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Gil Montoya DC, Ornelas-Guevara R, Diercks BP, Guse AH, Dupont G. T cell Ca 2+ microdomains through the lens of computational modeling. Front Immunol 2023; 14:1235737. [PMID: 37860008 PMCID: PMC10582754 DOI: 10.3389/fimmu.2023.1235737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Cellular Ca2+ signaling is highly organized in time and space. Locally restricted and short-lived regions of Ca2+ increase, called Ca2+ microdomains, constitute building blocks that are differentially arranged to create cellular Ca2+ signatures controlling physiological responses. Here, we focus on Ca2+ microdomains occurring in restricted cytosolic spaces between the plasma membrane and the endoplasmic reticulum, called endoplasmic reticulum-plasma membrane junctions. In T cells, these microdomains have been finely characterized. Enough quantitative data are thus available to develop detailed computational models of junctional Ca2+ dynamics. Simulations are able to predict the characteristics of Ca2+ increases at the level of single channels and in junctions of different spatial configurations, in response to various signaling molecules. Thanks to the synergy between experimental observations and computational modeling, a unified description of the molecular mechanisms that create Ca2+ microdomains in the first seconds of T cell stimulation is emerging.
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Affiliation(s)
- Diana C. Gil Montoya
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roberto Ornelas-Guevara
- Unit of Theoretical Chronobiology, Faculté des Sciences CP231, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Björn-Philipp Diercks
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas H. Guse
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Geneviève Dupont
- Unit of Theoretical Chronobiology, Faculté des Sciences CP231, Université Libre de Bruxelles (ULB), Brussels, Belgium
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2
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Gao ZX, Li TT, Jiang HY, He J. Calcium oscillation on homogeneous and heterogeneous networks of ryanodine receptor. Phys Rev E 2023; 107:024402. [PMID: 36932487 DOI: 10.1103/physreve.107.024402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Calcium oscillation is an important calcium homeostasis, imbalance of which is the key mechanism of initiation and progression of many major diseases. The formation and maintenance of calcium homeostasis are closely related to the spatial distribution of calcium channels on endoplasmic reticulum, whose complex structure was unveiled by recent observations with superresolution imaging techniques. In the current paper, a theoretical framework is established by abstracting the spatial distribution of the calcium channels as a nonlinear biological complex network with calcium channels as nodes and Ca^{2+} as edges. A dynamical model for a ryanodine receptor (RyR) is adopted to investigate the effect of spatial distribution on calcium oscillation. The mean-field model can be well reproduced from the complete graph and dense Erdös-Rényi network. The synchronization of RyRs is found important to generate a global calcium oscillation. Below a critical density of the Erdös-Rényi or BaraBási-Albert network, the amplitude and interspike interval decrease rapidly with the end of disappearance of oscillation due to the desynchronization. The clique graph with a cluster structure cannot produce a global oscillation due to the failure of synchronization between clusters. A more realistic geometric network is constructed in a two-dimensional plane based on the experimental information about the RyR arrangement of clusters and the frequency distribution of cluster sizes. Different from the clique graph, the global oscillation can be generated with reasonable parameters on the geometric network. The simulation also suggests that existence of small clusters and rogue RyRs plays an important role in the maintenance of global calcium oscillation through keeping synchronization between large clusters. Such results support the heterogeneous distribution of RyRs with different-size clusters, which is helpful to understand recent observations with superresolution nanoscale imaging techniques. The current theoretical framework can also be extent to investigate other phenomena in calcium signal transduction.
