed: 11/28/2022]
Abstract
Many clinically relevant forms of acute injury, such as stroke, traumatic brain injury, and myocardial infarction, have resisted treatments to prevent cell death following injury. The clinical failures can be linked to the currently used inductive models based on biological specifics of the injury system. Here we contrast the application of inductive and deductive models of acute cell injury. Using brain ischemia as a case study, we discuss limitations in inductive inferences, including the inability to unambiguously assign cell death causality and the lack of a systematic quantitative framework. These limitations follow from an overemphasis on qualitative molecular pathways specific to the injured system. Our recently developed nonlinear dynamical theory of cell injury provides a generic, systematic approach to cell injury in which attractor states and system parameters are used to quantitatively characterize acute injury systems. The theoretical, empirical, and therapeutic implications of shifting to a deductive framework are discussed. We illustrate how a deductive mathematical framework offers tangible advantages over qualitative inductive models for the development of therapeutics of acutely injured biological systems.
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Affiliation(s)
- Donald J. DeGracia
- Department of Physiology, Wayne State University, 4116 Scott Hall, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - Fika Tri Anggraini
- Department of Physiology, Wayne State University, 4116 Scott Hall, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | | | - Zhi-Feng Huang
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
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Sheppard PW, Sun X, Khammash M, Giffard RG. Overexpression of heat shock protein 72 attenuates NF-κB activation using a combination of regulatory mechanisms in microglia. PLoS Comput Biol 2014; 10:e1003471. [PMID: 24516376 PMCID: PMC3916226 DOI: 10.1371/journal.pcbi.1003471] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 12/30/2013] [Indexed: 12/16/2022] Open
Abstract
Overexpression of the inducible heat shock protein 70, Hsp72, has broadly cytoprotective effects and improves outcome following stroke. A full understanding of how Hsp72 protects cells against injury is elusive, though several distinct mechanisms are implicated. One mechanism is its anti-inflammatory effects. We study the effects of Hsp72 overexpression on activation of the transcription factor NF-κB in microglia combining experimentation and mathematical modeling, using TNFα to stimulate a microglial cell line stably overexpressing Hsp72. We find that Hsp72 overexpression reduces the amount of NF-κB DNA binding activity, activity of the upstream kinase IKK, and amount of IκBα inhibitor phosphorylated following TNFα application. Simulations evaluating several proposed mechanisms suggest that inhibition of IKK activation is an essential component of its regulatory activities. Unexpectedly we find that Hsp72 overexpression reduces the initial amount of the RelA/p65 NF-κB subunit in cells, contributing to the attenuated response. Neither mechanism in isolation, however, is sufficient to attenuate the response, providing evidence that Hsp72 relies upon multiple mechanisms to attenuate NF-κB activation. An additional observation from our study is that the induced expression of IκBα is altered significantly in Hsp72 expressing cells. While the mechanism responsible for this observation is not known, it points to yet another means by which Hsp72 may alter the NF-κB response. This study illustrates the multi-faceted nature of Hsp72 regulation of NF-κB activation in microglia and offers further clues to a novel mechanism by which Hsp72 may protect cells against injury. Inducing heat shock or overexpressing certain heat shock proteins (HSPs) is known to protect against brain injury, such as that resulting from stroke. Understanding the mechanisms underlying protection at the cellular and molecular level is a subject of intense research, as such knowledge may prove beneficial in designing future therapies. Regulation of the activation of the key inflammatory transcription factor Nuclear Factor κB (NF-κB) is believed to be one critical mechanism. However how its activation is altered by Hsp72 remains unresolved. Here we examine NF-κB signaling in microglia cells overexpressing Hsp72, combining experimentation and mathematical modeling. We show that Hsp72 affects signaling using at least two essential and distinct mechanisms: attenuation of upstream kinase (IKK) activity and reduction of steady state NF-κB protein levels. We provide numerical evidence suggesting that neither mechanism in isolation is sufficient to account for the observed signaling. Furthermore, our observations suggest an intriguing additional level of regulation of gene expression and protein synthesis of the IκBα inhibitor, which opens interesting new avenues of research. These results provide novel insight into the mechanisms by which Hsp72 may regulate inflammation and protect brain cells from injury.
