1
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Chew YH, Marucci L. Mechanistic Model-Driven Biodesign in Mammalian Synthetic Biology. Methods Mol Biol 2024; 2774:71-84. [PMID: 38441759 DOI: 10.1007/978-1-0716-3718-0_6] [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: 03/07/2024]
Abstract
Mathematical modeling plays a vital role in mammalian synthetic biology by providing a framework to design and optimize design circuits and engineered bioprocesses, predict their behavior, and guide experimental design. Here, we review recent models used in the literature, considering mathematical frameworks at the molecular, cellular, and system levels. We report key challenges in the field and discuss opportunities for genome-scale models, machine learning, and cybergenetics to expand the capabilities of model-driven mammalian cell biodesign.
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Affiliation(s)
- Yin Hoon Chew
- School of Mathematics, University of Birmingham, Birmingham, UK
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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2
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Oguma T, Takigawa-Imamura H, Shinoda T, Ogura S, Uemura A, Miyata T, Maini PK, Miura T. Analyzing the effect of cell rearrangement on Delta-Notch pattern formation. Phys Rev E 2023; 107:064404. [PMID: 37464594 DOI: 10.1103/physreve.107.064404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 04/24/2023] [Indexed: 07/20/2023]
Abstract
The Delta-Notch system plays a vital role in many areas of biology and typically forms a salt and pepper pattern in which cells strongly expressing Delta and cells strongly expressing Notch are alternately aligned via lateral inhibition. In this study, we consider cell rearrangement events, such as cell mixing and proliferation, that alter the spatial structure itself and affect the pattern dynamics. We model cell rearrangement events by a Poisson process and analyze the model while preserving the discrete properties of the spatial structure. We investigate the effects of the intermittent perturbations arising from these cell rearrangement events on the discrete spatial structure itself in the context of pattern formation and by using an analytical approach, coupled with numerical simulation. We find that the homogeneous expression pattern is stabilized if the frequency of cell rearrangement events is sufficiently large. We analytically obtain the balanced frequencies of the cell rearrangement events where the decrease of the pattern amplitude, as a result of cell rearrangement, is balanced by the increase in amplitude due to the Delta-Notch interaction dynamics. Our framework, while applied here to the specific case of the Delta-Notch system, is applicable more widely to other pattern formation mechanisms.
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Affiliation(s)
- Toshiki Oguma
- Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | | | - Tomoyasu Shinoda
- Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shuntaro Ogura
- Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Akiyoshi Uemura
- Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Takaki Miyata
- Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, Oxford OX2 6GG, United Kingdom
| | - Takashi Miura
- Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
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3
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Hartmann J, Mayor R. Self-organized collective cell behaviors as design principles for synthetic developmental biology. Semin Cell Dev Biol 2023; 141:63-73. [PMID: 35450765 DOI: 10.1016/j.semcdb.2022.04.009] [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: 01/23/2022] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
Abstract
Over the past two decades, molecular cell biology has graduated from a mostly analytic science to one with substantial synthetic capability. This success is built on a deep understanding of the structure and function of biomolecules and molecular mechanisms. For synthetic biology to achieve similar success at the scale of tissues and organs, an equally deep understanding of the principles of development is required. Here, we review some of the central concepts and recent progress in tissue patterning, morphogenesis and collective cell migration and discuss their value for synthetic developmental biology, emphasizing in particular the power of (guided) self-organization and the role of theoretical advances in making developmental insights applicable in synthesis.
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Affiliation(s)
- Jonas Hartmann
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Roberto Mayor
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
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4
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Sivakumar N, Warner HV, Peirce SM, Lazzara MJ. A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion. PLoS Comput Biol 2022; 18:e1010701. [PMID: 36441822 PMCID: PMC9747056 DOI: 10.1371/journal.pcbi.1010701] [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: 10/08/2021] [Revised: 12/13/2022] [Accepted: 11/01/2022] [Indexed: 11/29/2022] Open
Abstract
Physiological and pathological processes including embryogenesis and tumorigenesis rely on the ability of individual cells to work collectively to form multicell patterns. In these heterogeneous multicell systems, cell-cell signaling induces differential adhesion between cells that leads to tissue-level patterning. However, the sensitivity of pattern formation to changes in the strengths of signaling or cell adhesion processes is not well understood. Prior work has explored these issues using synthetically engineered heterogeneous multicell spheroid systems, in which cell subpopulations engage in bidirectional intercellular signaling to regulate the expression of different cadherins. While engineered cell systems provide excellent experimental tools to observe pattern formation in cell populations, computational models of these systems may be leveraged to explore more systematically how specific combinations of signaling and adhesion parameters can drive the emergence of unique patterns. We developed and validated two- and three-dimensional agent-based models (ABMs) of spheroid patterning for previously described cells engineered with a bidirectional signaling circuit that regulates N- and P-cadherin expression. Systematic exploration of model predictions, some of which were experimentally validated, revealed how cell seeding parameters, the order of signaling events, probabilities of induced cadherin expression, and homotypic adhesion strengths affect pattern formation. Unsupervised clustering was also used to map combinations of signaling and adhesion parameters to these unique spheroid patterns predicted by the ABM. Finally, we demonstrated how the model may be deployed to design new synthetic cell signaling circuits based on a desired final multicell pattern.