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Affiliation(s)
- Zhong-Xue Gao
- School of Physics and Technology, Nanjing Normal University, Nanjing 210097, China
| | - Tian-Tian Li
- School of Physics and Technology, Nanjing Normal University, Nanjing 210097, China
| | - Han-Yu Jiang
- School of Physics and Technology, Nanjing Normal University, Nanjing 210097, China
| | - Jun He
- School of Physics and Technology, Nanjing Normal University, Nanjing 210097, China
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3
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O'Grady S, Morgan MP. Calcium transport and signalling in breast cancer: Functional and prognostic significance. Semin Cancer Biol 2019; 72:19-26. [PMID: 31866475 DOI: 10.1016/j.semcancer.2019.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/03/2023]
Abstract
Comprised of a complex network of numerous intertwining pathways, the Ca2+ signalling nexus is an essential mediator of many normal cellular activities. Like many other such functions, the normal physiological activity of Ca2+ signalling is frequently co-opted and reshaped in cases of breast cancer, creating a potent oncogenic drive within the affected cell population. Such modifications can occur within pathways mediating either Ca2+ import (e.g. TRP channels, ORAI-STIM1) or Ca2+ export (e.g. PMCA), indicating that both increases and decreases within cellular Ca2+ levels have the potential to increase the malignant potential of a cell. Increased understanding of these pathways may offer clinical benefit in terms of both prognosis and treatment; patient survival has been linked to expression levels of certain Ca2+ transport proteins, whilst selective targeting of these factors with novel anti-cancer agents has demonstrated a variety of anti-tumour effects in in vitro studies. In addition, the activity of several Ca2+ signalling pathways has been shown to influence chemotherapy response, suggesting that a synergistic approach coupling traditional chemotherapy with Ca2+ targeting agents may also improve patient outcome. As such, targeted modulation of these pathways represents a novel approach in precision medicine and breast cancer therapy.
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Affiliation(s)
- Shane O'Grady
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Ireland
| | - Maria P Morgan
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Ireland.
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Miyamoto A, Mikoshiba K. A novel multi lines analysis tool of Ca 2+ dynamics reveals the nonuniformity of Ca 2+ propagation. Cell Calcium 2019; 78:76-80. [PMID: 30669073 DOI: 10.1016/j.ceca.2019.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/15/2018] [Accepted: 01/03/2019] [Indexed: 01/01/2023]
Abstract
Extracellular stimuli evoke a robust increase in the concentration of intracellular Ca2+ ([Ca2+]c) throughout the cell to trigger various cellular responses, such as gene expression and apoptosis. This robust expansion of [Ca2+]c is called Ca2+ propagation. To date, it is thought that intracellular second messengers, such as inositol 1,4,5-trisphosphate (IP3) and intracellular Ca2+, and clusters of IP3 receptors (IP3Rs) regulate Ca2+ propagation. However, little is known about how the elevation in the [Ca2+]c spreads throughout the cell, especially in non-polar cell, including HeLa cell. In this study, we developed a novel multi lines analysis tool. This tool revealed that the velocity of Ca2+ propagation was inconstant throughout cell and local concentration of intracellular Ca2+ did not contribute to the velocity of Ca2+ propagation. Our results suggest that intracellular Ca2+ propagation is not merely the result of diffusion of intracellular Ca2+, and that, on the contrary, intracellular Ca2+ propagation seems to be regulated by more complicated processes.
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Affiliation(s)
- Akitoshi Miyamoto
- Laboratory for Developmental Neurobiology, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, Japan; Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto, Japan.
| | - Katsuhiko Mikoshiba
- Laboratory for Developmental Neurobiology, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, Japan.
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5
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Bifurcations and limit cycles in cytosolic yeast calcium. Math Biosci 2017; 298:58-70. [PMID: 29104134 DOI: 10.1016/j.mbs.2017.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/30/2017] [Accepted: 11/01/2017] [Indexed: 11/20/2022]
Abstract
Calcium homeostasis is a fundamental cellular process in yeast. The regulation of the cytosolic calcium concentration is required for volume preservation and to regulate many vital calcium dependent processes such as mating and response to stress. The homeostatic mechanism is often studied by applying calcium pulses: sharply changing the calcium concentration in the yeast environment and observing the cellular response. To address these experimental investigations, several mathematical models have been proposed to describe this response. In this article we demonstrate that a previously studied model for this response predicts the presence of limit point instabilities and limit cycles in the dynamics of the calcium homeostasis system. We discuss the ways in which such dynamic characteristics can be observed with luminometric techniques. We contrast these predictions with experimentally observed responses and find that the experiments reveal a number of features that are consistent with modeling predictions. In particular, we find that equilibrium cytosolic concentrations have a sharp change in behavior as pulse size changes in the micromolar range. We show that such change is consistent with the presence of limit point instabilities. Additionally, we find that the response of synchronized yeast cells to millimolar range pulses is non-monotonic in its late stages. This response has characteristics similar to those associated with limit cycles.
