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Singh A, Sen S, Iter M, Adelaja A, Luecke S, Guo X, Hoffmann A. Stimulus-response signaling dynamics characterize macrophage polarization states. Cell Syst 2024; 15:563-577.e6. [PMID: 38843840 PMCID: PMC11226196 DOI: 10.1016/j.cels.2024.05.002] [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: 05/13/2022] [Revised: 12/03/2023] [Accepted: 05/10/2024] [Indexed: 06/22/2024]
Abstract
The functional state of cells is dependent on their microenvironmental context. Prior studies described how polarizing cytokines alter macrophage transcriptomes and epigenomes. Here, we characterized the functional responses of 6 differentially polarized macrophage populations by measuring the dynamics of transcription factor nuclear factor κB (NF-κB) in response to 8 stimuli. The resulting dataset of single-cell NF-κB trajectories was analyzed by three approaches: (1) machine learning on time-series data revealed losses of stimulus distinguishability with polarization, reflecting canalized effector functions. (2) Informative trajectory features driving stimulus distinguishability ("signaling codons") were identified and used for mapping a cell state landscape that could then locate macrophages conditioned by an unrelated condition. (3) Kinetic parameters, inferred using a mechanistic NF-κB network model, provided an alternative mapping of cell states and correctly predicted biochemical findings. Together, this work demonstrates that a single analyte's dynamic trajectories may distinguish the functional states of single cells and molecular network states underlying them. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Apeksha Singh
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Supriya Sen
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Iter
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Adewunmi Adelaja
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stefanie Luecke
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaolu Guo
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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2
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Kosmidis E, Shuttle CG, Preobraschenski J, Ganzella M, Johnson PJ, Veshaguri S, Holmkvist J, Møller MP, Marantos O, Marcoline F, Grabe M, Pedersen JL, Jahn R, Stamou D. Regulation of the mammalian-brain V-ATPase through ultraslow mode-switching. Nature 2022; 611:827-834. [PMID: 36418452 PMCID: PMC11212661 DOI: 10.1038/s41586-022-05472-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022]
Abstract
Vacuolar-type adenosine triphosphatases (V-ATPases)1-3 are electrogenic rotary mechanoenzymes structurally related to F-type ATP synthases4,5. They hydrolyse ATP to establish electrochemical proton gradients for a plethora of cellular processes1,3. In neurons, the loading of all neurotransmitters into synaptic vesicles is energized by about one V-ATPase molecule per synaptic vesicle6,7. To shed light on this bona fide single-molecule biological process, we investigated electrogenic proton-pumping by single mammalian-brain V-ATPases in single synaptic vesicles. Here we show that V-ATPases do not pump continuously in time, as suggested by observing the rotation of bacterial homologues8 and assuming strict ATP-proton coupling. Instead, they stochastically switch between three ultralong-lived modes: proton-pumping, inactive and proton-leaky. Notably, direct observation of pumping revealed that physiologically relevant concentrations of ATP do not regulate the intrinsic pumping rate. ATP regulates V-ATPase activity through the switching probability of the proton-pumping mode. By contrast, electrochemical proton gradients regulate the pumping rate and the switching of the pumping and inactive modes. A direct consequence of mode-switching is all-or-none stochastic fluctuations in the electrochemical gradient of synaptic vesicles that would be expected to introduce stochasticity in proton-driven secondary active loading of neurotransmitters and may thus have important implications for neurotransmission. This work reveals and emphasizes the mechanistic and biological importance of ultraslow mode-switching.
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Affiliation(s)
- Eleftherios Kosmidis
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Christopher G Shuttle
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Julia Preobraschenski
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute for Auditory Neuroscience, University Medical Center, Göttingen, Germany
- Multiscale Bioimaging Cluster of Excellence (MBExC), University of Göttingen, Göttingen, Germany
| | - Marcelo Ganzella
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Peter J Johnson
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Mathematics, University of Manchester, Manchester, UK
| | - Salome Veshaguri
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Novozymes A/S, Kgs Lyngby, Denmark
| | - Jesper Holmkvist
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Mads P Møller
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Orestis Marantos
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Frank Marcoline
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jesper L Pedersen
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Reinhard Jahn
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Dimitrios Stamou
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
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3
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Yasui K. Merits and Demerits of ODE Modeling of Physicochemical Systems for Numerical Simulations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27185860. [PMID: 36144593 PMCID: PMC9505051 DOI: 10.3390/molecules27185860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022]
Abstract
In comparison with the first-principles calculations mostly using partial differential equations (PDEs), numerical simulations with modeling by ordinary differential equations (ODEs) are sometimes superior in that they are computationally more economical and that important factors are more easily traced. However, a demerit of ODE modeling is the need of model validation through comparison with experimental data or results of the first-principles calculations. In the present review, examples of ODE modeling are reviewed such as sonochemical reactions inside a cavitation bubble, oriented attachment of nanocrystals, dynamic response of flexoelectric polarization, ultrasound-assisted sintering, and dynamics of a gas parcel in a thermoacoustic engine.
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Affiliation(s)
- Kyuichi Yasui
- National Institute of Advanced Industrial Science and Technology (AIST), Nagoya 463-8560, Japan
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4
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Miele Y, Jones SJ, Rossi F, Beales PA, Taylor AF. Collective Behavior of Urease pH Clocks in Nano- and Microvesicles Controlled by Fast Ammonia Transport. J Phys Chem Lett 2022; 13:1979-1984. [PMID: 35188399 PMCID: PMC9007528 DOI: 10.1021/acs.jpclett.2c00069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
The transmission of chemical signals via an extracellular solution plays a vital role in collective behavior in cellular biological systems and may be exploited in applications of lipid vesicles such as drug delivery. Here, we investigated chemical communication in synthetic micro- and nanovesicles containing urease in a solution of urea and acid. We combined experiments with simulations to demonstrate that the fast transport of ammonia to the external solution governs the pH-time profile and synchronizes the timing of the pH clock reaction in a heterogeneous population of vesicles. This study shows how the rate of production and emission of a small basic product controls pH changes in active vesicles with a distribution of sizes and enzyme amounts, which may be useful in bioreactor or healthcare applications.
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Affiliation(s)
- Ylenia Miele
- Department
of Chemistry and Biology, University of
Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Stephen J. Jones
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Federico Rossi
- Department
of Earth, Environmental and Physical Sciences, University of Siena, Pian dei Mantellini 44, 53100 Siena, Italy
| | - Paul A. Beales
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Annette F. Taylor
- Chemical
and Biological Engineering, University of
Sheffield, Sheffield S1 3JD, U.K.
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5
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Guha A, McGuire ML, Leriche G, Yang J, Mayer M. A single-liposome assay that enables temperature-dependent measurement of proton permeability of extremophile-inspired lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183567. [PMID: 33476579 DOI: 10.1016/j.bbamem.2021.183567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Affiliation(s)
- Anirvan Guha
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Melissa L McGuire
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland.
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