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Szischik CL, Reves Szemere J, Balderrama R, Sánchez de la Vega C, Ventura AC. Transient frequency preference responses in cell signaling systems. NPJ Syst Biol Appl 2024; 10:86. [PMID: 39128915 PMCID: PMC11317535 DOI: 10.1038/s41540-024-00413-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: 12/22/2023] [Accepted: 07/29/2024] [Indexed: 08/13/2024] Open
Abstract
Ligand-receptor systems, covalent modification cycles, and transcriptional networks are the fundamental components of cell signaling and gene expression systems. While their behavior in reaching a steady-state regime under step-like stimulation is well understood, their response under repetitive stimulation, particularly at early time stages is poorly characterized. Yet, early-stage responses to external inputs are arguably as informative as late-stage ones. In simple systems, a periodic stimulation elicits an initial transient response, followed by periodic behavior. Transient responses are relevant when the stimulation has a limited time span, or when the stimulated component's timescale is slow as compared to the timescales of the downstream processes, in which case the latter processes may be capturing only those transients. In this study, we analyze the frequency response of simple motifs at different time stages. We use dose-conserved pulsatile input signals and consider different metrics versus frequency curves. We show that in ligand-receptor systems, there is a frequency preference response in some specific metrics during the transient stages, which is not present in the periodic regime. We suggest this is a general system-level mechanism that cells may use to filter input signals that have consequences for higher order circuits. In addition, we evaluate how the described behavior in isolated motifs is reflected in similar types of responses in cascades and pathways of which they are a part. Our studies suggest that transient frequency preferences are important dynamic features of cell signaling and gene expression systems, which have been overlooked.
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Affiliation(s)
- Candela L Szischik
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física. Ciudad Universitaria, 1428, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE UBA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina-Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Juliana Reves Szemere
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física. Ciudad Universitaria, 1428, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE UBA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina-Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
- Universidad Pedagógica Nacional and Universidad Nacional de La Pampa, Facultad de Ciencias Exactas y Naturales, Departamento de Física, Santa Rosa, Argentina
| | - Rocío Balderrama
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Matemática. Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Investigaciones Matemáticas Luis A. Santaló (IMAS - CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina, Buenos Aires, Argentina
| | - Constanza Sánchez de la Vega
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Matemática. Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Cálculo, FCEyN, CONICET-UBA, Buenos Aires, Argentina
| | - Alejandra C Ventura
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física. Ciudad Universitaria, 1428, Buenos Aires, Argentina.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE UBA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina-Universidad de Buenos Aires, 1428, Buenos Aires, Argentina.
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Synthetic Cannabinoids Influence the Invasion of Glioblastoma Cell Lines in a Cell- and Receptor-Dependent Manner. Cancers (Basel) 2019; 11:cancers11020161. [PMID: 30709059 PMCID: PMC6406558 DOI: 10.3390/cancers11020161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 01/10/2023] Open
Abstract
The current treatment of glioblastoma is not sufficient, since they are heterogeneous and often resistant to chemotherapy. Earlier studies demonstrated effects of specific cannabinoid receptor (CB) agonists on the invasiveness of glioblastoma cell lines, but the exact mechanism remained unclear. Three human glioblastoma cell lines were treated with synthetic CB ligands. The effect of cannabinoids on microRNAs (miRs), Akt, and on the expression of proliferation and apoptosis markers were analyzed. Furthermore, in a model of organotypic hippocampal slice cultures cannabinoid mediated changes in the invasiveness were assessed. MicroRNAs and the activation of Akt which are related to cell migration, apoptosis, and proliferation were evaluated and found not to be associated with changes in the invasiveness after treatment with CB ligands. Also proliferation and/or apoptosis were not altered after treatment. The effects of cannabinoids on invasiveness could be blocked by the application of receptor antagonists and are likely mediated via CB₁/CB₂. In conclusion, our results suggest that cannabinoids can influence glioblastoma cell invasion in a receptor and cell type specific manner that is independent of proliferation and apoptosis. Thus, cannabinoids can potentially be used in the future as an addition to current therapy.
