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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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Kochel B. Negative feedback systems for modelling NF-κB transcription factor oscillatory activity. Transcription 2024:1-32. [PMID: 38739365 DOI: 10.1080/21541264.2024.2331887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/13/2024] [Indexed: 05/14/2024] Open
Abstract
Low-dimensional negative feedback systems (NFSs) were developed within a signal flow model to describe the oscillatory activities of NF-κB caused by interactions with its inhibitor IκBα. The NFSs were established as 3rd- and 4th-order linear systems containing unperturbed and perturbed negative feedback (NF) loops with constant or time-varying NF strengths and a feed-forward loop. NF-related analytical solutions to the NFSs representing the time courses of NF-κB and IκBα were determined and their exact mathematical relationship was found. The NFS's parameters were determined to fit the experimental time courses of NF-κB in TNF-α-stimulated embryonic fibroblasts, rela-/- embryonic fibroblasts reconstituted with RelA, C9L cells, GFP-p65 knock-in embryonic fibroblasts and embryogenic fibroblasts lacking Iκβ and IκBε, LPS-stimulated IC-21 macrophages treated or not with DCPA, and anti-IgM-stimulated DT40 B-lymphocytes. The unperturbed and perturbed NFSs describing the above biosystems generated isochronous and non-isochronous solutions, depending on a constant or time-varying NF strength, respectively. The oscillation period of the NF-coupled solutions, the phase difference between them and the time delays in the appearance of cytoplasmic IκBα after stimulation of NF-κB were determined. A significant divergence between the IκBα solutions to the NFSs and the IκBα experimental courses led to a rejection of the NF coupling between NF-κB and IκBα in the above biosystems. It was shown that neither the linearity nor the low dimensionality of the NFSs altered the NF relationship and the divergence between the IκBα solutions to the NFS and IκBα experimental time courses. Although the NF relationship between IκBα and NF-κB was not confirmed in all the experimental data analyzed, delayed negative feedback was found in some cases.
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Affiliation(s)
- Bonawentura Kochel
- Immunotherapy Central Europe, Wroclaw Medical University, Wrocław, Poland
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Wang M, Bennett ZT, Singh P, Feng Q, Wilhelm J, Huang G, Gao J. Elucidation of Protonation Cooperativity of a STING-Activating Polymer. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2305255. [PMID: 37541432 PMCID: PMC10838353 DOI: 10.1002/adma.202305255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/23/2023] [Indexed: 08/06/2023]
Abstract
Stimuli-responsive nanomaterials have the potential to improve the performance and overcome existing barriers of conventional nanotherapeutics. Molecular cooperativity design in stimuli-responsive nanomedicine can amplify physiological signals, enabling a cooperative response for improved diagnostic and therapeutic precision. Previously, this work reported an ultra-pH-sensitive polymer, PEG-b-PC7A, that possesses innate immune activating properties by binding to the stimulator of interferon genes (STING) through polyvalent phase condensation. This interaction enhances STING activation and synergizes with the endogenous STING ligand for robust cancer immunotherapy. Despite its successes in innate immune activation, the fundamental physicochemical and pH-responsive properties of PC7A require further investigation. Here, this study elucidates the protonation cooperativity driven by the phase transition of PC7A copolymer. The highly cooperative system displays an "all-or-nothing" proton distribution between highly charged unimer (all) and neutral micelle (nothing) states without gradually protonated intermediates. The binary protonation behavior is further illustrated in pH-precision-controlled release of a representative anticancer drug, β-lapachone, by PC7A micelles over a noncooperative PE5A polymer. Furthermore, the bimodal distribution of protons is represented by a high Hill coefficient (nH > 9), featuring strong positive cooperativity. This study highlights the nanoscale pH cooperativity of an immune activating polymer, providing insights into the physicochemical characterization and design parameters for future nanotherapeutics development.