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Affiliation(s)
- Nikita Sivakumar
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Helen V. Warner
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Shayn M. Peirce
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Matthew J. Lazzara
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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5
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Sánchez-Iranzo H, Halavatyi A, Diz-Muñoz A. Strength of interactions in the Notch gene regulatory network determines patterning and fate in the notochord. eLife 2022; 11:75429. [PMID: 35658971 PMCID: PMC9170247 DOI: 10.7554/elife.75429] [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: 11/11/2021] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Development of multicellular organisms requires the generation of gene expression patterns that determines cell fate and organ shape. Groups of genetic interactions known as Gene Regulatory Networks (GRNs) play a key role in the generation of such patterns. However, how the topology and parameters of GRNs determine patterning in vivo remains unclear due to the complexity of most experimental systems. To address this, we use the zebrafish notochord, an organ where coin-shaped precursor cells are initially arranged in a simple unidimensional geometry. These cells then differentiate into vacuolated and sheath cells. Using newly developed transgenic tools together with in vivo imaging, we identify jag1a and her6/her9 as the main components of a Notch GRN that generates a lateral inhibition pattern and determines cell fate. Making use of this experimental system and mathematical modeling we show that lateral inhibition patterning is promoted when ligand-receptor interactions are stronger within the same cell than in neighboring cells. Altogether, we establish the zebrafish notochord as an experimental system to study pattern generation, and identify and characterize how the properties of GRNs determine self-organization of gene patterning and cell fate.
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Affiliation(s)
- Héctor Sánchez-Iranzo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alba Diz-Muñoz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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6
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Ma Y, Budde MW, Mayalu MN, Zhu J, Lu AC, Murray RM, Elowitz MB. Synthetic mammalian signaling circuits for robust cell population control. Cell 2022; 185:967-979.e12. [PMID: 35235768 PMCID: PMC8995209 DOI: 10.1016/j.cell.2022.01.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/18/2021] [Accepted: 01/28/2022] [Indexed: 01/23/2023]
Abstract
In multicellular organisms, cells actively sense and control their own population density. Synthetic mammalian quorum-sensing circuits could provide insight into principles of population control and extend cell therapies. However, a key challenge is reducing their inherent sensitivity to "cheater" mutations that evade control. Here, we repurposed the plant hormone auxin to enable orthogonal mammalian cell-cell communication and quorum sensing. We designed a paradoxical population control circuit, termed "Paradaux," in which auxin stimulates and inhibits net cell growth at different concentrations. This circuit limited population size over extended timescales of up to 42 days of continuous culture. By contrast, when operating in a non-paradoxical regime, population control became more susceptible to mutational escape. These results establish auxin as a versatile "private" communication system and demonstrate that paradoxical circuit architectures can provide robust population control.
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Affiliation(s)
- Yitong Ma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark W Budde
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Primordium Labs, Arcadia, CA 91006, USA
| | - Michaëlle N Mayalu
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Junqin Zhu
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Andrew C Lu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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7
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Abstract
Increased control of biological growth and form is an essential gateway to transformative medical advances. Repairing of birth defects, restoring lost or damaged organs, normalizing tumors, all depend on understanding how cells cooperate to make specific, functional large-scale structures. Despite advances in molecular genetics, significant gaps remain in our understanding of the meso-scale rules of morphogenesis. An engineering approach to this problem is the creation of novel synthetic living forms, greatly extending available model systems beyond evolved plant and animal lineages. Here, we review recent advances in the emerging field of synthetic morphogenesis, the bioengineering of novel multicellular living bodies. Emphasizing emergent self-organization, tissue-level guided self-assembly, and active functionality, this work is the essential next generation of synthetic biology. Aside from useful living machines for specific functions, the rational design and analysis of new, coherent anatomies will greatly increase our understanding of foundational questions in evolutionary developmental and cell biology.