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Cao P, Falcke M, Sneyd J. Mapping Interpuff Interval Distribution to the Properties of Inositol Trisphosphate Receptors. Biophys J 2017; 112:2138-2146. [PMID: 28538151 DOI: 10.1016/j.bpj.2017.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/14/2017] [Accepted: 03/24/2017] [Indexed: 01/24/2023] Open
Abstract
Tightly clustered inositol trisphosphate receptors (IP3Rs) control localized Ca2+ liberation from the endoplasmic reticulum to generate repetitive Ca2+ puffs. Distributions of the interpuff interval (IPI), i.e., the waiting time between successive puffs, are found to be well characterized by a probability density function involving only two parameters, λ and ξ, which represent the basal rate of puff generation and the recovery rate from refractoriness, respectively. However, how the two parameters depend on the kinetic parameters of single IP3Rs in a cluster is still unclear. In this article, using a stochastic puff model and a single-channel data-based IP3R model, we establish the dependencies of λ and ξ on two important IP3R model parameters, IP3 concentration ([IP3]) and the recovery rate from Ca2+ inhibition (rlow). By varying [IP3] and rlow in physiologically plausible ranges, we find that the ξ-λ plane is comprised of only two disjoint regions, a biologically impermissible region and a region where each parameter set (ξ, λ) can be caused by using two different combinations of [IP3] and rlow. The two combinations utilize very different mechanisms to maintain the same IPI distribution, and the mechanistic difference provides a way of identifying IP3R kinetic parameters by observing properties of the IPI.
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Affiliation(s)
- Pengxing Cao
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - James Sneyd
- Department of Mathematics, The University of Auckland, Auckland, New Zealand.
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Ikebara JM, Takada SH, Cardoso DS, Dias NMM, de Campos BCV, Bretherick TAS, Higa GSV, Ferraz MSA, Kihara AH. Functional Role of Intracellular Calcium Receptor Inositol 1,4,5-Trisphosphate Type 1 in Rat Hippocampus after Neonatal Anoxia. PLoS One 2017; 12:e0169861. [PMID: 28072885 PMCID: PMC5225024 DOI: 10.1371/journal.pone.0169861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/22/2016] [Indexed: 01/13/2023] Open
Abstract
Anoxia is one of the most prevalent causes of neonatal morbidity and mortality, especially in preterm neonates, constituting an important public health problem due to permanent neurological sequelae observed in patients. Oxygen deprivation triggers a series of simultaneous cascades, culminating in cell death mainly located in more vulnerable metabolic brain regions, such as the hippocampus. In the process of cell death by oxygen deprivation, cytosolic calcium plays crucial roles. Intracellular inositol 1,4,5-trisphosphate receptors (IP3Rs) are important regulators of cytosolic calcium levels, although the role of these receptors in neonatal anoxia is completely unknown. This study focused on the functional role of inositol 1,4,5-trisphosphate receptor type 1 (IP3R1) in rat hippocampus after neonatal anoxia. Quantitative real-time PCR revealed a decrease of IP3R1 gene expression 24 hours after neonatal anoxia. We detected that IP3R1 accumulates specially in CA1, and this spatial pattern did not change after neonatal anoxia. Interestingly, we observed that anoxia triggers translocation of IP3R1 to nucleus in hippocampal cells. We were able to observe that anoxia changes distribution of IP3R1 immunofluorescence signals, as revealed by cluster size analysis. We next examined the role of IP3R1 in the neuronal cell loss triggered by neonatal anoxia. Intrahippocampal injection of non-specific IP3R1 blocker 2-APB clearly reduced the number of Fluoro-Jade C and Tunel positive cells, revealing that activation of IP3R1 increases cell death after neonatal anoxia. Finally, we aimed to disclose mechanistics of IP3R1 in cell death. We were able to determine that blockade of IP3R1 did not reduced the distribution and pixel density of activated caspase 3-positive cells, indicating that the participation of IP3R1 in neuronal cell loss is not related to classical caspase-mediated apoptosis. In summary, this study may contribute to new perspectives in the investigation of neurodegenerative mechanisms triggered by oxygen deprivation.
