1
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Emig AA, Hansen M, Grimm S, Coarfa C, Lord ND, Williams MK. Temporal dynamics of BMP/Nodal ratio drive tissue-specific gastrulation morphogenesis. Development 2025; 152:dev202931. [PMID: 39651654 PMCID: PMC12070064 DOI: 10.1242/dev.202931] [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: 04/05/2024] [Accepted: 11/29/2024] [Indexed: 12/11/2024]
Abstract
Anteroposterior elongation of the vertebrate body plan is driven by convergence and extension (C&E) gastrulation movements in both the mesoderm and neuroectoderm, but how or whether molecular regulation of C&E differs between tissues remains an open question. Using a zebrafish explant model of anteroposterior axis extension, we show that C&E of the neuroectoderm and mesoderm can be uncoupled ex vivo, and that morphogenesis of individual tissues results from distinct morphogen signaling dynamics. Using precise temporal manipulation of BMP and Nodal signaling, we identify a critical developmental window during which high or low BMP/Nodal ratios induce neuroectoderm- or mesoderm-driven C&E, respectively. Increased BMP activity similarly enhances C&E specifically in the ectoderm of intact zebrafish gastrulae, highlighting the in vivo relevance of our findings. Together, these results demonstrate that temporal dynamics of BMP and Nodal morphogen signaling activate distinct morphogenetic programs governing C&E gastrulation movements within individual tissues.
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Affiliation(s)
- Alyssa A. Emig
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Megan Hansen
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra Grimm
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nathan D. Lord
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Margot Kossmann Williams
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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2
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McNamara HM, Guyer AM, Jia BZ, Parot VJ, Dobbs CD, Schier AF, Cohen AE, Lord ND. Optogenetic control of Nodal signaling patterns. Development 2025; 152:dev204506. [PMID: 40145591 PMCID: PMC12070070 DOI: 10.1242/dev.204506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 03/20/2025] [Indexed: 03/28/2025]
Abstract
A crucial step in early embryogenesis is the establishment of spatial patterns of signaling activity. Tools to perturb morphogen signals with high resolution in space and time can help reveal how embryonic cells decode these signals to make appropriate fate decisions. Here, we present new optogenetic reagents and an experimental pipeline for creating designer Nodal signaling patterns in live zebrafish embryos. Nodal receptors were fused to the light-sensitive heterodimerizing pair Cry2/CIB1N, and the type II receptor was sequestered to the cytosol. The improved optoNodal2 reagents eliminate dark activity and improve response kinetics, without sacrificing dynamic range. We adapted an ultra-widefield microscopy platform for parallel light patterning in up to 36 embryos, and demonstrated precise spatial control over Nodal signaling activity and downstream gene expression. Patterned Nodal activation drove precisely controlled internalization of endodermal precursors. Furthermore, we used patterned illumination to generate synthetic signaling patterns in Nodal signaling mutants, rescuing several characteristic developmental defects. This study establishes an experimental toolkit for systematic exploration of Nodal signaling patterns in live embryos.
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Affiliation(s)
| | - Alison M. Guyer
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bill Z. Jia
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vicente J. Parot
- Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
| | - Caleb D. Dobbs
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | | | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Nathan D. Lord
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
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3
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Chen S, Shu W, Wang S, Yue L, Tan W. Bioinspired Nucleic Acid-Based Bandpass Filters and Their Concentration-Adaptive Functions. J Am Chem Soc 2025; 147:12786-12799. [PMID: 40178933 DOI: 10.1021/jacs.5c01331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2025]
Abstract
Natural signaling networks can act as bandpass filters to interpret external stimuli within defined concentration ranges for differential cellular activities. Replicating such a bandpass filtering mechanism by synthetic networks poses a significant challenge. Herein, we introduce a modular design of nucleic acid-based multilayer threshold-gated incoherent feedforward networks as multiband bandpass filters to produce mutually exclusive responses within defined input concentration ranges. In these networks, nucleic acids demonstrate triple functionality by acting as threshold-gated entities to discern input concentration levels, serving as network nodes to assemble incoherent feedforward loops for nonlinear signal processing, and functioning as signal transduction units for coupling downstream functional modules. These modular networks enable the fine-tuning of filtering performance in terms of band position, bandwidth, cascades, and responses. A mathematical simulation model allows us to predict the filtering behaviors under various conditions. Also, the networks are integrated with upstream signal conversion modules to process concentration information on molecules beyond nucleic acids, such as adenosine and its derivatives. Furthermore, connections to downstream functional modules allow the system to regulate various processes in a concentration bandpass manner, realizing concentration-adaptive DNAzyme biocatalysis, tristate logic operations, RNA transcription, and DNA condensate formation. These findings underscore the potential of enzyme-free DNA reaction networks in complex signal processing and lay a solid foundation for developing chemical and material systems with highly adaptive and autonomous behaviors.
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Affiliation(s)
- Si Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo and Biosensing, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Weijun Shu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo and Biosensing, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Shan Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo and Biosensing, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Liang Yue
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo and Biosensing, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, P. R. China
- Furong Laboratory, Changsha, Hunan 410082, P. R. China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo and Biosensing, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, P. R. China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P. R. China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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4
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Jashnsaz H, Neuert G. Phenotypic consequences of logarithmic signaling in MAPK stress response. iScience 2025; 28:111625. [PMID: 39886462 PMCID: PMC11780147 DOI: 10.1016/j.isci.2024.111625] [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: 12/15/2023] [Revised: 10/04/2024] [Accepted: 12/16/2024] [Indexed: 02/01/2025] Open
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
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN 37232, USA
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5
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Hartmann L, Kristofori P, Li C, Becker K, Hexemer L, Bohn S, Lenhardt S, Weiss S, Voss B, Loewer A, Legewie S. Transcriptional regulators ensuring specific gene expression and decision-making at high TGFβ doses. Life Sci Alliance 2025; 8:e202402859. [PMID: 39542693 PMCID: PMC11565188 DOI: 10.26508/lsa.202402859] [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: 06/02/2024] [Revised: 10/30/2024] [Accepted: 10/31/2024] [Indexed: 11/17/2024] Open
Abstract
TGFβ-signaling regulates cancer progression by controlling cell division, migration, and death. These outcomes are mediated by gene expression changes, but the mechanisms of decision-making toward specific fates remain unclear. Here, we combine SMAD transcription factor imaging, genome-wide RNA sequencing, and morphological assays to quantitatively link signaling, gene expression, and fate decisions in mammary epithelial cells. Fitting genome-wide kinetic models to our time-resolved data, we find that most of the TGFβ target genes can be explained as direct targets of SMAD transcription factors, whereas the remainder show signs of complex regulation, involving delayed regulation and strong amplification at high TGFβ doses. Knockdown experiments followed by global RNA sequencing revealed transcription factors interacting with SMADs in feedforward loops to control delayed and dose-discriminating target genes, thereby reinforcing the specific epithelial-to-mesenchymal transition at high TGFβ doses. We identified early repressors, preventing premature activation, and a late activator, boosting gene expression responses for a sufficiently strong TGFβ stimulus. Taken together, we present a global view of TGFβ-dependent gene regulation and describe specificity mechanisms reinforcing cellular decision-making.
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Affiliation(s)
- Laura Hartmann
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Panajot Kristofori
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Congxin Li
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Kolja Becker
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
| | - Lorenz Hexemer
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Stefan Bohn
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Sonja Lenhardt
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Sylvia Weiss
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Björn Voss
- Department of RNA-Biology & Bioinformatics, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
| | - Alexander Loewer
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
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6
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Follmer ML, Isner TJ, Ozekin YH, Levitt CH, Burek CL, Benninger RKP, Bates EA. Depolarization induces calcium-dependent BMP4 release from mouse embryonic palate mesenchymal cells. Nat Commun 2024; 15:9806. [PMID: 39532850 PMCID: PMC11558011 DOI: 10.1038/s41467-024-53642-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/17/2024] [Indexed: 11/16/2024] Open
Abstract
Bone Morphogenetic Protein (BMP) signaling is essential for craniofacial development, though little is known about the mechanisms that govern BMP secretion. We show that depolarization induces calcium-dependent BMP4 release from mouse embryonic palate mesenchyme. We show endogenous transient changes in intracellular calcium occur in cranial neural crest cells, the cells from which embryonic palate mesenchyme derives. Waves of transient changes in intracellular calcium suggest that these cells are electrically coupled and may temporally coordinate BMP release. These transient changes in intracellular calcium persist in palate mesenchyme cells from embryonic day 9.5 to 13.5 mice. Disruption of a potassium channel called Kcnj2 significantly decreases the amplitude of calcium transients and the ability of cells to secrete BMP. Kcnj2 knockout mice have cleft palate and reduced BMP signaling. Our data suggest that temporal control of developmental cues is regulated by ion channels, depolarization, and intracellular calcium for mammalian craniofacial morphogenesis.