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Affiliation(s)
- Mo R. Ebrahimkhani
- Department of Pathology, School of Medicine, University of Pittsburgh, A809B Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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8
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Ho C, Morsut L. Novel synthetic biology approaches for developmental systems. Stem Cell Reports 2021; 16:1051-1064. [PMID: 33979593 PMCID: PMC8185972 DOI: 10.1016/j.stemcr.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Recently, developmental systems are investigated with increasing technological power. Still, open questions remain, especially concerning self-organization capacity and its control. Here, we present three areas where synthetic biology tools are used in top-down and bottom-up approaches for studying and constructing developmental systems. First, we discuss how synthetic biology tools can improve stem cell-based organoid models. Second, we discuss recent studies employing user-defined perturbations to study embryonic patterning in model species. Third, we present "toy models" of patterning and morphogenesis using synthetic genetic circuits in non-developmental systems. Finally, we discuss how these tools and approaches can specifically benefit the field of embryo models.
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Affiliation(s)
- Christine Ho
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Leonardo Morsut
- Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA.
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9
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Gaut NJ, Adamala KP. Reconstituting Natural Cell Elements in Synthetic Cells. Adv Biol (Weinh) 2021; 5:e2000188. [DOI: 10.1002/adbi.202000188] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/05/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nathaniel J. Gaut
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
| | - Katarzyna P. Adamala
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
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10
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Yang ZJ, Yu ZY, Cai YM, Du RR, Cai L. Engineering of an enhanced synthetic Notch receptor by reducing ligand-independent activation. Commun Biol 2020; 3:116. [PMID: 32170210 PMCID: PMC7069970 DOI: 10.1038/s42003-020-0848-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/20/2020] [Indexed: 11/17/2022] Open
Abstract
Notch signaling is highly conserved in most animals and plays critical roles during neurogenesis as well as embryonic development. Synthetic Notch-based systems, modeled from Notch receptors, have been developed to sense and respond to a specific extracellular signal. Recent advancement of synNotch has shown promise for future use in cellular engineering to treat cancers. However, synNotch from Morsut et al. (2016) has a high level of ligand-independent activation, which limits its application. Here we show that adding an intracellular hydrophobic sequence (QHGQLWF, named as RAM7) present in native Notch, significantly reduced ligand-independent activation. Our enhanced synthetic Notch receptor (esNotch) demonstrates up to a 14.6-fold reduction in ligand-independent activation, without affecting its antigen-induced activation efficiency. Our work improves a previously reported transmembrane receptor and provides a powerful tool to develop better transmembrane signaling transduction modules for further advancement of eukaryotic synthetic biology.
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Affiliation(s)
- Zi-Jie Yang
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zi-Yan Yu
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yi-Ming Cai
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China
- Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, 77225, USA
| | - Rong-Rong Du
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China
| | - Liang Cai
- Department of Biochemistry, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China.
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.
- The Center for Faculty Development of Fudan University, Shanghai, China.
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11
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Santorelli M, Lam C, Morsut L. Synthetic development: building mammalian multicellular structures with artificial genetic programs. Curr Opin Biotechnol 2019; 59:130-140. [PMID: 31128430 PMCID: PMC6778502 DOI: 10.1016/j.copbio.2019.03.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/08/2019] [Accepted: 03/24/2019] [Indexed: 12/28/2022]
Abstract
Synthetic biology efforts began in simple single-cell systems, which were relatively easy to manipulate genetically (Cameron et al., 2014). The field grew exponentially in the last two decades, and one of the latest frontiers are synthetic developmental programs for multicellular mammalian systems (Black et al., 2017; Wieland and Fussenegger, 2012) to genetically control features such as patterning or morphogenesis. These programs rely on engineered cell-cell communications, multicellular gene regulatory networks and effector genes. Here, we contextualize the first of these synthetic developmental programs, examine molecular and computational tools that can be used to generate next generation versions, and present the general logic that underpins these approaches. These advances are exciting as they represent a novel way to address both control and understanding in the field of developmental biology and tissue development (Elowitz and Lim, 2010; Velazquez et al., 2018; White et al., 2018; Morsut, 2017). This field is just at the beginning, and it promises to be of major interest in the upcoming years of biomedical research.
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Affiliation(s)
- Marco Santorelli
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States
| | - Calvin Lam
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States
| | - Leonardo Morsut
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, United States; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, United States.
