1
|
Miller WB, Baluška F, Reber AS, Slijepčević P. Why death and aging ? All memories are imperfect. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 187:21-35. [PMID: 38316274 DOI: 10.1016/j.pbiomolbio.2024.02.001] [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: 10/30/2023] [Revised: 01/02/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Recent papers have emphasized the primary role of cellular information management in biological and evolutionary development. In this framework, intelligent cells collectively measure environmental cues to improve informational validity to support natural cellular engineering as collaborative decision-making and problem-solving in confrontation with environmental stresses. These collective actions are crucially dependent on cell-based memories as acquired patterns of response to environmental stressors. Notably, in a cellular self-referential framework, all biological information is ambiguous. This conditional requirement imposes a previously unexplored derivative. All cellular memories are imperfect. From this atypical background, a novel theory of aging and death is proposed. Since cellular decision-making is memory-dependent and biology is a continuous natural learning system, the accumulation of previously acquired imperfect memories eventually overwhelms the flexibility cells require to react adroitly to contemporaneous stresses to support continued cellular homeorhetic balance. The result is a gradual breakdown of the critical ability to efficiently measure environmental information and effect cell-cell communication. This age-dependent accretion governs senescence, ultimately ending in death as an organism-wide failure of cellular networking. This approach to aging and death is compatible with all prior theories. Each earlier approach illuminates different pertinent cellular signatures of this ongoing, obliged, living process.
Collapse
Affiliation(s)
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, Germany.
| | - Arthur S Reber
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada.
| | - Predrag Slijepčević
- Department of Life Sciences, College of Health, Medicine and Life Sciences, University of Brunel, UK.
| |
Collapse
|
2
|
Goetz A, Akl H, Dixit P. The ability to sense the environment is heterogeneously distributed in cell populations. eLife 2024; 12:RP87747. [PMID: 38293960 PMCID: PMC10942581 DOI: 10.7554/elife.87747] [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] [Indexed: 02/01/2024] Open
Abstract
Channel capacity of signaling networks quantifies their fidelity in sensing extracellular inputs. Low estimates of channel capacities for several mammalian signaling networks suggest that cells can barely detect the presence/absence of environmental signals. However, given the extensive heterogeneity and temporal stability of cell state variables, we hypothesize that the sensing ability itself may depend on the state of the cells. In this work, we present an information-theoretic framework to quantify the distribution of sensing abilities from single-cell data. Using data on two mammalian pathways, we show that sensing abilities are widely distributed in the population and most cells achieve better resolution of inputs compared to an 'average cell'. We verify these predictions using live-cell imaging data on the IGFR/FoxO pathway. Importantly, we identify cell state variables that correlate with cells' sensing abilities. This information-theoretic framework will significantly improve our understanding of how cells sense in their environment.
Collapse
Affiliation(s)
- Andrew Goetz
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
| | - Hoda Akl
- Department of Physics, University of FloridaGainesvilleUnited States
| | - Purushottam Dixit
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
- Systems Biology Institute, Yale UniversityWest HavenUnited States
| |
Collapse
|
3
|
Jashnsaz H, Neuert G. Phenotypic consequences of logarithmic signaling in MAPK stress response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570188. [PMID: 38106069 PMCID: PMC10723343 DOI: 10.1101/2023.12.05.570188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
How cells respond to dynamic environmental changes is crucial for understanding fundamental biological processes and cell physiology. In this study, we developed an experimental and quantitative analytical framework to explore how dynamic stress gradients that change over time regulate cellular volume, signaling activation, and growth phenotypes. Our findings reveal that gradual stress conditions substantially enhance cell growth compared to conventional acute stress. This growth advantage correlates with a minimal reduction in cell volume dependent on the dynamic of stress. We explain the growth phenotype with our finding of a logarithmic signal transduction mechanism in the yeast Mitogen-Activated Protein Kinase (MAPK) osmotic stress response pathway. These insights into the interplay between gradual environments, cell volume change, dynamic cell signaling, and growth, advance our understanding of fundamental cellular processes in gradual stress environments.