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Affiliation(s)
- Mikaela L Follmer
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Trevor J Isner
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yunus H Ozekin
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Claire H Levitt
- Department of Bioengineering, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Carolyn L Burek
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Richard K P Benninger
- Department of Bioengineering, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Emily Anne Bates
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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7
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Follmer ML, Isner T, Ozekin YH, Levitt C, Bates EA. Depolarization induces calcium-dependent BMP4 release from mouse embryonic palate mesenchyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598333. [PMID: 38915514 PMCID: PMC11195066 DOI: 10.1101/2024.06.11.598333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Ion channels are essential for proper morphogenesis of the craniofacial skeleton. However, the molecular mechanisms underlying this phenomenon are unknown. Loss of the Kcnj2 potassium channel disrupts Bone Morphogenetic Protein (BMP) signaling within the developing palate. BMP signaling is essential for the correct development of several skeletal structures, including the palate, though little is known about the mechanisms that govern BMP secretion. We introduce a tool to image the release of bone morphogenetic protein 4 (BMP4) from mammalian cells. Using this tool, we show that depolarization induces BMP4 release from mouse embryonic palate mesenchyme cells in a calcium-dependent manner. We show native transient changes in intracellular calcium occur in cranial neural crest cells, the cells from which embryonic palate mesenchyme derives. Waves of transient changes in intracellular calcium suggest that these cells are electrically coupled and may temporally coordinate BMP release. These transient changes in intracellular calcium persist in palate mesenchyme cells from embryonic day (E) 9.5 to 13.5 mice. Disruption of Kcnj2 significantly decreases the amplitude of calcium transients and the ability of cells to secrete BMP. Together, these data suggest that temporal control of developmental cues is regulated by ion channels, depolarization, and changes in intracellular calcium for mammalian craniofacial morphogenesis. SUMMARY We show that embryonic palate mesenchyme cells undergo transient changes in intracellular calcium. Depolarization of these cells induces BMP4 release suggesting that ion channels are a node in BMP4 signaling.
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8
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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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9
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McNamara HM, Jia BZ, Guyer A, Parot VJ, Dobbs C, Schier AF, Cohen AE, Lord ND. Optogenetic control of Nodal signaling patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.588875. [PMID: 38645239 PMCID: PMC11030342 DOI: 10.1101/2024.04.11.588875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
A crucial step in early embryogenesis is the establishment of spatial patterns of signaling activity. Tools to perturb morphogen signals with high resolution in space and time can help reveal how embryonic cells decode these signals to make appropriate fate decisions. Here, we present new optogenetic reagents and an experimental pipeline for creaHng designer Nodal signaling patterns in live zebrafish embryos. Nodal receptors were fused to the light-sensitive heterodimerizing pair Cry2/CIB1N, and the Type II receptor was sequestered to the cytosol. The improved optoNodal2 reagents eliminate dark activity and improve response kinetics, without sacrificing dynamic range. We adapted an ultra-widefield microscopy platform for parallel light patterning in up to 36 embryos and demonstrated precise spatial control over Nodal signaling activity and downstream gene expression. Patterned Nodal activation drove precisely controlled internalization of endodermal precursors. Further, we used patterned illumination to generate synthetic signaling patterns in Nodal signaling mutants, rescuing several characteristic developmental defects. This study establishes an experimental toolkit for systematic exploration of Nodal signaling patterns in live embryos.
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Affiliation(s)
| | - Bill Z. Jia
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Alison Guyer
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vicente J. Parot
- Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Caleb Dobbs
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Nathan D. Lord
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, USA
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10
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Emig AA, Hansen M, Grimm S, Coarfa C, Lord ND, Williams MK. Temporal dynamics of BMP/Nodal ratio drive tissue-specific gastrulation morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579243. [PMID: 38370754 PMCID: PMC10871350 DOI: 10.1101/2024.02.06.579243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Anteroposterior (AP) elongation of the vertebrate body plan is driven by convergence and extension (C&E) gastrulation movements in both the mesoderm and neuroectoderm, but how or whether molecular regulation of C&E differs between tissues remains an open question. Using a zebrafish explant model of AP axis extension, we show that C&E of the neuroectoderm and mesoderm can be uncoupled ex vivo, and that morphogenesis of individual tissues results from distinct morphogen signaling dynamics. Using precise temporal manipulation of BMP and Nodal signaling, we identify a critical developmental window during which high or low BMP/Nodal ratios induce neuroectoderm- or mesoderm-driven C&E, respectively. Increased BMP activity similarly enhances C&E specifically in the ectoderm of intact zebrafish gastrulae, highlighting the in vivo relevance of our findings. Together, these results demonstrate that temporal dynamics of BMP and Nodal morphogen signaling activate distinct morphogenetic programs governing C&E gastrulation movements within individual tissues.
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Affiliation(s)
- Alyssa A Emig
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Megan Hansen
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Sandra Grimm
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Cristian Coarfa
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Nathan D Lord
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA
| | - Margot Kossmann Williams
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Previous address: Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO
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11
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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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12
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George LF, Follmer ML, Fontenoy E, Moran HR, Brown JR, Ozekin YH, Bates EA. Endoplasmic Reticulum Calcium Mediates Drosophila Wing Development. Bioelectricity 2023; 5:290-306. [PMID: 38143873 PMCID: PMC10733776 DOI: 10.1089/bioe.2022.0036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023] Open
Abstract
Background The temporal dynamics of morphogen presentation impacts transcriptional responses and tissue patterning. However, the mechanisms controlling morphogen release are far from clear. We found that inwardly rectifying potassium (Irk) channels regulate endogenous transient increases in intracellular calcium and bone morphogenetic protein (BMP/Dpp) release for Drosophila wing development. Inhibition of Irk channels reduces BMP/Dpp signaling, and ultimately disrupts wing morphology. Ion channels impact development of several tissues and organisms in which BMP signaling is essential. In neurons and pancreatic beta cells, Irk channels modulate membrane potential to affect intracellular Ca++ to control secretion of neurotransmitters and insulin. Based on Irk activity in neurons, we hypothesized that electrical activity controls endoplasmic reticulum (ER) Ca++ release into the cytoplasm to regulate the release of BMP. Materials and Methods To test this hypothesis, we reduced expression of four proteins that control ER calcium, Stromal interaction molecule 1 (Stim), Calcium release-activated calcium channel protein 1 (Orai), SarcoEndoplasmic Reticulum Calcium ATPase (SERCA), small conductance calcium-activated potassium channel (SK), and Bestrophin 2 (Best2) using RNAi and documented wing phenotypes. We use live imaging to study calcium and Dpp release within pupal wings and larval wing discs. Additionally, we employed immunohistochemistry to characterize Small Mothers Against Decapentaplegic (SMAD) phosphorylation downstream of the BMP/Dpp pathway following RNAi knockdown. Results We found that reduced Stim and SERCA function decreases amplitude and frequency of endogenous calcium transients in the wing disc and reduced BMP/Dpp release. Conclusion Our results suggest control of ER calcium homeostasis is required for BMP/Dpp release, and Drosophila wing development.
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Affiliation(s)
- Laura Faith George
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mikaela Lynn Follmer
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Emily Fontenoy
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Hannah Rose Moran
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jeremy Ryan Brown
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Yunus H. Ozekin
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Emily Anne Bates
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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13
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Bohn S, Hexemer L, Huang Z, Strohmaier L, Lenhardt S, Legewie S, Loewer A. State- and stimulus-specific dynamics of SMAD signaling determine fate decisions in individual cells. Proc Natl Acad Sci U S A 2023; 120:e2210891120. [PMID: 36857347 PMCID: PMC10013741 DOI: 10.1073/pnas.2210891120] [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: 06/27/2022] [Accepted: 01/07/2023] [Indexed: 03/02/2023] Open
Abstract
SMAD-mediated signaling regulates apoptosis, cell cycle arrest, and epithelial-to-mesenchymal transition to safeguard tissue homeostasis. However, it remains elusive how the relatively simple pathway can determine such a broad range of cell fate decisions and how it differentiates between varying ligands. Here, we systematically investigate how SMAD-mediated responses are modulated by various ligands of the transforming growth factor β (TGFβ) family and compare these ligand responses in quiescent and proliferating MCF10A cells. We find that the nature of the phenotypic response is mainly determined by the proliferation status, with migration and cell cycle arrest being dominant in proliferating cells for all tested TGFβ family ligands, whereas cell death is the major outcome in quiescent cells. In both quiescent and proliferating cells, the identity of the ligand modulates the strength of the phenotypic response proportional to the dynamics of induced SMAD nuclear-to-cytoplasmic translocation and, as a consequence, the corresponding gene expression changes. Interestingly, the proliferation state of a cell has little impact on the set of genes induced by SMAD signaling; instead, it modulates the relative cellular sensitivity to TGFβ superfamily members. Taken together, diversity of SMAD-mediated responses is mediated by differing cellular states, which determine ligand sensitivity and phenotypic effects, while the pathway itself merely serves as a quantitative relay from the cell membrane to the nucleus.
