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Helenek C, Krzysztoń R, Petreczky J, Wan Y, Cabral M, Coraci D, Balázsi G. Synthetic gene circuit evolution: Insights and opportunities at the mid-scale. Cell Chem Biol 2024; 31:1447-1459. [PMID: 38925113 PMCID: PMC11330362 DOI: 10.1016/j.chembiol.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
Directed evolution focuses on optimizing single genetic components for predefined engineering goals by artificial mutagenesis and selection. In contrast, experimental evolution studies the adaptation of entire genomes in serially propagated cell populations, to provide an experimental basis for evolutionary theory. There is a relatively unexplored gap at the middle ground between these two techniques, to evolve in vivo entire synthetic gene circuits with nontrivial dynamic function instead of single parts or whole genomes. We discuss the requirements for such mid-scale evolution, with hypothetical examples for evolving synthetic gene circuits by appropriate selection and targeted shuffling of a seed set of genetic components in vivo. Implementing similar methods should aid the rapid generation, functionalization, and optimization of synthetic gene circuits in various organisms and environments, accelerating both the development of biomedical and technological applications and the understanding of principles guiding regulatory network evolution.
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Affiliation(s)
- Christopher Helenek
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Rafał Krzysztoń
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julia Petreczky
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yiming Wan
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mariana Cabral
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Damiano Coraci
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA.
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2
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Li Y, Deng D, Höfer CT, Kim J, Do Heo W, Xu Q, Liu X, Zi Z. Liebig's law of the minimum in the TGF-β/SMAD pathway. PLoS Comput Biol 2024; 20:e1012072. [PMID: 38753874 PMCID: PMC11135686 DOI: 10.1371/journal.pcbi.1012072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/29/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Cells use signaling pathways to sense and respond to their environments. The transforming growth factor-β (TGF-β) pathway produces context-specific responses. Here, we combined modeling and experimental analysis to study the dependence of the output of the TGF-β pathway on the abundance of signaling molecules in the pathway. We showed that the TGF-β pathway processes the variation of TGF-β receptor abundance using Liebig's law of the minimum, meaning that the output-modifying factor is the signaling protein that is most limited, to determine signaling responses across cell types and in single cells. We found that the abundance of either the type I (TGFBR1) or type II (TGFBR2) TGF-β receptor determined the responses of cancer cell lines, such that the receptor with relatively low abundance dictates the response. Furthermore, nuclear SMAD2 signaling correlated with the abundance of TGF-β receptor in single cells depending on the relative expression levels of TGFBR1 and TGFBR2. A similar control principle could govern the heterogeneity of signaling responses in other signaling pathways.
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Affiliation(s)
- Yuchao Li
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory, Berlin, Germany
| | - Difan Deng
- German Federal Institute for Risk Assessment, Department of Experimental Toxicology and ZEBET, Berlin, Germany
| | - Chris Tina Höfer
- German Federal Institute for Risk Assessment, Department of Experimental Toxicology and ZEBET, Berlin, Germany
| | - Jihye Kim
- Department of Biological Sciences, KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Won Do Heo
- Department of Biological Sciences, KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Quanbin Xu
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Xuedong Liu
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Zhike Zi
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory, Berlin, Germany
- German Federal Institute for Risk Assessment, Department of Experimental Toxicology and ZEBET, Berlin, Germany
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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3
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Andrews SS, Wiley HS, Sauro HM. Design patterns of biological cells. Bioessays 2024; 46:e2300188. [PMID: 38247191 PMCID: PMC10922931 DOI: 10.1002/bies.202300188] [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: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.
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Affiliation(s)
- Steven S. Andrews
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Herbert M. Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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4
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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.
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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
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5
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Fan Y, Chai C, Li P, Zou X, Ferrell JE, Wang B. Ultrafast distant wound response is essential for whole-body regeneration. Cell 2023; 186:3606-3618.e16. [PMID: 37480850 PMCID: PMC10957142 DOI: 10.1016/j.cell.2023.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/11/2023] [Accepted: 06/23/2023] [Indexed: 07/24/2023]
Abstract
Injury induces systemic responses, but their functions remain elusive. Mechanisms that can rapidly synchronize wound responses through long distances are also mostly unknown. Using planarian flatworms capable of whole-body regeneration, we report that injury induces extracellular signal-regulated kinase (Erk) activity waves to travel at a speed 10-100 times faster than those in other multicellular tissues. This ultrafast propagation requires longitudinal body-wall muscles, elongated cells forming dense parallel tracks running the length of the organism. The morphological properties of muscles allow them to act as superhighways for propagating and disseminating wound signals. Inhibiting Erk propagation prevents tissues distant to the wound from responding and blocks regeneration, which can be rescued by a second injury to distal tissues shortly after the first injury. Our findings provide a mechanism for long-range signal propagation in large, complex tissues to coordinate responses across cell types and highlight the function of feedback between spatially separated tissues during whole-body regeneration.
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Affiliation(s)
- Yuhang Fan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Chew Chai
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Pengyang Li
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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Martin-Vega A, Earnest S, Augustyn A, Wichaidit C, Gazdar A, Girard L, Peyton M, Kollipara RK, Minna JD, Johnson JE, Cobb MH. ASCL1-ERK1/2 Axis: ASCL1 restrains ERK1/2 via the dual specificity phosphatase DUSP6 to promote survival of a subset of neuroendocrine lung cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545148. [PMID: 37398419 PMCID: PMC10312738 DOI: 10.1101/2023.06.15.545148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The transcription factor achaete-scute complex homolog 1 (ASCL1) is a lineage oncogene that is central for the growth and survival of small cell lung cancers (SCLC) and neuroendocrine non-small cell lung cancers (NSCLC-NE) that express it. Targeting ASCL1, or its downstream pathways, remains a challenge. However, a potential clue to overcoming this challenage has been information that SCLC and NSCLC-NE that express ASCL1 exhibit extremely low ERK1/2 activity, and efforts to increase ERK1/2 activity lead to inhibition of SCLC growth and surival. Of course, this is in dramatic contrast to the majority of NSCLCs where high activity of the ERK pathway plays a major role in cancer pathogenesis. A major knowledge gap is defining the mechanism(s) underlying the low ERK1/2 activity in SCLC, determining if ERK1/2 activity and ASCL1 function are inter-related, and if manipulating ERK1/2 activity provides a new therapeutic strategy for SCLC. We first found that expression of ERK signaling and ASCL1 have an inverse relationship in NE lung cancers: knocking down ASCL1 in SCLCs and NE-NSCLCs increased active ERK1/2, while inhibition of residual SCLC/NSCLC-NE ERK1/2 activity with a MEK inhibitor increased ASCL1 expression. To determine the effects of ERK activity on expression of other genes, we obtained RNA-seq from ASCL1-expressing lung tumor cells treated with an ERK pathway MEK inhibitor and identified down-regulated genes (such as SPRY4, ETV5, DUSP6, SPRED1) that potentially could influence SCLC/NSCLC-NE tumor cell survival. This led us to discover that genes regulated by MEK inhibition suppress ERK activation and CHIP-seq demonstrated these are bound by ASCL1. In addition, SPRY4, DUSP6, SPRED1 are known suppressors of the ERK1/2 pathway, while ETV5 regulates DUSP6. Survival of NE lung tumors was inhibited by activation of ERK1/2 and a subset of ASCL1-high NE lung tumors expressed DUSP6. Because the dual specificity phosphatase 6 (DUSP6) is an ERK1/2-selective phosphatase that inactivates these kinases and has a pharmacologic inhibitor, we focused mechanistic studies on DUSP6. These studies showed: Inhibition of DUSP6 increased active ERK1/2, which accumulated in the nucleus; pharmacologic and genetic inhibition of DUSP6 affected proliferation and survival of ASCL1-high NE lung cancers; and that knockout of DUSP6 "cured" some SCLCs while in others resistance rapidly developed indicating a bypass mechanism was activated. Thus, our findings fill this knowledge gap and indicate that combined expression of ASCL1, DUSP6 and low phospho-ERK1/2 identify some neuroendocrine lung cancers for which DUSP6 may be a therapeutic target.
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7
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Sarma U, Ripka L, Anyaegbunam UA, Legewie S. Modeling Cellular Signaling Variability Based on Single-Cell Data: The TGFβ-SMAD Signaling Pathway. Methods Mol Biol 2023; 2634:215-251. [PMID: 37074581 DOI: 10.1007/978-1-0716-3008-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Nongenetic heterogeneity is key to cellular decisions, as even genetically identical cells respond in very different ways to the same external stimulus, e.g., during cell differentiation or therapeutic treatment of disease. Strong heterogeneity is typically already observed at the level of signaling pathways that are the first sensors of external inputs and transmit information to the nucleus where decisions are made. Since heterogeneity arises from random fluctuations of cellular components, mathematical models are required to fully describe the phenomenon and to understand the dynamics of heterogeneous cell populations. Here, we review the experimental and theoretical literature on cellular signaling heterogeneity, with special focus on the TGFβ/SMAD signaling pathway.
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Affiliation(s)
- Uddipan Sarma
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Lorenz Ripka
- Institute of Molecular Biology (IMB), Mainz, Germany
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Uchenna Alex Anyaegbunam
- Institute of Molecular Biology (IMB), Mainz, Germany
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, Stuttgart, Germany
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Mainz, Germany.