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Affiliation(s)
- Maggie Wang
- Department of Biomedical Engineering, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zachary T Bennett
- Department of Biomedical Engineering, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Parnavi Singh
- Department of Biomedical Engineering, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Qiang Feng
- Department of Biomedical Engineering, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jonathan Wilhelm
- Department of Biomedical Engineering, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Gang Huang
- Department of Biomedical Engineering, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jinming Gao
- Department of Biomedical Engineering, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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The Hedgehog Signaling Pathway in Idiopathic Pulmonary Fibrosis: Resurrection Time. Int J Mol Sci 2021; 23:ijms23010171. [PMID: 35008597 PMCID: PMC8745434 DOI: 10.3390/ijms23010171] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 02/07/2023] Open
Abstract
The hedgehog (Hh) pathway is a sophisticated conserved cell signaling pathway that plays an essential role in controlling cell specification and proliferation, survival factors, and tissue patterning formation during embryonic development. Hh signal activity does not entirely disappear after development and may be reactivated in adulthood within tissue-injury-associated diseases, including idiopathic pulmonary fibrosis (IPF). The dysregulation of Hh-associated activating transcription factors, genomic abnormalities, and microenvironments is a co-factor that induces the initiation and progression of IPF.
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Szemere JR, Rotstein HG, Ventura AC. Frequency-preference response in covalent modification cycles under substrate sequestration conditions. NPJ Syst Biol Appl 2021; 7:32. [PMID: 34404807 PMCID: PMC8371027 DOI: 10.1038/s41540-021-00192-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Covalent modification cycles (CMCs) are basic units of signaling systems and their properties are well understood. However, their behavior has been mostly characterized in situations where the substrate is in excess over the modifying enzymes. Experimental data on protein abundance suggest that the enzymes and their target proteins are present in comparable concentrations, leading to substrate sequestration by the enzymes. In this enzyme-in-excess regime, CMCs have been shown to exhibit signal termination, the ability of the product to return to a stationary value lower than its peak in response to constant stimulation, while this stimulation is still active, with possible implications for the ability of systems to adapt to environmental inputs. We characterize the conditions leading to signal termination in CMCs in the enzyme-in-excess regime. We also demonstrate that this behavior leads to a preferred frequency response (band-pass filters) when the cycle is subjected to periodic stimulation, whereas the literature reports that CMCs investigated so far behave as low-pass filters. We characterize the relationship between signal termination and the preferred frequency response to periodic inputs and we explore the dynamic mechanism underlying these phenomena. Finally, we describe how the behavior of CMCs is reflected in similar types of responses in the cascades of which they are part. Evidence of protein abundance in vivo shows that enzymes and substrates are present in comparable concentrations, thus suggesting that signal termination and frequency-preference response to periodic inputs are also important dynamic features of cell signaling systems, which have been overlooked.
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Affiliation(s)
- Juliana Reves Szemere
- grid.482261.b0000 0004 1794 2491Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Horacio G. Rotstein
- grid.260896.30000 0001 2166 4955Federated Department of Biological Sciences, New Jersey Institute of Technology & Rutgers University, Newark, NJ United States
| | - Alejandra C. Ventura
- grid.482261.b0000 0004 1794 2491Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina ,grid.7345.50000 0001 0056 1981Departamento de Física, FCEyN UBA, Ciudad Universitaria, Buenos Aires, Argentina
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Sevlever F, Di Bella JP, Ventura AC. Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves. PLoS Comput Biol 2020; 16:e1007929. [PMID: 32497065 PMCID: PMC7297384 DOI: 10.1371/journal.pcbi.1007929] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/16/2020] [Accepted: 05/06/2020] [Indexed: 12/02/2022] Open
Abstract
Negative cooperativity is a phenomenon in which the binding of a first ligand or substrate molecule decreases the rate of subsequent binding. This definition is not exclusive to ligand-receptor binding, it holds whenever two or more molecules undergo two successive binding events. Negative cooperativity turns the binding curve more graded and cannot be distinguished from two independent and different binding events based on equilibrium measurements only. The need of kinetic data for this purpose was already reported. Here, we study the binding response as a function of the amount of ligand, at different times, from very early times since ligand is added and until equilibrium is reached. Over those binding curves measured at different times, we compute the dynamic range: the fold change required in input to elicit a change from 10 to 90% of maximum output, finding that it evolves in time differently and controlled by different parameters in the two situations that are identical in equilibrium. Deciphering which is the microscopic model that leads to a given binding curve adds understanding on the molecular mechanisms at play, and thus, is a valuable tool. The methods developed in this article were tested both with simulated and experimental data, showing to be robust to noise and experimental constraints.
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Affiliation(s)
- Federico Sevlever
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina
- Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
| | - Juan Pablo Di Bella
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina
- Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
| | - Alejandra C. Ventura
- Department of Physiology, Molecular and Cellular Biology, University of Buenos Aires, Buenos Aires, Argentina
- Institute of Physiology, Molecular Biology and Neurosciences, National Research Council (CONICET), Buenos Aires, Argentina
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