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Affiliation(s)
- Stefan Bohn
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
| | - Lorenz Hexemer
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, 70569Stuttgart, Germany
| | - Zixin Huang
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
| | - Laura Strohmaier
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, 70569Stuttgart, Germany
| | - Sonja Lenhardt
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics, University of Stuttgart, 70569Stuttgart, Germany
- Stuttgart Research Center for Systems Biology, University of Stuttgart, 70569Stuttgart, Germany
| | - Alexander Loewer
- Department of Biology, Technical University Darmstadt, 64287Darmstadt, Germany
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14
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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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15
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Thiemicke A, Neuert G. Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments. Front Cell Dev Biol 2023; 11:1124874. [PMID: 37025183 PMCID: PMC10072286 DOI: 10.3389/fcell.2023.1124874] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
All cells employ signal transduction pathways to respond to physiologically relevant extracellular cytokines, stressors, nutrient levels, hormones, morphogens, and other stimuli that vary in concentration and rate in healthy and diseased states. A central unsolved fundamental question in cell signaling is whether and how cells sense and integrate information conveyed by changes in the rate of extracellular stimuli concentrations, in addition to the absolute difference in concentration. We propose that different environmental changes over time influence cell behavior in addition to different signaling molecules or different genetic backgrounds. However, most current biomedical research focuses on acute environmental changes and does not consider how cells respond to environments that change slowly over time. As an example of such environmental change, we review cell sensitivity to environmental rate changes, including the novel mechanism of rate threshold. A rate threshold is defined as a threshold in the rate of change in the environment in which a rate value below the threshold does not activate signaling and a rate value above the threshold leads to signal activation. We reviewed p38/Hog1 osmotic stress signaling in yeast, chemotaxis and stress response in bacteria, cyclic adenosine monophosphate signaling in Amoebae, growth factors signaling in mammalian cells, morphogen dynamics during development, temporal dynamics of glucose and insulin signaling, and spatio-temproral stressors in the kidney. These reviewed examples from the literature indicate that rate thresholds are widespread and an underappreciated fundamental property of cell signaling. Finally, by studying cells in non-linear environments, we outline future directions to understand cell physiology better in normal and pathophysiological conditions.
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Affiliation(s)
- Alexander Thiemicke
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, United States
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, United States
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Gregor Neuert,
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16
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Feng J, Han X, Yuan Y, Cho CK, Janečková E, Guo T, Pareek S, Rahman MS, Zheng B, Bi J, Jing J, Zhang M, Xu J, Ho TV, Chai Y. TGF-β signaling and Creb5 cooperatively regulate Fgf18 to control pharyngeal muscle development. eLife 2022; 11:e80405. [PMID: 36542062 PMCID: PMC9771365 DOI: 10.7554/elife.80405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
The communication between myogenic cells and their surrounding connective tissues is indispensable for muscle morphogenesis. During late embryonic development in mice, myogenic progenitors migrate to discrete sites to form individual muscles. The detailed mechanism of this process remains unclear. Using mouse levator veli palatini (LVP) development as a model, we systematically investigated how a distinct connective tissue subpopulation, perimysial fibroblasts, communicates with myogenic cells to regulate mouse pharyngeal myogenesis. Using single-cell RNAseq data analysis, we identified that TGF-β signaling is a key regulator for the perimysial fibroblasts. Loss of TGF-β signaling in the neural crest-derived palatal mesenchyme leads to defects in perimysial fibroblasts and muscle malformation in the soft palate in Osr2Cre;Tgfbr1fl/fl mice. In particular, Creb5, a transcription factor expressed in the perimysial fibroblasts, cooperates with TGF-β signaling to activate expression of Fgf18. Moreover, Fgf18 supports pharyngeal muscle development in vivo and exogenous Fgf18 can partially rescue myogenic cell numbers in Osr2Cre;Tgfbr1fl/fl samples, illustrating that TGF-β-regulated Fgf18 signaling is required for LVP development. Collectively, our findings reveal the mechanism by which TGF-β signaling achieves its functional specificity in defining the perimysial-to-myogenic signals for pharyngeal myogenesis.
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Affiliation(s)
- Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Xia Han
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Yuan Yuan
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Courtney Kyeong Cho
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Eva Janečková
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Tingwei Guo
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Siddhika Pareek
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Md Shaifur Rahman
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Banghong Zheng
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Jing Bi
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Junjun Jing
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Mingyi Zhang
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Jian Xu
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
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17
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Abstract
Transforming growth factor-beta (TGF-β) is a double-edged sword in cancer treatment because of its pivotal yet complex and roles played during cancer initiation/development. Current anti-cancer strategies involving TGF-β largely view TGF-β as an onco-therapeutic target that not only substantially hinders its full utilisation for cancer control, but also considerably restricts innovations in this field. Thereby, how to take advantages of therapeutically favourable properties of TGF-β for cancer management represents an interesting and less investigated problem. Here, by categorising cancer hallmarks into four critical transition events and one enabling characteristic controlling cancer initiation and progression, and delineating TGF-β complexities according to these cancer traits, we identify the suppressive role of TGF-β in tumour initiation and early-stage progression and its promotive functionalities in cancer metastasis as well as other cancer hallmarks. We also propose the feasibility and possible scenarios of combining cold atmospheric plasma (CAP) with onco-therapeutics utilising TGF-β for cancer control given the intrinsic properties of CAP against cancer hallmarks.
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18
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Duan X, Luo M, Li J, Shen Z, Xie K. Overcoming therapeutic resistance to platinum-based drugs by targeting Epithelial–Mesenchymal transition. Front Oncol 2022; 12:1008027. [PMID: 36313710 PMCID: PMC9614084 DOI: 10.3389/fonc.2022.1008027] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022] Open
Abstract
Platinum-based drugs (PBDs), including cisplatin, carboplatin, and oxaliplatin, have been widely used in clinical practice as mainstay treatments for various types of cancer. Although there is firm evidence of notable achievements with PBDs in the management of cancers, the acquisition of resistance to these agents is still a major challenge to efforts at cure. The introduction of the epithelial-mesenchymal transition (EMT) concept, a critical process during embryonic morphogenesis and carcinoma progression, has offered a mechanistic explanation for the phenotypic switch of cancer cells upon PBD exposure. Accumulating evidence has suggested that carcinoma cells can enter a resistant state via induction of the EMT. In this review, we discussed the underlying mechanism of PBD-induced EMT and the current understanding of its role in cancer drug resistance, with emphasis on how this novel knowledge can be exploited to overcome PBD resistance via EMT-targeted compounds, especially those under clinical trials.
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Affiliation(s)
- Xirui Duan
- Department of Oncology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Maochao Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Jian Li
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Zhisen Shen
- Department of Otorhinolaryngology and Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
- *Correspondence: Ke Xie, ; Zhisen Shen,
| | - Ke Xie
- Department of Oncology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Ke Xie, ; Zhisen Shen,
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19
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Tischler J, Swank Z, Hsiung HA, Vianello S, Lutolf MP, Maerkl SJ. An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates. CELL REPORTS METHODS 2022; 2:100244. [PMID: 35880022 PMCID: PMC9308133 DOI: 10.1016/j.crmeth.2022.100244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022]
Abstract
We present a low-cost, do-it-yourself system for complex mammalian cell culture under dynamically changing medium formulations by integrating conventional multi-well tissue culture plates with simple microfluidic control and system automation. We demonstrate the generation of complex concentration profiles, enabling the investigation of sophisticated input-response relations. We further apply our automated cell-culturing platform to the dynamic stimulation of two widely employed stem-cell-based in vitro models for early mammalian development: the conversion of naive mouse embryonic stem cells into epiblast-like cells and mouse 3D gastruloids. Performing automated medium-switch experiments, we systematically investigate cell fate commitment along the developmental trajectory toward mouse epiblast fate and examine symmetry-breaking, germ layer formation, and cardiac differentiation in mouse 3D gastruloids as a function of time-varying Wnt pathway activation. With these proof-of-principle examples, we demonstrate a highly versatile and scalable tool that can be adapted to specific research questions, experimental demands, and model systems.