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, Stuttgart, Germany.
- Stuttgart Research Center for Systems Biology, University of Stuttgart, Stuttgart, Germany.
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8
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Hanson RL, Batchelor E. Coordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress. Mol Syst Biol 2022; 18:e11401. [PMID: 36472304 PMCID: PMC9724178 DOI: 10.15252/msb.202211401] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
In response to different cellular stresses, the transcription factor p53 undergoes different dynamics. p53 dynamics, in turn, control cell fate. However, distinct stresses can generate the same p53 dynamics but different cell fate outcomes, suggesting integration of dynamic information from other pathways is important for cell fate regulation. To determine how MAPK activities affect p53-mediated responses to DNA breaks and oxidative stress, we simultaneously tracked p53 and either ERK, JNK, or p38 activities in single cells. While p53 dynamics were comparable between the stresses, cell fate outcomes were distinct. Combining MAPK dynamics with p53 dynamics was important for distinguishing between the stresses and for generating temporal ordering of cell fate pathways. Furthermore, cross-talk between MAPKs and p53 controlled the balance between proliferation and cell death. These findings provide insight into how cells integrate signaling pathways with distinct temporal patterns of activity to encode stress specificity and drive different cell fate decisions.
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Affiliation(s)
- Ryan L Hanson
- Department of Integrative Biology and PhysiologyUniversity of MinnesotaMinneapolisMNUSA
| | - Eric Batchelor
- Department of Integrative Biology and PhysiologyUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
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9
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Abstract
Metazoan embryos develop from a single cell into three-dimensional structured organisms while groups of genetically identical cells attain specialized identities. Cells of the developing embryo both create and accurately interpret morphogen gradients to determine their positions and make specific decisions in response. Here, we first cover intellectual roots of morphogen and positional information concepts. Focusing on animal embryos, we then provide a review of current understanding on how morphogen gradients are established and how their spans are controlled. Lastly, we cover how gradients evolve in time and space during development, and how they encode information to control patterning. In sum, we provide a list of patterning principles for morphogen gradients and review recent advances in quantitative methodologies elucidating information provided by morphogens.
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Affiliation(s)
- M. Fethullah Simsek
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ertuğrul M. Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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10
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Giri R, Brady S, Papadopoulos DK, Carthew RW. Single-cell Senseless protein analysis reveals metastable states during the transition to a sensory organ fate. iScience 2022; 25:105097. [PMID: 36157584 PMCID: PMC9494244 DOI: 10.1016/j.isci.2022.105097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/02/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
Cell fate decisions can be envisioned as bifurcating dynamical systems, and the decision that Drosophila cells make during sensory organ differentiation has been described as such. We extended these studies by focusing on the Senseless protein which orchestrates sensory cell fate transitions. Wing cells contain intermediate Senseless numbers before their fate transition, after which they express much greater numbers of Senseless molecules as they differentiate. However, the dynamics are inconsistent with it being a simple bistable system. Cells with intermediate Senseless are best modeled as residing in four discrete states, each with a distinct protein number and occupying a specific region of the tissue. Although the states are stable over time, the number of molecules in each state vary with time. The fold change in molecule number between adjacent states is invariant and robust to absolute protein number variation. Thus, cells transitioning to sensory fates exhibit metastability with relativistic properties.
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Affiliation(s)
- Ritika Giri
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Shannon Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Dimitrios K. Papadopoulos
- Center for Molecular Medicine (CMM), Department of Clinical Neuroscience, Karolinska Institute, 17176 Stockholm, Sweden,Department of Biology, University of Crete, Voutes University Campus, Heraklion, Crete 70013, Greece
| | - 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,Corresponding author
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11
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Seenivasan P, Narayanan R. Efficient information coding and degeneracy in the nervous system. Curr Opin Neurobiol 2022; 76:102620. [PMID: 35985074 PMCID: PMC7613645 DOI: 10.1016/j.conb.2022.102620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 11/25/2022]
Abstract
Efficient information coding (EIC) is a universal biological framework rooted in the fundamental principle that system responses should match their natural stimulus statistics for maximizing environmental information. Quantitatively assessed through information theory, such adaptation to the environment occurs at all biological levels and timescales. The context dependence of environmental stimuli and the need for stable adaptations make EIC a daunting task. We argue that biological complexity is the principal architect that subserves deft execution of stable EIC. Complexity in a system is characterized by several functionally segregated subsystems that show a high degree of functional integration when they interact with each other. Complex biological systems manifest heterogeneities and degeneracy, wherein structurally different subsystems could interact to yield the same functional outcome. We argue that complex systems offer several choices that effectively implement EIC and homeostasis for each of the different contexts encountered by the system.
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Affiliation(s)
- Pavithraa Seenivasan
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India. https://twitter.com/PaveeSeeni
| | - Rishikesh Narayanan
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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12
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Wen Y, Xie D, Liu Z. Advances in protein analysis in single live cells: principle, instrumentation and applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Valls PO, Esposito A. Signalling dynamics, cell decisions, and homeostatic control in health and disease. Curr Opin Cell Biol 2022; 75:102066. [PMID: 35245783 PMCID: PMC9097822 DOI: 10.1016/j.ceb.2022.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/13/2022]
Abstract
Cell signalling engenders cells with the capability to receive and process information from the intracellular and extracellular environments, trigger and execute biological responses, and communicate with each other. Ultimately, cell signalling is responsible for maintaining homeostasis at the cellular, tissue and systemic level. For this reason, cell signalling is a topic of intense research efforts aimed to elucidate how cells coordinate transitions between states in developing and adult organisms in physiological and pathological conditions. Here, we review current knowledge of how cell signalling operates at multiple spatial and temporal scales, focusing on how single-cell analytical techniques reveal mechanisms underpinning cell-to-cell variability, signalling plasticity, and collective cellular responses.
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Affiliation(s)
- Pablo Oriol Valls
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
| | - Alessandro Esposito
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom; Centre for Genome Engineering and Maintenance, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom.
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14
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Feldman D, Funk L, Le A, Carlson RJ, Leiken MD, Tsai F, Soong B, Singh A, Blainey PC. Pooled genetic perturbation screens with image-based phenotypes. Nat Protoc 2022; 17:476-512. [PMID: 35022620 PMCID: PMC9654597 DOI: 10.1038/s41596-021-00653-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022]
Abstract
Discovery of the genetic components underpinning fundamental and disease-related processes is being rapidly accelerated by combining efficient, programmable genetic engineering with phenotypic readouts of high spatial, temporal and/or molecular resolution. Microscopy is a fundamental tool for studying cell biology, but its lack of high-throughput sequence readouts hinders integration in large-scale genetic screens. Optical pooled screens using in situ sequencing provide massively scalable integration of barcoded lentiviral libraries (e.g., CRISPR perturbation libraries) with high-content imaging assays, including dynamic processes in live cells. The protocol uses standard lentiviral vectors and molecular biology, providing single-cell resolution of phenotype and engineered genotype, scalability to millions of cells and accurate sequence reads sufficient to distinguish >106 perturbations. In situ amplification takes ~2 d, while sequencing can be performed in ~1.5 h per cycle. The image analysis pipeline provided enables fully parallel automated sequencing analysis using a cloud or cluster computing environment.
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Affiliation(s)
- David Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Luke Funk
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna Le
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rebecca J Carlson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - FuNien Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Brian Soong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cellular and Tissue Genomics, Genentech Inc., South San Francisco, CA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
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15
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microRNA-Mediated Encoding and Decoding of Time-Dependent Signals in Tumorigenesis. Biomolecules 2022; 12:biom12020213. [PMID: 35204714 PMCID: PMC8961662 DOI: 10.3390/biom12020213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
microRNAs, pivotal post-transcriptional regulators of gene expression, in the past decades have caught the attention of researchers for their involvement in different biological processes, ranging from cell development to cancer. Although lots of effort has been devoted to elucidate the topological features and the equilibrium properties of microRNA-mediated motifs, little is known about how the information encoded in frequency, amplitude, duration, and other features of their regulatory signals can affect the resulting gene expression patterns. Here, we review the current knowledge about microRNA-mediated gene regulatory networks characterized by time-dependent input signals, such as pulses, transient inputs, and oscillations. First, we identify the general characteristic of the main motifs underlying temporal patterns. Then, we analyze their impact on two commonly studied oncogenic networks, showing how their dysfunction can lead to tumorigenesis.
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16
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Huang WYC, Alvarez S, Kondo Y, Kuriyan J, Groves JT. Relating cellular signaling timescales to single-molecule kinetics: A first-passage time analysis of Ras activation by SOS. Proc Natl Acad Sci U S A 2021; 118:e2103598118. [PMID: 34740968 PMCID: PMC8694064 DOI: 10.1073/pnas.2103598118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2021] [Indexed: 12/27/2022] Open
Abstract
Son of Sevenless (SOS) is a Ras guanine nucleotide exchange factor (GEF) that plays a central role in numerous cellular signaling pathways. Like many other signaling molecules, SOS is autoinhibited in the cytosol and activates only after recruitment to the membrane. The mean activation time of individual SOS molecules has recently been measured to be ∼60 s, which is unexpectedly long and seemingly contradictory with cellular signaling timescales, which have been measured to be as fast as several seconds. Here, we rectify this discrepancy using a first-passage time analysis to reconstruct the effective signaling timescale of multiple SOS molecules from their single-molecule activation kinetics. Along with corresponding experimental measurements, this analysis reveals how the functional response time, comprised of many slowly activating molecules, can become substantially faster than the average molecular kinetics. This consequence stems from the enzymatic processivity of SOS in a highly out-of-equilibrium reaction cycle during receptor triggering. Ultimately, rare, early activation events dominate the macroscopic reaction dynamics.