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Zhang J, Tian XJ, Chen YJ, Wang W, Watkins S, Xing J. Pathway crosstalk enables cells to interpret TGF-β duration. NPJ Syst Biol Appl 2018; 4:18. [PMID: 29872541 PMCID: PMC5972147 DOI: 10.1038/s41540-018-0060-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/28/2018] [Accepted: 05/07/2018] [Indexed: 02/07/2023] Open
Abstract
The detection and transmission of the temporal quality of intracellular and extracellular signals is an essential cellular mechanism. It remains largely unexplored how cells interpret the duration information of a stimulus. In this paper, we performed an integrated quantitative and computational analysis on TGF-β induced activation of SNAIL1, a key transcription factor that regulates several subsequent cell fate decisions such as apoptosis and epithelial-to-mesenchymal transition. We demonstrate that crosstalk among multiple TGF-β activated pathways forms a relay from SMAD to GLI1 that initializes and maintains SNAILl expression, respectively. SNAIL1 functions as a key integrator of information from TGF-β signaling distributed through upstream divergent pathways. The intertwined network serves as a temporal checkpoint, so that cells can generate a transient or sustained expression of SNAIL1 depending on TGF-β duration. Furthermore, we observed that TGF-β treatment leads to an unexpected accumulation of GSK3 molecules in an enzymatically active tyrosine phosphorylation form in Golgi apparatus and ER, followed by accumulation of GSK3 molecules in an enzymatically inhibitive serine phosphorylation in the nucleus. Subsequent model analysis and inhibition experiments revealed that the initial localized increase of GSK3 enzymatic activity couples to the positive feedback loop of the substrate Gli1 to form a network motif with multi-objective functions. That is, the motif is robust against stochastic fluctuations, and has a narrow distribution of response time that is insensitive to initial conditions. Specifically for TGF-β signaling, the motif ensures a smooth relay from SMAD to GLI1 on regulating SNAIL1 expression.
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Affiliation(s)
- Jingyu Zhang
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Xiao-Jun Tian
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA.,4Present Address: School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287 USA
| | - Yi-Jiun Chen
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Weikang Wang
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Simon Watkins
- 2Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Jianhua Xing
- 1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260 USA.,3UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232 USA
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Weddell JC, Imoukhuede PI. Integrative meta-modeling identifies endocytic vesicles, late endosome and the nucleus as the cellular compartments primarily directing RTK signaling. Integr Biol (Camb) 2018; 9:464-484. [PMID: 28436498 DOI: 10.1039/c7ib00011a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recently, intracellular receptor signaling has been identified as a key component mediating cell responses for various receptor tyrosine kinases (RTKs). However, the extent each endocytic compartment (endocytic vesicle, early endosome, recycling endosome, late endosome, lysosome and nucleus) contributes to receptor signaling has not been quantified. Furthermore, our understanding of endocytosis and receptor signaling is complicated by cell- or receptor-specific endocytosis mechanisms. Therefore, towards understanding the differential endocytic compartment signaling roles, and identifying how to achieve signal transduction control for RTKs, we delineate how endocytosis regulates RTK signaling. We achieve this via a meta-analysis across eight RTKs, integrating computational modeling with experimentally derived cell (compartment volume, trafficking kinetics and pH) and ligand-receptor (ligand/receptor concentration and interaction kinetics) physiology. Our simulations predict the abundance of signaling from eight RTKs, identifying the following hierarchy in RTK signaling: PDGFRβ > IGFR1 > EGFR > PDGFRα > VEGFR1 > VEGFR2 > Tie2 > FGFR1. We find that endocytic vesicles are the primary cell signaling compartment; over 43% of total receptor signaling occurs within the endocytic vesicle compartment for these eight RTKs. Mechanistically, we found that high RTK signaling within endocytic vesicles may be attributed to their low volume (5.3 × 10-19 L) which facilitates an enriched ligand concentration (3.2 μM per ligand molecule within the endocytic vesicle). Under the analyzed physiological conditions, we identified extracellular ligand concentration as the most sensitive parameter to change; hence the most significant one to modify when regulating absolute compartment signaling. We also found that the late endosome and nucleus compartments are important contributors to receptor signaling, where 26% and 18%, respectively, of average receptor signaling occurs across the eight RTKs. Conversely, we found very low membrane-based receptor signaling, exhibiting <1% of the total receptor signaling for these eight RTKs. Moreover, we found that nuclear translocation, mechanistically, requires late endosomal transport; when we blocked receptor trafficking from late endosomes to the nucleus we found a 57% reduction in nuclear translocation. In summary, our research has elucidated the significance of endocytic vesicles, late endosomes and the nucleus in RTK signal propagation.
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Affiliation(s)
- Jared C Weddell
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1304 W Springfield Ave., 3233 Digital Computer Laboratory, Urbana, IL 61801, USA.