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Affiliation(s)
- Julia Tischler
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Zoe Swank
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hao-An Hsiung
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Stefano Vianello
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Matthias P. Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
- Roche Institute for Translational Bioengineering (TB), Pharma Research and Early Development (pRED), F. Hoffman-La Roche Ltd, Basel, Switzerland
| | - Sebastian J. Maerkl
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
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20
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Kolbe N, Hexemer L, Bammert LM, Loewer A, Lukáčová-Medvid’ová M, Legewie S. Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling. PLoS Comput Biol 2022; 18:e1010266. [PMID: 35759468 PMCID: PMC9269928 DOI: 10.1371/journal.pcbi.1010266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 07/08/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
Cells sense their surrounding by employing intracellular signaling pathways that transmit hormonal signals from the cell membrane to the nucleus. TGF-β/SMAD signaling encodes various cell fates, controls tissue homeostasis and is deregulated in diseases such as cancer. The pathway shows strong heterogeneity at the single-cell level, but quantitative insights into mechanisms underlying fluctuations at various time scales are still missing, partly due to inefficiency in the calibration of stochastic models that mechanistically describe signaling processes. In this work we analyze single-cell TGF-β/SMAD signaling and show that it exhibits temporal stochastic bursts which are dose-dependent and whose number and magnitude correlate with cell migration. We propose a stochastic modeling approach to mechanistically describe these pathway fluctuations with high computational efficiency. Employing high-order numerical integration and fitting to burst statistics we enable efficient quantitative parameter estimation and discriminate models that assume noise in different reactions at the receptor level. This modeling approach suggests that stochasticity in the internalization of TGF-β receptors into endosomes plays a key role in the observed temporal bursting. Further, the model predicts the single-cell dynamics of TGF-β/SMAD signaling in untested conditions, e.g., successfully reflects memory effects of signaling noise and cellular sensitivity towards repeated stimulation. Taken together, our computational framework based on burst analysis, noise modeling and path computation scheme is a suitable tool for the data-based modeling of complex signaling pathways, capable of identifying the source of temporal noise.
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Affiliation(s)
- Niklas Kolbe
- Institute of Geometry and Practical Mathematics, RWTH Aachen University, Aachen, Germany
| | - Lorenz Hexemer
- Institute of Molecular Biology (IMB), Mainz, Germany
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
| | | | - Alexander Loewer
- Systems Biology of the Stress Response, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | | | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
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21
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Dynamic Visualization of TGF-β/SMAD3 Transcriptional Responses in Single Living Cells. Cancers (Basel) 2022; 14:cancers14102508. [PMID: 35626109 PMCID: PMC9139966 DOI: 10.3390/cancers14102508] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary How a single cytokine can induce a variety of cellular responses in the same cell or in different cells is a longstanding question. Transforming growth factor β (TGF-β) is a prototypical multifunctional cytokine of which biological responses are highly dependent on in a cellular context. TGF-β signals via intracellular SMAD transcription factors, and the duration and intensity of SMAD activation are key determinants for the responses that are elicited by TGF-β. To visualize the TGF-β signaling kinetics, we developed a dynamic TGF-β/SMAD3 transcriptional reporter using a quickly folded and highly unstable green florescent protein. We demonstrate the specificity and sensitivity of this reporter and its wide application to monitor dynamic TGF-β-induced responses in cells cultured on plastic dishes, and in living animals. This tool allows for the analysis of TGF-β signaling at a single living cell level, and allows for the discovery of dynamic TGF-β SMAD- induced transcriptional responses in multi-step biological processes. Abstract Transforming growth factor-β (TGF-β) signaling is tightly controlled in duration and intensity during embryonic development and in the adult to maintain tissue homeostasis. To visualize the TGF-β/SMAD3 signaling kinetics, we developed a dynamic TGF-β/SMAD3 transcriptional fluorescent reporter using multimerized SMAD3/4 binding elements driving the expression of a quickly folded and highly unstable GFP protein. We demonstrate the specificity and sensitivity of this reporter and its wide application to monitor dynamic TGF-β/SMAD3 transcriptional responses in both 2D and 3D systems in vitro, as well as in vivo, using live-cell and intravital imaging. Using this reporter in B16F10 cells, we observed single cell heterogeneity in response to TGF-β challenge, which can be categorized into early, late, and non-responders. Because of its broad application potential, this reporter allows for new discoveries into how TGF-β/SMAD3-dependent transcriptional dynamics are affected during multistep and reversible biological processes.
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22
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Furfaro F, Vias C, Sorre B. Using Microfluidics and Live Cell Reporters to Dissect the Dynamics of TGF-β Signaling in Mouse Embryonic Stem Cells. Methods Mol Biol 2022; 2488:125-143. [PMID: 35347687 DOI: 10.1007/978-1-0716-2277-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The TGF-β pathway is known to behave as a classical morphogen, meaning that it can dictate cell fate decisions in a dose-dependent manner. Recent observations however showed that in addition to the absolute value of morphogen concentration, cells could also extract information from its temporal variations. In the present article we describe how to use automated microfluidics cell culture to stimulate cells with precisely defined temporal profiles of morphogens and how to engineer mouse embryonic stem cells with fluorescent reporters of pathway activity to record in real time their response to the applied stimulations. The combination of automated cell culture and of live cell reporter provides a complete toolbox to study how cells encode the information carried by time-varying TGF-β signals.
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Affiliation(s)
- Fabien Furfaro
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, Université de Paris, Paris Cedex 13, France
| | - Carine Vias
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, Université de Paris, Paris Cedex 13, France
| | - Benoit Sorre
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, Université de Paris, Paris Cedex 13, France.
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France.
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23
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Abstract
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types that elaborate this complexity results from the activity of gene networks and was likened by Waddington to a flow through a landscape in which valleys represent alternative fates. Geometric methods allow the formal representation of such landscapes and codify the types of behaviors that result from systems of differential equations. Results from Smale and coworkers imply that systems encompassing gene network models can be represented as potential gradients with a Riemann metric, justifying the Waddington metaphor. Here, we extend this representation to include parameter dependence and enumerate all three-way cellular decisions realizable by tuning at most two parameters, which can be generalized to include spatial coordinates in a tissue. All diagrams of cell states vs. model parameters are thereby enumerated. We unify a number of standard models for spatial pattern formation by expressing them in potential form (i.e., as topographic elevation). Turing systems appear nonpotential, yet in suitable variables the dynamics are low dimensional and potential. A time-independent embedding recovers the original variables. Lateral inhibition is described by a saddle point with many unstable directions. A model for the patterning of the Drosophila eye appears as relaxation in a bistable potential. Geometric reasoning provides intuitive dynamic models for development that are well adapted to fit time-lapse data.
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24
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Viswanathan R, Hartmann J, Pallares Cartes C, De Renzis S. Desensitisation of Notch signalling through dynamic adaptation in the nucleus. EMBO J 2021; 40:e107245. [PMID: 34396565 PMCID: PMC8441390 DOI: 10.15252/embj.2020107245] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 07/21/2021] [Accepted: 07/24/2021] [Indexed: 11/13/2022] Open
Abstract
During embryonic development, signalling pathways orchestrate organogenesis by controlling tissue‐specific gene expression programmes and differentiation. Although the molecular components of many common developmental signalling systems are known, our current understanding of how signalling inputs are translated into gene expression outputs in real‐time is limited. Here we employ optogenetics to control the activation of Notch signalling during Drosophila embryogenesis with minute accuracy and follow target gene expression by quantitative live imaging. Light‐induced nuclear translocation of the Notch Intracellular Domain (NICD) causes a rapid activation of target mRNA expression. However, target gene transcription gradually decays over time despite continuous photo‐activation and nuclear NICD accumulation, indicating dynamic adaptation to the signalling input. Using mathematical modelling and molecular perturbations, we show that this adaptive transcriptional response fits to known motifs capable of generating near‐perfect adaptation and can be best explained by state‐dependent inactivation at the target cis‐regulatory region. Taken together, our results reveal dynamic nuclear adaptation as a novel mechanism controlling Notch signalling output during tissue differentiation.
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Affiliation(s)
- Ranjith Viswanathan
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
| | - Jonas Hartmann
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany.,Department of Cell and Developmental Biology, University College London, London, UK
| | | | - Stefano De Renzis
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
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25
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Mateus R, Fuhrmann JF, Dye NA. Growth across scales: Dynamic signaling impacts tissue size and shape. Curr Opin Cell Biol 2021; 73:50-57. [PMID: 34182209 DOI: 10.1016/j.ceb.2021.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/06/2021] [Indexed: 12/20/2022]
Abstract
Organ and tissue growth result from an integration of biophysical communication across biological scales, both in time and space. In this review, we highlight new insight into the dynamic connections between control mechanisms operating at different length scales. First, we consider how the dynamics of chemical and electrical signaling in the shape of gradients or waves affect spatiotemporal signal interpretation. Then, we discuss the mechanics underlying dynamic cell behavior during oriented tissue growth, followed by the connections between signaling at the tissue and organismal levels.