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Affiliation(s)
- William Y C Huang
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Steven Alvarez
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720
| | - Yasushi Kondo
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - John Kuriyan
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- HHMI, University of California, Berkeley, CA 94720
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720;
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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17
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Hirose S, Rieu JP, Anjard C, Cochet-Escartin O, Kikuchi H, Funamoto K. Aerotaxis and aerokinesis of Dictyostelium discoideum under hypoxic microenvironments. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:1187-1190. [PMID: 34891499 DOI: 10.1109/embc46164.2021.9629752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Although spatiotemporal changes of oxygen in a microenvironment are known to affect the cellular dynamics of various eukaryotes, the details are not fully understood. Here, we describe the aerotaxis and aerokinesis of Dictyostelium discoideum (Dd), which has long been employed as a model organism for eukaryotic cells. We developed a microfluidic device capable of time-lapse observation of cultured cells while controlling oxygen concentrations in microchannels. Migratory behaviors of Dd were observed and quantitatively evaluated under an oxygen concentration gradient from 0% to 21% O2, as well as in various uniform oxygen conditions. In a hypoxic region within the oxygen concentration gradient, Dd migrated toward regions of higher oxygen concentration at increased velocity, which was independent of cell density. Observed under uniform oxygen concentrations of 1%, 2%, 3%, and 21%, the migration velocity of Dd increased significantly in hypoxic environments of 2% O2 or less. Thus, Dd shows aerotaxis, directed by the oxygen concentration gradient, and simultaneously shows aerokinesis, changing the migration velocity according to the oxygen concentration itself.
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18
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Loree JM, Wang Y, Syed MA, Sorokin AV, Coker O, Xiu J, Weinberg BA, Vanderwalde AM, Tesfaye A, Raymond VM, Miron B, Tarcic G, Zelichov O, Broaddus RR, Ng PKS, Jeong KJ, Tsang YH, Mills GB, Overman MJ, Grothey A, Marshall JL, Kopetz S. Clinical and Functional Characterization of Atypical KRAS/ NRAS Mutations in Metastatic Colorectal Cancer. Clin Cancer Res 2021; 27:4587-4598. [PMID: 34117033 PMCID: PMC8364867 DOI: 10.1158/1078-0432.ccr-21-0180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/29/2021] [Accepted: 06/09/2021] [Indexed: 01/13/2023]
Abstract
PURPOSE Mutations in KRAS/NRAS (RAS) predict lack of anti-EGFR efficacy in metastatic colorectal cancer (mCRC). However, it is unclear if all RAS mutations have similar impact, and atypical mutations beyond those in standard guidelines exist. EXPERIMENTAL DESIGN We reviewed 7 tissue and 1 cell-free DNA cohorts of 9,485 patients to characterize atypical RAS variants. Using an in vitro cell-based assay (functional annotation for cancer treatment), Ba/F3 transformation, and in vivo xenograft models of transduced isogenic clones, we assessed signaling changes across mutations. RESULTS KRAS exon 2, extended RAS, and atypical RAS mutations were noted in 37.8%, 9.5%, and 1.2% of patients, respectively. Among atypical variants, KRAS L19F, Q22K, and D33E occurred at prevalence ≥0.1%, whereas no NRAS codon 117/146 and only one NRAS codon 59 mutation was noted. Atypical RAS mutations had worse overall survival than RAS/BRAF wild-type mCRC (HR, 2.90; 95% confidence interval, 1.24-6.80; P = 0.014). We functionally characterized 114 variants with the FACT assay. All KRAS exon 2 and extended RAS mutations appeared activating. Of 57 atypical RAS variants characterized, 18 (31.6%) had signaling below wild-type, 23 (40.4%) had signaling between wild-type and activating control, and 16 (28.1%) were hyperactive beyond the activating control. Ba/F3 transformation (17/18 variants) and xenograft model (7/8 variants) validation was highly concordant with FACT results, and activating atypical variants were those that occurred at highest prevalence in clinical cohorts. CONCLUSIONS We provide best available evidence to guide treatment when atypical RAS variants are identified. KRAS L19F, Q22K, D33E, and T50I are more prevalent than many guideline-included RAS variants and functionally relevant.
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Affiliation(s)
| | | | - Muddassir A Syed
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexey V Sorokin
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Oluwadara Coker
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Benjamin A Weinberg
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | | | | | | | | | | | | | | | | | - Kang Jin Jeong
- Oregon Health Sciences University Knight Cancer Institute, Portland, Oregon
| | - Yiu Huen Tsang
- Oregon Health Sciences University Knight Cancer Institute, Portland, Oregon
| | - Gordon B Mills
- Oregon Health Sciences University Knight Cancer Institute, Portland, Oregon
| | | | | | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, Texas.
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19
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Gillies TE, Pargett M, Silva JM, Teragawa CK, McCormick F, Albeck JG. Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway. Mol Syst Biol 2021; 16:e9518. [PMID: 33073539 PMCID: PMC7569415 DOI: 10.15252/msb.20209518] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/02/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
Activating mutations in RAS are present in ~ 30% of human tumors, and the resulting aberrations in ERK/MAPK signaling play a central role in oncogenesis. However, the form of these signaling changes is uncertain, with activating RAS mutants linked to both increased and decreased ERK activation in vivo. Rationally targeting the kinase activity of this pathway requires clarification of the quantitative effects of RAS mutations. Here, we use live‐cell imaging in cells expressing only one RAS isoform to quantify ERK activity with a new level of accuracy. We find that despite large differences in their biochemical activity, mutant KRAS isoforms within cells have similar ranges of ERK output. We identify roles for pathway‐level effects, including variation in feedback strength and feedforward modulation of phosphatase activity, that act to rescale pathway sensitivity, ultimately resisting changes in the dynamic range of ERK activity while preserving responsiveness to growth factor stimuli. Our results reconcile seemingly inconsistent reports within the literature and imply that the signaling changes induced by RAS mutations early in oncogenesis are subtle.
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Affiliation(s)
- Taryn E Gillies
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Jillian M Silva
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Carolyn K Teragawa
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.,Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
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20
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Gene Expression at a Single Molecule Level: Implications for MDS and AML. Blood 2021; 138:625-636. [PMID: 34157070 DOI: 10.1182/blood.2019004261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Non-genetic heterogeneity, or gene expression stochasticity, is an important source of variability in biological systems. With the advent and improvement of single molecule resolution technologies, it has been shown that transcription dynamics and resultant transcript number fluctuations generate significant cell-to-cell variability that has important biological effects and may contribute substantially to both tissue homeostasis and disease. In this respect, the pathophysiology of stem cell-derived malignancies such as AML and MDS, which has historically been studied at the ensemble level, may require re-evaluation. To that end, it is our aim in this review to highlight the results of recent single-molecule, biophysical, and systems studies of gene expression dynamics, with the explicit purpose of demonstrating how the insights from these basic science studies may help inform and progress the field of leukemia biology and, ultimately, research into novel therapies.
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21
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Benary M, Bohn S, Lüthen M, Nolis IK, Blüthgen N, Loewer A. Disentangling Pro-mitotic Signaling during Cell Cycle Progression using Time-Resolved Single-Cell Imaging. Cell Rep 2021; 31:107514. [PMID: 32294432 DOI: 10.1016/j.celrep.2020.03.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/19/2020] [Accepted: 03/23/2020] [Indexed: 11/26/2022] Open
Abstract
Cells rely on input from extracellular growth factors to control their proliferation during development and adult homeostasis. Such mitogenic inputs are transmitted through multiple signaling pathways that synergize to precisely regulate cell cycle entry and progression. Although the architecture of these signaling networks has been characterized in molecular detail, their relative contribution, especially at later cell cycle stages, remains largely unexplored. By combining quantitative time-resolved measurements of fluorescent reporters in untransformed human cells with targeted pharmacological inhibitors and statistical analysis, we quantify epidermal growth factor (EGF)-induced signal processing in individual cells over time and dissect the dynamic contribution of downstream pathways. We define signaling features that encode information about extracellular ligand concentrations and critical time windows for inducing cell cycle transitions. We show that both extracellular signal-regulated kinase (ERK) and phosphatidylinositol 3-kinase (PI3K) activity are necessary for initial cell cycle entry, whereas only PI3K affects the duration of S phase at later stages of mitogenic signaling.
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Affiliation(s)
- Manuela Benary
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, 10115 Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany
| | - Stefan Bohn
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Mareen Lüthen
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ilias K Nolis
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, 13125 Berlin, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, 10115 Berlin, Germany; Integrative Research Institute Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Alexander Loewer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany; Berlin Institute for Medical Systems Biology, Max Delbrueck Center in the Helmholtz Association, 13125 Berlin, Germany.
