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Castaneda Ruan P, Benson JC, Trebak M, Kirk V, Sneyd J. A Model for the Coexistence of Competing Mechanisms for Ca 2 + Oscillations in T-lymphocytes. Bull Math Biol 2024; 86:86. [PMID: 38869652 PMCID: PMC11176111 DOI: 10.1007/s11538-024-01317-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024]
Abstract
Ca 2 + is a ubiquitous signaling mechanism across different cell types. In T-cells, it is associated with cytokine production and immune function. Benson et al. have shown the coexistence of competing Ca 2 + oscillations during antigen stimulation of T-cell receptors, depending on the presence of extracellular Ca 2 + influx through the Ca 2 + release-activated Ca 2 + channel (Benson in J Biol Chem 29:105310, 2023). In this paper, we construct a mathematical model consisting of five ordinary differential equations and analyze the relationship between the competing oscillatory mechanisms.. We perform bifurcation analysis on two versions of our model, corresponding to the two oscillatory types, to find the defining characteristics of these two families.
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Affiliation(s)
- Paco Castaneda Ruan
- Department of Mathematics, University of Auckland, Auckland Central, 1142, Auckland, New Zealand.
| | - J Cory Benson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 1526, USA
- Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 1526, USA
- Graduate Program in Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, 17033, USA
| | - Mohamed Trebak
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 1526, USA
- Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 1526, USA
| | - Vivien Kirk
- Department of Mathematics, University of Auckland, Auckland Central, 1142, Auckland, New Zealand
| | - James Sneyd
- Department of Mathematics, University of Auckland, Auckland Central, 1142, Auckland, New Zealand
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2
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Fung SYS, Xǔ XJ, Wu M. Nonlinear dynamics in phosphoinositide metabolism. Curr Opin Cell Biol 2024; 88:102373. [PMID: 38797149 PMCID: PMC11186694 DOI: 10.1016/j.ceb.2024.102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024]
Abstract
Phosphoinositides broadly impact membrane dynamics, signal transduction and cellular physiology. The orchestration of signaling complexity by this seemingly simple metabolic pathway remains an open question. It is increasingly evident that comprehending the complexity of the phosphoinositides metabolic network requires a systems view based on nonlinear dynamics, where the products of metabolism can either positively or negatively modulate enzymatic function. These feedback and feedforward loops may be paradoxical, leading to counterintuitive effects. In this review, we introduce the framework of nonlinear dynamics, emphasizing distinct dynamical regimes such as the excitable state, oscillations, and mixed-mode oscillations-all of which have been experimentally observed in phosphoinositide metabolisms. We delve into how these dynamical behaviors arise from one or multiple network motifs, including positive and negative feedback loops, coherent and incoherent feedforward loops. We explore the current understanding of the molecular circuits responsible for these behaviors. While mapping these circuits presents both conceptual and experimental challenges, redefining cellular behavior based on dynamical state, lipid fluxes, time delay, and network topology is likely essential for a comprehensive understanding of this fundamental metabolic network.
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Affiliation(s)
- Suet Yin Sarah Fung
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8002, USA
| | - X J Xǔ
- Department of Physics, Yale University, New Haven, CT, 06511, USA
| | - Min Wu
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8002, USA.
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3
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Cacciotti A, Beccaccioli M, Reverberi M. The CRZ1 transcription factor in plant fungi: regulation mechanism and impact on pathogenesis. Mol Biol Rep 2024; 51:647. [PMID: 38727981 PMCID: PMC11087348 DOI: 10.1007/s11033-024-09593-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Calcium (Ca2+) is a universal signaling molecule that is tightly regulated, and a fleeting elevation in cytosolic concentration triggers a signal cascade within the cell, which is crucial for several processes such as growth, tolerance to stress conditions, and virulence in fungi. The link between calcium and calcium-dependent gene regulation in cells relies on the transcription factor Calcineurin-Responsive Zinc finger 1 (CRZ1). The direct regulation of approximately 300 genes in different stress pathways makes it a hot topic in host-pathogen interactions. Notably, CRZ1 can modulate several pathways and orchestrate cellular responses to different types of environmental insults such as osmotic stress, oxidative stress, and membrane disruptors. It is our belief that CRZ1 provides the means for tightly modulating and synchronizing several pathways allowing pathogenic fungi to install into the apoplast and eventually penetrate plant cells (i.e., ROS, antimicrobials, and quick pH variation). This review discusses the structure, function, regulation of CRZ1 in fungal physiology and its role in plant pathogen virulence.
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Affiliation(s)
- A Cacciotti
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - M Beccaccioli
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
| | - M Reverberi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
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Ajjour H, Pallafacchina G, Lenzini L, Caroccia B, Rossi GP. Intracellular Calcium Dynamics in Primary Human Adrenocortical Cells Deciphered with a Novel Pipeline. High Blood Press Cardiovasc Prev 2024; 31:299-308. [PMID: 38763953 DOI: 10.1007/s40292-024-00641-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/02/2024] [Indexed: 05/21/2024] Open
Abstract
INTRODUCTION The fluctuations of the intracellular Ca2+ concentration ([Ca2+]i) are key physiological signals for cell function under normal conditions and can undergo profound alterations in disease states, as high blood pressure due to endocrine disorders like primary aldosteronism (PA). However, when assessing such fluctuations several parameters in the Ca2+ signal dynamics need to be considered, which renders their assessment challenging. AIM Aim to develop an observer-independent custom-made pipeline to analyze Ca2+ dynamics in terms of frequency and peak parameters, as amplitude, full width at half maximum (FWHM) and area under the curve (AUC). METHODS We applied a custom-made methodology to aldosterone-producing adenoma (APA) and APA adjacent cells (AAC) and found this pipeline to be suitable for monitoring and processing a wide-range of [Ca2+]i events in these cell types delivering reproducible results. CONCLUSION The designed pipeline can provide a useful tool for [Ca2+]i signal analysis that allows comparisons of Ca2+ dynamics not only in PA, but in other cell phenotypes that are relevant for the regulation of blood pressure.
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Affiliation(s)
- Hala Ajjour
- Specialized Center of Excellence for Hypertension of the European Society of Hypertension and Emergency Medicine Unit, Department of Medicine-DIMED, University Hospital, University of Padua, Padua, 35126, Italy
| | - Giorgia Pallafacchina
- Neuroscience Institute, Italian National Research Council (CNR) and Department of Biomedical Sciences, University of Padua, Padua, 35131, Italy
| | - Livia Lenzini
- Specialized Center of Excellence for Hypertension of the European Society of Hypertension and Emergency Medicine Unit, Department of Medicine-DIMED, University Hospital, University of Padua, Padua, 35126, Italy
| | - Brasilina Caroccia
- Specialized Center of Excellence for Hypertension of the European Society of Hypertension and Emergency Medicine Unit, Department of Medicine-DIMED, University Hospital, University of Padua, Padua, 35126, Italy
| | - Gian Paolo Rossi
- Specialized Center of Excellence for Hypertension of the European Society of Hypertension and Emergency Medicine Unit, Department of Medicine-DIMED, University Hospital, University of Padua, Padua, 35126, Italy.
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5
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Lee L, Yoast R, Emrich S, Trebak M, Kirk V, Sneyd J. Emergence of broad cytosolic Ca 2+ oscillations in the absence of CRAC channels: A model for CRAC-mediated negative feedback on PLC and Ca 2+ oscillations through PKC. J Theor Biol 2024; 581:111740. [PMID: 38253220 DOI: 10.1016/j.jtbi.2024.111740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/28/2023] [Accepted: 01/16/2024] [Indexed: 01/24/2024]
Abstract
The role of Ca2+ release-activated Ca2+ (CRAC) channels mediated by ORAI isoforms in calcium signalling has been extensively investigated. It has been shown that the presence or absence of different isoforms has a significant effect on store-operated calcium entry (SOCE). Yoast et al. (2020) showed that, in addition to the reported narrow-spike oscillations (whereby cytosolic calcium decreases quickly after a sharp increase), ORAI1 knockout HEK293 cells were able to oscillate with broad-spike oscillations (whereby cytosolic calcium decreases in a prolonged manner after a sharp increase) when stimulated with a muscarinic agonist. This suggests that Ca2+ influx through ORAI-mediated CRAC channels negatively regulates the duration of Ca2+ oscillations. We hypothesise that, through the activation of protein kinase C (PKC), ORAI1 negatively regulates phospholipase C (PLC) activity to decrease inositol 1,4,5-trisphosphate (IP3) production and limit the duration of agonist-evoked Ca2+ oscillations. Based on this hypothesis, we construct a new mathematical model, which shows that the formation of broad-spike oscillations is highly dependent on the absence of ORAI1. Predictions of this model are consistent with the experimental results.
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Affiliation(s)
- Lloyd Lee
- Department of Mathematics, University of Auckland, 1142 Auckland, New Zealand.
| | - Ryan Yoast
- Graduate Program in Cellular and Molecular Physiology, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Scott Emrich
- Graduate Program in Cellular and Molecular Physiology, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Mohamed Trebak
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 1526, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 1526, USA; UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 1526, USA
| | - Vivien Kirk
- Department of Mathematics, University of Auckland, 1142 Auckland, New Zealand
| | - James Sneyd
- Department of Mathematics, University of Auckland, 1142 Auckland, New Zealand
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6
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Sanders KM, Drumm BT, Cobine CA, Baker SA. Ca 2+ dynamics in interstitial cells: foundational mechanisms for the motor patterns in the gastrointestinal tract. Physiol Rev 2024; 104:329-398. [PMID: 37561138 PMCID: PMC11281822 DOI: 10.1152/physrev.00036.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/29/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023] Open
Abstract
The gastrointestinal (GI) tract displays multiple motor patterns that move nutrients and wastes through the body. Smooth muscle cells (SMCs) provide the forces necessary for GI motility, but interstitial cells, electrically coupled to SMCs, tune SMC excitability, transduce inputs from enteric motor neurons, and generate pacemaker activity that underlies major motor patterns, such as peristalsis and segmentation. The interstitial cells regulating SMCs are interstitial cells of Cajal (ICC) and PDGF receptor (PDGFR)α+ cells. Together these cells form the SIP syncytium. ICC and PDGFRα+ cells express signature Ca2+-dependent conductances: ICC express Ca2+-activated Cl- channels, encoded by Ano1, that generate inward current, and PDGFRα+ cells express Ca2+-activated K+ channels, encoded by Kcnn3, that generate outward current. The open probabilities of interstitial cell conductances are controlled by Ca2+ release from the endoplasmic reticulum. The resulting Ca2+ transients occur spontaneously in a stochastic manner. Ca2+ transients in ICC induce spontaneous transient inward currents and spontaneous transient depolarizations (STDs). Neurotransmission increases or decreases Ca2+ transients, and the resulting depolarizing or hyperpolarizing responses conduct to other cells in the SIP syncytium. In pacemaker ICC, STDs activate voltage-dependent Ca2+ influx, which initiates a cluster of Ca2+ transients and sustains activation of ANO1 channels and depolarization during slow waves. Regulation of GI motility has traditionally been described as neurogenic and myogenic. Recent advances in understanding Ca2+ handling mechanisms in interstitial cells and how these mechanisms influence motor patterns of the GI tract suggest that the term "myogenic" should be replaced by the term "SIPgenic," as this review discusses.