Collapse
Affiliation(s)
- Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232 USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232 USA
- Lead Contact
| |
Collapse
|
4
|
Goetz A, Akl H, Dixit P. The ability to sense the environment is heterogeneously distributed in cell populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531554. [PMID: 36945613 PMCID: PMC10028875 DOI: 10.1101/2023.03.07.531554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Channel capacity of signaling networks quantifies their fidelity in sensing extracellular inputs. Low estimates of channel capacities for several mammalian signaling networks suggest that cells can barely detect the presence/absence of environmental signals. However, given the extensive heterogeneity and temporal stability of cell state variables, we hypothesize that the sensing ability itself may depend on the state of the cells. In this work, we present an information theoretic framework to quantify the distribution of sensing abilities from single cell data. Using data on two mammalian pathways, we show that sensing abilities are widely distributed in the population and most cells achieve better resolution of inputs compared to an " average cell ". We verify these predictions using live cell imaging data on the IGFR/FoxO pathway. Importantly, we identify cell state variables that correlate with cells' sensing abilities. This information theoretic framework will significantly improve our understanding of how cells sense in their environment.
Collapse
|
5
|
Bernasek SM, Hur SSJ, Peláez-Restrepo N, Boisclair Lachance JF, Bakker R, Navarro HT, Sanchez-Luege N, Amaral LAN, Bagheri N, Rebay I, Carthew RW. Ratiometric sensing of Pnt and Yan transcription factor levels confers ultrasensitivity to photoreceptor fate transitions in Drosophila. Development 2023; 150:dev201467. [PMID: 36942737 PMCID: PMC10163347 DOI: 10.1242/dev.201467] [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: 11/21/2022] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
Cell state transitions are often triggered by large changes in the concentrations of transcription factors and therefore large differences in their stoichiometric ratios. Whether cells can elicit transitions using modest changes in the ratios of co-expressed factors is unclear. Here, we investigate how cells in the Drosophila eye resolve state transitions by quantifying the expression dynamics of the ETS transcription factors Pnt and Yan. Eye progenitor cells maintain a relatively constant ratio of Pnt/Yan protein, despite expressing both proteins with pulsatile dynamics. A rapid and sustained twofold increase in the Pnt/Yan ratio accompanies transitions to photoreceptor fates. Genetic perturbations that modestly disrupt the Pnt/Yan ratio produce fate transition defects consistent with the hypothesis that transitions are normally driven by a twofold shift in the ratio. A biophysical model based on cooperative Yan-DNA binding coupled with non-cooperative Pnt-DNA binding illustrates how twofold ratio changes could generate ultrasensitive changes in target gene transcription to drive fate transitions. Thus, coupling cell state transitions to the Pnt/Yan ratio sensitizes the system to modest fold-changes, conferring robustness and ultrasensitivity to the developmental program.
Collapse
Affiliation(s)
- Sebastian M. Bernasek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Suzy S. J. Hur
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Nicolás Peláez-Restrepo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute (HHMI), Hanna H. Gray Fellows Program
| | | | - Rachael Bakker
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | | | - Nicelio Sanchez-Luege
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Luís A. N. Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes, Northwestern University, Evanston, IL 60208, USA
| | - Ilaria Rebay
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Richard W. Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, IL 60611, USA
| |
Collapse
|
6
|
Kalliara E, Kardynska M, Bagnall J, Spiller DG, Müller W, Ruckerl D, Śmieja J, Biswas SK, Paszek P. Post-transcriptional regulatory feedback encodes JAK-STAT signal memory of interferon stimulation. Front Immunol 2022; 13:947213. [PMID: 36238296 PMCID: PMC9552616 DOI: 10.3389/fimmu.2022.947213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Immune cells fine tune their responses to infection and inflammatory cues. Here, using live-cell confocal microscopy and mathematical modelling, we investigate interferon-induced JAK-STAT signalling in innate immune macrophages. We demonstrate that transient exposure to IFN-γ stimulation induces a long-term desensitisation of STAT1 signalling and gene expression responses, revealing a dose- and time-dependent regulatory feedback that controls JAK-STAT responses upon re-exposure to stimulus. We show that IFN-α/β1 elicit different level of desensitisation from IFN-γ, where cells refractory to IFN-α/β1 are sensitive to IFN-γ, but not vice versa. We experimentally demonstrate that the underlying feedback mechanism involves regulation of STAT1 phosphorylation but is independent of new mRNA synthesis and cognate receptor expression. A new feedback model of the protein tyrosine phosphatase activity recapitulates experimental data and demonstrates JAK-STAT network’s ability to decode relative changes of dose, timing, and type of temporal interferon stimulation. These findings reveal that STAT desensitisation renders cells with signalling memory of type I and II interferon stimulation, which in the future may improve administration of interferon therapy.