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Affiliation(s)
- Patrick W. Sheppard
- Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Department of Biosystems Science and Engineering, ETH-Zurich, Basel, Switzerland
- * E-mail:
| | - Xiaoyun Sun
- Department of Anesthesia, Stanford University, Stanford, California, United States of America
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH-Zurich, Basel, Switzerland
| | - Rona G. Giffard
- Department of Anesthesia, Stanford University, Stanford, California, United States of America
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11
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Ouyang YB, Giffard RG. MicroRNAs regulate the chaperone network in cerebral ischemia. Transl Stroke Res 2013; 4:693-703. [PMID: 24323423 PMCID: PMC3864745 DOI: 10.1007/s12975-013-0280-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/24/2013] [Accepted: 07/30/2013] [Indexed: 01/17/2023]
Abstract
The highly evolutionarily conserved 70 kDa heat shock protein (HSP70) family was first understood for its role in protein folding and response to stress. Subsequently, additional functions have been identified for it in regulation of organelle interaction, of the inflammatory response, and of cell death and survival. Overexpression of HSP70 family members is associated with increased resistance to and improved recovery from cerebral ischemia. MicroRNAs (miRNAs) are important posttranscriptional regulators that interact with multiple target messenger RNAs (mRNA) coordinately regulating target genes, including chaperones. The members of the HSP70 family are now appreciated to work together as networks to facilitate organelle communication and regulate inflammatory signaling and cell survival after cerebral ischemia. This review will focus on the new concept of the role of the chaperone network in the organelle network and its novel regulation by miRNA.
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Affiliation(s)
- Yi-Bing Ouyang
- Department of Anesthesia, Stanford University School of Medicine, 300 Pasteur Drive, S272A and S290, Stanford, CA, 94305-5117, USA,
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12
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Han D, Moon S, Kim Y, Kim J, Jin J, Kim Y. In-depth proteomic analysis of mouse microglia using a combination of FASP and StageTip-based, high pH, reversed-phase fractionation. Proteomics 2013; 13:2984-8. [PMID: 23943505 DOI: 10.1002/pmic.201300091] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 06/02/2013] [Accepted: 07/20/2013] [Indexed: 11/07/2022]
Abstract
Microglia are major immune cells in the central nervous system. A characterization of microglia proteome would facilitate on the study of microglial functions in association with various neurodegenerative diseases. To build a reference proteome, we established a BV-2 microglial proteome to a depth of 5494 unique protein groups using a novel strategy that combined FASP, StageTip-based high pH fractionation, and high-resolution MS quickly and cost efficiently. By bioinformatics analysis, the BV-2 proteome is a valuable resource for studies of microglial function, such as in the immune response, inflammatory response, and phagocytosis. All MS data have been deposited in the ProteomeXchange with identifier PXD000168.
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Affiliation(s)
- Dohyun Han
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Korea; Institute of Medical & Biological Engineering, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
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Zhang W, Zou X. Systematic analysis of the mechanisms of virus-triggered type I IFN signaling pathways through mathematical modeling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:771-779. [PMID: 24091409 DOI: 10.1109/tcbb.2013.31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Based on biological experimental data, we developed a mathematical model of the virus-triggered signaling pathways that lead to induction of type I IFNs and systematically analyzed the mechanisms of the cellular antiviral innate immune responses, including the negative feedback regulation of ISG56 and the positive feedback regulation of IFNs. We found that the time between 5 and 48 hours after viral infection is vital for the control and/or elimination of the virus from the host cells and demonstrated that the ISG56-induced inhibition of MITA activation is stronger than the ISG56-induced inhibition of TBK1 activation. The global parameter sensitivity analysis suggests that the positive feedback regulation of IFNs is very important in the innate antiviral system. Furthermore, the robustness of the innate immune signaling network was demonstrated using a new robustness index. These results can help us understand the mechanisms of the virus-induced innate immune response at a system level and provide instruction for further biological experiments.