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Affiliation(s)
- Kenton M Sanders
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada-Reno, Reno, Nevada, United States
| | - Bernard T Drumm
- Smooth Muscle Research Centre, Dundalk Institute of Technology, Dundalk, Ireland
| | - Caroline A Cobine
- Smooth Muscle Research Centre, Dundalk Institute of Technology, Dundalk, Ireland
| | - Salah A Baker
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada-Reno, Reno, Nevada, United States
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7
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Benson JC, Romito O, Abdelnaby AE, Xin P, Pathak T, Weir SE, Kirk V, Castaneda F, Yoast RE, Emrich SM, Tang PW, Yule DI, Hempel N, Potier-Cartereau M, Sneyd J, Trebak M. A multiple-oscillator mechanism underlies antigen-induced Ca 2+ oscillations in Jurkat T-cells. J Biol Chem 2023; 299:105310. [PMID: 37778728 PMCID: PMC10641176 DOI: 10.1016/j.jbc.2023.105310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 09/11/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023] Open
Abstract
T-cell receptor stimulation triggers cytosolic Ca2+ signaling by inositol-1,4,5-trisphosphate (IP3)-mediated Ca2+ release from the endoplasmic reticulum (ER) and Ca2+ entry through Ca2+ release-activated Ca2+ (CRAC) channels gated by ER-located stromal-interacting molecules (STIM1/2). Physiologically, cytosolic Ca2+ signaling manifests as regenerative Ca2+ oscillations, which are critical for nuclear factor of activated T-cells-mediated transcription. In most cells, Ca2+ oscillations are thought to originate from IP3 receptor-mediated Ca2+ release, with CRAC channels indirectly sustaining them through ER refilling. Here, experimental and computational evidence support a multiple-oscillator mechanism in Jurkat T-cells whereby both IP3 receptor and CRAC channel activities oscillate and directly fuel antigen-evoked Ca2+ oscillations, with the CRAC channel being the major contributor. KO of either STIM1 or STIM2 significantly reduces CRAC channel activity. As such, STIM1 and STIM2 synergize for optimal Ca2+ oscillations and activation of nuclear factor of activated T-cells 1 and are essential for ER refilling. The loss of both STIM proteins abrogates CRAC channel activity, drastically reduces ER Ca2+ content, severely hampers cell proliferation and enhances cell death. These results clarify the mechanism and the contribution of STIM proteins to Ca2+ oscillations in T-cells.
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Affiliation(s)
- J Cory Benson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Graduate Program in Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Olivier Romito
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Inserm UMR 1069, Nutrition Croissance Cancer, Faculté de Médecine, Université de Tours, Tours, France
| | - Ahmed Emam Abdelnaby
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ping Xin
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Trayambak Pathak
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sierra E Weir
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vivien Kirk
- Department of Mathematics, University of Auckland, Auckland, New Zealand
| | | | - Ryan E Yoast
- Graduate Program in Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Scott M Emrich
- Graduate Program in Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Priscilla W Tang
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - David I Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, USA
| | - Nadine Hempel
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marie Potier-Cartereau
- Inserm UMR 1069, Nutrition Croissance Cancer, Faculté de Médecine, Université de Tours, Tours, France
| | - James Sneyd
- Department of Mathematics, University of Auckland, Auckland, New Zealand
| | - Mohamed Trebak
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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8
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Paknejad N, Sapuru V, Hite RK. Structural titration reveals Ca 2+-dependent conformational landscape of the IP 3 receptor. Nat Commun 2023; 14:6897. [PMID: 37898605 PMCID: PMC10613215 DOI: 10.1038/s41467-023-42707-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023] Open
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are endoplasmic reticulum Ca2+ channels whose biphasic dependence on cytosolic Ca2+ gives rise to Ca2+ oscillations that regulate fertilization, cell division and cell death. Despite the critical roles of IP3R-mediated Ca2+ responses, the structural underpinnings of the biphasic Ca2+ dependence that underlies Ca2+ oscillations are incompletely understood. Here, we collect cryo-EM images of an IP3R with Ca2+ concentrations spanning five orders of magnitude. Unbiased image analysis reveals that Ca2+ binding does not explicitly induce conformational changes but rather biases a complex conformational landscape consisting of resting, preactivated, activated, and inhibited states. Using particle counts as a proxy for relative conformational free energy, we demonstrate that Ca2+ binding at a high-affinity site allows IP3Rs to activate by escaping a low-energy resting state through an ensemble of preactivated states. At high Ca2+ concentrations, IP3Rs preferentially enter an inhibited state stabilized by a second, low-affinity Ca2+ binding site. Together, these studies provide a mechanistic basis for the biphasic Ca2+-dependence of IP3R channel activity.
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Affiliation(s)
- Navid Paknejad
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Physiology, Biophysics, and Systems Biology (PBSB) Program, Weill Cornell Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY, 10065, USA
| | - Vinay Sapuru
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Physiology, Biophysics, and Systems Biology (PBSB) Program, Weill Cornell Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY, 10065, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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9
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Szigeti K, Ihnatovych I, Rosas N, Dorn RP, Notari E, Cortes Gomez E, He M, Maly I, Prasad S, Nimmer E, Heo Y, Fuchsova B, Bennett DA, Hofmann WA, Pralle A, Bae Y, Wang J. Neuronal actin cytoskeleton gain of function in the human brain. EBioMedicine 2023; 95:104725. [PMID: 37517100 PMCID: PMC10404607 DOI: 10.1016/j.ebiom.2023.104725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND While advancements in imaging techniques have led to major strides in deciphering the human brain, successful interventions are elusive and represent some of the most persistent translational gaps in medicine. Human restricted CHRFAM7A has been associated with neuropsychiatric disorders. METHODS The physiological role of CHRFAM7A in human brain is explored using multiomics approach on 600 post mortem human brain tissue samples. The emerging pathways and mechanistic hypotheses are tested and validated in an isogenic hiPSC model of CHRFAM7A knock-in medial ganglionic eminence progenitors and neurons. FINDINGS CHRFAM7A is identified as a modulator of intracellular calcium dynamics and an upstream regulator of Rac1. Rac1 activation re-designs the actin cytoskeleton leading to dynamic actin driven remodeling of membrane protrusion and a switch from filopodia to lamellipodia. The reinforced cytoskeleton leads to an advantage to tolerate stiffer mechanical properties of the extracellular environment. INTERPRETATION CHRFAM7A modifies the actin cytoskeleton to a more dynamic and stiffness resistant state in an α7nAChR dependent manner. CHRFAM7A may facilitate neuronal adaptation to changes in the brain environment in physiological and pathological conditions contributing to risk or recovery. Understanding how CHRFAM7A affects human brain requires human studies in the areas of memory formation and erasure, cognitive reserve, and neuronal plasticity. FUNDING This work is supported in part by the Community Foundation for Greater Buffalo (Kinga Szigeti). Also, in part by the International Society for Neurochemistry (ISN) and The Company of Biologists (Nicolas Rosas). ROSMAP is supported by NIA grants P30AG10161, P30AG72975, R01AG15819, R01AG17917. U01AG46152, and U01AG61356.
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Affiliation(s)
- Kinga Szigeti
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA.
| | - Ivanna Ihnatovych
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Nicolás Rosas
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA; Instituto de Investigaciones Biotecnológicas, Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de, Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - Ryu P Dorn
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Emily Notari
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | | | - Muye He
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Ivan Maly
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Shreyas Prasad
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Erik Nimmer
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Yuna Heo
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Beata Fuchsova
- Instituto de Investigaciones Biotecnológicas, Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de, Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Wilma A Hofmann
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Arnd Pralle
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Yongho Bae
- State University of New York at Buffalo, 875 Ellicott St., Buffalo, NY, 14203, USA
| | - Jianmin Wang
- Roswell Park Comprehensive Cancer Center, 665 Elm St, Buffalo, NY 14203, USA
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10
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Friedhoff VN, Lindner B, Falcke M. Modeling IP 3-induced Ca 2+ signaling based on its interspike interval statistics. Biophys J 2023; 122:2818-2831. [PMID: 37312455 PMCID: PMC10398346 DOI: 10.1016/j.bpj.2023.06.004] [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: 03/10/2023] [Revised: 04/24/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023] Open
Abstract
Inositol 1,4,5-trisphosphate (IP3)-induced Ca2+ signaling is a second messenger system used by almost all eukaryotic cells. Recent research demonstrated randomness of Ca2+ signaling on all structural levels. We compile eight general properties of Ca2+ spiking common to all cell types investigated and suggest a theory of Ca2+ spiking starting from the random behavior of IP3 receptor channel clusters mediating the release of Ca2+ from the endoplasmic reticulum capturing all general properties and pathway-specific behavior. Spike generation begins after the absolute refractory period of the previous spike. According to its hierarchical spreading from initiating channel openings to cell level, we describe it as a first passage process from none to all clusters open while the cell recovers from the inhibition which terminated the previous spike. Our theory reproduces the exponential stimulation response relation of the average interspike interval Tav and its robustness properties, random spike timing with a linear moment relation between Tav and the interspike interval SD and its robustness properties, sensitive dependency of Tav on diffusion properties, and nonoscillatory local dynamics. We explain large cell variability of Tav observed in experiments by variability of channel cluster coupling by Ca2+-induced Ca2+ release, the number of clusters, and IP3 pathway component expression levels. We predict the relation between puff probability and agonist concentration and [IP3] and agonist concentration. Differences of spike behavior between cell types and stimulating agonists are explained by the different types of negative feedback terminating spikes. In summary, the hierarchical random character of spike generation explains all of the identified general properties.
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Affiliation(s)
- Victor Nicolai Friedhoff
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Department of Physics, Humboldt University, Berlin, Germany
| | - Benjamin Lindner
- Bernstein Center for Computational Neuroscience Berlin, Berlin, Germany; Department of Physics, Humboldt University, Berlin, Germany
| | - Martin Falcke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Department of Physics, Humboldt University, Berlin, Germany.
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11
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Zeng Z, Cheng M, Li M, Wang T, Wen F, Sanderson MJ, Sneyd J, Shen Y, Chen J. Inherent differences of small airway contraction and Ca 2+ oscillations in airway smooth muscle cells between BALB/c and C57BL/6 mouse strains. Front Cell Dev Biol 2023; 11:1202573. [PMID: 37346175 PMCID: PMC10279852 DOI: 10.3389/fcell.2023.1202573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
BALB/c and C57BL/6 mouse strains are widely used as animal model in studies of respiratory diseases, such as asthma. Asthma is characterized by airway hyperresponsiveness, which is eventually resulted from the excessive airway smooth muscle (ASM) contraction mediated by Ca2+ oscillations in ASM cells. It is reported that BALB/c mice have inherently higher airway responsiveness, but show no different contractive response of tracheal ring as compared to C57BL/6 mice. However, whether the different airway responsiveness is due to the different extents of small airway contraction, and what's underlying mechanism remains unknown. Here, we assess agonist-induced small airway contraction and Ca2+ oscillations in ASM cells between BALB/c and C57BL/6 mice by using precision-cut lung slices (PCLS). We found that BALB/c mice showed an intrinsically stronger extent of small airway narrowing and faster Ca2+ oscillations in ASM cells in response to agonists. These differences were associated with a higher magnitude of Ca2+ influx via store-operated Ca2+ entry (SOCE), as a result of increased expression of SOCE components (STIM1, Orai1) in the ASM cells of small airway of BALB/c mice. An established mathematical model and experimental results suggested that the increased SOC current could result in increased agonist-induced Ca2+ oscillations. Therefore, the inherently higher SOC underlies the increased Ca2+ oscillation frequency in ASM cells and stronger small airway contraction in BALB/c mice, thus higher airway responsiveness in BALB/c than C57BL/6 mouse strain.