Collapse
Affiliation(s)
- Eirini Kalliara
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Malgorzata Kardynska
- Department of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Zabrze, Poland
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - James Bagnall
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - David G. Spiller
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Werner Müller
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Dominik Ruckerl
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jarosław Śmieja
- Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Subhra K. Biswas
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pawel Paszek
- School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- *Correspondence: Pawel Paszek,
| |
Collapse
|
7
|
Zamir A, Li G, Chase K, Moskovitch R, Sun B, Zaritsky A. Emergence of synchronized multicellular mechanosensing from spatiotemporal integration of heterogeneous single-cell information transfer. Cell Syst 2022; 13:711-723.e7. [PMID: 35921844 PMCID: PMC9509451 DOI: 10.1016/j.cels.2022.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/14/2021] [Accepted: 07/07/2022] [Indexed: 01/26/2023]
Abstract
Multicellular synchronization is a ubiquitous phenomenon in living systems. However, how noisy and heterogeneous behaviors of individual cells are integrated across a population toward multicellular synchronization is unclear. Here, we study the process of multicellular calcium synchronization of the endothelial cell monolayer in response to mechanical stimuli. We applied information theory to quantify the asymmetric information transfer between pairs of cells and defined quantitative measures to how single cells receive or transmit information within a multicellular network. Our analysis revealed that multicellular synchronization was established by gradual enhancement of information spread from the single cell to the multicellular scale. Synchronization was associated with heterogeneity in the cells' communication properties, reinforcement of the cells' state, and information flow. Altogether, we suggest a phenomenological model where cells gradually learn their local environment, adjust, and reinforce their internal state to stabilize the multicellular network architecture to support information flow from local to global scales toward multicellular synchronization.
Collapse
Affiliation(s)
- Amos Zamir
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Guanyu Li
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Katelyn Chase
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Robert Moskovitch
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Bo Sun
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA.
| | - Assaf Zaritsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| |
Collapse
|
8
|
Borba C, Kourakis MJ, Schwennicke S, Brasnic L, Smith WC. Fold Change Detection in Visual Processing. Front Neural Circuits 2021; 15:705161. [PMID: 34497492 PMCID: PMC8419522 DOI: 10.3389/fncir.2021.705161] [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: 05/04/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Visual processing transforms the complexities of the visual world into useful information. Ciona, an invertebrate chordate and close relative of the vertebrates, has one of the simplest nervous systems known, yet has a range of visuomotor behaviors. This simplicity has facilitated studies linking behavior and neural circuitry. Ciona larvae have two distinct visuomotor behaviors - a looming shadow response and negative phototaxis. These are mediated by separate neural circuits that initiate from different clusters of photoreceptors, with both projecting to a CNS structure called the posterior brain vesicle (pBV). We report here that inputs from both circuits are processed to generate fold change detection (FCD) outputs. In FCD, the behavioral response scales with the relative fold change in input, but is invariant to the overall magnitude of the stimulus. Moreover, the two visuomotor behaviors have fundamentally different stimulus/response relationships - indicative of differing circuit strategies, with the looming shadow response showing a power relationship to fold change, while the navigation behavior responds linearly. Pharmacological modulation of the FCD response points to the FCD circuits lying outside of the visual organ (the ocellus), with the pBV being the most likely location. Consistent with these observations, the connectivity and properties of pBV interneurons conform to known FCD circuit motifs, but with different circuit architectures for the two circuits. The negative phototaxis circuit forms a putative incoherent feedforward loop that involves interconnecting cholinergic and GABAergic interneurons. The looming shadow circuit uses the same cholinergic and GABAergic interneurons, but with different synaptic inputs to create a putative non-linear integral feedback loop. These differing circuit architectures are consistent with the behavioral outputs of the two circuits. Finally, while some reports have highlighted parallels between the pBV and the vertebrate midbrain, suggesting a common origin for the two, others reports have disputed this, suggesting that invertebrate chordates lack a midbrain homolog. The convergence of visual inputs at the pBV, and its putative role in visual processing reported here and in previous publications, lends further support to the proposed common origin of the pBV and the vertebrate midbrain.