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Affiliation(s)
- Rita Mateus
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany.
| | - Jana F Fuhrmann
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Natalie A Dye
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany; Mildred Scheel Nachwuchszentrum (MSNZ) P2, Medical Faculty, Technische Universität Dresden, Germany.
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26
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Gritti N, Oriola D, Trivedi V. Rethinking embryology in vitro: A synergy between engineering, data science and theory. Dev Biol 2021; 474:48-61. [DOI: 10.1016/j.ydbio.2020.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
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Phan-Everson T, Etoc F, Li S, Khodursky S, Yoney A, Brivanlou AH, Siggia ED. Differential compartmentalization of BMP4/NOGGIN requires NOGGIN trans-epithelial transport. Dev Cell 2021; 56:1930-1944.e5. [PMID: 34051144 DOI: 10.1016/j.devcel.2021.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/01/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
Using self-organizing human models of gastrulation, we previously showed that (1) BMP4 initiates the cascade of events leading to gastrulation, (2) BMP4 signal reception is restricted to the basolateral domain, and (3) in a human-specific manner, BMP4 directly induces the expression of NOGGIN. Here, we report the surprising discovery that in human epiblasts, NOGGIN and BMP4 were secreted into opposite extracellular spaces. Interestingly, apically presented NOGGIN could inhibit basally delivered BMP4. Apically imposed microfluidic flow demonstrated that NOGGIN traveled in the apical extracellular space. Our co-localization analysis detailed the endocytotic route that trafficked NOGGIN from the apical space to the basolateral intercellular space where BMP4 receptors were located. This apical-basal transcytosis was indispensable for NOGGIN inhibition. Taken together, the segregation of activator/inhibitor into distinct extracellular spaces challenges classical views of morphogen movement. We propose that the transport of morphogen inhibitors regulates the spatial availability of morphogens during embryogenesis.
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Affiliation(s)
- Tien Phan-Everson
- Laboratory of Stem Cell Biology and Molecular Embryology, the Rockefeller University, New York, NY 10065, USA; Center for Studies in Physics and Biology, the Rockefeller University, New York, NY 10065, USA
| | - Fred Etoc
- Laboratory of Stem Cell Biology and Molecular Embryology, the Rockefeller University, New York, NY 10065, USA
| | - Shu Li
- Laboratory of Stem Cell Biology and Molecular Embryology, the Rockefeller University, New York, NY 10065, USA
| | - Samuel Khodursky
- Center for Studies in Physics and Biology, the Rockefeller University, New York, NY 10065, USA
| | - Anna Yoney
- Laboratory of Stem Cell Biology and Molecular Embryology, the Rockefeller University, New York, NY 10065, USA; Center for Studies in Physics and Biology, the Rockefeller University, New York, NY 10065, USA; Department of Genetics and Development, Columbia University, New York, NY 10032
| | - Ali H Brivanlou
- Laboratory of Stem Cell Biology and Molecular Embryology, the Rockefeller University, New York, NY 10065, USA.
| | - Eric D Siggia
- Center for Studies in Physics and Biology, the Rockefeller University, New York, NY 10065, USA.
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28
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Liu L, Warmflash A. Self-organized signaling in stem cell models of embryos. Stem Cell Reports 2021; 16:1065-1077. [PMID: 33979594 PMCID: PMC8185436 DOI: 10.1016/j.stemcr.2021.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Mammalian embryonic development is a complex process driven by self-organization. Understanding how a fertilized egg develops into an embryo composed of more than 200 cell types in precise spatial patterns remains one of the fundamental challenges in biology. Pluripotent stem cells have been used as in vitro models for investigating mammalian development, and represent promising building blocks for regenerative therapies. Recently, sophisticated stem cell-based models that recapitulate early embryonic fate patterning and morphogenesis have been developed. In this article, we review recent advances in stem cell models of embryos in particular focusing on signaling activities underpinning cell fate decisions in space and time.
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Affiliation(s)
- Lizhong Liu
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Aryeh Warmflash
- Department of Biosciences, Rice University, Houston, TX 77005, USA; Department of Bioengineering, Rice University, Houston, TX 77005, USA.
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29
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Mark KG, Rape M. Ubiquitin-dependent regulation of transcription in development and disease. EMBO Rep 2021; 22:e51078. [PMID: 33779035 DOI: 10.15252/embr.202051078] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/29/2020] [Accepted: 03/01/2021] [Indexed: 12/19/2022] Open
Abstract
Transcription is an elaborate process that is required to establish and maintain the identity of the more than two hundred cell types of a metazoan organism. Strict regulation of gene expression is therefore vital for tissue formation and homeostasis. An accumulating body of work found that ubiquitylation of histones, transcription factors, or RNA polymerase II is crucial for ensuring that transcription occurs at the right time and place during development. Here, we will review principles of ubiquitin-dependent control of gene expression and discuss how breakdown of these regulatory circuits leads to a wide array of human diseases.
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Affiliation(s)
- Kevin G Mark
- Department of Molecular Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Michael Rape
- Department of Molecular Cell Biology, University of California at Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
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30
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Thiemicke A, Neuert G. Kinetics of osmotic stress regulate a cell fate switch of cell survival. SCIENCE ADVANCES 2021; 7:7/8/eabe1122. [PMID: 33608274 PMCID: PMC7895434 DOI: 10.1126/sciadv.abe1122] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/06/2021] [Indexed: 05/02/2023]
Abstract
Exposure of cells to diverse types of stressful environments differentially regulates cell fate. Although many types of stresses causing this differential regulation are known, it is unknown how changes over time of the same stressor regulate cell fate. Changes in extracellular osmolarity are critically involved in physiological and pathophysiological processes in several tissues. We observe that human cells survive gradual but not acute hyperosmotic stress. We find that stress, caspase, and apoptosis signaling do not activate during gradual stress in contrast to acute treatments. Contrary to the current paradigm, we see a substantial accumulation of proline in cells treated with gradual but not acute stresses. We show that proline can protect cells from hyperosmotic stress similar to the osmoprotection in plants and bacteria. Our studies found a cell fate switch that enables cells to survive gradually changing stress environments by preventing caspase activation and protect cells through proline accumulation.
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Affiliation(s)
- Alexander Thiemicke
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Gregor Neuert
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA.
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, USA
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31
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Johnson AN, Li G, Jashnsaz H, Thiemicke A, Kesler BK, Rogers DC, Neuert G. A rate threshold mechanism regulates MAPK stress signaling and survival. Proc Natl Acad Sci U S A 2021; 118:e2004998118. [PMID: 33443180 PMCID: PMC7812835 DOI: 10.1073/pnas.2004998118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cells are exposed to changes in extracellular stimulus concentration that vary as a function of rate. However, how cells integrate information conveyed from stimulation rate along with concentration remains poorly understood. Here, we examined how varying the rate of stress application alters budding yeast mitogen-activated protein kinase (MAPK) signaling and cell behavior at the single-cell level. We show that signaling depends on a rate threshold that operates in conjunction with stimulus concentration to determine the timing of MAPK signaling during rate-varying stimulus treatments. We also discovered that the stimulation rate threshold and stimulation rate-dependent cell survival are sensitive to changes in the expression levels of the Ptp2 phosphatase, but not of another phosphatase that similarly regulates osmostress signaling during switch-like treatments. Our results demonstrate that stimulation rate is a regulated determinant of cell behavior and provide a paradigm to guide the dissection of major stimulation rate dependent mechanisms in other systems.