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Affiliation(s)
- Zijian Zeng
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University and Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, Chengdu, Sichuan, China
| | - Mengxin Cheng
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University and Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, Chengdu, Sichuan, China
| | - Meng Li
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University and Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, Chengdu, Sichuan, China
| | - Tao Wang
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University and Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, Chengdu, Sichuan, China
| | - Fuqiang Wen
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University and Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, Chengdu, Sichuan, China
| | - Michael J. Sanderson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
| | - James Sneyd
- Department of Mathematics, The University of Auckland, Auckland, New Zealand
| | - Yongchun Shen
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University and Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, Chengdu, Sichuan, China
| | - Jun Chen
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University and Division of Pulmonary Diseases, State Key Laboratory of Biotherapy, Chengdu, Sichuan, China
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12
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Benson JC, Trebak M. Too much of a good thing: The case of SOCE in cellular apoptosis. Cell Calcium 2023; 111:102716. [PMID: 36931194 PMCID: PMC10481469 DOI: 10.1016/j.ceca.2023.102716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/13/2023]
Abstract
Intracellular calcium (Ca2+) is an essential second messenger in eukaryotic cells regulating numerous cellular functions such as contraction, secretion, immunity, growth, and metabolism. Ca2+ signaling is also a key signal transducer in the intrinsic apoptosis pathway. The store-operated Ca2+ entry pathway (SOCE) is ubiquitously expressed in eukaryotic cells, and is the primary Ca2+ influx pathway in non-excitable cells. SOCE is mediated by the endoplasmic reticulum Ca2+ sensing STIM proteins, and the plasma membrane Ca2+-selective Orai channels. A growing number of studies have implicated SOCE in regulating cell death primarily via the intrinsic apoptotic pathway in a variety of tissues and in response to physiological stressors such as traumatic brain injury, ischemia reperfusion injury, sepsis, and alcohol toxicity. Notably, the literature points to excessive cytosolic Ca2+ influx through SOCE in vulnerable cells as a key factor tipping the balance towards cellular apoptosis. While the literature primarily addresses the functions of STIM1 and Orai1, STIM2, Orai2 and Orai3 are also emerging as potential regulators of cell death. Here, we review the functions of STIM and Orai proteins in regulating cell death and the implications of this regulation to human pathologies.
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Affiliation(s)
- J Cory Benson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 1526, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 1526, USA; Department of Cellular and Molecular Physiology, Graduate Program, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Mohamed Trebak
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 1526, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 1526, USA; UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA 1526, USA.
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13
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Kim DS, Pessah IN, Santana CM, Purnell BS, Li R, Buchanan GF, Rumbeiha WK. Investigations into hydrogen sulfide-induced suppression of neuronal activity in vivo and calcium dysregulation in vitro. Toxicol Sci 2023; 192:kfad022. [PMID: 36882182 PMCID: PMC10109532 DOI: 10.1093/toxsci/kfad022] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Acute exposure to high concentrations of hydrogen sulfide (H2S) leads to sudden death and, if survived, lingering neurological disorders. Clinical signs include seizures, loss of consciousness, and dyspnea. The proximate mechanisms underlying H2S-induced acute toxicity and death have not been clearly elucidated. We investigated electrocerebral, cardiac and respiratory activity during H2S exposure using electroencephalogram (EEG), electrocardiogram (EKG) and plethysmography. H2S suppressed electrocerebral activity and disrupted breathing. Cardiac activity was comparatively less affected. To test whether Ca2+ dysregulation contributes to H2S-induced EEG suppression, we developed an in vitro real-time rapid throughput assay measuring patterns of spontaneous synchronized Ca2+ oscillations in cultured primary cortical neuronal networks loaded with the indicator Fluo-4 using the fluorescent imaging plate reader (FLIPR-Tetra®). Sulfide >5 ppm dysregulated synchronous calcium oscillation (SCO) patterns in a dose-dependent manner. Inhibitors of NMDA and AMPA receptors magnified H2S-induced SCO suppression. Inhibitors of L-type voltage gated Ca2+ channels and transient receptor potential channels prevented H2S-induced SCO suppression. Inhibitors of T-type voltage gated Ca2+ channels, ryanodine receptors, and sodium channels had no measurable influence on H2S-induced SCO suppression. Exposures to > 5 ppm sulfide also suppressed neuronal electrical activity in primary cortical neurons measured by multi-electrode array (MEA), an effect alleviated by pretreatment with the nonselective transient receptor potential channel inhibitor, 2-APB. 2-APB also reduced primary cortical neuronal cell death from sulfide exposure. These results improve our understanding of the role of different Ca2+ channels in acute H2S-induced neurotoxicity and identify transient receptor potential channel modulators as novel structures with potential therapeutic benefits.
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Affiliation(s)
- Dong-Suk Kim
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, California 95616, USA
| | - Isaac N Pessah
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, California 95616, USA
| | - Cristina M Santana
- VDPAM, College of Veterinary Medicine, Iowa State University, Ames, Iowa 50011, USA
- MRIGlobal, Kansas City, Missouri 64110, USA
| | - Benton S Purnell
- Department of Neurology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52246, USA
- Department of Nerosurgery, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Rui Li
- Department of Neurology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52246, USA
| | - Gordon F Buchanan
- Department of Neurology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52246, USA
| | - Wilson K Rumbeiha
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, California 95616, USA
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14
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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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15
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Sneyd J, Rugis J, Su S, Suresh V, Wahl AM, Yule DI. Simulation of Calcium Dynamics in Realistic Three-Dimensional Domains. Biomolecules 2022; 12:1455. [PMID: 36291663 PMCID: PMC9599163 DOI: 10.3390/biom12101455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
The cytosolic concentration of free calcium ions ([Ca2+]) is an important intracellular messenger in most cell types, and the spatial distribution of [Ca2+] is often critical. In a salivary gland acinar cell, a polarised epithelial cell, whose principal function is to transport water and thus secrete saliva, [Ca2+] controls the secretion of primary saliva, but increases in [Ca2+] are localised to the apical regions of the cell. Hence, any quantitative explanation of how [Ca2+] controls saliva secretion must take into careful account the spatial distribution of the various Ca2+ sources, Ca2+ sinks, and Ca2+-sensitive ion channels. Based on optical slices, we have previously constructed anatomically accurate three-dimensional models of seven salivary gland acinar cells, and thus shown that a model in which Ca2+ responses are confined to the apical regions of the cell is sufficient to provide a quantitative and predictive explanation of primary saliva secretion. However, reconstruction of such anatomically accurate cells is extremely time consuming and inefficient. Here, we present an alternative, mostly automated method of constructing three-dimensional cells that are approximately anatomically accurate and show that the new construction preserves the quantitative accuracy of the model.
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Affiliation(s)
- James Sneyd
- Department of Mathematics, University of Auckland, Auckland 1142, New Zealand
| | - John Rugis
- Department of Mathematics, University of Auckland, Auckland 1142, New Zealand
| | - Shan Su
- Department of Mathematics, University of Auckland, Auckland 1142, New Zealand
| | - Vinod Suresh
- Department of Engineering Science, University of Auckland, Auckland 1142, New Zealand
| | - Amanda M. Wahl
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
| | - David I. Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY 14642, USA
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16
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Chen M, Liu H, Wang R. Dynamical behaviors of quorum sensing network mediated by combinatorial perturbation. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:4812-4840. [PMID: 35430842 DOI: 10.3934/mbe.2022225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The dynamical behaviors of the quorum sensing (QS) system are closely related to the release drugs and control the PH value in microorganisms and plants. However, the effect of the main molecules AiiA, LuxI, H$ _2 $O$ _2 $, and time delayed individual and combinatorial perturbation on the QS system dynamics and the above-mentioned biological phenomena is still unclear, which are seen as a key consideration in our paper. This paper formulates a QS computational model by incorporating these several substances. First, for the protein production time delay, a critical value is given by Hopf bifurcation theory. It is found that a larger time delay can lead to a larger amplitude and a longer period. This indicates that the length of time for protein synthesis has a regulatory effect on the release of drugs from the bacterial population. Second, hen the concentrations of AiiA, LuxI, and H$ _2 $O$ _2 $ is modulated individually, the QS system undergoes periodic oscillation and bistable state. Meanwhile, oscillatory and bistable regions can be significantly affected by simultaneously perturbing any two parameters related to AiiA, LuxI, and H$ _2 $O$ _2 $. This means that the individual or simultaneous changes of the three intrinsic molecular concentrations can effectively control the drugs release and the PH value in microorganisms and plants. Finally, the sensitivity relationship between the critical value of the delay and AiiA, LuxI, H$ _2 $O$ _2 $ parameters is analyzed.
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Affiliation(s)
- Menghan Chen
- Department of Mathematics, Shanghai University, Shanghai 200444, China
| | - Haihong Liu
- Department of Mathematics, Yunnan Normal University, Kunming 650500, China
| | - Ruiqi Wang
- Department of Mathematics, Shanghai University, Shanghai 200444, China
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17
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Hancock EJ, Zawieja SD, Macaskill C, Davis MJ, Bertram CD. Modelling the coupling of the M-clock and C-clock in lymphatic muscle cells. Comput Biol Med 2022; 142:105189. [PMID: 34995957 PMCID: PMC9132416 DOI: 10.1016/j.compbiomed.2021.105189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 01/01/2023]
Abstract
Chronic dysfunction of the lymphatic vascular system results in fluid accumulation between cells: lymphoedema. The condition is commonly acquired secondary to diseases such as cancer or the associated therapies. The primary driving force for fluid return through the lymphatic vasculature is provided by contractions of the muscularized lymphatic collecting vessels, driven by electrochemical oscillations. However, there is an incomplete understanding of the molecular and bioelectric mechanisms involved in lymphatic muscle cell excitation, hampering the development and use of pharmacological therapies. Modelling in silico has contributed greatly to understanding the contributions of specific ion channels to the cardiac action potential, but modelling of these processes in lymphatic muscle remains limited. Here, we propose a model of oscillations in the membrane voltage (M-clock) and intracellular calcium concentrations (C-clock) of lymphatic muscle cells. We modify a model by Imtiaz and colleagues to enable the M-clock to drive the C-clock oscillations. This approach differs from typical models of calcium oscillators in lymphatic and related cell types, but is required to fit recent experimental data. We include an additional voltage dependence in the gating variable control for the L-type calcium channel, enabling the M-clock to oscillate independently of the C-clock. We use phase-plane analysis to show that these M-clock oscillations are qualitatively similar to those of a generalised FitzHugh-Nagumo model. We also provide phase plane analysis to understand the interaction of the M-clock and C-clock oscillations. The model and methods have the potential to help determine mechanisms and find targets for pharmacological treatment of lymphoedema.
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Affiliation(s)
- E J Hancock
- School of Mathematics & Statistics, University of Sydney, NSW, 2006, Australia
| | - S D Zawieja
- Dept. of Medical Pharmacology & Physiology, Univ. of Missouri, Columbia, MI, 65212, USA
| | - C Macaskill
- School of Mathematics & Statistics, University of Sydney, NSW, 2006, Australia
| | - M J Davis
- Dept. of Medical Pharmacology & Physiology, Univ. of Missouri, Columbia, MI, 65212, USA
| | - C D Bertram
- School of Mathematics & Statistics, University of Sydney, NSW, 2006, Australia.
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18
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Developing a Mathematical Model of Intracellular Calcium Dynamics for Evaluating Combined Anticancer Effects of Afatinib and RP4010 in Esophageal Cancer. Int J Mol Sci 2022; 23:ijms23031763. [PMID: 35163685 PMCID: PMC8836083 DOI: 10.3390/ijms23031763] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 01/27/2023] Open
Abstract
Targeting dysregulated Ca2+ signaling in cancer cells is an emerging chemotherapy approach. We previously reported that store-operated Ca2+ entry (SOCE) blockers, such as RP4010, are promising antitumor drugs for esophageal cancer. As a tyrosine kinase inhibitor (TKI), afatinib received FDA approval to be used in targeted therapy for patients with EGFR mutation-positive cancers. While preclinical studies and clinical trials have shown that afatinib has benefits for esophageal cancer patients, it is not known whether a combination of afatinib and RP4010 could achieve better anticancer effects. Since TKI can alter intracellular Ca2+ dynamics through EGFR/phospholipase C-γ pathway, in this study, we evaluated the inhibitory effect of afatinib and RP4010 on intracellular Ca2+ oscillations in KYSE-150, a human esophageal squamous cell carcinoma cell line, using both experimental and mathematical simulations. Our mathematical simulation of Ca2+ oscillations could fit well with experimental data responding to afatinib or RP4010, both separately or in combination. Guided by simulation, we were able to identify a proper ratio of afatinib and RP4010 for combined treatment, and such a combination presented synergistic anticancer-effect evidence by experimental measurement of intracellular Ca2+ and cell proliferation. This intracellular Ca2+ dynamic-based mathematical simulation approach could be useful for a rapid and cost-effective evaluation of combined targeting therapy drugs.