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De la Fuente IM, Cortés JM, Valero E, Desroches M, Rodrigues S, Malaina I, Martínez L. On the dynamics of the adenylate energy system: homeorhesis vs homeostasis. PLoS One 2014; 9:e108676. [PMID: 25303477 PMCID: PMC4193753 DOI: 10.1371/journal.pone.0108676] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 09/03/2014] [Indexed: 11/20/2022] Open
Abstract
Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Institute of Parasitology and Biomedicine “López-Neyra”, CSIC, Granada, Spain
- Department of Mathematics, University of the Basque Country UPV/EHU, Leioa, Spain
- Unit of Biophysics (CSIC, UPV/EHU), and Department of Biochemistry and Molecular Biology University of the Basque Country, Bilbao, Spain
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
| | - Jesús M. Cortés
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
- Ikerbasque: The Basque Foundation for Science, Bilbao, Basque Country, Spain
| | - Edelmira Valero
- Department of Physical Chemistry, School of Industrial Engineering, University of Castilla-La Mancha, Albacete, Spain
| | | | - Serafim Rodrigues
- School of Computing and Mathematics, University of Plymouth, Plymouth, United Kingdom
| | - Iker Malaina
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
- Department of Physiology, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Luis Martínez
- Department of Mathematics, University of the Basque Country UPV/EHU, Leioa, Spain
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
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Tunable signal processing through a kinase control cycle: the IKK signaling node. Biophys J 2014; 105:231-41. [PMID: 23823243 DOI: 10.1016/j.bpj.2013.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 04/19/2013] [Accepted: 05/02/2013] [Indexed: 12/31/2022] Open
Abstract
The transcription factor NFκB, a key component of the immune system, shows intricate stimulus-specific temporal dynamics. Those dynamics are thought to play a role in controlling the physiological response to cytokines and pathogens. Biochemical evidence suggests that the NFκB inducing kinase, IKK, a signaling hub onto which many signaling pathways converge, is regulated via a regulatory cycle comprising a poised, an active, and an inactive state. We hypothesize that it operates as a modulator of signal dynamics, actively reshaping the signals generated at the receptor proximal level. Here we show that a regulatory cycle can function in at least three dynamical regimes, tunable by regulating a single kinetic parameter. In particular, the simplest three-state regulatory cycle can generate signals with two well-defined phases, each with distinct coding capabilities in terms of the information they can carry about the stimulus. We also demonstrate that such a kinase cycle can function as a signal categorizer classifying diverse incoming signals into outputs with a limited set of temporal activity profiles. Finally, we discuss the extension of the results to other regulatory motifs that could be understood in terms of the regimes of the three-state cycle.
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Estrada J, Guantes R. Dynamic and structural constraints in signal propagation by regulatory networks. ACTA ACUST UNITED AC 2013; 9:268-84. [DOI: 10.1039/c2mb25243k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Behar M, Hoffmann A. Understanding the temporal codes of intra-cellular signals. Curr Opin Genet Dev 2010; 20:684-93. [PMID: 20956081 DOI: 10.1016/j.gde.2010.09.007] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 01/07/2023]
Abstract
The health of organisms and cells depends on appropriate responses to diverse internal and external cues, stimuli, or challenges, such as changes in hormone or cytokine levels, or exposure to a pathogen. Cellular responses must be tailored to the identity and intensity of the stimulus and therefore intra-cellular signals must carry information about both. However, signaling mediators often form intricate networks that react to multiple stimuli yet manage to produce stimulus-specific responses. The multi-functionality ('functional pleiotropism') of signaling nodes suggests that biological networks have evolved ways of passing physiologically relevant stimulus information through shared channels. Increasing evidence supports the notion that this is achieved in part through temporal regulation of signaling mediators' activities. The present challenge is to identify the features of temporal activity profile that represent information about a given stimulus and understand how cells read the temporal codes to control their responses.