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22
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Functional measurement of mitogen-activated protein kinase pathway activation predicts responsiveness of RAS-mutant cancers to MEK inhibitors. Eur J Cancer 2021; 149:184-192. [PMID: 33865203 DOI: 10.1016/j.ejca.2021.01.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 01/17/2023]
Abstract
BACKGROUND RAS variant-related functional impact on the mitogen-activated protein kinase (MAPK) pathway, and correlation between MAPK activation and MAPK/ERK kinase (MEK) inhibitor responsiveness, is not established. PATIENTS AND METHODS Of 1,693 tumours sequenced, 576 harboured a RAS alteration; 62 patients received an MEK inhibitor (MEKi) and had RAS mutations that were functionally characterised. We report that RAS mutants have variable levels of MAPK activity, as measured by a functional cell-based assay that quantified MAPK pathway activation after transfection with a variety of RAS mutations. RESULTS Patients with tumours harbouring RAS alterations with high versus low MAPK activity who were treated with an MEKi showed significantly longer median progression-free survival (PFS) (5.0 vs. 2.3 months; p = 0.0034) and overall survival (20.0 vs. 5.0 months; p = 0.0146) and a trend towards higher rates of clinical benefit (stable disease ≥6 months or partial/complete remission) (38% versus 15%; p = 0.095) (p-values as per univariate analysis). PFS remained statistically significant after the multivariate analysis (p = 0.003). CONCLUSIONS These results support a correlation between RAS-mutant cancers with greater MAPK signalling and PFS after MEKi treatment.
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23
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De S, Campbell C, Venkitaraman AR, Esposito A. Pulsatile MAPK Signaling Modulates p53 Activity to Control Cell Fate Decisions at the G2 Checkpoint for DNA Damage. Cell Rep 2021; 30:2083-2093.e5. [PMID: 32075732 PMCID: PMC7029415 DOI: 10.1016/j.celrep.2020.01.074] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 12/04/2019] [Accepted: 01/22/2020] [Indexed: 01/01/2023] Open
Abstract
Cell-autonomous changes in p53 expression govern the duration and outcome of cell-cycle arrest at the G2 checkpoint for DNA damage. Here, we report that mitogen-activated protein kinase (MAPK) signaling integrates extracellular cues with p53 dynamics to determine cell fate at the G2 checkpoint. Optogenetic tools and quantitative cell biochemistry reveal transient oscillations in MAPK activity dependent on ataxia-telangiectasia-mutated kinase after DNA damage. MAPK inhibition alters p53 dynamics and p53-dependent gene expression after checkpoint enforcement, prolonging G2 arrest. In contrast, sustained MAPK signaling induces the phosphorylation of CDC25C, and consequently, the accumulation of pro-mitotic kinases, thereby relaxing checkpoint stringency and permitting cells to evade prolonged G2 arrest and senescence induction. We propose a model in which this MAPK-mediated mechanism integrates extracellular cues with cell-autonomous p53-mediated signals, to safeguard genomic integrity during tissue proliferation. Early steps in oncogene-driven carcinogenesis may imbalance this tumor-suppressive mechanism to trigger genome instability. DNA damage elicits opposing pro-survival and pro-arrest responses via MAPK and p53 MAPK pulsations modulate p53-dependent transcription to determine cell fate MAPK/p53 signal dynamics control the stringency of the G2 DNA damage checkpoint MAPK/p53 integrate extracellular and intracellular cues to protect genome integrity
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Affiliation(s)
- Siddharth De
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Callum Campbell
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
| | - Alessandro Esposito
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
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24
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Haggerty RA, Purvis JE. Inferring the structures of signaling motifs from paired dynamic traces of single cells. PLoS Comput Biol 2021; 17:e1008657. [PMID: 33539338 PMCID: PMC7889133 DOI: 10.1371/journal.pcbi.1008657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/17/2021] [Accepted: 12/26/2020] [Indexed: 11/18/2022] Open
Abstract
Individual cells show variability in their signaling dynamics that often correlates with phenotypic responses, indicating that cell-to-cell variability is not merely noise but can have functional consequences. Based on this observation, we reasoned that cell-to-cell variability under the same treatment condition could be explained in part by a single signaling motif that maps different upstream signals into a corresponding set of downstream responses. If this assumption holds, then repeated measurements of upstream and downstream signaling dynamics in a population of cells could provide information about the underlying signaling motif for a given pathway, even when no prior knowledge of that motif exists. To test these two hypotheses, we developed a computer algorithm called MISC (Motif Inference from Single Cells) that infers the underlying signaling motif from paired time-series measurements from individual cells. When applied to measurements of transcription factor and reporter gene expression in the yeast stress response, MISC predicted signaling motifs that were consistent with previous mechanistic models of transcription. The ability to detect the underlying mechanism became less certain when a cell's upstream signal was randomly paired with another cell's downstream response, demonstrating how averaging time-series measurements across a population obscures information about the underlying signaling mechanism. In some cases, motif predictions improved as more cells were added to the analysis. These results provide evidence that mechanistic information about cellular signaling networks can be systematically extracted from the dynamical patterns of single cells.
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Affiliation(s)
- Raymond A. Haggerty
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Computational Medicine Program, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeremy E. Purvis
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Computational Medicine Program, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Curriculum for Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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25
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Banerjee M, Volpert V. Stochastic intracellular regulation can remove oscillations in a model of tissue growth. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2020; 37:551-568. [PMID: 32735317 DOI: 10.1093/imammb/dqaa009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/28/2020] [Accepted: 06/19/2020] [Indexed: 01/06/2023]
Abstract
The work is devoted to the analysis of cell population dynamics where cells make a choice between differentiation and apoptosis. This choice is based on the values of intracellular proteins whose concentrations are described by a system of ordinary differential equations with bistable dynamics. Intracellular regulation and cell fate are controlled by the extracellular regulation through the number of differentiated cells. It is shown that the total cell number necessarily oscillates if the initial condition in the intracellular regulation is fixed. These oscillations can be suppressed if the initial condition is a random variable with a sufficiently large variation. Thus, the result of the work suggests a possible answer to the question about the role of stochasticity in the intracellular regulation.
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Affiliation(s)
- M Banerjee
- Department of Mathematics and Statistics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - V Volpert
- Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, 69622 Villeurbanne, France.,INRIA, Université de Lyon, Université Lyon 1, Institut Camille Jordan, 43 Bd. du 11 Novembre 1918, 69200 Villeurbanne Cedex, France.,Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow 117198, Russian Federation
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26
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Ma M, Bordignon P, Dotto GP, Pelet S. Visualizing cellular heterogeneity by quantifying the dynamics of MAPK activity in live mammalian cells with synthetic fluorescent biosensors. Heliyon 2020; 6:e05574. [PMID: 33319088 PMCID: PMC7723811 DOI: 10.1016/j.heliyon.2020.e05574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/26/2020] [Accepted: 11/18/2020] [Indexed: 01/19/2023] Open
Abstract
Mitogen-Activated Protein Kinases (MAPKs) control a wide array of cellular functions by transducing extracellular information into defined biological responses. In order to understand how these pathways are regulated, dynamic single cell measurements are highly needed. Fluorescence microscopy is well suited to perform these measurements. However, more dynamic and sensitive biosensors that allow the quantification of signaling activity in living mammalian cells are required. We have engineered a synthetic fluorescent substrate for human MAPKs (ERK, JNK and p38) that relocates from the nucleus to the cytoplasm when phosphorylated by the kinases. We demonstrate that this reporter displays an improved response compared to other relocation biosensors. This assay allows to monitor the heterogeneity in the MAPK response in a population of isogenic cells, revealing pulses of ERK activity upon a physiological EGFR stimulation. We show applicability of this approach to the analysis of multiple cancer cell lines and primary cells as well as its application in vivo to developing tumors. Using this ERK biosensor, dynamic single cell measurements with high temporal resolution can be obtained. These MAPK reporters can be widely applied to the analysis of molecular mechanisms of MAPK signaling in healthy and diseased state, in cell culture assays or in vivo.
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Affiliation(s)
- Min Ma
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- Department of Biochemistry, University of Lausanne, Switzerland
| | - Pino Bordignon
- Department of Biochemistry, University of Lausanne, Switzerland
| | | | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
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27
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Shaaya M, Fauser J, Zhurikhina A, Conage-Pough JE, Huyot V, Brennan M, Flower CT, Matsche J, Khan S, Natarajan V, Rehman J, Kota P, White FM, Tsygankov D, Karginov AV. Light-regulated allosteric switch enables temporal and subcellular control of enzyme activity. eLife 2020; 9:e60647. [PMID: 32965214 PMCID: PMC7577742 DOI: 10.7554/elife.60647] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/22/2020] [Indexed: 12/24/2022] Open
Abstract
Engineered allosteric regulation of protein activity provides significant advantages for the development of robust and broadly applicable tools. However, the application of allosteric switches in optogenetics has been scarce and suffers from critical limitations. Here, we report an optogenetic approach that utilizes an engineered Light-Regulated (LightR) allosteric switch module to achieve tight spatiotemporal control of enzymatic activity. Using the tyrosine kinase Src as a model, we demonstrate efficient regulation of the kinase and identify temporally distinct signaling responses ranging from seconds to minutes. LightR-Src off-kinetics can be tuned by modulating the LightR photoconversion cycle. A fast cycling variant enables the stimulation of transient pulses and local regulation of activity in a selected region of a cell. The design of the LightR module ensures broad applicability of the tool, as we demonstrate by achieving light-mediated regulation of Abl and bRaf kinases as well as Cre recombinase.