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19
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Flesia AG, Nieto PS, Aon MA, Kembro JM. Computational Approaches and Tools as Applied to the Study of Rhythms and Chaos in Biology. Methods Mol Biol 2022; 2399:277-341. [PMID: 35604562 DOI: 10.1007/978-1-0716-1831-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The temporal dynamics in biological systems displays a wide range of behaviors, from periodic oscillations, as in rhythms, bursts, long-range (fractal) correlations, chaotic dynamics up to brown and white noise. Herein, we propose a comprehensive analytical strategy for identifying, representing, and analyzing biological time series, focusing on two strongly linked dynamics: periodic (oscillatory) rhythms and chaos. Understanding the underlying temporal dynamics of a system is of fundamental importance; however, it presents methodological challenges due to intrinsic characteristics, among them the presence of noise or trends, and distinct dynamics at different time scales given by molecular, dcellular, organ, and organism levels of organization. For example, in locomotion circadian and ultradian rhythms coexist with fractal dynamics at faster time scales. We propose and describe the use of a combined approach employing different analytical methodologies to synergize their strengths and mitigate their weaknesses. Specifically, we describe advantages and caveats to consider for applying probability distribution, autocorrelation analysis, phase space reconstruction, Lyapunov exponent estimation as well as different analyses such as harmonic, namely, power spectrum; continuous wavelet transforms; synchrosqueezing transform; and wavelet coherence. Computational harmonic analysis is proposed as an analytical framework for using different types of wavelet analyses. We show that when the correct wavelet analysis is applied, the complexity in the statistical properties, including temporal scales, present in time series of signals, can be unveiled and modeled. Our chapter showcase two specific examples where an in-depth analysis of rhythms and chaos is performed: (1) locomotor and food intake rhythms over a 42-day period of mice subjected to different feeding regimes; and (2) chaotic calcium dynamics in a computational model of mitochondrial function.
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Affiliation(s)
- Ana Georgina Flesia
- Universidad Nacional de Córdoba, Facultad de Matemática, Astronomía y Física, Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro de Investigaciones y Estudios de Matemática (CIEM, CONICET), Ciudad Universitaria, Córdoba, Argentina
| | - Paula Sofia Nieto
- Universidad Nacional de Córdoba, Facultad de Matemática, Astronomía y Física, Córdoba, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Física Enrique Gaviola (IFEG, CONICET-UNC), Ciudad Universitaria, Córdoba, Argentina
| | - Miguel A Aon
- Laboratory of Cardiovascular Science, and Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jackelyn Melissa Kembro
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Instituto de Ciencia y Tecnología de los Alimentos (ICTA) and Catedra de Química Biológica. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Biológicas y Tecnológicas (IIByT, CONICET-UNC), Vélez Sarsfield 1611, Ciudad Universitaria, Córdoba, Argentina.
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20
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Schulte A, Bieniussa L, Gupta R, Samtleben S, Bischler T, Doering K, Sodmann P, Rittner H, Blum R. Homeostatic calcium fluxes, ER calcium release, SOCE, and calcium oscillations in cultured astrocytes are interlinked by a small calcium toolkit. Cell Calcium 2021; 101:102515. [PMID: 34896701 DOI: 10.1016/j.ceca.2021.102515] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/27/2022]
Abstract
How homeostatic ER calcium fluxes shape cellular calcium signals is still poorly understood. Here we used dual-color calcium imaging (ER-cytosol) and transcriptome analysis to link candidates of the calcium toolkit of astrocytes with homeostatic calcium signals. We found molecular and pharmacological evidence that P/Q-type channel Cacna1a contributes to depolarization-dependent calcium entry in astrocytes. For stimulated ER calcium release, the cells express the phospholipase Cb3, IP3 receptors Itpr1 and Itpr2, but no ryanodine receptors (Ryr1-3). After IP3-induced calcium release, Stim1/2 - Orai1/2/3 most likely mediate SOCE. The Serca2 (Atp2a2) is the candidate for refilling of the ER calcium store. The cells highly express adenosine receptor Adora1a for IP3-induced calcium release. Accordingly, adenosine induces fast ER calcium release and subsequent ER calcium oscillations. After stimulation, calcium refilling of the ER depends on extracellular calcium. In response to SOCE, astrocytes show calcium-induced calcium release, notably even after ER calcium was depleted by extracellular calcium removal in unstimulated cells. In contrast, spontaneous ER-cytosol calcium oscillations were not fully dependent on extracellular calcium, as ER calcium oscillations could persist over minutes in calcium-free solution. Additionally, cell-autonomous calcium oscillations show a second-long spatial and temporal delay in the signal dynamics of ER and cytosolic calcium. Our data reveal a rather strong contribution of homeostatic calcium fluxes in shaping IP3-induced and calcium-induced calcium release as well as spatiotemporal components of intracellular calcium oscillations.
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Affiliation(s)
- Annemarie Schulte
- Department of Neurology, University Hospital of Würzburg, Würzburg, 97080 Germany; Institute of Clinical Neurobiology, University Hospital of Würzburg, Würzburg, 97078 Germany
| | - Linda Bieniussa
- Institute of Clinical Neurobiology, University Hospital of Würzburg, Würzburg, 97078 Germany; Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Würzburg, Germany
| | - Rohini Gupta
- Department of Neurology, University Hospital of Würzburg, Würzburg, 97080 Germany; Institute of Clinical Neurobiology, University Hospital of Würzburg, Würzburg, 97078 Germany
| | - Samira Samtleben
- Institute of Clinical Neurobiology, University Hospital of Würzburg, Würzburg, 97078 Germany; Department of Cell Biology, University of Alberta, MSM, Edmonton, T6G 2H7 Canada
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, Würzburg, 97080 Germany
| | - Kristina Doering
- Core Unit Systems Medicine, University of Würzburg, Würzburg, 97080 Germany; Department of Human Genetics, Ruhr University Bochum, Bochum, Germany
| | - Philipp Sodmann
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, 97080 Germany
| | - Heike Rittner
- Department of Anesthesiology, Intensive Care, Emergency Medicine and Pain Therapy, University Hospital of Würzburg, Würzburg, 97074 Germany
| | - Robert Blum
- Department of Neurology, University Hospital of Würzburg, Würzburg, 97080 Germany; Institute of Clinical Neurobiology, University Hospital of Würzburg, Würzburg, 97078 Germany.
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21
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Xiong X, Li Y, Zheng D. Dynamic mechanism of multiple bursting patterns in a whole-cell multiscale model with calcium oscillations. JOURNAL OF BIOLOGICAL DYNAMICS 2021; 15:308-326. [PMID: 34092205 DOI: 10.1080/17513758.2021.1925753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
The dynamic mechanism of a whole-cell model containing electrical signalling and two-compartment Ca2+ signalling in gonadotrophs is investigated. The transition from spiking to bursting by Hopf bifurcation of the fast subsystem about the slow variable is detected via the suitable parameters. When the timescale of K+ gating variable is changed, the relaxation oscillation with locally small fluctuation, chaotic bursting and mixed-mode bursting (MMB) are revealed through chaos. In addition, the bifurcation of [Ca2+]i with regard to [IP3] is analysed, showing periodic solutions, torus, period doubling solutions and chaos. Finally, hyperpolarizations and torus canard-like behaviours of the full system under a set of specific parameters are elucidated.
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Affiliation(s)
- Xiaowen Xiong
- School of Physical and Mathematical Sciences, Nanjing Tech University, Nanjing, People's Republic of China
| | - Yanqiu Li
- School of Physical and Mathematical Sciences, Nanjing Tech University, Nanjing, People's Republic of China
| | - Dongmei Zheng
- School of Physical and Mathematical Sciences, Nanjing Tech University, Nanjing, People's Republic of China
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22
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Maćešić S, Tóth Á, Horváth D. Origins of oscillatory dynamics in the model of reactive oxygen species in the rhizosphere. J Chem Phys 2021; 155:175102. [PMID: 34742207 DOI: 10.1063/5.0062139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oscillatory processes are essential for normal functioning and survival of biological systems, and reactive oxygen species have a prominent role in many of them. A mechanism representing the dynamics of these species in the rhizosphere is analyzed using stoichiometric network analysis with the aim to determine its capabilities to simulate various dynamical states, including oscillations. A detailed analysis has shown that unstable steady states result from four destabilizing feedback cycles, among which the cycle involving hydroquinone, an electron acceptor, and its semi-reduced form is the dominant one responsible for the existence of saddle-node and Andronov-Hopf bifurcations. This requires a higher steady-state concentration for the reduced electron acceptor compared to that of the remaining species, where the level of oxygen steady-state concentration determines whether the Andronov-Hopf or saddle-node bifurcation will occur.
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Affiliation(s)
- Stevan Maćešić
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, 6720 Szeged, Hungary
| | - Ágota Tóth
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, 6720 Szeged, Hungary
| | - Dezső Horváth
- Department of Applied and Environmental Chemistry, University of Szeged, Rerrich Béla tér 1, 6720 Szeged, Hungary
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23
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From spikes to intercellular waves: Tuning intercellular calcium signaling dynamics modulates organ size control. PLoS Comput Biol 2021; 17:e1009543. [PMID: 34723960 PMCID: PMC8601605 DOI: 10.1371/journal.pcbi.1009543] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 11/18/2021] [Accepted: 10/07/2021] [Indexed: 12/18/2022] Open
Abstract
Information flow within and between cells depends significantly on calcium (Ca2+) signaling dynamics. However, the biophysical mechanisms that govern emergent patterns of Ca2+ signaling dynamics at the organ level remain elusive. Recent experimental studies in developing Drosophila wing imaginal discs demonstrate the emergence of four distinct patterns of Ca2+ activity: Ca2+ spikes, intercellular Ca2+ transients, tissue-level Ca2+ waves, and a global “fluttering” state. Here, we used a combination of computational modeling and experimental approaches to identify two different populations of cells within tissues that are connected by gap junction proteins. We term these two subpopulations “initiator cells,” defined by elevated levels of Phospholipase C (PLC) activity, and “standby cells,” which exhibit baseline activity. We found that the type and strength of hormonal stimulation and extent of gap junctional communication jointly determine the predominate class of Ca2+ signaling activity. Further, single-cell Ca2+ spikes are stimulated by insulin, while intercellular Ca2+ waves depend on Gαq activity. Our computational model successfully reproduces how the dynamics of Ca2+ transients varies during organ growth. Phenotypic analysis of perturbations to Gαq and insulin signaling support an integrated model of cytoplasmic Ca2+ as a dynamic reporter of overall tissue growth. Further, we show that perturbations to Ca2+ signaling tune the final size of organs. This work provides a platform to further study how organ size regulation emerges from the crosstalk between biochemical growth signals and heterogeneous cell signaling states. Calcium (Ca2+) is a universal second messenger that regulates a myriad of cellular processes such as cell division, cell proliferation and apoptosis. Multiple patterns of Ca2+ signaling including single-cell spikes, multicellular Ca2+ transients, large-scale Ca2+ waves, and global “fluttering” have been observed in epithelial systems during organ development. Key molecular players and biophysical mechanisms involved in formation of these patterns during organ development are not well understood. In this work, we developed a generalized multicellular model of Ca2+ that captures all the key categories of Ca2+ activity as a function of key hormonal signals. Integration of model predictions and experiments reveals two subclasses of cell populations and demonstrates that Ca2+ signaling activity at the organ scale is defined by a general decrease in gap junction communication as an organ grows. Our experiments also reveal that a “goldilocks zone” of optimal Ca2+ activity is required to achieve optimal growth at the organ level.