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Affiliation(s)
- Marcelo Behar
- Signaling Systems Laboratory, BioCircuits Institute, and San Diego Center for Systems Biology of Cellular Stress Responses, University of California, San Diego, 9500 Gillman Dr, La Jolla, CA 92093, United States
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de Ronde WH, Tostevin F, ten Wolde PR. Effect of feedback on the fidelity of information transmission of time-varying signals. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:031914. [PMID: 21230115 DOI: 10.1103/physreve.82.031914] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Indexed: 05/30/2023]
Abstract
Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating environment, we therefore have to understand how reliably biochemical networks can transmit time-varying signals. To this end, we must understand both the noise characteristics and the amplification properties of networks. In this paper, we use information theory to study how reliably signaling cascades employing autoregulation and feedback can transmit time-varying signals. We calculate the frequency dependence of the gain-to-noise ratio, which reflects how reliably a network transmits signals at different frequencies. We find that the gain-to-noise ratio may differ qualitatively from the power spectrum of the output, showing that the latter does not directly reflect signaling performance. Moreover, we find that autoactivation and autorepression increase and decrease the gain-to-noise ratio for all of frequencies, respectively. Positive feedback specifically enhances information transmission at low frequencies, while negative feedback increases signal fidelity at high frequencies. Our analysis not only elucidates the role of autoregulation and feedback in naturally occurring biological networks, but also reveals design principles that can be used for the reliable transmission of time-varying signals in synthetic gene circuits.
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Affiliation(s)
- Wiet Hendrik de Ronde
- FOM Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands.
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Hashimoto M, Feng J, York RL, Ellerbee AK, Morrison G, Thomas SW, Mahadevan L, Whitesides GM. Infochemistry: encoding information as optical pulses using droplets in a microfluidic device. J Am Chem Soc 2009; 131:12420-9. [PMID: 19655796 DOI: 10.1021/ja904788m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article describes a new procedure for generating and transmitting a message--a sequence of optical pulses--by aligning a mask (an opaque sheet containing transparent "windows") below a microfluidic channel in which flows an opaque continuous fluid containing transparent droplets. The optical mask encodes the message as a unique sequence of windows that can transmit or block light; the flow of transparent droplets in the channel converts this message into a sequence of optical pulses. The properties of the windows on the mask (e.g., their size, wavelength of transmittance, orientation of polarization) determine the information carried in these optical pulses (e.g., intensity, color, polarization). The structure of a transmitted signal depends on the number and spacing of droplets in the channel. Fourier transformation can deconvolve superimposed signals created by the flow of multiple droplets into the message that a single droplet would transmit. The research described in this contribution explores a new field at the intersection of chemistry, materials science, and information technology: infochemistry.
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Affiliation(s)
- Michinao Hashimoto
- Department of Chemistry and Chemical Biology, 12 Oxford Street, Harvard University, Cambridge, Massachusetts 02138, USA
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Cournac A, Sepulchre JA. Simple molecular networks that respond optimally to time-periodic stimulation. BMC SYSTEMS BIOLOGY 2009; 3:29. [PMID: 19257878 PMCID: PMC2666635 DOI: 10.1186/1752-0509-3-29] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 03/03/2009] [Indexed: 01/10/2023]
Abstract
Background Bacteria or cells receive many signals from their environment and from other organisms. In order to process this large amount of information, Systems Biology shows that a central role is played by regulatory networks composed of genes and proteins. The objective of this paper is to present and to discuss simple regulatory network motifs having the property to maximize their responses under time-periodic stimulations. In elucidating the mechanisms underlying these responses through simple networks the goal is to pinpoint general principles which optimize the oscillatory responses of molecular networks. Results We took a look at basic network motifs studied in the literature such as the Incoherent Feedforward Loop (IFFL) or the interlerlocked negative feedback loop. The former is also generalized to a diamond pattern, with network components being either purely genetic or combining genetic and signaling pathways. Using standard mathematics and numerical simulations, we explain the types of responses exhibited by the IFFL with respect to a train of periodic pulses. We show that this system has a non-vanishing response only if the inter-pulse interval is above a threshold. A slight generalisation of the IFFL (the diamond) is shown to work as an ideal pass-band filter. We next show a mechanism by which average of oscillatory response can be maximized by bursting temporal patterns. Finally we study the interlerlocked negative feedback loop, i.e. a 2-gene motif forming a loop where the nodes respectively activate and repress each other, and show situations where this system possesses a resonance under periodic stimulation. Conclusion We present several simple motif designs of molecular networks producing optimal output in response to periodic stimulations of the system. The identified mechanisms are simple and based on known network motifs in the literature, so that that they could be embodied in existing organisms, or easily implementable by means of synthetic biology. Moreover we show that these designs can be studied in different contexts of molecular biology, as for example in genetic networks or in signaling pathways.
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Affiliation(s)
- Axel Cournac
- Institut Non Linéaire de Nice, Université de Nice Sophia-Antipolis, CNRS, Valbonne, France.
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