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Affiliation(s)
- Amanda N Johnson
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232
| | - Guoliang Li
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232
| | - Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232
| | - Alexander Thiemicke
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232
| | - Benjamin K Kesler
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232
| | - Dustin C Rogers
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232;
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN 37232
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN 37232
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32
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Papadopoulos A, Chalmantzi V, Mikhaylichenko O, Hyvönen M, Stellas D, Kanhere A, Heath J, Cunningham DL, Fotsis T, Murphy C. Combined transcriptomic and phosphoproteomic analysis of BMP4 signaling in human embryonic stem cells. Stem Cell Res 2020; 50:102133. [PMID: 33383406 DOI: 10.1016/j.scr.2020.102133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/08/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022] Open
Abstract
Human embryonic stem cells (hESCs) are an invaluable tool in the fields of embryology and regenerative medicine. Activin A and BMP4 are well-characterised growth factors implicated in pluripotency and differentiation. In the current study, hESCs are cultured in a modified version of mTeSR1, where low concentrations of ActivinA substitute for TGFβ. This culture system is further used to investigate the changes induced by BMP4 on hESCs by employing a combination of transcriptomic and phosphoproteomic approaches. Results indicate that in a pluripotent state, hESCs maintain WNT signaling under negative regulation by expressing pathway inhibitors. Initial stages of differentiation are characterized by upregulation of WNT pathway ligands, TGFβ pathway inhibitors which have been shown in Xenopus to expand the BMP signaling range essential for embryonic patterning, and mesendodermal transcripts. Moreover, BMP4 enhances the phosphorylation of proteins associated with migration and transcriptional regulation. Results further indicate the vital regulatory role of Activin A and BMP4 in crucial fate decisions in hESCs.
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Affiliation(s)
- Angelos Papadopoulos
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London SE5 9NU, United Kingdom
| | - Varvara Chalmantzi
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Olga Mikhaylichenko
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London SE5 9NU, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, United Kingdom
| | - Dimitris Stellas
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Aditi Kanhere
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - John Heath
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Debbie L Cunningham
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Theodore Fotsis
- Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, University Campus of Ioannina, 45110 Ioannina, Greece; Laboratory of Biology, Medical School, University of Ioannina, 45110 Ioannina, Greece
| | - Carol Murphy
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, University Campus of Ioannina, 45110 Ioannina, Greece.
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33
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F M, M V, C B, O G, M M, N E. Development of a microfluidic approach for the real-time analysis of extrinsic TGF-β signalling. Biochem Biophys Res Commun 2020; 532:32-39. [PMID: 32826061 DOI: 10.1016/j.bbrc.2020.07.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
Autocrine and paracrine signalling are traditionally difficult to study due to the sub-micromolar concentrations involved. This has proven to be especially limiting in the study of embryonic stem cells that rely on such signalling for viability, self-renewal, and proliferation. Microfluidics allows to achieve local concentrations of ligands representative of the in vivo stem cell niche, gaining more precise control over the cell microenvironment, as well as to manipulate ligands availability with high temporal resolution and minimal amount of reagents. Here we developed a microfluidics-based system for monitoring the dynamics of TGF-β pathway activity by means of a SMAD2/3-dependent luciferase reporter. We first validated our system by showing dose-dependent transcriptional activation. We then tested the effects of pulsatile stimulation and delayed inhibition of TGF-β activity on signalling dynamics. Finally, we show that our microfluidic system, unlike conventional culture systems, can detect TGF-β ligands secreted in the conditioned medium from hESCs.
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Affiliation(s)
- Michielin F
- Department of Industrial Engineering, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine (VIMM), Padova, Italy; Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Vetralla M
- Department of Industrial Engineering, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Bolego C
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Italy
| | - Gagliano O
- Department of Industrial Engineering, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Montagner M
- Department of Molecular Medicine, University of Padova, Italy
| | - Elvassore N
- Department of Industrial Engineering, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine (VIMM), Padova, Italy; Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China.
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34
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Jashnsaz H, Fox ZR, Hughes JJ, Li G, Munsky B, Neuert G. Diverse Cell Stimulation Kinetics Identify Predictive Signal Transduction Models. iScience 2020; 23:101565. [PMID: 33083733 PMCID: PMC7549069 DOI: 10.1016/j.isci.2020.101565] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 08/18/2020] [Accepted: 09/11/2020] [Indexed: 11/28/2022] Open
Abstract
Computationally understanding the molecular mechanisms that give rise to cell signaling responses upon different environmental, chemical, and genetic perturbations is a long-standing challenge that requires models that fit and predict quantitative responses for new biological conditions. Overcoming this challenge depends not only on good models and detailed experimental data but also on the rigorous integration of both. We propose a quantitative framework to perturb and model generic signaling networks using multiple and diverse changing environments (hereafter "kinetic stimulations") resulting in distinct pathway activation dynamics. We demonstrate that utilizing multiple diverse kinetic stimulations better constrains model parameters and enables predictions of signaling dynamics that would be impossible using traditional dose-response or individual kinetic stimulations. To demonstrate our approach, we use experimentally identified models to predict signaling dynamics in normal, mutated, and drug-treated conditions upon multitudes of kinetic stimulations and quantify which proteins and reaction rates are most sensitive to which extracellular stimulations.
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Affiliation(s)
- Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Zachary R. Fox
- Inria Saclay Ile-de-France, Palaiseau 91120, France
- Institut Pasteur, USR 3756 IP CNRS, Paris 75015, France
- Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Jason J. Hughes
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Guoliang Li
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Brian Munsky
- Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN 37232, USA
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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35
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Maity A, Wollman R. Information transmission from NFkB signaling dynamics to gene expression. PLoS Comput Biol 2020; 16:e1008011. [PMID: 32797040 PMCID: PMC7478807 DOI: 10.1371/journal.pcbi.1008011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 09/08/2020] [Accepted: 06/02/2020] [Indexed: 02/06/2023] Open
Abstract
The dynamic signal encoding paradigm suggests that information flows from the extracellular environment into specific signaling patterns (encoding) that are then read by downstream effectors to control cellular behavior. Previous work empirically quantified the information content of dynamic signaling patterns. However, whether this information can be faithfully transmitted to the gene expression level is unclear. Here we used NFkB signaling as a model to understand the accuracy of information transmission from signaling dynamics into gene expression. Using a detailed mathematical model, we simulated realistic NFkB signaling patterns with different degrees of variability. The NFkB patterns were used as an input to a simple gene expression model. Analysis of information transmission between ligand and NFkB and ligand and gene expression allows us to determine information loss in transmission between receptors to dynamic signaling patterns and between signaling dynamics to gene expression. Information loss could occur due to biochemical noise or due to a lack of specificity. We found that noise-free gene expression has very little information loss suggesting that gene expression can preserve specificity in NFkB patterns. As expected, the addition of noise to the gene expression model results in information loss. Interestingly, this effect can be mitigated by a specific choice of parameters that can substantially reduce information loss due to biochemical noise during gene expression. Overall our results show that the cellular capacity for information transmission from dynamic signaling patterns to gene expression can be high enough to preserve ligand specificity and thereby the accuracy of cellular response to environmental cues.
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Affiliation(s)
- Alok Maity
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| | - Roy Wollman
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
- Departments of Integrative Biology and Physiology and Chemistry and Biochemistry, University of California UCLA, California, United States of America
- * E-mail:
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36
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Guo Y, Gao Z, Liu Y, Li S, Zhu J, Chen P, Liu BF. Multichannel Synchronous Hydrodynamic Gating Coupling with Concentration Gradient Generator for High-Throughput Probing Dynamic Signaling of Single Cells. Anal Chem 2020; 92:12062-12070. [DOI: 10.1021/acs.analchem.0c02746] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yiran Guo
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhaolong Gao
- The Key Laboratory of Ministry of Education for Image Processing and Intelligent Control, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yinan Liu
- Department of Genetics, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jinchi Zhu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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37
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Teixeira AF, Ten Dijke P, Zhu HJ. On-Target Anti-TGF-β Therapies Are Not Succeeding in Clinical Cancer Treatments: What Are Remaining Challenges? Front Cell Dev Biol 2020; 8:605. [PMID: 32733895 PMCID: PMC7360684 DOI: 10.3389/fcell.2020.00605] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/19/2020] [Indexed: 12/24/2022] Open
Abstract
Metastasis is the leading cause of death for cancer patients. During cancer progression, the initial detachment of cells from the primary tumor and the later colonization of a secondary organ are characterized as limiting steps for metastasis. Epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) are opposite dynamic multistep processes that enable these critical events in metastasis by altering the phenotype of cancer cells and improving their ability to migrate, invade and seed at distant organs. Among the molecular pathways that promote tumorigenesis in late-stage cancers, transforming growth factor-β (TGF-β) is described as an EMT master inducer by controlling different genes and proteins related to cytoskeleton assembly, cell-cell attachment and extracellular matrix remodeling. Still, despite the successful outcomes of different TGF-β pharmacological inhibitors in cell culture (in vitro) and animal models (in vivo), results in cancer clinical trials are poor or inconsistent at least, highlighting the existence of crucial components in human cancers that have not been properly explored. Here we review most recent findings to provide perspectives bridging the gap between on-target anti-TGF-β therapies in vitro and in pre-clinical models and the poor clinical outcomes in treating cancer patients. Specifically, we focus on (i) the dual roles of TGF-β signaling in cancer metastasis; (ii) dynamic signaling; (iii) functional differences of TGF-β free in solution vs. in exosomes; (iv) the regulatory effects of tumor microenvironment (TME) – particularly by cancer-associated fibroblasts – on TGF-β signaling pathway. Clearly identifying and establishing those missing links may provide strategies to revitalize and clinically improve the efficacy of TGF-β targeted therapies.