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24
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Yoast RE, Emrich SM, Zhang X, Xin P, Arige V, Pathak T, Benson JC, Johnson MT, Abdelnaby AE, Lakomski N, Hempel N, Han JM, Dupont G, Yule DI, Sneyd J, Trebak M. The Mitochondrial Ca 2+ uniporter is a central regulator of interorganellar Ca 2+ transfer and NFAT activation. J Biol Chem 2021; 297:101174. [PMID: 34499925 PMCID: PMC8496184 DOI: 10.1016/j.jbc.2021.101174] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial Ca2+ uptake tailors the strength of stimulation of plasma membrane phospholipase C–coupled receptors to that of cellular bioenergetics. However, how Ca2+ uptake by the mitochondrial Ca2+ uniporter (MCU) shapes receptor-evoked interorganellar Ca2+ signaling is unknown. Here, we used CRISPR/Cas9 gene knockout, subcellular Ca2+ imaging, and mathematical modeling to show that MCU is a universal regulator of intracellular Ca2+ signaling across mammalian cell types. MCU activity sustains cytosolic Ca2+ signaling by preventing Ca2+-dependent inactivation of store-operated Ca2+ release–activated Ca2+ channels and by inhibiting Ca2+ extrusion. Paradoxically, MCU knockout (MCU-KO) enhanced cytosolic Ca2+ responses to store depletion. Physiological agonist stimulation in MCU-KO cells led to enhanced frequency of cytosolic Ca2+ oscillations, endoplasmic reticulum Ca2+ refilling, nuclear translocation of nuclear factor for activated T cells transcription factors, and cell proliferation, without altering inositol-1,4,5-trisphosphate receptor activity. Our data show that MCU has dual counterbalancing functions at the cytosol–mitochondria interface, whereby the cell-specific MCU-dependent cytosolic Ca2+ clearance and buffering capacity of mitochondria reciprocally regulate interorganellar Ca2+ transfer and nuclear factor for activated T cells nuclear translocation during receptor-evoked signaling. These findings highlight the critical dual function of the MCU not only in the acute Ca2+ buffering by mitochondria but also in shaping endoplasmic reticulum and cytosolic Ca2+ signals that regulate cellular transcription and function.
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Affiliation(s)
- Ryan E Yoast
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Scott M Emrich
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Xuexin Zhang
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ping Xin
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vikas Arige
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, USA
| | - Trayambak Pathak
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - J Cory Benson
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Martin T Johnson
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ahmed Emam Abdelnaby
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Natalia Lakomski
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Nadine Hempel
- Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Jung Min Han
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Geneviève Dupont
- Unité de Chronobiologie Théorique, Université Libre de Bruxelles, Brussels, Belgium
| | - David I Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, New York, USA
| | - James Sneyd
- Department of Mathematics, The University of Auckland, Auckland, New Zealand
| | - Mohamed Trebak
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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25
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Long Y, He P, Shao Z, Li Z, Kim H, Yao AM, Peng Y, Xu R, Ahn CH, Lee SW, Zhong J, Lin L. Moisture-induced autonomous surface potential oscillations for energy harvesting. Nat Commun 2021; 12:5287. [PMID: 34489424 PMCID: PMC8421362 DOI: 10.1038/s41467-021-25554-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 07/30/2021] [Indexed: 11/09/2022] Open
Abstract
A variety of autonomous oscillations in nature such as heartbeats and some biochemical reactions have been widely studied and utilized for applications in the fields of bioscience and engineering. Here, we report a unique phenomenon of moisture-induced electrical potential oscillations on polymers, poly([2-(methacryloyloxy)ethyl] dimethyl-(3-sulfopropyl) ammonium hydroxide-co-acrylic acid), during the diffusion of water molecules. Chemical reactions are modeled by kinetic simulations while system dynamic equations and the stability matrix are analyzed to show the chaotic nature of the system which oscillates with hidden attractors to induce the autonomous surface potential oscillation. Using moisture in the ambient environment as the activation source, this self-excited chemoelectrical reaction could have broad influences and usages in surface-reaction based devices and systems. As a proof-of-concept demonstration, an energy harvester is constructed and achieved the continuous energy production for more than 15,000 seconds with an energy density of 16.8 mJ/cm2. A 2-Volts output voltage has been produced to power a liquid crystal display toward practical applications with five energy harvesters connected in series.
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Affiliation(s)
- Yu Long
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Peisheng He
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Zhichun Shao
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Zhaoyang Li
- Department of Electromechanical Engineering and Centre for Artificial Intelligence and Robotics, University of Macau, Macau, SAR, China
| | - Han Kim
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Archie Mingze Yao
- Department of Engineering Mechanics, Tsinghua University, Beijing, China
| | - Yande Peng
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Renxiao Xu
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Christine Heera Ahn
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Seung-Wuk Lee
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Junwen Zhong
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Electromechanical Engineering and Centre for Artificial Intelligence and Robotics, University of Macau, Macau, SAR, China.
| | - Liwei Lin
- Department of Mechanical Engineering, University of California Berkeley, Berkeley, CA, USA.
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26
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Lyu Z, Park J, Kim KM, Jin HJ, Wu H, Rajadas J, Kim DH, Steinberg GK, Lee W. A neurovascular-unit-on-a-chip for the evaluation of the restorative potential of stem cell therapies for ischaemic stroke. Nat Biomed Eng 2021; 5:847-863. [PMID: 34385693 PMCID: PMC8524779 DOI: 10.1038/s41551-021-00744-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
The therapeutic efficacy of stem cells transplanted into an ischaemic brain depends primarily on the responses of the neurovascular unit. Here, we report the development and applicability of a functional neurovascular unit on a microfluidic chip as a microphysiological model of ischaemic stroke that recapitulates the function of the blood-brain barrier as well as interactions between therapeutic stem cells and host cells (human brain microvascular endothelial cells, pericytes, astrocytes, microglia and neurons). We used the model to track the infiltration of a number of candidate stem cells and to characterize the expression levels of genes associated with post-stroke pathologies. We observed that each type of stem cell showed unique neurorestorative effects, primarily by supporting endogenous recovery rather than through direct cell replacement, and that the recovery of synaptic activities is correlated with the recovery of the structural and functional integrity of the neurovascular unit rather than with the regeneration of neurons.
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Affiliation(s)
- Zhonglin Lyu
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jon Park
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kwang-Min Kim
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hye-Jin Jin
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Haodi Wu
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jayakumar Rajadas
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Deok-Ho Kim
- Departments of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, U.S.A.,Departments of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, U.S.A
| | - Gary K. Steinberg
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA.,Stanford Stroke Center, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wonjae Lee
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA.,Stanford Stroke Center, Stanford University School of Medicine, Stanford, CA 94305, USA.,Correspondence and requests for materials should be addressed to: Corresponding author, Wonjae Lee, or
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27
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Takano T, Wahl AM, Huang KT, Narita T, Rugis J, Sneyd J, Yule DI. Highly localized intracellular Ca 2+ signals promote optimal salivary gland fluid secretion. eLife 2021; 10:66170. [PMID: 34240705 PMCID: PMC8352588 DOI: 10.7554/elife.66170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 07/08/2021] [Indexed: 11/23/2022] Open
Abstract
Salivary fluid secretion involves an intricate choreography of membrane transporters to result in the trans-epithelial movement of NaCl and water into the acinus lumen. Current models are largely based on experimental observations in enzymatically isolated cells where the Ca2+ signal invariably propagates globally and thus appears ideally suited to activate spatially separated Cl and K channels, present on the apical and basolateral plasma membrane, respectively. We monitored Ca2+ signals and salivary secretion in live mice expressing GCamp6F, following stimulation of the nerves innervating the submandibular gland. Consistent with in vitro studies, Ca2+ signals were initiated in the apical endoplasmic reticulum. In marked contrast to in vitro data, highly localized trains of Ca2+ transients that failed to fully propagate from the apical region were observed. Following stimuli optimum for secretion, large apical-basal gradients were elicited. A new mathematical model, incorporating these data was constructed to probe how salivary secretion can be optimally stimulated by apical Ca2+ signals.
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Affiliation(s)
- Takahiro Takano
- Department of Pharmacology and Physiology, University of Rochester, Rochester, United States
| | - Amanda M Wahl
- Department of Pharmacology and Physiology, University of Rochester, Rochester, United States
| | - Kai-Ting Huang
- Department of Pharmacology and Physiology, University of Rochester, Rochester, United States
| | - Takanori Narita
- Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - John Rugis
- Department of Mathematics, University of Auckland, Auckland, New Zealand
| | - James Sneyd
- Department of Mathematics, University of Auckland, Auckland, New Zealand
| | - David I Yule
- Department of Pharmacology and Physiology, University of Rochester, Rochester, United States
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28
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Abstract
Living systems maintain or increase local order by working against the second law of thermodynamics. Thermodynamic consistency is restored as they consume free energy, thereby increasing the net entropy of their environment. Recently introduced estimators for the entropy production rate have provided major insights into the efficiency of important cellular processes. In experiments, however, many degrees of freedom typically remain hidden to the observer, and, in these cases, existing methods are not optimal. Here, by reformulating the problem within an optimization framework, we are able to infer improved bounds on the rate of entropy production from partial measurements of biological systems. Our approach yields provably optimal estimates given certain measurable transition statistics. In contrast to prevailing methods, the improved estimator reveals nonzero entropy production rates even when nonequilibrium processes appear time symmetric and therefore may pretend to obey detailed balance. We demonstrate the broad applicability of this framework by providing improved bounds on the energy consumption rates in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells.
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Affiliation(s)
- Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139
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29
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Emrich SM, Yoast RE, Xin P, Arige V, Wagner LE, Hempel N, Gill DL, Sneyd J, Yule DI, Trebak M. Omnitemporal choreographies of all five STIM/Orai and IP 3Rs underlie the complexity of mammalian Ca 2+ signaling. Cell Rep 2021; 34:108760. [PMID: 33657364 PMCID: PMC7968378 DOI: 10.1016/j.celrep.2021.108760] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/16/2020] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
Stromal-interaction molecules (STIM1/2) sense endoplasmic reticulum (ER) Ca2+ depletion and activate Orai channels. However, the choreography of interactions between native STIM/Orai proteins under physiological agonist stimulation is unknown. We show that the five STIM1/2 and Orai1/2/3 proteins are non-redundant and function together to ensure the graded diversity of mammalian Ca2+ signaling. Physiological Ca2+ signaling requires functional interactions between STIM1/2, Orai1/2/3, and IP3Rs, ensuring that receptor-mediated Ca2+ release is tailored to Ca2+ entry and nuclear factor of activated T cells (NFAT) activation. The N-terminal Ca2+-binding ER-luminal domains of unactivated STIM1/2 inhibit IP3R-evoked Ca2+ release. A gradual increase in agonist intensity and STIM1/2 activation relieves IP3R inhibition. Concomitantly, activated STIM1/2 C termini differentially interact with Orai1/2/3 as agonist intensity increases. Thus, coordinated and omnitemporal functions of all five STIM/Orai and IP3Rs translate the strength of agonist stimulation to precise levels of Ca2+ signaling and NFAT induction, ensuring the fidelity of complex mammalian Ca2+ signaling.