Collapse
Affiliation(s)
- Cezar Borba
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Matthew J Kourakis
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Shea Schwennicke
- College of Creative Studies, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lorena Brasnic
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States.,Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - William C Smith
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States.,College of Creative Studies, University of California, Santa Barbara, Santa Barbara, CA, United States
| |
Collapse
|
9
|
Karin O, Raz M, Alon U. An opponent process for alcohol addiction based on changes in endocrine gland mass. iScience 2021; 24:102127. [PMID: 33665551 PMCID: PMC7903339 DOI: 10.1016/j.isci.2021.102127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/17/2020] [Accepted: 01/27/2021] [Indexed: 12/03/2022] Open
Abstract
Consuming addictive drugs is often initially pleasurable, but escalating drug intake eventually recruits physiological anti-reward systems called opponent processes that cause tolerance and withdrawal symptoms. Opponent processes are fundamental for the addiction process, but their physiological basis is not fully characterized. Here, we propose an opponent processes mechanism centered on the endocrine stress response, the hypothalamic-pituitary-adrenal (HPA) axis. We focus on alcohol addiction, where the HPA axis is activated and secretes β-endorphin, causing euphoria and analgesia. Using a mathematical model, we show that slow changes in the functional mass of HPA glands act as an opponent process for β-endorphin secretion. The model explains hormone dynamics in alcohol addiction and experiments on alcohol preference in rodents. The opponent process is based on fold-change detection (FCD) where β-endorphin responses are relative rather than absolute; FCD confers vulnerability to addiction but has adaptive roles for learning. Our model suggests gland mass changes as potential targets for intervention in addiction. Addiction involves tolerance and withdrawal over weeks Model of the HPA-axis and β-endorphins explains tolerance and withdrawal Effects due to changes in the functional mass of endocrine glands Fold-change detection makes circuit prone to addiction but boosts learning
Collapse
Affiliation(s)
- Omer Karin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moriya Raz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
10
|
Molecular switch architecture determines response properties of signaling pathways. Proc Natl Acad Sci U S A 2021; 118:2013401118. [PMID: 33688042 DOI: 10.1073/pnas.2013401118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Many intracellular signaling pathways are composed of molecular switches, proteins that transition between two states-on and off Typically, signaling is initiated when an external stimulus activates its cognate receptor that, in turn, causes downstream switches to transition from off to on using one of the following mechanisms: activation, in which the transition rate from the off state to the on state increases; derepression, in which the transition rate from the on state to the off state decreases; and concerted, in which activation and derepression operate simultaneously. We use mathematical modeling to compare these signaling mechanisms in terms of their dose-response curves, response times, and abilities to process upstream fluctuations. Our analysis elucidates several operating principles for molecular switches. First, activation increases the sensitivity of the pathway, whereas derepression decreases sensitivity. Second, activation generates response times that decrease with signal strength, whereas derepression causes response times to increase with signal strength. These opposing features allow the concerted mechanism to not only show dose-response alignment, but also to decouple the response time from stimulus strength. However, these potentially beneficial properties come at the expense of increased susceptibility to upstream fluctuations. We demonstrate that these operating principles also hold when the models are extended to include additional features, such as receptor removal, kinetic proofreading, and cascades of switches. In total, we show how the architecture of molecular switches govern their response properties. We also discuss the biological implications of our findings.
Collapse
|
11
|
Berenguer J, Celià-Terrassa T. Cell memory of epithelial-mesenchymal plasticity in cancer. Curr Opin Cell Biol 2021; 69:103-110. [PMID: 33578288 DOI: 10.1016/j.ceb.2021.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022]
Abstract
Fundamental biological processes of cell identity and cell fate determination are controlled by complex regulatory networks. These processes require molecular mechanisms that confer cellular phenotypic memory and state persistence. In this minireview, we will summarize mechanisms of cell memory based on regulatory hysteretic feedback loops and explore epigenetic mechanisms widely represented in nature, with special focus on epithelial-to-mesenchymal plasticity. We will also discuss the functional consequences of cell memory and epithelial-to-mesenchymal plasticity dynamics during development and cancer metastasis.