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12
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Kojima R, Fussenegger M. Synthetic Biology: Engineering Mammalian Cells To Control Cell-to-Cell Communication at Will. Chembiochem 2019; 20:994-1002. [PMID: 30589185 DOI: 10.1002/cbic.201800682] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Indexed: 12/12/2022]
Abstract
Cell-to-cell communication plays a key role in the regulation of many natural biological processes. Recent advances in mammalian synthetic biology are making it possible to rationally engineer cell-to-cell communication for therapeutic and other purposes. Here, we review state-of-the-art engineering principles to control cell-to-cell communication, focusing on communication between mammalian cells with diffusible factors (e.g., small molecules or exosomes) or direct cell contact, and on interkingdom communication between mammalian cells and bacteria. Potential applications include construction of artificial tissues able to perform complex computations, sophisticated cell-based cancer therapies, use of mammalian cells as a new class of cargo delivery modality, development of design principles to control pattern formation of cell populations, and treatment of infectious diseases. We also discuss the challenges facing practical applications, and possible enabling technologies to overcome them.
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Affiliation(s)
- Ryosuke Kojima
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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13
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Rewiring T-cell responses to soluble factors with chimeric antigen receptors. Nat Chem Biol 2018; 14:317-324. [PMID: 29377003 PMCID: PMC6035732 DOI: 10.1038/nchembio.2565] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/12/2017] [Indexed: 12/22/2022]
Abstract
Chimeric antigen receptor (CAR)-expressing T cells targeting surface-bound tumor antigens have yielded promising clinical outcomes, with two CD19 CAR-T cell therapies recently receiving FDA approval for the treatment of B-cell malignancies. The adoption of CARs for the recognition of soluble ligands, a distinct class of biomarkers in physiology and disease, could considerably broaden the utility of CARs in disease treatment. In this study, we demonstrate that CAR-T cells can be engineered to respond robustly to diverse soluble ligands, including the CD19 ectodomain, GFP variants, and transforming growth factor beta (TGF-β). We additionally show that CAR signaling in response to soluble ligands relies on ligand-mediated CAR dimerization and that CAR responsiveness to soluble ligands can be fine-tuned by adjusting the mechanical coupling between the CAR's ligand-binding and signaling domains. Our results support a role for mechanotransduction in CAR signaling and demonstrate an approach for systematically engineering immune-cell responses to soluble, extracellular ligands.
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14
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Luna-Escalante JC, Formosa-Jordan P, Ibañes M. Redundancy and cooperation in Notch intercellular signaling. Development 2018; 145:dev.154807. [PMID: 29242285 DOI: 10.1242/dev.154807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022]
Abstract
During metazoan development, Notch signaling drives spatially coordinated differentiation by establishing communication between adjacent cells. This occurs through either lateral inhibition, in which adjacent cells acquire distinct fates, or lateral induction, in which all cells become equivalent. Notch signaling is commonly activated by several distinct ligands, each of which drives signaling with a different efficiency upon binding to the Notch receptor of adjacent cells. Moreover, these ligands can also be distinctly regulated by Notch signaling. Under such complex circumstances, the overall spatial coordination becomes elusive. Here, we address this issue through both mathematical and computational analyses. Our results show that when two ligands have distinct efficiencies and compete for the same Notch receptor, they cooperate to drive new signaling states, thereby conferring additional robustness and evolvability to Notch signaling. Counterintuitively, whereas antagonistically regulated ligands cooperate to drive and enhance the response that is expected from the more efficient ligand, equivalently regulated ligands coordinate emergent spatial responses that are dependent on both ligands. Our study highlights the importance of ligand efficiency in multi-ligand scenarios, and can explain previously reported complex phenotypes.
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Affiliation(s)
- Juan C Luna-Escalante
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona 08028, Spain
| | - Pau Formosa-Jordan
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona 08028, Spain
| | - Marta Ibañes
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona 08028, Spain .,Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona 08028, Spain
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15
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Jiménez A, Cotterell J, Munteanu A, Sharpe J. A spectrum of modularity in multi-functional gene circuits. Mol Syst Biol 2017; 13:925. [PMID: 28455348 PMCID: PMC5408781 DOI: 10.15252/msb.20167347] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A major challenge in systems biology is to understand the relationship between a circuit's structure and its function, but how is this relationship affected if the circuit must perform multiple distinct functions within the same organism? In particular, to what extent do multi‐functional circuits contain modules which reflect the different functions? Here, we computationally survey a range of bi‐functional circuits which show no simple structural modularity: They can switch between two qualitatively distinct functions, while both functions depend on all genes of the circuit. Our analysis reveals two distinct classes: hybrid circuits which overlay two simpler mono‐functional sub‐circuits within their circuitry, and emergent circuits, which do not. In this second class, the bi‐functionality emerges from more complex designs which are not fully decomposable into distinct modules and are consequently less intuitive to predict or understand. These non‐intuitive emergent circuits are just as robust as their hybrid counterparts, and we therefore suggest that the common bias toward studying modular systems may hinder our understanding of real biological circuits.