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Affiliation(s)
- Scott M Emrich
- Department of Cellular and Molecular Physiology, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Ryan E Yoast
- Department of Cellular and Molecular Physiology, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Ping Xin
- Department of Cellular and Molecular Physiology, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Vikas Arige
- Department of Pharmacology and Physiology, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Larry E Wagner
- Department of Pharmacology and Physiology, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Nadine Hempel
- Department of Pharmacology, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA; Penn State Cancer Institute, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Donald L Gill
- Department of Cellular and Molecular Physiology, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - James Sneyd
- Department of Mathematics, The University of Auckland, 38 Princes Street, Auckland 1010, New Zealand
| | - David I Yule
- Department of Pharmacology and Physiology, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Mohamed Trebak
- Department of Cellular and Molecular Physiology, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA; Penn State Cancer Institute, the Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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30
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Cloete I, Corrêa-Velloso JC, Bartlett PJ, Kirk V, Thomas AP, Sneyd J. A Tale of two receptors. J Theor Biol 2021; 518:110629. [PMID: 33607144 DOI: 10.1016/j.jtbi.2021.110629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/10/2021] [Accepted: 02/05/2021] [Indexed: 11/26/2022]
Abstract
Calcium (Ca2+) oscillations in hepatocytes have a wide dynamic range. In particular, recent experimental evidence shows that agonist stimulation of the P2Y family of receptors leads to qualitatively diverse Ca2+ oscillations. We present a new model of Ca2+ oscillations in hepatocytes based on these experiments to investigate the mechanisms controlling P2Y-activated Ca2+ oscillations. The model accounts for Ca2+ regulation of the IP3 receptor (IP3R), the positive feedback from Ca2+ on phospholipase C (PLC) and the P2Y receptor phosphorylation by protein kinase C (PKC). Furthermore, PKC is shown to control multiple cellular substrates. Utilising the model, we suggest the activity and intensity of PLC and PKC necessary to explain the qualitatively diverse Ca2+ oscillations in response to P2Y receptor activation.
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Affiliation(s)
- Ielyaas Cloete
- Department of Mathematics, University of Auckland, Auckland 1142, New Zealand
| | - Juliana C Corrêa-Velloso
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School Rutgers, The State University of New Jersey, Newark, NJ 07103, United States
| | - Paula J Bartlett
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School Rutgers, The State University of New Jersey, Newark, NJ 07103, United States
| | - Vivien Kirk
- Department of Mathematics, University of Auckland, Auckland 1142, New Zealand
| | - Andrew P Thomas
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School Rutgers, The State University of New Jersey, Newark, NJ 07103, United States
| | - James Sneyd
- Department of Mathematics, University of Auckland, Auckland 1142, New Zealand
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31
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Sneyd J, Vera-Sigüenza E, Rugis J, Pages N, Yule DI. Calcium Dynamics and Water Transport in Salivary Acinar Cells. Bull Math Biol 2021; 83:31. [PMID: 33594615 PMCID: PMC8018713 DOI: 10.1007/s11538-020-00841-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/25/2020] [Indexed: 01/07/2023]
Abstract
Saliva is secreted from the acinar cells of the salivary glands, using mechanisms that are similar to other types of water-transporting epithelial cells. Using a combination of theoretical and experimental techniques, over the past 20 years we have continually developed and modified a quantitative model of saliva secretion, and how it is controlled by the dynamics of intracellular calcium. However, over approximately the past 5 years there have been significant developments both in our understanding of the underlying mechanisms and in the way these mechanisms should best be modelled. Here, we review the traditional understanding of how saliva is secreted, and describe how our work has suggested important modifications to this traditional view. We end with a brief description of the most recent data from living animals and discuss how this is now contributing to yet another iteration of model construction and experimental investigation.
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Affiliation(s)
- James Sneyd
- Department of Mathematics, The University of Auckland, Level 2, Building 303, 38 Princes Street, Auckland, New Zealand.
| | | | | | | | - David I Yule
- School of Medicine and Dentistry, University of Rochester Medical Center, 601 Elmwood Ave, Box 711, Rochester, NY, USA
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32
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Hsu IS, Moses AM. Stochastic models for single-cell data: Current challenges and the way forward. FEBS J 2021; 289:647-658. [PMID: 33570798 DOI: 10.1111/febs.15760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/22/2020] [Accepted: 02/10/2021] [Indexed: 11/28/2022]
Abstract
Although the quantity and quality of single-cell data have progressed rapidly, making quantitative predictions with single-cell stochastic models remains challenging. The stochastic nature of cellular processes leads to at least three challenges in building models with single-cell data: (a) because variability in single-cell data can be attributed to multiple different sources, it is difficult to rule out conflicting mechanistic models that explain the same data equally well; (b) the distinction between interesting biological variability and experimental variability is sometimes ambiguous; (c) the nonstandard distributions of single-cell data can lead to violations of the assumption of symmetric errors in least-squares fitting. In this review, we first discuss recent studies that overcome some of the challenges or set up a promising direction and then introduce some powerful statistical approaches utilized in these studies. We conclude that applying and developing statistical approaches could lead to further progress in building stochastic models for single-cell data.
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Affiliation(s)
- Ian S Hsu
- Department of Cell & Systems Biology, University of Toronto, ON, Canada
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, ON, Canada
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33
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Kaimachnikov NP, Kotova PD, Kochkina EN, Rogachevskaja OA, Khokhlov AA, Bystrova MF, Kolesnikov SS. Modeling of Ca2+ transients initiated by GPCR agonists in mesenchymal stromal cells. BBA ADVANCES 2021; 1:100012. [PMID: 37082025 PMCID: PMC10074909 DOI: 10.1016/j.bbadva.2021.100012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 10/21/2022] Open
Abstract
The integrative study that included experimentation and mathematical modeling was carried out to analyze dynamic aspects of transient Ca2+ signaling induced by brief pulses of GPCR agonists in mesenchymal stromal cells from the human adipose tissue (AD-MSCs). The experimental findings argued for IP3/Ca2+-regulated Ca2+ release via IP3 receptors (IP3Rs) as a key mechanism mediating agonist-dependent Ca2+ transients. The consistent signaling circuit was proposed to formalize coupling of agonist binding to Ca2+ mobilization for mathematical modeling. The model properly simulated the basic phenomenology of agonist transduction in AD-MSCs, which mostly produced single Ca2+ spikes upon brief stimulation. The spike-like responses were almost invariantly shaped at different agonist doses above a threshold, while response lag markedly decreased with stimulus strength. In AD-MSCs, agonists and IP3 uncaging elicited similar Ca2+ transients but IP3 pulses released Ca2+ without pronounced delay. This suggested that IP3 production was rate-limiting in agonist transduction. In a subpopulation of AD-MSCs, brief agonist pulses elicited Ca2+ bursts crowned by damped oscillations. With properly adjusted parameters of IP3R inhibition by cytosolic Ca2+, the model reproduced such oscillatory Ca2+ responses as well. GEM-GECO1 and R-CEPIA1er, the genetically encoded sensors of cytosolic and reticular Ca2+, respectively, were co-expressed in HEK-293 cells that also responded to agonists in an "all-or-nothing" manner. The experimentally observed Ca2+ signals triggered by ACh in both compartments were properly simulated with the suggested signaling circuit. Thus, the performed modeling of the transduction process provides sufficient theoretical basis for deeper interpretation of experimental findings on agonist-induced Ca2+ signaling in AD-MSCs.
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34
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Cohen O, Nitsan I, Tzlil S, Safran SA. Long-Time Phase Correlations Reveal Regulation of Beating Cardiomyocytes. PHYSICAL REVIEW LETTERS 2020; 125:258101. [PMID: 33416366 DOI: 10.1103/physrevlett.125.258101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Spontaneous contractions of cardiomyocytes are driven by calcium oscillations due to the activity of ionic calcium channels and pumps. The beating phase is related to the time-dependent deviation of the oscillations from their average frequency, due to noise and the resulting cellular response. Here, we demonstrate experimentally that, in addition to the short-time (1-2 Hz), beat-to-beat variability, there are long-time correlations (tens of minutes) in the beating phase dynamics of isolated cardiomyocytes. Our theoretical model relates these long-time correlations to cellular regulation that restores the frequency to its average, homeostatic value in response to stochastic perturbations.
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Affiliation(s)
- Ohad Cohen
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ido Nitsan
- Faculty of Mechanical Engineering, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Shelly Tzlil
- Faculty of Mechanical Engineering, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Samuel A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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35
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Qi H, Li X, Jin Z, Simmen T, Shuai J. The Oscillation Amplitude, Not the Frequency of Cytosolic Calcium, Regulates Apoptosis Induction. iScience 2020; 23:101671. [PMID: 33196017 PMCID: PMC7644924 DOI: 10.1016/j.isci.2020.101671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/15/2020] [Accepted: 10/08/2020] [Indexed: 01/06/2023] Open
Abstract
Although a rising concentration of cytosolic Ca2+ has long been recognized as an essential signal for apoptosis, the dynamical mechanisms by which Ca2+ regulates apoptosis are not clear yet. To address this, we constructed a computational model that integrates known biochemical reactions and can reproduce the dynamical behaviors of Ca2+-induced apoptosis as observed in experiments. Model analysis shows that oscillating Ca2+ signals first convert into gradual signals and eventually transform into a switch-like apoptotic response. Via the two processes, the apoptotic signaling pathway filters the frequency of Ca2+ oscillations effectively but instead responds acutely to their amplitude. Collectively, our results suggest that Ca2+ regulates apoptosis mainly via oscillation amplitude, rather than frequency, modulation. This study not only provides a comprehensive understanding of how oscillatory Ca2+ dynamically regulates the complex apoptotic signaling network but also presents a typical example of how Ca2+ controls cellular responses through amplitude modulation.
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Affiliation(s)
- Hong Qi
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China.,Shanxi Key Laboratory of Mathematical Techniques and Big Data Analysis on Disease Control and Prevention, Shanxi University, Taiyuan 030006, China
| | - Xiang Li
- Department of Physics, Xiamen University, Xiamen 361005, China.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361102, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
| | - Zhen Jin
- Complex Systems Research Center, Shanxi University, Taiyuan 030006, China.,Shanxi Key Laboratory of Mathematical Techniques and Big Data Analysis on Disease Control and Prevention, Shanxi University, Taiyuan 030006, China
| | - Thomas Simmen
- Faculty of Medicine and Dentistry, Department of Cell Biology, University of Alberta, Edmonton, AB T6G2H7, Canada
| | - Jianwei Shuai
- Department of Physics, Xiamen University, Xiamen 361005, China.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361102, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
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36
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Dual mechanisms of Ca2+ oscillations in hepatocytes. J Theor Biol 2020; 503:110390. [DOI: 10.1016/j.jtbi.2020.110390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 11/30/2022]
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37
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Marchena M, Echebarria B, Shiferaw Y, Alvarez-Lacalle E. Buffering and total calcium levels determine the presence of oscillatory regimes in cardiac cells. PLoS Comput Biol 2020; 16:e1007728. [PMID: 32970668 PMCID: PMC7537911 DOI: 10.1371/journal.pcbi.1007728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/06/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022] Open
Abstract
Calcium oscillations and waves induce depolarization in cardiac cells which are believed to cause life-threathening arrhythimas. In this work, we study the conditions for the appearance of calcium oscillations in both a detailed subcellular model of calcium dynamics and a minimal model that takes into account just the minimal ingredients of the calcium toolkit. To avoid the effects of homeostatic changes and the interaction with the action potential we consider the somewhat artificial condition of a cell without pacing and with no calcium exchange with the extracellular medium. Both the full subcellular model and the minimal model present the same scenarios depending on the calcium load: two stationary states, one with closed ryanodine receptors (RyR) and most calcium in the cell stored in the sarcoplasmic reticulum (SR), and another, with open RyRs and a depleted SR. In between, calcium oscillations may appear. The robustness of these oscillations is determined by the amount of calsequestrin (CSQ). The lack of this buffer in the SR enhances the appearance of oscillations. The minimal model allows us to relate the stability of the oscillating state to the nullcline structure of the system, and find that its range of existence is bounded by a homoclinic and a Hopf bifurcation, resulting in a sudden transition to the oscillatory regime as the cell calcium load is increased. Adding a small amount of noise to the RyR behavior increases the parameter region where oscillations appear and provides a gradual transition from the resting state to the oscillatory regime, as observed in the subcellular model and experimentally. In cardiac cells, calcium plays a very important role. An increase in calcium levels is the trigger used by the cell to initiate contraction. Besides, calcium modulates several transmembrane currents, affecting the cell transmembrane potential. Thus, dysregulations in calcium handling have been associated with the appearance of arrhythmias. Often, this dysregulation results in the appearance of periodic calcium waves or global oscillations, providing a pro-arrhythmic substrate. In this paper, we study the onset of calcium oscillations in cardiac cells using both a detailed subcellular model of calcium dynamics and a minimal model that takes into account the essential ingredients of the calcium toolkit. Both reproduce the main experimental results and link this behavior with the presence of different steady-state solutions and bifurcations that depend on the total amount of calcium in the cell and in the level of buffering present. We expect that this work will help to clarify the conditions under which calcium oscillations appear in cardiac myocytes and, therefore, will represent a step further in the understanding of the origin of cardiac arrhythmias.