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Affiliation(s)
- Mark Shaaya
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Anastasia Zhurikhina
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of MedicineAtlantaUnited States
| | - Jason E Conage-Pough
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Center for Precision Cancer Medicine, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Vincent Huyot
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Martin Brennan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Cameron T Flower
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Center for Precision Cancer Medicine, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Program in Computational and Systems Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Jacob Matsche
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Shahzeb Khan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Viswanathan Natarajan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
- University of Illinois Cancer Center, The University of Illinois at ChicagoChicagoUnited States
- Division of Cardiology, Department of Medicine, The University of Illinois, College of MedicineChicagoUnited States
| | - Pradeep Kota
- Marsico Lung Institute, Cystic Fibrosis Center and Department of Medicine, University of North CarolinaChapel HillUnited States
| | - Forest M White
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Center for Precision Cancer Medicine, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Program in Computational and Systems Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Denis Tsygankov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of MedicineAtlantaUnited States
| | - Andrei V Karginov
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
- University of Illinois Cancer Center, The University of Illinois at ChicagoChicagoUnited States
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28
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Persson S, Welkenhuysen N, Shashkova S, Cvijovic M. Fine-Tuning of Energy Levels Regulates SUC2 via a SNF1-Dependent Feedback Loop. Front Physiol 2020; 11:954. [PMID: 32922308 PMCID: PMC7456839 DOI: 10.3389/fphys.2020.00954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/15/2020] [Indexed: 11/22/2022] Open
Abstract
Nutrient sensing pathways are playing an important role in cellular response to different energy levels. In budding yeast, Saccharomyces cerevisiae, the sucrose non-fermenting protein kinase complex SNF1 is a master regulator of energy homeostasis. It is affected by multiple inputs, among which energy levels is the most prominent. Cells which are exposed to a switch in carbon source availability display a change in the gene expression machinery. It has been shown that the magnitude of the change varies from cell to cell. In a glucose rich environment Snf1/Mig1 pathway represses the expression of its downstream target, such as SUC2. However, upon glucose depletion SNF1 is activated which leads to an increase in SUC2 expression. Our single cell experiments indicate that upon starvation, gene expression pattern of SUC2 shows rapid increase followed by a decrease to initial state with high cell-to-cell variability. The mechanism behind this behavior is currently unknown. In this work we study the long-term behavior of the Snf1/Mig1 pathway upon glucose starvation with a microfluidics and non-linear mixed effect modeling approach. We show a negative feedback mechanism, involving Snf1 and Reg1, which reduces SUC2 expression after the initial strong activation. Snf1 kinase activity plays a key role in this feedback mechanism. Our systems biology approach proposes a negative feedback mechanism that works through the SNF1 complex and is controlled by energy levels. We further show that Reg1 likely is involved in the negative feedback mechanism.
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Affiliation(s)
- Sebastian Persson
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Niek Welkenhuysen
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Sviatlana Shashkova
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
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29
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Tang J, Wu Z, Tian Y, Yang R. ICGEC: a comparative method for measuring epigenetic conservation of genes via the integrated signal from multiple histone modifications between cell types. BMC Genomics 2020; 21:356. [PMID: 32398001 PMCID: PMC7216622 DOI: 10.1186/s12864-020-6771-1] [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: 09/29/2019] [Accepted: 05/04/2020] [Indexed: 11/17/2022] Open
Abstract
Background Histone post-translational modifications play crucial roles in epigenetic regulation of gene expression and are known to be associated with the phenotypic differences of different cell types. Therefore, it is of fundamental importance to dissect the genes and pathways involved in such a phenotypic variation at the level of epigenetics. However, the existing comparative approaches are largely based on the differences, especially the absolute difference in the levels of individual histone modifications of genes under contrasting conditions. Thus, a method for measuring the overall change in the epigenetic circumstance of each gene underpinned by multiple types of histone modifications between cell types is lacking. Results To address this challenge, we developed ICGEC, a new method for estimating the degree of epigenetic conservation of genes between two cell lines. Different from existing comparative methods, ICGEC provides a reliable score for measuring the relative change in the epigenetic context of corresponding gene between two conditions and simultaneously produces a score for each histone mark. The application of ICGEC to the human embryonic stem cell line H1 and four H1-derived cell lines with available epigenomic data for the same 16 types of histone modifications indicated high robustness and reliability of ICGEC. Furthermore, the analysis of the epigenetically dynamic and conserved genes which were defined based on the ICGEC output results demonstrated that ICGEC can deepen our understanding of the biological processes of cell differentiation to overcome the limitations of traditional expression analysis. Specifically, the ICGEC-derived differentiation-direction-specific genes were shown to have putative functions that are well-matched with cell identity. Additionally, H3K79me1 and H3K27ac were found to be the main histone marks accounting for whether an epigenetically dynamic gene was differentially expressed between two cell lines. Conclusions The use of ICGEC creates a convenient and robust way to measure the overall epigenetic conservation of individual genes and marks between two conditions. Thus, it provides a basis for exploring the epigenotype-phenotype relationship. ICGEC can be deemed a state-of-the-art method tailored for comparative epigenomic analysis of changes in cell dynamics.
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Affiliation(s)
- Jing Tang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zefeng Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuhan Tian
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
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30
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Vink CS, Calero-Nieto FJ, Wang X, Maglitto A, Mariani SA, Jawaid W, Göttgens B, Dzierzak E. Iterative Single-Cell Analyses Define the Transcriptome of the First Functional Hematopoietic Stem Cells. Cell Rep 2020; 31:107627. [PMID: 32402290 PMCID: PMC7225750 DOI: 10.1016/j.celrep.2020.107627] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/18/2020] [Accepted: 04/18/2020] [Indexed: 01/06/2023] Open
Abstract
Whereas hundreds of cells in the mouse embryonic aorta transdifferentiate to hematopoietic cells, only very few establish hematopoietic stem cell (HSC) identity at a single time point. The Gata2 transcription factor is essential for HSC generation and function. In contrast to surface-marker-based cell isolation, Gata2-based enrichment provides a direct link to the internal HSC regulatory network. Here, we use iterations of index-sorting of Gata2-expressing intra-aortic hematopoietic cluster (IAHC) cells, single-cell transcriptomics, and functional analyses to connect HSC identity to specific gene expression. Gata2-expressing IAHC cells separate into 5 major transcriptomic clusters. Iterative analyses reveal refined CD31, cKit, and CD27 phenotypic parameters that associate specific molecular profiles in one cluster with distinct HSC and multipotent progenitor function. Thus, by iterations of single-cell approaches, we identify the transcriptome of the first functional HSCs as they emerge in the mouse embryo and localize them to aortic clusters containing 1-2 cells.
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Affiliation(s)
- Chris Sebastiaan Vink
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, Midlothian, Scotland EH16 4TJ, UK
| | - Fernando Jose Calero-Nieto
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire, England CB2 0AW, UK
| | - Xiaonan Wang
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire, England CB2 0AW, UK
| | - Antonio Maglitto
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, Midlothian, Scotland EH16 4TJ, UK
| | - Samanta Antonella Mariani
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, Midlothian, Scotland EH16 4TJ, UK
| | - Wajid Jawaid
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire, England CB2 0AW, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire, England CB2 0AW, UK
| | - Elaine Dzierzak
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, Midlothian, Scotland EH16 4TJ, UK.