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Affiliation(s)
- Alba Jiménez
- EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Cotterell
- EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andreea Munteanu
- EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Sharpe
- EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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16
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Mathur M, Xiang JS, Smolke CD. Mammalian synthetic biology for studying the cell. J Cell Biol 2016; 216:73-82. [PMID: 27932576 PMCID: PMC5223614 DOI: 10.1083/jcb.201611002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/25/2022] Open
Abstract
Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology.
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Affiliation(s)
- Melina Mathur
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Joy S Xiang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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17
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Abstract
Throughout biology, function is intimately linked with form. Across scales ranging from subcellular to multiorganismal, the identity and organization of a biological structure's subunits dictate its properties. The field of molecular morphogenesis has traditionally been concerned with describing these links, decoding the molecular mechanisms that give rise to the shape and structure of cells, tissues, organs, and organisms. Recent advances in synthetic biology promise unprecedented control over these molecular mechanisms; this opens the path to not just probing morphogenesis but directing it. This review explores several frontiers in the nascent field of synthetic morphogenesis, including programmable tissues and organs, synthetic biomaterials and programmable matter, and engineering complex morphogenic systems de novo. We will discuss each frontier's objectives, current approaches, constraints and challenges, and future potential.
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Affiliation(s)
- Brian P Teague
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Patrick Guye
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Ron Weiss
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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Borek B, Hasty J, Tsimring L. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules. PLoS One 2016; 11:e0153679. [PMID: 27148743 PMCID: PMC4858293 DOI: 10.1371/journal.pone.0153679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/01/2016] [Indexed: 01/30/2023] Open
Abstract
The Turing instability was proposed more than six decades ago as a mechanism leading to spatial patterning, but it has yet to be exploited in a synthetic biology setting. Here we characterize the Turing instability in a specific gene circuit that can be implemented in vitro or in populations of clonal cells producing short-range activator N-Acyl homoserine lactone (AHL) and long-range inhibitor hydrogen peroxide (H2O2) gas. Slowing the production rate of the AHL-degrading enzyme, AiiA, generates stable fixed states, limit cycle oscillations and Turing patterns. Further tuning of signaling parameters determines local robustness and controls the range of unstable wavenumbers in the patterning regime. These findings provide a roadmap for optimizing spatial patterns of gene expression based on familiar quorum and gas sensitive E. coli promoters. The circuit design and predictions may be useful for (re)programming spatial dynamics in synthetic and natural gene expression systems.
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Affiliation(s)
- Bartłomiej Borek
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
| | - Jeff Hasty
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0412, United States of America
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0116, United States of America
| | - Lev Tsimring
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
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19
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Morsut L, Roybal KT, Xiong X, Gordley RM, Coyle SM, Thomson M, Lim WA. Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors. Cell 2016; 164:780-91. [PMID: 26830878 DOI: 10.1016/j.cell.2016.01.012] [Citation(s) in RCA: 563] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/04/2016] [Accepted: 01/08/2016] [Indexed: 01/12/2023]
Abstract
The Notch protein is one of the most mechanistically direct transmembrane receptors-the intracellular domain contains a transcriptional regulator that is released from the membrane when engagement of the cognate extracellular ligand induces intramembrane proteolysis. We find that chimeric forms of Notch, in which both the extracellular sensor module and the intracellular transcriptional module are replaced with heterologous protein domains, can serve as a general platform for generating novel cell-cell contact signaling pathways. Synthetic Notch (synNotch) pathways can drive user-defined functional responses in diverse mammalian cell types. Because individual synNotch pathways do not share common signaling intermediates, the pathways are functionally orthogonal. Thus, multiple synNotch receptors can be used in the same cell to achieve combinatorial integration of environmental cues, including Boolean response programs, multi-cellular signaling cascades, and self-organized cellular patterns. SynNotch receptors provide extraordinary flexibility in engineering cells with customized sensing/response behaviors to user-specified extracellular cues.
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Affiliation(s)
- Leonardo Morsut
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | - Kole T Roybal
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | - Xin Xiong
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | - Russell M Gordley
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | - Scott M Coyle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | - Matthew Thomson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute.