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Affiliation(s)
- Miquel Marchena
- Departament de Física, Universitat Politècnica de Catalunya-BarcelonaTech, Barcelona, Spain
| | - Blas Echebarria
- Departament de Física, Universitat Politècnica de Catalunya-BarcelonaTech, Barcelona, Spain
| | - Yohannes Shiferaw
- Physics Department, California State University, Northridge, California 91330, USA
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Calcium signaling and epigenetics: A key point to understand carcinogenesis. Cell Calcium 2020; 91:102285. [PMID: 32942140 DOI: 10.1016/j.ceca.2020.102285] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/22/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023]
Abstract
Calcium (Ca2+) signaling controls a wide range of cellular processes, including the hallmarks of cancer. The Ca2+ signaling system encompasses several types of proteins, such as receptors, channels, pumps, exchangers, buffers, and sensors, of which several are mutated or with altered expression in cancer cells. Since epigenetic mechanisms are disrupted in all stages of carcinogenesis, and reversibly regulate gene expression, they have been studied by different research groups to understand their role in Ca2+ signaling remodeling in cancer cells and the carcinogenic process. In this review, we link Ca2+ signaling, cancer, and epigenetics fields to generate a comprehensive landscape of this complex group of diseases.
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Zhang Y, Liu H, Li Z, Miao Z, Zhou J. Oscillatory Dynamics of p53-Mdm2 Circuit in Response to DNA Damage Caused by Ionizing Radiation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1703-1713. [PMID: 30762566 DOI: 10.1109/tcbb.2019.2899574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although the dynamical behavior of the p53-Mdm2 loop has been extensively studied, the understanding of the mechanism underlying the regulation of this pathway still remains limited. Herein, we developed an integrated model with five basic components and three ubiquitous time delays for the p53-Mdm2 interaction in response to DNA damage following ionizing radiation (IR). We showed that a sufficient amount of activated ATM level can initiate the p53 oscillations with nearly the same amplitude over a wide range of the ATM level; a proper range of p53 level is also required for generating the oscillations, for too high or too low levels it would fail to generate the oscillations; and increased Mdm2 level leads to decreased amplitude of the p53 oscillation and reduced expression of the p53 activity. Moreover, we found that the negative feedback loop formed between p53 and nuclear Mdm2 plays a dominant role in determining the p53 dynamics, whereas when interaction strength of the negative feedback loop becomes weaker, the positive feedback loop formed between p53 and cytoplasmatic Mdm2 can induce different types of dynamics. Furthermore, we demonstrated that the total time delay required for protein production and nuclear translocation of Mdm2 can induce p53 oscillations even when the p53 level is at a certain stable high steady state or at a certain stable low steady state. In addition, the two important features of the oscillatory dynamics-amplitude and period-can be controlled by such time delay. These results are in agreement with multiple experimental observations and may enrich our understanding of the dynamics of the p53 network.
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40
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Zhou A, Liu X, Zhang S, Huo B. Effects of store-operated and receptor-operated calcium channels on synchronization of calcium oscillations in astrocytes. Biosystems 2020; 198:104233. [PMID: 32858094 DOI: 10.1016/j.biosystems.2020.104233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 10/23/2022]
Abstract
Intercellular calcium signaling allows cells to communicate with each other and to interact with adjacent cells. Gap junction is the most common and important way for cellular communication. Recently, mathematical models have been widely used to gain a precise and quantitative understanding of the dynamics of intracellular calcium ions (Ca2+). In this paper, we establish a mathematical model considering the gap junction permeable to Ca2+ and to IP3 for describing the calcium oscillations in coupled astrocytes. Store-operated calcium entry (SOCE) is viewed as the main process which controls the non-excitable cells, hence, we focus on the effect of store-operated calcium channel (SOCC) and receptor-operated calcium channel (ROCC) on the intercellular synchronization, respectively. By employing bifurcation analysis on this model, the dynamic behaviors of the coupled system with different physiological state cells is obtained with changes in the maximum capacity of the SOCC and the ROCC. The synchronization boundaries for different conditions are gained in the two parameters space of the channel parameters and the coupling strength. The results suggest that the variation of the maximum flow for different calcium channels determines the stable oscillations of the coupled system, as well as for the frequency and amplitude of oscillations. The SOCC has an expected effect on the change of the oscillatory interval while the ROCC demonstrated the influence on the amplitude modulation. Furthermore, the coupling strength and channel parameters could induce 1:1 locking of intercellular Ca2+ oscillations and the synchronization region like Arnol'd tongue is found.
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Affiliation(s)
- Anqi Zhou
- Department of Mechanics, Tianjin University, Tianjin, 300354, PR China
| | - Xijun Liu
- Department of Mechanics, Tianjin University, Tianjin, 300354, PR China
| | - Suxia Zhang
- Department of Mechanics, Tianjin University, Tianjin, 300354, PR China.
| | - Bing Huo
- College of Mechanical Engineering, Tianjin University of Science & Technology, Tianjin, 300222, PR China
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41
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Ca 2+ Release via IP 3 Receptors Shapes the Cardiac Ca 2+ Transient for Hypertrophic Signaling. Biophys J 2020; 119:1178-1192. [PMID: 32871099 DOI: 10.1016/j.bpj.2020.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/16/2020] [Accepted: 08/04/2020] [Indexed: 12/27/2022] Open
Abstract
Calcium (Ca2+) plays a central role in mediating both contractile function and hypertrophic signaling in ventricular cardiomyocytes. L-type Ca2+ channels trigger release of Ca2+ from ryanodine receptors for cellular contraction, whereas signaling downstream of G-protein-coupled receptors stimulates Ca2+ release via inositol 1,4,5-trisphosphate receptors (IP3Rs), engaging hypertrophic signaling pathways. Modulation of the amplitude, duration, and duty cycle of the cytosolic Ca2+ contraction signal and spatial localization have all been proposed to encode this hypertrophic signal. Given current knowledge of IP3Rs, we develop a model describing the effect of functional interaction (cross talk) between ryanodine receptor and IP3R channels on the Ca2+ transient and examine the sensitivity of the Ca2+ transient shape to properties of IP3R activation. A key result of our study is that IP3R activation increases Ca2+ transient duration for a broad range of IP3R properties, but the effect of IP3R activation on Ca2+ transient amplitude is dependent on IP3 concentration. Furthermore we demonstrate that IP3-mediated Ca2+ release in the cytosol increases the duty cycle of the Ca2+ transient, the fraction of the cycle for which [Ca2+] is elevated, across a broad range of parameter values and IP3 concentrations. When coupled to a model of downstream transcription factor (NFAT) activation, we demonstrate that there is a high correspondence between the Ca2+ transient duty cycle and the proportion of activated NFAT in the nucleus. These findings suggest increased cytosolic Ca2+ duty cycle as a plausible mechanism for IP3-dependent hypertrophic signaling via Ca2+-sensitive transcription factors such as NFAT in ventricular cardiomyocytes.
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42
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Nair V, Yi J, Isheim D, Rotenberg M, Meng L, Shi F, Chen X, Gao X, Prominski A, Jiang Y, Yue J, Gallagher CT, Seidman DN, Tian B. Laser writing of nitrogen-doped silicon carbide for biological modulation. SCIENCE ADVANCES 2020; 6:6/34/eaaz2743. [PMID: 32937377 PMCID: PMC7442483 DOI: 10.1126/sciadv.aaz2743] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 07/08/2020] [Indexed: 05/05/2023]
Abstract
Conducting or semiconducting materials embedded in insulating polymeric substrates can be useful in biointerface applications; however, attainment of this composite configuration by direct chemical processes is challenging. Laser-assisted synthesis has evolved as a fast and inexpensive technique to prepare various materials, but its utility in the construction of biophysical tools or biomedical devices is less explored. Here, we use laser writing to convert portions of polydimethylsiloxane (PDMS) into nitrogen-doped cubic silicon carbide (3C-SiC). The dense 3C-SiC surface layer is connected to the PDMS matrix via a spongy graphite layer, facilitating electrochemical and photoelectrochemical activity. We demonstrate the fabrication of arbitrary two-dimensional (2D) SiC-based patterns in PDMS and freestanding 3D constructs. To establish the functionality of the laser-produced composite, we apply it as flexible electrodes for pacing isolated hearts and as photoelectrodes for local peroxide delivery to smooth muscle sheets.
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Affiliation(s)
- Vishnu Nair
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Jaeseok Yi
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Dieter Isheim
- Northwestern University Center for Atom-Probe Tomography, Evanston, IL 60208, USA
| | - Menahem Rotenberg
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Lingyuan Meng
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Fengyuan Shi
- Electron Microscopy Core, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Xinqi Chen
- Keck Interdisciplinary Surface Science Center, Northwestern University, Evanston, IL 60208, USA
| | - Xiang Gao
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Aleksander Prominski
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Yuanwen Jiang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Jiping Yue
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | | | - David N Seidman
- Northwestern University Center for Atom-Probe Tomography, Evanston, IL 60208, USA
| | - Bozhi Tian
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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43
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Bartlett PJ, Cloete I, Sneyd J, Thomas AP. IP 3-Dependent Ca 2+ Oscillations Switch into a Dual Oscillator Mechanism in the Presence of PLC-Linked Hormones. iScience 2020; 23:101062. [PMID: 32353764 PMCID: PMC7191650 DOI: 10.1016/j.isci.2020.101062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 12/11/2019] [Accepted: 04/09/2020] [Indexed: 11/28/2022] Open
Abstract
Ca2+ oscillations that depend on inositol-1,4,5-trisphosphate (IP3) have been ascribed to biphasic Ca2+ regulation of the IP3 receptor (IP3R) or feedback mechanisms controlling IP3 levels in different cell types. IP3 uncaging in hepatocytes elicits Ca2+ transients that are often localized at the subcellular level and increase in magnitude with stimulus strength. However, this does not reproduce the broad baseline-separated global Ca2+ oscillations elicited by vasopressin. Addition of hormone to cells activated by IP3 uncaging initiates a qualitative transition from high-frequency spatially disorganized Ca2+ transients, to low-frequency, oscillatory Ca2+ waves that propagate throughout the cell. A mathematical model with dual coupled oscillators that integrates Ca2+-induced Ca2+ release at the IP3R and mutual feedback mechanisms of cross-coupling between Ca2+ and IP3 reproduces this behavior. Thus, multiple Ca2+ oscillation modes can coexist in the same cell, and hormonal stimulation can switch from the simpler to the more complex to yield robust signaling.
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Affiliation(s)
- Paula J Bartlett
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Ielyaas Cloete
- Department of Mathematics, The University of Auckland, Auckland, New Zealand
| | - James Sneyd
- Department of Mathematics, The University of Auckland, Auckland, New Zealand
| | - Andrew P Thomas
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School Rutgers, The State University of New Jersey, Newark, NJ 07103, USA.