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Affiliation(s)
- Adilson Fonseca Teixeira
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Peter Ten Dijke
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Hong-Jian Zhu
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
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38
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Chen P, Li S, Guo Y, Zeng X, Liu BF. A review on microfluidics manipulation of the extracellular chemical microenvironment and its emerging application to cell analysis. Anal Chim Acta 2020; 1125:94-113. [PMID: 32674786 DOI: 10.1016/j.aca.2020.05.065] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Spatiotemporal manipulation of extracellular chemical environments with simultaneous monitoring of cellular responses plays an essential role in exploring fundamental biological processes and expands our understanding of underlying mechanisms. Despite the rapid progress and promising successes in manipulation strategies, many challenges remain due to the small size of cells and the rapid diffusion of chemical molecules. Fortunately, emerging microfluidic technology has become a powerful approach for precisely controlling the extracellular chemical microenvironment, which benefits from its integration capacity, automation, and high-throughput capability, as well as its high resolution down to submicron. Here, we summarize recent advances in microfluidics manipulation of the extracellular chemical microenvironment, including the following aspects: i) Spatial manipulation of chemical microenvironments realized by convection flow-, diffusion-, and droplet-based microfluidics, and surface chemical modification; ii) Temporal manipulation of chemical microenvironments enabled by flow switching/shifting, moving/flowing cells across laminar flows, integrated microvalves/pumps, and droplet manipulation; iii) Spatiotemporal manipulation of chemical microenvironments implemented by a coupling strategy and open-space microfluidics; and iv) High-throughput manipulation of chemical microenvironments. Finally, we briefly present typical applications of the above-mentioned technical advances in cell-based analyses including cell migration, cell signaling, cell differentiation, multicellular analysis, and drug screening. We further discuss the future improvement of microfluidics manipulation of extracellular chemical microenvironments to fulfill the needs of biological and biomedical research and applications.
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Affiliation(s)
- Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yiran Guo
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xuemei Zeng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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39
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Heemskerk I. Full of potential: Pluripotent stem cells for the systems biology of embryonic patterning. Dev Biol 2020; 460:86-98. [DOI: 10.1016/j.ydbio.2019.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 02/07/2023]
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40
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Mateus R, Holtzer L, Seum C, Hadjivasiliou Z, Dubois M, Jülicher F, Gonzalez-Gaitan M. BMP Signaling Gradient Scaling in the Zebrafish Pectoral Fin. Cell Rep 2020; 30:4292-4302.e7. [PMID: 32209485 PMCID: PMC7109522 DOI: 10.1016/j.celrep.2020.03.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 02/07/2020] [Accepted: 03/09/2020] [Indexed: 01/25/2023] Open
Abstract
Secreted growth factors can act as morphogens that form spatial concentration gradients in developing organs, thereby controlling growth and patterning. For some morphogens, adaptation of the gradients to tissue size allows morphological patterns to remain proportioned as the organs grow. In the zebrafish pectoral fin, we found that BMP signaling forms a two-dimensional gradient. The length of the gradient scales with tissue length and its amplitude increases with fin size according to a power-law. Gradient scaling and amplitude power-laws are signatures of growth control by time derivatives of morphogenetic signaling: cell division correlates with the fold change over time of the cellular signaling levels. We show that Smoc1 regulates BMP gradient scaling and growth in the fin. Smoc1 scales the gradient by means of a feedback loop: Smoc1 is a BMP agonist and BMP signaling represses Smoc1 expression. Our work uncovers a layer of morphogen regulation during vertebrate appendage development.
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Affiliation(s)
- Rita Mateus
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Laurent Holtzer
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Carole Seum
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Zena Hadjivasiliou
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Marine Dubois
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
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41
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Huizar F, Soundarrajan D, Paravitorghabeh R, Zartman J. Interplay between morphogen-directed positional information systems and physiological signaling. Dev Dyn 2020; 249:328-341. [PMID: 31794137 PMCID: PMC7328709 DOI: 10.1002/dvdy.140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
The development of an organism from an undifferentiated single cell into a spatially complex structure requires spatial patterning of cell fates across tissues. Positional information, proposed by Lewis Wolpert in 1969, has led to the characterization of many components involved in regulating morphogen signaling activity. However, how morphogen gradients are established, maintained, and interpreted by cells still is not fully understood. Quantitative and systems-based approaches are increasingly needed to define general biological design rules that govern positional information systems in developing organisms. This short review highlights a selective set of studies that have investigated the roles of physiological signaling in modulating and mediating morphogen-based pattern formation. Similarities between neural transmission and morphogen-based pattern formation mechanisms suggest underlying shared principles of active cell-based communication. Within larger tissues, neural networks provide directed information, via physiological signaling, that supplements positional information through diffusion. Further, mounting evidence demonstrates that physiological signaling plays a role in ensuring robustness of morphogen-based signaling. We conclude by highlighting several outstanding questions regarding the role of physiological signaling in morphogen-based pattern formation. Elucidating how physiological signaling impacts positional information is critical for understanding the close coupling of developmental and cellular processes in the context of development, disease, and regeneration.
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Affiliation(s)
- Francisco Huizar
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, South Bend, Indiana
- Bioengineering Graduate Program, University of Notre Dame, South Bend, Indiana
| | - Dharsan Soundarrajan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, South Bend, Indiana
| | - Ramezan Paravitorghabeh
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, South Bend, Indiana
| | - Jeremiah Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, South Bend, Indiana
- Bioengineering Graduate Program, University of Notre Dame, South Bend, Indiana
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42
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Camacho-Aguilar E, Warmflash A. Insights into mammalian morphogen dynamics from embryonic stem cell systems. Curr Top Dev Biol 2020; 137:279-305. [PMID: 32143746 PMCID: PMC7713707 DOI: 10.1016/bs.ctdb.2019.11.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Morphogens play an essential role in cell fate specification and patterning including in laying out the mammalian body plan during gastrulation. In vivo studies have shed light on the signaling pathways involved in this process and the phenotypes associated with their disruption, however, several important open questions remain regarding how morphogens function in space and time. Self-organized patterning systems based on embryonic stem cells have emerged as a powerful platform for beginning to address these questions that is complementary to in vivo approaches. Here we review recent progress in understanding morphogen signaling dynamics and patterning in early mammalian development by taking advantage of cutting-edge embryonic stem cell technology.
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Affiliation(s)
| | - Aryeh Warmflash
- Department of Biosciences, Rice University, Houston, TX, United States; Department of Bioengineering, Rice University, Houston, TX, United States.
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43
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Abstract
Specificity in signal transduction is determined by the ability of cells to "encode" and subsequently "decode" different environmental signals. Akin to computer software, this "signaling code" governs context-dependent execution of cellular programs through modulation of signaling dynamics and can be corrupted by disease-causing mutations. Class IA phosphoinositide 3-kinase (PI3K) signaling is critical for normal growth and development and is dysregulated in human disorders such as benign overgrowth syndromes, cancer, primary immune deficiency, and metabolic syndrome. Despite decades of PI3K research, understanding of context-dependent regulation of the PI3K pathway and of the underlying signaling code remains rudimentary. Here, we review current knowledge on context-specific PI3K signaling and how technological advances now make it possible to move from a qualitative to quantitative understanding of this pathway. Insight into how cellular PI3K signaling is encoded or decoded may open new avenues for rational pharmacological targeting of PI3K-associated diseases. The principles of PI3K context-dependent signal encoding and decoding described here are likely applicable to most, if not all, major cell signaling pathways.
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Affiliation(s)
- Ralitsa R Madsen
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6DD, UK.
| | - Bart Vanhaesebroeck
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London WC1E 6DD, UK.