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20
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Yaffe MB, Gough NR, VanHook AM. Science Signaling
Podcast for 5 January 2016: New directions in signaling research. Sci Signal 2016. [DOI: 10.1126/scisignal.aaf1448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Science Signaling
editors discuss the current state of signal transduction research and the journal's place in this dynamic landscape.
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Affiliation(s)
- Michael B. Yaffe
- Chief Scientific Editor, Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue, NW, Washington, DC 20005, USA
- David H. Koch Institute for Integrative Cancer Research, The Broad Institute, and the Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nancy R. Gough
- Editor, Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue, NW, Washington, DC 20005, USA
| | - Annalisa M. VanHook
- Web Editor, Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue, NW, Washington, DC 20005, USA
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21
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Kolar K, Wischhusen HM, Müller K, Karlsson M, Weber W, Zurbriggen MD. A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication. BMC SYSTEMS BIOLOGY 2015; 9:97. [PMID: 26714638 PMCID: PMC4696150 DOI: 10.1186/s12918-015-0252-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 12/15/2015] [Indexed: 02/05/2023]
Abstract
Background Multicellular organisms depend on the exchange of information between specialized cells. This communication is often difficult to decipher in its native context, but synthetic biology provides tools to engineer well-defined systems that allow the convenient study and manipulation of intercellular communication networks. Results Here, we present the first mammalian synthetic network for reciprocal cell-cell communication to compute the border between a sender/receiver and a processing cell population. The two populations communicate via L-tryptophan and interleukin-4 to highlight the population border by the production of a fluorescent protein. The sharpness of that visualized edge can be adjusted by modulating key parameters of the network. Conclusions We anticipate that this network will on the one hand be a useful tool to gain deeper insights into the mechanisms of tissue formation in nature and will on the other hand contribute to our ability to engineer artificial tissues. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0252-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katja Kolar
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany
| | - Hanna M Wischhusen
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: DMK GmbH, Head of Quality Assurance, DE-26939, Ovelgönne, Germany
| | - Konrad Müller
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: Novartis Pharma AG, Biologics Process R&D, CH-4002, Basel, Switzerland
| | - Maria Karlsson
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,Present address: Respiratory, Inflammation and Autoimmunity (RIA) iMED, AstraZeneca, SE-431 83, Mölndal, Sweden
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, DE-79104, Freiburg, Germany
| | - Matias D Zurbriggen
- Faculty of Biology, University of Freiburg, DE-79104, Freiburg, Germany. .,Present address: Institute of Synthetic Biology and Cluster of Excellence on Plant Science (CEPLAS), University of Düsseldorf, DE-40225, Düsseldorf, Germany.
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22
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Artificial cell-cell communication as an emerging tool in synthetic biology applications. J Biol Eng 2015; 9:13. [PMID: 26265937 PMCID: PMC4531478 DOI: 10.1186/s13036-015-0011-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/25/2015] [Indexed: 01/14/2023] Open
Abstract
Cell-cell communication is a widespread phenomenon in nature, ranging from bacterial quorum sensing and fungal pheromone communication to cellular crosstalk in multicellular eukaryotes. These communication modes offer the possibility to control the behavior of an entire community by modifying the performance of individual cells in specific ways. Synthetic biology, i.e., the implementation of artificial functions within biological systems, is a promising approach towards the engineering of sophisticated, autonomous devices based on specifically functionalized cells. With the growing complexity of the functions performed by such systems, both the risk of circuit crosstalk and the metabolic burden resulting from the expression of numerous foreign genes are increasing. Therefore, systems based on a single type of cells are no longer feasible. Synthetic biology approaches with multiple subpopulations of specifically functionalized cells, wired by artificial cell-cell communication systems, provide an attractive and powerful alternative. Here we review recent applications of synthetic cell-cell communication systems with a specific focus on recent advances with fungal hosts.