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Yoast RE, Emrich SM, Zhang X, Xin P, Johnson MT, Fike AJ, Walter V, Hempel N, Yule DI, Sneyd J, Gill DL, Trebak M. The native ORAI channel trio underlies the diversity of Ca 2+ signaling events. Nat Commun 2020; 11:2444. [PMID: 32415068 PMCID: PMC7229178 DOI: 10.1038/s41467-020-16232-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/16/2020] [Indexed: 12/30/2022] Open
Abstract
The essential role of ORAI1 channels in receptor-evoked Ca2+ signaling is well understood, yet little is known about the physiological activation of the ORAI channel trio natively expressed in all cells. The roles of ORAI2 and ORAI3 have remained obscure. We show that ORAI2 and ORAI3 channels play a critical role in mediating the regenerative Ca2+ oscillations induced by physiological receptor activation, yet ORAI1 is dispensable in generation of oscillations. We reveal that ORAI2 and ORAI3 channels multimerize with ORAI1 to expand the range of sensitivity of receptor-activated Ca2+ signals, reflecting their enhanced basal STIM1-binding and heightened Ca2+-dependent inactivation. This broadened bandwidth of Ca2+ influx is translated by cells into differential activation of NFAT1 and NFAT4 isoforms. Our results uncover a long-sought role for ORAI2 and ORAI3, revealing an intricate control mechanism whereby heteromerization of ORAI channels mediates graded Ca2+ signals that extend the agonist-sensitivity to fine-tune transcriptional control.
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Affiliation(s)
- Ryan E Yoast
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Scott M Emrich
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Xuexin Zhang
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Ping Xin
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Martin T Johnson
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Adam J Fike
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Vonn Walter
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
- Penn State Cancer Institute and The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Nadine Hempel
- Penn State Cancer Institute and The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
- Department of Pharmacology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - David I Yule
- Department of Pharmacology and Physiology, University of Rochester Medical Center School of Medicine and Dentistry, 601 Elmwood Avenue, Box 711, Rochester, NY, 14642, USA
| | - James Sneyd
- Department of Mathematics, The University of Auckland, 38 Princes Street, Auckland, 1010, New Zealand
| | - Donald L Gill
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Mohamed Trebak
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA.
- Penn State Cancer Institute and The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA.
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45
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Lock JT, Parker I. IP 3 mediated global Ca 2+ signals arise through two temporally and spatially distinct modes of Ca 2+ release. eLife 2020; 9:e55008. [PMID: 32396066 PMCID: PMC7253181 DOI: 10.7554/elife.55008] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
The 'building-block' model of inositol trisphosphate (IP3)-mediated Ca2+ liberation posits that cell-wide cytosolic Ca2+ signals arise through coordinated activation of localized Ca2+ puffs generated by stationary clusters of IP3 receptors (IP3Rs). Here, we revise this hypothesis, applying fluctuation analysis to resolve Ca2+ signals otherwise obscured during large Ca2+ elevations. We find the rising phase of global Ca2+ signals is punctuated by a flurry of puffs, which terminate before the peak by a mechanism involving partial ER Ca2+ depletion. The continuing rise in Ca2+, and persistence of global signals even when puffs are absent, reveal a second mode of spatiotemporally diffuse Ca2+ signaling. Puffs make only small, transient contributions to global Ca2+ signals, which are sustained by diffuse release of Ca2+ through a functionally distinct process. These two modes of IP3-mediated Ca2+ liberation have important implications for downstream signaling, imparting spatial and kinetic specificity to Ca2+-dependent effector functions and Ca2+ transport.
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Affiliation(s)
- Jeffrey T Lock
- Department of Neurobiology & Behavior, UC IrvineIrvineUnited States
| | - Ian Parker
- Department of Neurobiology & Behavior, UC IrvineIrvineUnited States
- Department of Physiology & Biophysics, UC IrvineIrvineUnited States
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46
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Cohen O, Safran SA. Cardiomyocyte Calcium Ion Oscillations-Lessons From Physics. Front Physiol 2020; 11:164. [PMID: 32184736 PMCID: PMC7058634 DOI: 10.3389/fphys.2020.00164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/12/2020] [Indexed: 12/22/2022] Open
Abstract
We review a theoretical, coarse-grained description for cardiomyocytes calcium dynamics that is motivated by experiments on RyR channel dynamics and provides an analogy to other spontaneously oscillating systems. We show how a minimal model, that focuses on calcium channel and pump dynamics and kinetics, results in a single, easily understood equation for spontaneous calcium oscillations (the Van-der-Pol equation). We analyze experiments on isolated RyR channels to quantify how the channel dynamics depends both on the local calcium concentration, as well as its temporal behavior (“adaptation”). Our oscillator model analytically predicts the conditions for spontaneous oscillations, their frequency and amplitude, and how each of those scale with the small number of relevant parameters related to calcium channel and pump activity. The minimal model is easily extended to include the effects of noise and external pacing (electrical or mechanical). We show how our simple oscillator predicts and explains the experimental observations of synchronization, “bursting” and reduction of apparent noise in the beating dynamics of paced cells. Thus, our analogy and theoretical approach provides robust predictions for the beating dynamics, and their biochemical and mechanical modulation.
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Affiliation(s)
- Ohad Cohen
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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47
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Powell J, Falcke M, Skupin A, Bellamy TC, Kypraios T, Thul R. A Statistical View on Calcium Oscillations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:799-826. [PMID: 31646535 DOI: 10.1007/978-3-030-12457-1_32] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transient rises and falls of the intracellular calcium concentration have been observed in numerous cell types and under a plethora of conditions. There is now a growing body of evidence that these whole-cell calcium oscillations are stochastic, which poses a significant challenge for modelling. In this review, we take a closer look at recently developed statistical approaches to calcium oscillations. These models describe the timing of whole-cell calcium spikes, yet their parametrisations reflect subcellular processes. We show how non-stationary calcium spike sequences, which e.g. occur during slow depletion of intracellular calcium stores or in the presence of time-dependent stimulation, can be analysed with the help of so-called intensity functions. By utilising Bayesian concepts, we demonstrate how values of key parameters of the statistical model can be inferred from single cell calcium spike sequences and illustrate what information whole-cell statistical models can provide about the subcellular mechanistic processes that drive calcium oscillations. In particular, we find that the interspike interval distribution of HEK293 cells under constant stimulation is captured by a Gamma distribution.
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Affiliation(s)
- Jake Powell
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Martin Falcke
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Department of Physics, Humboldt University, Berlin, Germany
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg.,National Biomedical Computation Resource, University California San Diego, La Jolla, CA, USA
| | - Tomas C Bellamy
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Theodore Kypraios
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK
| | - Rüdiger Thul
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK.
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48
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Ohadi D, Schmitt DL, Calabrese B, Halpain S, Zhang J, Rangamani P. Computational Modeling Reveals Frequency Modulation of Calcium-cAMP/PKA Pathway in Dendritic Spines. Biophys J 2019; 117:1963-1980. [PMID: 31668749 PMCID: PMC7031750 DOI: 10.1016/j.bpj.2019.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/30/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022] Open
Abstract
Dendritic spines are the primary excitatory postsynaptic sites that act as subcompartments of signaling. Ca2+ is often the first and most rapid signal in spines. Downstream of calcium, the cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) pathway plays a critical role in the regulation of spine formation, morphological modifications, and ultimately, learning and memory. Although the dynamics of calcium are reasonably well-studied, calcium-induced cAMP/PKA dynamics, particularly with respect to frequency modulation, are not fully explored. In this study, we present a well-mixed model for the dynamics of calcium-induced cAMP/PKA dynamics in dendritic spines. The model is constrained using experimental observations in the literature. Further, we measured the calcium oscillation frequency in dendritic spines of cultured hippocampal CA1 neurons and used these dynamics as model inputs. Our model predicts that the various steps in this pathway act as frequency modulators for calcium, and the high frequency of calcium input is filtered by adenylyl cyclase 1 and phosphodiesterases in this pathway such that cAMP/PKA only responds to lower frequencies. This prediction has important implications for noise filtering and long-timescale signal transduction in dendritic spines. A companion manuscript presents a three-dimensional spatial model for the same pathway.
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Affiliation(s)
- Donya Ohadi
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California
| | - Danielle L Schmitt
- Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Barbara Calabrese
- Division of Biological Sciences and Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, California
| | - Shelley Halpain
- Division of Biological Sciences and Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, California
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California.
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A mathematical model of calcium dynamics: Obesity and mitochondria-associated ER membranes. PLoS Comput Biol 2019; 15:e1006661. [PMID: 31437152 PMCID: PMC6726250 DOI: 10.1371/journal.pcbi.1006661] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 09/04/2019] [Accepted: 08/03/2019] [Indexed: 12/27/2022] Open
Abstract
Multiple cellular organelles tightly orchestrate intracellular calcium (Ca2+) dynamics to regulate cellular activities and maintain homeostasis. The interplay between the endoplasmic reticulum (ER), a major store of intracellular Ca2+, and mitochondria, an important source of adenosine triphosphate (ATP), has been the subject of much research, as their dysfunction has been linked with metabolic diseases. Interestingly, throughout the cell’s cytosolic domain, these two organelles share common microdomains called mitochondria-associated ER membranes (MAMs), where their membranes are in close apposition. The role of MAMs is critical for intracellular Ca2+ dynamics as they provide hubs for direct Ca2+ exchange between the organelles. A recent experimental study reported correlation between obesity and MAM formation in mouse liver cells, and obesity-related cellular changes that are closely associated with the regulation of Ca2+ dynamics. We constructed a mathematical model to study the effects of MAM Ca2+ dynamics on global Ca2+ activities. Through a series of model simulations, we investigated cellular mechanisms underlying the altered Ca2+ dynamics in the cells under obesity. We predict that, as the dosage of stimulus gradually increases, liver cells from obese mice will reach the state of saturated cytosolic Ca2+ concentration at a lower stimulus concentration, compared to cells from healthy mice. It is well known that intracellular Ca2+ oscillations carry encoded signals in their amplitude and frequency to regulate various cellular processes, and accumulating evidence supports the importance of the interplay between the ER and mitochondria in cellular Ca2+ homeostasis. Miscommunications between the organelles may be involved in the development of metabolic diseases. Based on a recent experimental study that spotlighted a correlation between obesity and physical interactions of the ER and mitochondria in mouse hepatic cells, we constructed a mathematical model as a tool to probe the effects of the cellular changes linked with obesity on global cellular Ca2+ dynamics. Our model successfully reproduced the experimental study that observed a positive correlation between an increase in ER-mitochondrial junctions and the magnitude of mitochondrial Ca2+ responses. We postulate that hepatic cells from lean animals exhibit Ca2+ oscillations that are more robust under higher concentrations of stimulus, compared to cells from obese animals.
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Wang C, Liu H, Zhou J. Oscillatory Dynamics of p53 Genetic Network Induced by Feedback Loops and Time Delays. IEEE Trans Nanobioscience 2019; 18:611-621. [PMID: 31226080 DOI: 10.1109/tnb.2019.2924079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
DNA damage caused by γ -irradiation initiates oscillatory expression of the p53 genetic network. Although many studies revealed the effects of the p53-Mdm2 circuit on p53 dynamics, a few studies explored the contribution of upstream kinases to p53 oscillation. In this paper, an integrated mathematical model of the p53 network in response to γ -irradiation is studied, which consists of five basic components, two ubiquitous time delays, and two negative feedback loops. It is found that recurrent p53 pulses are externally initiated by ataxia telangiectasia mutated (ATM), and the negative feedback loop formed between ATM and p53, via Wip1, plays a dominant role in generating p53 oscillation. In addition, p53 oscillation requires not only an appropriate Mdm2 negative strength but also a threshold level of Wip1 negative strength. Furthermore, the time delays required for transcription and translation of Mdm2 and Wip1 proteins are essential for p53 oscillation. In particular, the critical value of time delay for inducing oscillation and the properties of delay-driven Hopf bifurcation are theoretically analyzed. As expected, the results are clearly in consistence with biological experiments and observations.
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