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44
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Teixeira AF, Ten Dijke P, Zhu HJ. On-Target Anti-TGF-β Therapies Are Not Succeeding in Clinical Cancer Treatments: What Are Remaining Challenges? Front Cell Dev Biol 2020. [PMID: 32733895 DOI: 10.3389/fcell.2020.00605.pmid:32733895;pmcid:pmc7360684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Metastasis is the leading cause of death for cancer patients. During cancer progression, the initial detachment of cells from the primary tumor and the later colonization of a secondary organ are characterized as limiting steps for metastasis. Epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) are opposite dynamic multistep processes that enable these critical events in metastasis by altering the phenotype of cancer cells and improving their ability to migrate, invade and seed at distant organs. Among the molecular pathways that promote tumorigenesis in late-stage cancers, transforming growth factor-β (TGF-β) is described as an EMT master inducer by controlling different genes and proteins related to cytoskeleton assembly, cell-cell attachment and extracellular matrix remodeling. Still, despite the successful outcomes of different TGF-β pharmacological inhibitors in cell culture (in vitro) and animal models (in vivo), results in cancer clinical trials are poor or inconsistent at least, highlighting the existence of crucial components in human cancers that have not been properly explored. Here we review most recent findings to provide perspectives bridging the gap between on-target anti-TGF-β therapies in vitro and in pre-clinical models and the poor clinical outcomes in treating cancer patients. Specifically, we focus on (i) the dual roles of TGF-β signaling in cancer metastasis; (ii) dynamic signaling; (iii) functional differences of TGF-β free in solution vs. in exosomes; (iv) the regulatory effects of tumor microenvironment (TME) - particularly by cancer-associated fibroblasts - on TGF-β signaling pathway. Clearly identifying and establishing those missing links may provide strategies to revitalize and clinically improve the efficacy of TGF-β targeted therapies.
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Affiliation(s)
- Adilson Fonseca Teixeira
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Peter Ten Dijke
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Hong-Jian Zhu
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
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45
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Abstract
Spatially distributed signaling molecules, known as morphogens, provide spatial information during development. A host of different morphogens have now been identified, from subcellular gradients through to morphogens that act across a whole embryo. These gradients form over a wide-range of timescales, from seconds to hours, and their time windows for interpretation are also highly variable; the processes of morphogen gradient formation and interpretation are highly dynamic. The morphogen Bicoid (Bcd), present in the early Drosophila embryo, is essential for setting up the future Drosophila body segments. Due to its accessibility for both genetic perturbations and imaging, this system has provided key insights into how precise patterning can occur within a highly dynamic system. Here, we review the temporal scales of Bcd gradient formation and interpretation. In particular, we discuss the quantitative evidence for different models of Bcd gradient formation, outline the time windows for Bcd interpretation, and describe how Bcd temporally adapts its own ability to be interpreted. The utilization of temporal information in morphogen readout may provide crucial inputs to ensure precise spatial patterning, particularly in rapidly developing systems.
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46
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Rogers KW, Müller P. Optogenetic approaches to investigate spatiotemporal signaling during development. Curr Top Dev Biol 2019; 137:37-77. [PMID: 32143750 DOI: 10.1016/bs.ctdb.2019.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Embryogenesis is coordinated by signaling pathways that pattern the developing organism. Many aspects of this process are not fully understood, including how signaling molecules spread through embryonic tissues, how signaling amplitude and dynamics are decoded, and how multiple signaling pathways cooperate to pattern the body plan. Optogenetic approaches can be used to address these questions by providing precise experimental control over a variety of biological processes. Here, we review how these strategies have provided new insights into developmental signaling and discuss how they could contribute to future investigations.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany; Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.
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47
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Morgani SM, Hadjantonakis AK. Signaling regulation during gastrulation: Insights from mouse embryos and in vitro systems. Curr Top Dev Biol 2019; 137:391-431. [PMID: 32143751 DOI: 10.1016/bs.ctdb.2019.11.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gastrulation is the process whereby cells exit pluripotency and concomitantly acquire and pattern distinct cell fates. This is driven by the convergence of WNT, BMP, Nodal and FGF signals, which are tightly spatially and temporally controlled, resulting in regional and stage-specific signaling environments. The combination, level and duration of signals that a cell is exposed to, according its position within the embryo and the developmental time window, dictates the fate it will adopt. The key pathways driving gastrulation exhibit complex interactions, which are difficult to disentangle in vivo due to the complexity of manipulating multiple signals in parallel with high spatiotemporal resolution. Thus, our current understanding of the signaling dynamics regulating gastrulation is limited. In vitro stem cell models have been established, which undergo organized cellular differentiation and patterning. These provide amenable, simplified, deconstructed and scalable models of gastrulation. While the foundation of our understanding of gastrulation stems from experiments in embryos, in vitro systems are now beginning to reveal the intricate details of signaling regulation. Here we discuss the current state of knowledge of the role, regulation and dynamic interaction of signaling pathways that drive mouse gastrulation.
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Affiliation(s)
- Sophie M Morgani
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Cambridge, United Kingdom.
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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48
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Hoover KM, Gratz SJ, Qi N, Herrmann KA, Liu Y, Perry-Richardson JJ, Vanderzalm PJ, O'Connor-Giles KM, Broihier HT. The calcium channel subunit α 2δ-3 organizes synapses via an activity-dependent and autocrine BMP signaling pathway. Nat Commun 2019; 10:5575. [PMID: 31811118 PMCID: PMC6898181 DOI: 10.1038/s41467-019-13165-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/23/2019] [Indexed: 12/17/2022] Open
Abstract
Synapses are highly specialized for neurotransmitter signaling, yet activity-dependent growth factor release also plays critical roles at synapses. While efficient neurotransmitter signaling relies on precise apposition of release sites and neurotransmitter receptors, molecular mechanisms enabling high-fidelity growth factor signaling within the synaptic microenvironment remain obscure. Here we show that the auxiliary calcium channel subunit α2δ-3 promotes the function of an activity-dependent autocrine Bone Morphogenetic Protein (BMP) signaling pathway at the Drosophila neuromuscular junction (NMJ). α2δ proteins have conserved synaptogenic activity, although how they execute this function has remained elusive. We find that α2δ-3 provides an extracellular scaffold for an autocrine BMP signal, suggesting a mechanistic framework for understanding α2δ's conserved role in synapse organization. We further establish a transcriptional requirement for activity-dependent, autocrine BMP signaling in determining synapse density, structure, and function. We propose that activity-dependent, autocrine signals provide neurons with continuous feedback on their activity state for modulating both synapse structure and function.
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Affiliation(s)
- Kendall M Hoover
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Scott J Gratz
- Department of Neuroscience, Brown University, Providence, RI, 02912, USA
| | - Nova Qi
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Kelsey A Herrmann
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Yizhou Liu
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jahci J Perry-Richardson
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Pamela J Vanderzalm
- Department of Biology, John Carroll University, University Heights, OH, 44118, USA
| | | | - Heather T Broihier
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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49
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Karamched BR, Ott W, Timofeyev I, Alnahhas RN, Bennett MR, Josić K. Moran Model of Spatial Alignment in Microbial Colonies. PHYSICA D. NONLINEAR PHENOMENA 2019; 395:1-6. [PMID: 31889737 PMCID: PMC6936756 DOI: 10.1016/j.physd.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We describe a spatial Moran model that captures mechanical interactions and directional growth in spatially extended populations. The model is analytically tractable and completely solvable under a mean-field approximation and can elucidate the mechanisms that drive the formation of population-level patterns. As an example we model a population of E. coli growing in a rectangular microfluidic trap. We show that spatial patterns can arise as a result of a tug-of-war between boundary effects and growth rate modulations due to cell-cell interactions: Cells align parallel to the long side of the trap when boundary effects dominate. However, when cell-cell interactions exceed a critical value, cells align orthogonally to the trap's long side. This modeling approach and analysis can be extended to directionally-growing cells in a variety of domains to provide insight into how local and global interactions shape collective behavior.
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Affiliation(s)
- B R Karamched
- Department of Mathematics, University of Houston, Houston, Texas 77004, USA
| | - W Ott
- Department of Mathematics, University of Houston, Houston, Texas 77004, USA
| | - I Timofeyev
- Department of Mathematics, University of Houston, Houston, Texas 77004, USA
| | - R N Alnahhas
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - M R Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - K Josić
- Department of Mathematics, University of Houston, Houston, Texas 77004, USA
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
- Department of Biosciences, University of Houston, Houston, Texas 77004, USA
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50
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Sonnen KF, Merten CA. Microfluidics as an Emerging Precision Tool in Developmental Biology. Dev Cell 2019; 48:293-311. [PMID: 30753835 DOI: 10.1016/j.devcel.2019.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/13/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022]
Abstract
Microfluidics has become a precision tool in modern biology. It enables omics data to be obtained from individual cells, as compared to averaged signals from cell populations, and it allows manipulation of biological specimens in entirely new ways. Cells and organisms can be perturbed at extraordinary spatiotemporal resolution, revealing mechanistic insights that would otherwise remain hidden. In this perspective article, we discuss the current and future impact of microfluidic technology in the field of developmental biology. In addition, we provide detailed information on how to start using this technology even without prior experience.
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Affiliation(s)
| | - Christoph A Merten
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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