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23
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Matsuda M, Koga M, Woltjen K, Nishida E, Ebisuya M. Synthetic lateral inhibition governs cell-type bifurcation with robust ratios. Nat Commun 2015; 6:6195. [PMID: 25652697 DOI: 10.1038/ncomms7195] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 01/05/2015] [Indexed: 01/20/2023] Open
Abstract
Cell-type diversity in multicellular organisms is created through a series of binary cell fate decisions. Lateral inhibition controlled by Delta-Notch signalling is the core mechanism for the choice of alternative cell types by homogeneous neighbouring cells. Here, we show that cells engineered with a Delta-Notch-dependent lateral inhibition circuit spontaneously bifurcate into Delta-positive and Notch-active cell populations. The synthetic lateral inhibition circuit comprises transcriptional repression of Delta and intracellular feedback of Lunatic fringe (Lfng). The Lfng-feedback subcircuit, even alone, causes the autonomous cell-type bifurcation. Furthermore, the ratio of two cell populations bifurcated by lateral inhibition is reproducible and robust against perturbation. The cell-type ratio is adjustable by the architecture of the lateral inhibition circuit as well as the degree of cell-cell attachment. Thus, the minimum lateral inhibition mechanism between adjacent cells not only serves as a binary cell-type switch of individual cells but also governs the cell-type ratio at the cell-population level.
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Affiliation(s)
- Mitsuhiro Matsuda
- 1] RIKEN Center for Developmental Biology, Kobe 650-0047, Japan [2] Career-Path Promotion Unit for Young Life Scientists, Kyoto University, Kyoto 606-8501, Japan [3] Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Makito Koga
- 1] RIKEN Center for Developmental Biology, Kobe 650-0047, Japan [2] Career-Path Promotion Unit for Young Life Scientists, Kyoto University, Kyoto 606-8501, Japan [3] Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Knut Woltjen
- 1] Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan [2] Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
| | - Eisuke Nishida
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Miki Ebisuya
- 1] RIKEN Center for Developmental Biology, Kobe 650-0047, Japan [2] Career-Path Promotion Unit for Young Life Scientists, Kyoto University, Kyoto 606-8501, Japan [3] Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
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24
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Barcena Menendez D, Senthivel VR, Isalan M. Sender-receiver systems and applying information theory for quantitative synthetic biology. Curr Opin Biotechnol 2015; 31:101-7. [PMID: 25282688 PMCID: PMC4332572 DOI: 10.1016/j.copbio.2014.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/21/2014] [Indexed: 12/31/2022]
Abstract
Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning.
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Affiliation(s)
- Diego Barcena Menendez
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Vivek Raj Senthivel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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25
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A yeast pheromone-based inter-species communication system. Appl Microbiol Biotechnol 2014; 99:1299-308. [PMID: 25331280 DOI: 10.1007/s00253-014-6133-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/01/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
Abstract
We report on a pheromone-based inter-species communication system, allowing for a controlled cell-cell communication between the two species Saccharomyces cerevisiae and Schizosaccharomyces pombe as a proof of principle. It exploits the mating response pathways of the two yeast species employing the pheromones, α- or P-factor, as signaling molecules. The authentic and chimeric pheromone-encoding genes were engineered to code for the P-factor in S. cerevisiae and the α-factor in S. pombe. Upon transformation of the respective constructs, cells were enabled to express the mating pheromone of the opposite species. The supernatant of cultures of S. pombe cells expressing α-factor were able to induce a G1 arrest in the cell cycle, a change in morphology to the typical shmoo effect and expression driven by the pheromone-responsive FIG1 promoter in S. cerevisiae. The supernatant of cultures of S. cerevisiae cells expressing P-factor similarly induced cell cycle arrest in G1, an alteration in morphology typical for mating as well as the activation of the pheromone-responsive promoters of the rep1 and sxa2 genes in a pheromone-hypersensitive reporter strain of S. pombe. Apparently, both heterologous pheromones were correctly processed and secreted in an active form by the cells of the other species. Our data clearly show that the species-specific pheromone systems of yeast species can be exploited for a controlled inter-species communication.
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26
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Petrovic J, Formosa-Jordan P, Luna-Escalante JC, Abelló G, Ibañes M, Neves J, Giraldez F. Ligand-dependent Notch signaling strength orchestrates lateral induction and lateral inhibition in the developing inner ear. Development 2014; 141:2313-24. [PMID: 24821984 DOI: 10.1242/dev.108100] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
During inner ear development, Notch exhibits two modes of operation: lateral induction, which is associated with prosensory specification, and lateral inhibition, which is involved in hair cell determination. These mechanisms depend respectively on two different ligands, jagged 1 (Jag1) and delta 1 (Dl1), that rely on a common signaling cascade initiated after Notch activation. In the chicken otocyst, expression of Jag1 and the Notch target Hey1 correlates well with lateral induction, whereas both Jag1 and Dl1 are expressed during lateral inhibition, as are Notch targets Hey1 and Hes5. Here, we show that Jag1 drives lower levels of Notch activity than Dl1, which results in the differential expression of Hey1 and Hes5. In addition, Jag1 interferes with the ability of Dl1 to elicit high levels of Notch activity. Modeling the sensory epithelium when the two ligands are expressed together shows that ligand regulation, differential signaling strength and ligand competition are crucial to allow the two modes of operation and for establishing the alternate pattern of hair cells and supporting cells. Jag1, while driving lateral induction on its own, facilitates patterning by lateral inhibition in the presence of Dl1. This novel behavior emerges from Jag1 acting as a competitive inhibitor of Dl1 for Notch signaling. Both modeling and experiments show that hair cell patterning is very robust. The model suggests that autoactivation of proneural factor Atoh1, upstream of Dl1, is a fundamental component for robustness. The results stress the importance of the levels of Notch signaling and ligand competition for Notch function.