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31
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Miller RC, Aplin CP, Kay TM, Leighton R, Libal C, Simonet R, Cembran A, Heikal AA, Boersma AJ, Sheets ED. FRET Analysis of Ionic Strength Sensors in the Hofmeister Series of Salt Solutions Using Fluorescence Lifetime Measurements. J Phys Chem B 2020; 124:3447-3458. [PMID: 32267692 DOI: 10.1021/acs.jpcb.9b10498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Living cells are complex, crowded, and dynamic and continually respond to environmental and intracellular stimuli. They also have heterogeneous ionic strength with compartmentalized variations in both intracellular concentrations and types of ions. These challenges would benefit from the development of quantitative, noninvasive approaches for mapping the heterogeneous ionic strength fluctuations in living cells. Here, we investigated a class of recently developed ionic strength sensors that consists of mCerulean3 (a cyan fluorescent protein) and mCitrine (a yellow fluorescent protein) tethered via a linker made of two charged α-helices and a flexible loop. The two helices are designed to bear opposite charges, which is hypothesized to increase the ionic screening and therefore a larger intermolecular distance. In these protein constructs, mCerulean3 and mCitrine act as a donor-acceptor pair undergoing Förster resonance energy transfer (FRET) that is dependent on both the linker amino acids and the environmental ionic strength. Using time-resolved fluorescence of the donor (mCerulean3), we determined the sensitivity of the energy transfer efficiencies and the donor-acceptor distances of these sensors at variable concentrations of the Hofmeister series of salts (KCl, LiCl, NaCl, NaBr, NaI, Na2SO4). As controls, similar measurements were carried out on the FRET-incapable, enzymatically cleaved counterparts of these sensors as well as a construct designed with two electrostatically neutral α-helices (E6G2). Our results show that the energy transfer efficiencies of these sensors are sensitive to both the linker amino acid sequence and the environmental ionic strength, whereas the sensitivity of these sensors to the identity of the dissolved ions of the Hofmeister series of salts seems limited. We also developed a theoretical framework to explain the observed trends as a function of the ionic strength in terms of the Debye screening of the electrostatic interaction between the two charged α-helices in the linker region. These controlled solution studies represent an important step toward the development of rationally designed FRET-based environmental sensors while offering different models for calculating the energy transfer efficiency using time-resolved fluorescence that is compatible with future in vivo studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
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32
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Zimmerman L, Zelichov O, Aizenmann A, Barbash Z, Vidne M, Tarcic G. A Novel System for Functional Determination of Variants of Uncertain Significance using Deep Convolutional Neural Networks. Sci Rep 2020; 10:4192. [PMID: 32144301 PMCID: PMC7060242 DOI: 10.1038/s41598-020-61173-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/24/2020] [Indexed: 11/08/2022] Open
Abstract
Many drugs are developed for commonly occurring, well studied cancer drivers such as vemurafenib for BRAF V600E and erlotinib for EGFR exon 19 mutations. However, most tumors also harbor mutations which have an uncertain role in disease formation, commonly called Variants of Uncertain Significance (VUS), which are not studied or characterized and could play a significant role in drug resistance and relapse. Therefore, the determination of the functional significance of VUS and their response to Molecularly Targeted Agents (MTA) is essential for developing new drugs and predicting response of patients. Here we present a multi-scale deep convolutional neural network (DCNN) architecture combined with an in-vitro functional assay to investigate the functional role of VUS and their response to MTA's. Our method achieved high accuracy and precision on a hold-out set of examples (0.98 mean AUC for all tested genes) and was used to predict the oncogenicity of 195 VUS in 6 genes. 63 (32%) of the assayed VUS's were classified as pathway activating, many of them to a similar extent as known driver mutations. Finally, we show that responses of various mutations to FDA approved MTAs are accurately predicted by our platform in a dose dependent manner. Taken together this novel system can uncover the treatable mutational landscape of a drug and be a useful tool in drug development.
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33
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Lyashenko E, Niepel M, Dixit PD, Lim SK, Sorger PK, Vitkup D. Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks. eLife 2020; 9:50342. [PMID: 31961323 PMCID: PMC7046471 DOI: 10.7554/elife.50342] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Detecting relative rather than absolute changes in extracellular signals enables cells to make decisions in constantly fluctuating environments. It is currently not well understood how mammalian signaling networks store the memories of past stimuli and subsequently use them to compute relative signals, that is perform fold change detection. Using the growth factor-activated PI3K-Akt signaling pathway, we develop here computational and analytical models, and experimentally validate a novel non-transcriptional mechanism of relative sensing in mammalian cells. This mechanism relies on a new form of cellular memory, where cells effectively encode past stimulation levels in the abundance of cognate receptors on the cell surface. The surface receptor abundance is regulated by background signal-dependent receptor endocytosis and down-regulation. We show the robustness and specificity of relative sensing for two physiologically important ligands, epidermal growth factor (EGF) and hepatocyte growth factor (HGF), and across wide ranges of background stimuli. Our results suggest that similar mechanisms of cell memory and fold change detection may be important in diverse signaling cascades and multiple biological contexts.
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Affiliation(s)
- Eugenia Lyashenko
- Department of Systems Biology, Columbia University, New York, United States
| | - Mario Niepel
- HMS LINCS Center Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Purushottam D Dixit
- Department of Systems Biology, Columbia University, New York, United States.,Department of Physics, University of Florida, Gainesville, United States
| | - Sang Kyun Lim
- HMS LINCS Center Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Peter K Sorger
- Department of Systems Biology, Columbia University, New York, United States.,HMS LINCS Center Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Dennis Vitkup
- Department of Systems Biology, Columbia University, New York, United States.,Center for Computational Biology and Bioinformatics, Columbia University, New York, United States.,Department of Biomedical Informatics, Columbia University, New York, United States
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34
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Simsek MF, Özbudak EM. Spatial Fold Change of FGF Signaling Encodes Positional Information for Segmental Determination in Zebrafish. Cell Rep 2019; 24:66-78.e8. [PMID: 29972792 PMCID: PMC6063364 DOI: 10.1016/j.celrep.2018.06.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/08/2018] [Accepted: 06/05/2018] [Indexed: 01/15/2023] Open
Abstract
Signal gradients encode instructive information for numerous decision-making processes during embryonic development. A striking example of precise, scalable tissue-level patterning is the segmentation of somites—the precursors of the vertebral column—during which the fibroblast growth factor (FGF), Wnt, and retinoic acid (RA) pathways establish spatial gradients. Despite decades of studies proposing roles for all three pathways, the dynamic feature of these gradients that encodes instructive information determining segment sizes remained elusive. We developed a non-elongating tail explant system, integrated quantitative measurements with computational modeling, and tested alternative models to show that positional information is encoded solely by spatial fold change (SFC) in FGF signal output. Neighboring cells measure SFC to accurately position the determination front and thus determine segment size. The SFC model successfully recapitulates results of spatiotemporal perturbation experiments on both explants and intact embryos, and it shows that Wnt signaling acts permissively upstream of FGF signaling and that RA gradient is dispensable. Simsek et al. use an elongation-arrested 3D explant system, integrated with quantitative measurements and computational modeling, to show that positional information for segmentation is encoded solely by spatial fold change (SFC) in FGF signal output. Neighboring cells measure SFC to accurately determine somite segment sizes. Wnt signaling acts permissively upstream of FGF signaling.
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Affiliation(s)
- M Fethullah Simsek
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ertuğrul M Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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35
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Abstract
Collective oscillations of cells in a population appear under diverse biological contexts. Here, we establish a set of common principles by categorising the response of individual cells against a time-varying signal. A positive intracellular signal relay of sufficient gain from participating cells is required to sustain the oscillations, together with phase matching. The two conditions yield quantitative predictions for the onset cell density and frequency in terms of measured single-cell and signal response functions. Through mathematical constructions, we show that cells that adapt to a constant stimulus fulfil the phase requirement by developing a leading phase in an active frequency window that enables cell-to-signal energy flow. Analysis of dynamical quorum sensing in several cellular systems with increasing biological complexity reaffirms the pivotal role of adaptation in powering oscillations in an otherwise dissipative cell-to-cell communication channel. The physical conditions identified also apply to synthetic oscillatory systems. There are many examples of cell populations exhibiting density-dependent collective oscillatory behaviour. Here, the authors show that sustained collective oscillations emerge when cells anticipate variation in signal and attempt to amplify it, a property that can be linked to adaptation.
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36
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Information Theory: New Look at Oncogenic Signaling Pathways. Trends Cell Biol 2019; 29:862-875. [DOI: 10.1016/j.tcb.2019.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 12/23/2022]
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37
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Blum Y, Mikelson J, Dobrzyński M, Ryu H, Jacques M, Jeon NL, Khammash M, Pertz O. Temporal perturbation of ERK dynamics reveals network architecture of FGF2/MAPK signaling. Mol Syst Biol 2019; 15:e8947. [PMID: 31777174 PMCID: PMC6864398 DOI: 10.15252/msb.20198947] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/27/2019] [Accepted: 10/21/2019] [Indexed: 01/09/2023] Open
Abstract
Stimulation of PC-12 cells with epidermal (EGF) versus nerve (NGF) growth factors (GFs) biases the distribution between transient and sustained single-cell ERK activity states, and between proliferation and differentiation fates within a cell population. We report that fibroblast GF (FGF2) evokes a distinct behavior that consists of a gradually changing population distribution of transient/sustained ERK signaling states in response to increasing inputs in a dose response. Temporally controlled GF perturbations of MAPK signaling dynamics applied using microfluidics reveal that this wider mix of ERK states emerges through the combination of an intracellular feedback, and competition of FGF2 binding to FGF receptors (FGFRs) and heparan sulfate proteoglycan (HSPG) co-receptors. We show that the latter experimental modality is instructive for model selection using a Bayesian parameter inference. Our results provide novel insights into how different receptor tyrosine kinase (RTK) systems differentially wire the MAPK network to fine-tune fate decisions at the cell population level.