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Affiliation(s)
- Juliane Midori Ikebara
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
| | - Silvia Honda Takada
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
| | - Débora Sterzeck Cardoso
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
| | | | | | | | - Guilherme Shigueto Vilar Higa
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Alexandre Hiroaki Kihara
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
- Departamento de Fisiologia e Biofísica, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
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Cai X, Li X, Qi H, Wei F, Chen J, Shuai J. Comparison of gating dynamics of different IP 3R channels with immune algorithm searching for channel parameter distributions. Phys Biol 2016; 13:056005. [PMID: 27749281 DOI: 10.1088/1478-3975/13/5/056005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The gating properties of the inositol 1, 4, 5-trisphosphate (IP3) receptor (IP3R) are determined by the binding and unbinding capability of Ca2+ ions and IP3 messengers. With the patch clamp experiments, the stationary properties have been discussed for Xenopus oocyte type-1 IP3R (Oo-IP3R1), type-3 IP3R (Oo-IP3R3) and Spodoptera frugiperda IP3R (Sf-IP3R). In this paper, in order to provide insights about the relation between the observed gating characteristics and the gating parameters in different IP3Rs, we apply the immune algorithm to fit the parameters of a modified DeYoung-Keizer model. By comparing the fitting parameter distributions of three IP3Rs, we suggest that the three types of IP3Rs have the similar open sensitivity in responding to IP3. The Oo-IP3R3 channel is easy to open in responding to low Ca2+ concentration, while Sf-IP3R channel is easily inhibited in responding to high Ca2+ concentration. We also show that the IP3 binding rate is not a sensitive parameter for stationary gating dynamics for three IP3Rs, but the inhibitory Ca2+ binding/unbinding rates are sensitive parameters for gating dynamics for both Oo-IP3R1 and Oo-IP3R3 channels. Such differences may be important in generating the spatially and temporally complex Ca2+ oscillations in cells. Our study also demonstrates that the immune algorithm can be applied for model parameter searching in biological systems.
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Affiliation(s)
- Xiuhong Cai
- Department of Physics, Xiamen University, Xiamen 361000, People's Republic of China
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Chen Y, Qi H, Li X, Cai M, Chen X, Liu W, Shuai J. Suppressing effect of Ca^{2+} blips on puff amplitudes by inhibiting channels to prevent recovery. Phys Rev E 2016; 94:022411. [PMID: 27627339 DOI: 10.1103/physreve.94.022411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Indexed: 11/07/2022]
Abstract
As local signals, calcium puffs arise from the concerted opening of a few nearby inositol 1,4,5-trisphospate receptor channels to release Ca^{2+} ions from the endoplasmic reticulum. Although Ca^{2+} puffs have been well studied, little is known about the modulation of cytosolic basal Ca^{2+} concentration ([Ca^{2+}]_{Basal}) on puff dynamics. In this paper we consider a puff model to study how the statistical properties of puffs are modulated by [Ca^{2+}]_{Basal}. The puff frequency and lifetime trivially increase with the increasing [Ca^{2+}]_{Basal}, but an unexpected result is that the puff amplitude and the maximum open-channel number of the puff show decreasing relationship with the increasing [Ca^{2+}]_{Basal}. The underlying dynamics is related not only to the increasing puff frequency which gives a shorter recovery time, but also to the increasing frequency of blips with only one channel open. We indicate that Ca^{2+} blips cause the channels to be inhibited and prevent their recovery during interpuff intervals, resulting in the suppressing effect on puff amplitudes. With increasing [Ca^{2+}]_{Basal}, more blips occur to cause more channels to be inhibited, leaving fewer channels available for puff events. This study shows that the blips may play relevant functions in global Ca^{2+} waves through modulating puff dynamics.
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Affiliation(s)
- Yuan Chen
- Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China
| | - Hong Qi
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China
| | - Xiang Li
- Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China
| | - Meichun Cai
- Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China
| | - Xingqiang Chen
- Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China
| | - Wen Liu
- Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China
| | - Jianwei Shuai
- Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361102, China
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陈 圆. Modeling of Ca<sup>2+</sup> Channels and Ca<sup>2+</sup> Signal Oscillations. Biophysics (Nagoya-shi) 2016. [DOI: 10.12677/biphy.2016.41001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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