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Li J, Zhang S, Lu M, Chen Z, Chen C, Han L, Zhang M, Xu Y. Hydroxysafflor yellow A suppresses inflammatory responses of BV2 microglia after oxygen–glucose deprivation. Neurosci Lett 2013; 535:51-6. [DOI: 10.1016/j.neulet.2012.12.056] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 12/11/2012] [Accepted: 12/28/2012] [Indexed: 01/30/2023]
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Chtarto A, Bockstael O, Gebara E, Vermoesen K, Melas C, Pythoud C, Levivier M, De Witte O, Luthi-Carter R, Clinkers R, Tenenbaum L. An adeno-associated virus-based intracellular sensor of pathological nuclear factor-κB activation for disease-inducible gene transfer. PLoS One 2013; 8:e53156. [PMID: 23301037 PMCID: PMC3536800 DOI: 10.1371/journal.pone.0053156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 11/26/2012] [Indexed: 11/20/2022] Open
Abstract
Stimulation of resident cells by NF-κB activating cytokines is a central element of inflammatory and degenerative disorders of the central nervous system (CNS). This disease-mediated NF-κB activation could be used to drive transgene expression selectively in affected cells, using adeno-associated virus (AAV)-mediated gene transfer. We have constructed a series of AAV vectors expressing GFP under the control of different promoters including NF-κB -responsive elements. As an initial screen, the vectors were tested in vitro in HEK-293T cells treated with TNF-α. The best profile of GFP induction was obtained with a promoter containing two blocks of four NF-κB -responsive sequences from the human JCV neurotropic polyoma virus promoter, fused to a new tight minimal CMV promoter, optimally distant from each other. A therapeutical gene, glial cell line-derived neurotrophic factor (GDNF) cDNA under the control of serotype 1-encapsidated NF-κB -responsive AAV vector (AAV-NF) was protective in senescent cultures of mouse cortical neurons. AAV-NF was then evaluated in vivo in the kainic acid (KA)-induced status epilepticus rat model for temporal lobe epilepsy, a major neurological disorder with a central pathophysiological role for NF-κB activation. We demonstrate that AAV-NF, injected in the hippocampus, responded to disease induction by mediating GFP expression, preferentially in CA1 and CA3 neurons and astrocytes, specifically in regions where inflammatory markers were also induced. Altogether, these data demonstrate the feasibility to use disease-activated transcription factor-responsive elements in order to drive transgene expression specifically in affected cells in inflammatory CNS disorders using AAV-mediated gene transfer.
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Affiliation(s)
- Abdelwahed Chtarto
- Laboratory of Experimental Neurosurgery, Université Libre de Bruxelles, Brussels, Belgium.
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Mice lacking the β2 adrenergic receptor have a unique genetic profile before and after focal brain ischaemia. ASN Neuro 2012; 4:AN20110020. [PMID: 22867428 PMCID: PMC3436074 DOI: 10.1042/an20110020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The role of the β2AR (β2 adrenergic receptor) after stroke is unclear as pharmacological manipulations of the β2AR have produced contradictory results. We previously showed that mice deficient in the β2AR (β2KO) had smaller infarcts compared with WT (wild-type) mice (FVB) after MCAO (middle cerebral artery occlusion), a model of stroke. To elucidate mechanisms of this neuroprotection, we evaluated changes in gene expression using microarrays comparing differences before and after MCAO, and differences between genotypes. Genes associated with inflammation and cell deaths were enriched after MCAO in both genotypes, and we identified several genes not previously shown to increase following ischaemia (Ccl9, Gem and Prg4). In addition to networks that were similar between genotypes, one network with a central core of GPCR (G-protein-coupled receptor) and including biological functions such as carbohydrate metabolism, small molecule biochemistry and inflammation was identified in FVB mice but not in β2KO mice. Analysis of differences between genotypes revealed 11 genes differentially expressed by genotype both before and after ischaemia. We demonstrate greater Glo1 protein levels and lower Pmaip/Noxa mRNA levels in β2KO mice in both sham and MCAO conditions. As both genes are implicated in NF-κB (nuclear factor κB) signalling, we measured p65 activity and TNFα (tumour necrosis factor α) levels 24 h after MCAO. MCAO-induced p65 activation and post-ischaemic TNFα production were both greater in FVB compared with β2KO mice. These results suggest that loss of β2AR signalling results in a neuroprotective phenotype in part due to decreased NF-κB signalling, decreased inflammation and decreased apoptotic signalling in the brain.
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