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Affiliation(s)
- Yannick Blum
- Institute of Cell BiologyUniversity of BernBernSwitzerland
| | - Jan Mikelson
- Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
| | | | - Hyunryul Ryu
- Institute of Advanced Machinery and DesignSeoul National UniversitySeoulKorea
- Present address:
Research Laboratory of ElectronicsMassachusetts Institute of TechnologyCambridgeMAUSA
| | | | - Noo Li Jeon
- Institute of Advanced Machinery and DesignSeoul National UniversitySeoulKorea
| | - Mustafa Khammash
- Department of Biosystems Science and EngineeringETH ZurichBaselSwitzerland
| | - Olivier Pertz
- Institute of Cell BiologyUniversity of BernBernSwitzerland
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38
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Chen EP, Song RS, Chen X. Mathematical model of hypoxia and tumor signaling interplay reveals the importance of hypoxia and cell-to-cell variability in tumor growth inhibition. BMC Bioinformatics 2019; 20:507. [PMID: 31638911 PMCID: PMC6802183 DOI: 10.1186/s12859-019-3098-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 09/13/2019] [Indexed: 01/10/2023] Open
Abstract
Background Human tumor is a complex tissue with multiple heterogeneous hypoxic regions and significant cell-to-cell variability. Due to the complexity of the disease, the explanation of why anticancer therapies fail cannot be attributed to intrinsic or acquired drug resistance alone. Furthermore, there are inconsistent reports of hypoxia-induced kinase activities in different cancer cell-lines, where increase, decreases, or no change has been observed. Thus, we asked, why are there widely contrasting results in kinase activity under hypoxia in different cancer cell-lines and how does hypoxia play a role in anti-cancer drug sensitivity? Results We took a modeling approach to address these questions by analyzing the model simulation to explain why hypoxia driven signals can have dissimilar impact on tumor growth and alter the efficacy of anti-cancer drugs. Repeated simulations with varying concentrations of biomolecules followed by decision tree analysis reveal that the highly differential effects among heterogeneous subpopulation of tumor cells could be governed by varying concentrations of just a few key biomolecules. These biomolecules include activated serine/threonine-specific protein kinases (pRAF), mitogen-activated protein kinase kinase (pMEK), protein kinase B (pAkt), or phosphoinositide-4,5-bisphosphate 3-kinase (pPI3K). Additionally, the ratio of activated extracellular signal-regulated kinases (pERK) or pAkt to its respective total was a key factor in determining the sensitivity of pERK or pAkt to hypoxia. Conclusion This work offers a mechanistic insight into how hypoxia can affect the efficacy of anti-cancer drug that targets tumor signaling and provides a framework to identify the types of tumor cells that are either sensitive or resistant to anti-cancer therapy.
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Affiliation(s)
- Emile P Chen
- Computational Sciences, GlaxoSmithKline, Collegeville, PA, 19426, USA.
| | - Roy S Song
- Computational Sciences, GlaxoSmithKline, Collegeville, PA, 19426, USA
| | - Xueer Chen
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15206-3701, USA
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39
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Hu W, Li Q, Li B, Ma K, Zhang C, Fu X. Optogenetics sheds new light on tissue engineering and regenerative medicine. Biomaterials 2019; 227:119546. [PMID: 31655444 DOI: 10.1016/j.biomaterials.2019.119546] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 01/23/2023]
Abstract
Optogenetics has demonstrated great potential in the fields of tissue engineering and regenerative medicine, from basic research to clinical applications. Spatiotemporal encoding during individual development has been widely identified and is considered a novel strategy for regeneration. A as a noninvasive method with high spatiotemporal resolution, optogenetics are suitable for this strategy. In this review, we discuss roles of dynamic signal coding in cell physiology and embryonic development. Several optogenetic systems are introduced as ideal optogenetic tools, and their features are compared. In addition, potential applications of optogenetics for tissue engineering are discussed, including light-controlled genetic engineering and regulation of signaling pathways. Furthermore, we present how emerging biomaterials and photoelectric technologies have greatly promoted the clinical application of optogenetics and inspired new concepts for optically controlled therapies. Our summation of currently available data conclusively demonstrates that optogenetic tools are a promising method for elucidating and simulating developmental processes, thus providing vast prospects for tissue engineering and regenerative medicine applications.
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Affiliation(s)
- Wenzhi Hu
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Qiankun Li
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Bingmin Li
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Kui Ma
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Cuiping Zhang
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China.
| | - Xiaobing Fu
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China.
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40
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Meyer AS, Heiser LM. Systems biology approaches to measure and model phenotypic heterogeneity in cancer. CURRENT OPINION IN SYSTEMS BIOLOGY 2019; 17:35-40. [PMID: 32864511 PMCID: PMC7449235 DOI: 10.1016/j.coisb.2019.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The recent wide-spread adoption of single cell profiling technologies has revealed that individual cancers are not homogenous collections of deregulated cells, but instead are comprised of multiple genetically and phenotypically distinct cell subpopulations that exhibit a wide range of responses to extracellular signals and therapeutic insult. Such observations point to the urgent need to understand cancer as a complex, adaptive system. Cancer systems biology studies seek to develop the experimental and theoretical methods required to understand how biological components work together to determine how cancer cells function. Ultimately, such approaches will lead to improvements in how cancer is managed and treated. In this review, we discuss recent advances in cancer systems biology approaches to quantify, model, and elucidate mechanisms of heterogeneity.
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Affiliation(s)
- Aaron S. Meyer
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Laura M. Heiser
- Department of Biomedical Engineering and OHSU Center for Spatial Systems Biomedicine, OHSU, Portland, OR, USA
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41
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Wong VC, Bass VL, Bullock ME, Chavali AK, Lee REC, Mothes W, Gaudet S, Miller-Jensen K. NF-κB-Chromatin Interactions Drive Diverse Phenotypes by Modulating Transcriptional Noise. Cell Rep 2019; 22:585-599. [PMID: 29346759 DOI: 10.1016/j.celrep.2017.12.080] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/27/2017] [Accepted: 12/21/2017] [Indexed: 10/18/2022] Open
Abstract
Noisy gene expression generates diverse phenotypes, but little is known about mechanisms that modulate noise. Combining experiments and modeling, we studied how tumor necrosis factor (TNF) initiates noisy expression of latent HIV via the transcription factor nuclear factor κB (NF-κB) and how the HIV genomic integration site modulates noise to generate divergent (low-versus-high) phenotypes of viral activation. We show that TNF-induced transcriptional noise varies more than mean transcript number and that amplification of this noise explains low-versus-high viral activation. For a given integration site, live-cell imaging shows that NF-κB activation correlates with viral activation, but across integration sites, NF-κB activation cannot account for differences in transcriptional noise and phenotypes. Instead, differences in transcriptional noise are associated with differences in chromatin state and RNA polymerase II regulation. We conclude that, whereas NF-κB regulates transcript abundance in each cell, the chromatin environment modulates noise in the population to support diverse HIV activation in response to TNF.
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Affiliation(s)
- Victor C Wong
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Victor L Bass
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - M Elise Bullock
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Arvind K Chavali
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Robin E C Lee
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
| | - Suzanne Gaudet
- Department of Cancer Biology and Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Kathryn Miller-Jensen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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42
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Hard Limits and Performance Tradeoffs in a Class of Antithetic Integral Feedback Networks. Cell Syst 2019; 9:49-63.e16. [PMID: 31279505 DOI: 10.1016/j.cels.2019.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/28/2019] [Accepted: 05/30/2019] [Indexed: 12/18/2022]
Abstract
Feedback regulation is pervasive in biology at both the organismal and cellular level. In this article, we explore the properties of a particular biomolecular feedback mechanism called antithetic integral feedback, which can be implemented using the binding of two molecules. Our work develops an analytic framework for understanding the hard limits, performance tradeoffs, and architectural properties of this simple model of biological feedback control. Using tools from control theory, we show that there are simple parametric relationships that determine both the stability and the performance of these systems in terms of speed, robustness, steady-state error, and leakiness. These findings yield a holistic understanding of the behavior of antithetic integral feedback and contribute to a more general theory of biological control systems.
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43
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Abstract
A handful of core intercellular signaling pathways play pivotal roles in a broad variety of developmental processes. It has remained puzzling how so few pathways can provide the precision and specificity of cell-cell communication required for multicellular development. Solving this requires us to quantitatively understand how developmentally relevant signaling information is actively sensed, transformed and spatially distributed by signaling pathways. Recently, single cell analysis and cell-based reconstitution, among other approaches, have begun to reveal the 'communication codes' through which information is represented in the identities, concentrations, combinations and dynamics of extracellular ligands. They have also revealed how signaling pathways decipher these features and control the spatial distribution of signaling in multicellular contexts. Here, we review recent work reporting the discovery and analysis of communication codes and discuss their implications for diverse developmental processes.
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Affiliation(s)
- Pulin Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, Pasadena, CA 91125, USA
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44
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Deathridge J, Antolović V, Parsons M, Chubb JR. Live imaging of ERK signalling dynamics in differentiating mouse embryonic stem cells. Development 2019; 146:dev172940. [PMID: 31064783 PMCID: PMC6602347 DOI: 10.1242/dev.172940] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/29/2019] [Indexed: 12/18/2022]
Abstract
Stimulation of the ERK/MAPK pathway is required for the exit from pluripotency and onset of differentiation in mouse embryonic stem cells (ESCs). The dynamic behaviour of ERK activity in individual cells during this transition is unclear. Using a FRET-based biosensor, we monitored ERK signalling dynamics of single mouse ESCs during differentiation. ERK activity was highly heterogeneous, with considerable variability in ERK signalling between single cells within ESC colonies. Different triggers of differentiation induced distinct ERK activity profiles. Surprisingly, the dynamic features of ERK signalling were not strongly coupled to loss of pluripotency marker expression, regardless of the differentiation stimulus, suggesting the normal dynamic range of ERK signalling is not rate-limiting in single cells during differentiation. ERK signalling dynamics were sensitive to the degree of cell crowding and were similar in neighbouring cells. Sister cells from a mitotic division also showed more similar ERK activity, an effect that was apparent whether cells remained adjacent or moved apart after division. These data suggest a combination of cell lineage and niche contributes to the absolute level of ERK signalling in mouse ESCs.