Collapse
Affiliation(s)
- Jordi Berenguer
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
| | - Toni Celià-Terrassa
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.
| |
Collapse
|
12
|
Son M, Wang AG, Tu HL, Metzig MO, Patel P, Husain K, Lin J, Murugan A, Hoffmann A, Tay S. NF-κB responds to absolute differences in cytokine concentrations. Sci Signal 2021; 14. [PMID: 34211635 DOI: 10.1126/scisignal.aaz4382] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cells receive a wide range of dynamic signaling inputs during immune regulation, but how gene regulatory networks measure such dynamic inputs is not well understood. Here, we used microfluidic single-cell analysis and mathematical modeling to study how the NF-κB pathway responds to immune inputs that vary over time such as increasing, decreasing, or fluctuating cytokine signals. We found that NF-κB activity responded to the absolute difference in cytokine concentration and not to the concentration itself. Our analyses revealed that negative feedback by the regulatory proteins A20 and IκBα enabled differential responses to changes in cytokine dose by providing a short-term memory of previous cytokine concentrations and by continuously resetting kinase cycling and receptor abundance. Investigation of NF-κB target gene expression showed that cells exhibited distinct transcriptional responses under different dynamic cytokine profiles. Our results demonstrate how cells use simple network motifs and transcription factor dynamics to efficiently extract information from complex signaling environments.
Collapse
Affiliation(s)
- Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Andrew G Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Hsiung-Lin Tu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.,Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Marie Oliver Metzig
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
| | - Parthiv Patel
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Kabir Husain
- James Franck Institute and Department of Physics, University of Chicago, Chicago, IL 60637, USA
| | - Jing Lin
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Arvind Murugan
- James Franck Institute and Department of Physics, University of Chicago, Chicago, IL 60637, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
13
|
Hongdusit A, Liechty ET, Fox JM. Optogenetic interrogation and control of cell signaling. Curr Opin Biotechnol 2020; 66:195-206. [PMID: 33053496 DOI: 10.1016/j.copbio.2020.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 02/05/2023]
Abstract
Signaling networks control the flow of information through biological systems and coordinate the chemical processes that constitute cellular life. Optogenetic actuators - genetically encoded proteins that undergo light-induced changes in activity or conformation - are useful tools for probing signaling networks over time and space. They have permitted detailed dissections of cellular proliferation, differentiation, motility, and death, and enabled the assembly of synthetic systems with applications in areas as diverse as photography, chemical synthesis, and medicine. In this review, we provide a brief introduction to optogenetic systems and describe their application to molecular-level analyses of cell signaling. Our discussion highlights important research achievements and speculates on future opportunities to exploit optogenetic systems in the study and assembly of complex biochemical networks.
Collapse
Affiliation(s)
- Akarawin Hongdusit
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA
| | - Evan T Liechty
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA.
| |
Collapse
|
14
|
Dixit PD, Lyashenko E, Niepel M, Vitkup D. Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks. Cell Syst 2020; 10:204-212.e8. [PMID: 31864963 PMCID: PMC7047530 DOI: 10.1016/j.cels.2019.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 07/30/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022]
Abstract
Predictive models of signaling networks are essential for understanding cell population heterogeneity and designing rational interventions in disease. However, using computational models to predict heterogeneity of signaling dynamics is often challenging because of the extensive variability of biochemical parameters across cell populations. Here, we describe a maximum entropy-based framework for inference of heterogeneity in dynamics of signaling networks (MERIDIAN). MERIDIAN estimates the joint probability distribution over signaling network parameters that is consistent with experimentally measured cell-to-cell variability of biochemical species. We apply the developed approach to investigate the response heterogeneity in the EGFR/Akt signaling network. Our analysis demonstrates that a significant fraction of cells exhibits high phosphorylated Akt (pAkt) levels hours after EGF stimulation. Our findings also suggest that cells with high EGFR levels predominantly contribute to the subpopulation of cells with high pAkt activity. We also discuss how MERIDIAN can be extended to accommodate various experimental measurements.
Collapse
Affiliation(s)
- Purushottam D Dixit
- Department of Systems Biology, Columbia University, New York, NY, USA; Department of Physics, University of Florida, Gainesville, FL, USA.
| | - Eugenia Lyashenko
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Mario Niepel
- Laboratory of Systems Pharmacology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis Vitkup
- Department of Systems Biology, Columbia University, New York, NY, USA; Department of Biomedical Informatics, Columbia University, New York, NY, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA.
| |
Collapse
|