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Affiliation(s)
- Julia Deathridge
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guys Campus, London SE1 1UL, UK
| | - Vlatka Antolović
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guys Campus, London SE1 1UL, UK
| | - Jonathan R Chubb
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
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45
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Sullivan CR, Mielnik CA, O'Donovan SM, Funk AJ, Bentea E, DePasquale EA, Alganem K, Wen Z, Haroutunian V, Katsel P, Ramsey AJ, Meller J, McCullumsmith RE. Connectivity Analyses of Bioenergetic Changes in Schizophrenia: Identification of Novel Treatments. Mol Neurobiol 2019; 56:4492-4517. [PMID: 30338483 PMCID: PMC7584383 DOI: 10.1007/s12035-018-1390-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/11/2018] [Indexed: 01/21/2023]
Abstract
We utilized a cell-level approach to examine glycolytic pathways in the DLPFC of subjects with schizophrenia (n = 16) and control (n = 16) and found decreased mRNA expression of glycolytic enzymes in pyramidal neurons, but not astrocytes. To replicate these novel bioenergetic findings, we probed independent datasets for bioenergetic targets and found similar abnormalities. Next, we used a novel strategy to build a schizophrenia bioenergetic profile by a tailored application of the Library of Integrated Network-Based Cellular Signatures data portal (iLINCS) and investigated connected cellular pathways, kinases, and transcription factors using Enrichr. Finally, with the goal of identifying drugs capable of "reversing" the bioenergetic schizophrenia signature, we performed a connectivity analysis with iLINCS and identified peroxisome proliferator-activated receptor (PPAR) agonists as promising therapeutic targets. We administered a PPAR agonist to the GluN1 knockdown model of schizophrenia and found it improved long-term memory. Taken together, our findings suggest that tailored bioinformatics approaches, coupled with the LINCS library of transcriptional signatures of chemical and genetic perturbagens, may be employed to identify novel treatment strategies for schizophrenia and related diseases.
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Affiliation(s)
| | - Catharine A Mielnik
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | | | - Adam J Funk
- Department of Neuroscience, University of Toledo, Toledo, OH, USA
| | - Eduard Bentea
- Neurosciences TA Biology, UCB BioPharma SPRL, Braine-l'Alleud, Belgium
| | - Erica A DePasquale
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Khaled Alganem
- Department of Neuroscience, University of Toledo, Toledo, OH, USA
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Vahram Haroutunian
- Department of Psychiatry and Neuroscience, The Icahn School of Medicine at Mount Sinai, Bronx, NY, USA
| | - Pavel Katsel
- Department of Psychiatry and Neuroscience, The Icahn School of Medicine at Mount Sinai, Bronx, NY, USA
| | - Amy J Ramsey
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jarek Meller
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Informatics, Nicolaus Copernicus University, Torun, Poland
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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46
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Olsman N, Xiao F, Doyle JC. Architectural Principles for Characterizing the Performance of Antithetic Integral Feedback Networks. iScience 2019; 14:277-291. [PMID: 31015073 PMCID: PMC6479019 DOI: 10.1016/j.isci.2019.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/14/2019] [Accepted: 04/01/2019] [Indexed: 02/06/2023] Open
Abstract
As we begin to design increasingly complex synthetic biomolecular systems, it is essential to develop rational design methodologies that yield predictable circuit performance. Here we apply mathematical tools from the theory of control and dynamical systems to yield practical insights into the architecture and function of a particular class of biological feedback circuit. Specifically, we show that it is possible to analytically characterize both the operating regime and performance tradeoffs of an antithetic integral feedback circuit architecture. Furthermore, we demonstrate how these principles can be applied to inform the design process of a particular synthetic feedback circuit.
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Affiliation(s)
- Noah Olsman
- Department of Control and Dynamical Systems, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02215, USA.
| | - Fangzhou Xiao
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - John C Doyle
- Department of Control and Dynamical Systems, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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47
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Sheng C, Mendler IH, Rieke S, Snyder P, Jentsch M, Friedrich D, Drossel B, Loewer A. PCNA-Mediated Degradation of p21 Coordinates the DNA Damage Response and Cell Cycle Regulation in Individual Cells. Cell Rep 2019; 27:48-58.e7. [DOI: 10.1016/j.celrep.2019.03.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/03/2019] [Accepted: 03/08/2019] [Indexed: 12/29/2022] Open
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48
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Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells. Sci Rep 2019; 9:5372. [PMID: 30926874 PMCID: PMC6440972 DOI: 10.1038/s41598-019-41870-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/20/2019] [Indexed: 12/22/2022] Open
Abstract
The transduction of extracellular signals through signaling pathways that culminate in a transcriptional response is central to many biological processes. However, quantitative relationships between activities of signaling pathway components and transcriptional output of target genes remain poorly explored. Here we developed a dual bioluminescence imaging strategy allowing simultaneous monitoring of nuclear translocation of the SMAD4 and SMAD2 transcriptional activators upon TGF-β stimulation, and the transcriptional response of the endogenous connective tissue growth factor (ctgf) gene. Using cell lines allowing to vary exogenous SMAD4/2 expression levels, we performed quantitative measurements of the temporal profiles of SMAD4/2 translocation and ctgf transcription kinetics in hundreds of individual cells at high temporal resolution. We found that while nuclear translocation efficiency had little impact on initial ctgf transcriptional activation, high total cellular SMAD4 but not SMAD2 levels increased the probability of cells to exhibit a sustained ctgf transcriptional response. The approach we present here allows time-resolved single cell quantification of transcription factor dynamics and transcriptional responses and thereby sheds light on the quantitative relationship between SMADs and target gene responses.
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49
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Synergy with TGFβ ligands switches WNT pathway dynamics from transient to sustained during human pluripotent cell differentiation. Proc Natl Acad Sci U S A 2019; 116:4989-4998. [PMID: 30819898 DOI: 10.1073/pnas.1815363116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
WNT/β-catenin signaling is crucial to all stages of life. It controls early morphogenetic events in embryos, maintains stem cell niches in adults, and is dysregulated in many types of cancer. Despite its ubiquity, little is known about the dynamics of signal transduction or whether it varies across contexts. Here we probe the dynamics of signaling by monitoring nuclear accumulation of β-catenin, the primary transducer of canonical WNT signals, using quantitative live cell imaging. We show that β-catenin signaling responds adaptively to constant WNT signaling in pluripotent stem cells, and that these dynamics become sustained on differentiation. Varying dynamics were also observed in the response to WNT in commonly used mammalian cell lines. Signal attenuation in pluripotent cells is observed even at saturating doses, where ligand stability does not affect the dynamics. TGFβ superfamily ligands Activin and BMP, which coordinate with WNT signaling to pattern the gastrula, increase the β-catenin response in a manner independent of their ability to induce new WNT ligand production. Our results reveal how variables external to the pathway, including differentiation status and cross-talk with other pathways, dramatically alter WNT/β-catenin dynamics.
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50
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Wong VC, Mathew S, Ramji R, Gaudet S, Miller-Jensen K. Fold-Change Detection of NF-κB at Target Genes with Different Transcript Outputs. Biophys J 2019; 116:709-724. [PMID: 30704857 PMCID: PMC6382958 DOI: 10.1016/j.bpj.2019.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/29/2018] [Accepted: 01/04/2019] [Indexed: 11/19/2022] Open
Abstract
The transcription factor nuclear factor (NF)-κB promotes inflammatory and stress-responsive gene transcription across a range of cell types in response to the cytokine tumor necrosis factor (TNF). Although NF-κB signaling exhibits significant variability across single cells, some target genes supporting high levels of TNF-inducible transcription exhibit fold-change detection of NF-κB, which may buffer against stochastic variation in signaling molecules. It is unknown whether fold-change detection is maintained at NF-κB target genes with low levels of TNF-inducible transcription, for which stochastic promoter events may be more pronounced. Here, we used a microfluidic cell-trapping device to measure how TNF-induced activation of NF-κB controls transcription in single Jurkat T cells at the promoters of integrated HIV and the endogenous cytokine gene IL6, which produce only a few transcripts per cell. We tracked TNF-stimulated NF-κB RelA nuclear translocation by live-cell imaging and then quantified transcript number by RNA FISH in the same cell. We found that TNF-induced transcript abundance at 2 h for low- and high-abundance target genes correlates with similar strength with the fold change in nuclear NF-κB. A computational model of TNF-NF-κB signaling, which implements fold-change detection from competition for binding to κB motifs, could reproduce fold-change detection across the experimentally measured range of transcript outputs. However, multiple model parameters affecting transcription had to be simultaneously varied across promoters to maintain fold-change detection while also matching other trends in the single-cell data for low-abundance transcripts. Our results suggest that cells use multiple biological mechanisms to tune transcriptional output while maintaining robustness of NF-κB fold-change detection.
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Affiliation(s)
- Victor C Wong
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut
| | - Shibin Mathew
- Department of Cancer Biology and Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Ramesh Ramji
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Suzanne Gaudet
- Department of Cancer Biology and Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts.
| | - Kathryn Miller-Jensen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut; Department of Biomedical Engineering, Yale University, New Haven, Connecticut.
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