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Affiliation(s)
- Jelena Petrovic
- Developmental Biology Unit, CEXS, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain
| | - Pau Formosa-Jordan
- Departament d'Estructura i Constituents de la Matèria, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Juan C Luna-Escalante
- Departament d'Estructura i Constituents de la Matèria, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Gina Abelló
- Developmental Biology Unit, CEXS, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain
| | - Marta Ibañes
- Departament d'Estructura i Constituents de la Matèria, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Joana Neves
- Developmental Biology Unit, CEXS, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain
| | - Fernando Giraldez
- Developmental Biology Unit, CEXS, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Spain
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27
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Abstract
Theoretical and computational approaches for understanding different aspects of Notch signaling and Notch dependent patterning are gaining popularity in recent years. These in silico methodologies can provide dynamic insights that are often not intuitive and may help guide experiments aimed at elucidating these processes. This chapter is an introductory tutorial intended to allow someone with basic mathematical and computational knowledge to explore new mathematical models of Notch-mediated processes and perform numerical simulations of these models. In particular, we explain how to define and simulate models of lateral inhibition patterning processes. We provide a Matlab code for simulating various lateral inhibition models in a simple and intuitive manner, and show how to present the results from the computational models. This code can be used as a starting point for exploring more specific models that include additional aspects of the Notch pathway and its regulation.
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Affiliation(s)
- Pau Formosa-Jordan
- Department of Structure and Constituents of Matter, Physics, University of Barcelona, Martí i Franquès 1, Barcelona, 08028, Spain
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28
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Immune signal transduction in leishmaniasis from natural to artificial systems: Role of feedback loop insertion. Biochim Biophys Acta Gen Subj 2014; 1840:71-9. [DOI: 10.1016/j.bbagen.2013.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/31/2013] [Accepted: 08/23/2013] [Indexed: 12/17/2022]
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29
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Blagovic K, Gong ES, Milano DF, Natividad RJ, Asthagiri AR. Engineering cell-cell signaling. Curr Opin Biotechnol 2013; 24:940-947. [PMID: 23856592 DOI: 10.1016/j.copbio.2013.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/25/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
Juxtacrine cell-cell signaling mediated by the direct interaction of adjoining mammalian cells is arguably the mode of cell communication that is most recalcitrant to engineering. Overcoming this challenge is crucial for progress in biomedical applications, such as tissue engineering, regenerative medicine, immune system engineering and therapeutic design. Here, we describe the significant advances that have been made in developing synthetic platforms (materials and devices) and synthetic cells (cell surface engineering and synthetic gene circuits) to modulate juxtacrine cell-cell signaling. In addition, significant progress has been made in elucidating design rules and strategies to modulate juxtacrine signaling on the basis of quantitative, engineering analysis of the mechanical and regulatory role of juxtacrine signals in the context of other cues and physical constraints in the microenvironment. These advances in engineering juxtacrine signaling lay a strong foundation for an integrative approach to utilize synthetic cells, advanced 'chassis' and predictive modeling to engineer the form and function of living tissues.
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Affiliation(s)
- Katarina Blagovic
- Department of Chemical Engineering, Northeastern University, Boston, MA
| | - Emily S Gong
- Department of Chemical Engineering, Northeastern University, Boston, MA
| | - Daniel F Milano
- Department of Chemical Engineering, Northeastern University, Boston, MA
| | | | - Anand R Asthagiri
- Department of Chemical Engineering, Northeastern University, Boston, MA
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30
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Simakov DSA, Pismen LM. Discrete model of periodic pattern formation through a combined autocrine–juxtacrine cell signaling. Phys Biol 2013; 10:046001. [DOI: 10.1088/1478-3975/10/4/046001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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31
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Engineered cell-cell communication and its applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 146:97-121. [PMID: 24002441 DOI: 10.1007/10_2013_249] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past several decades, biologists have become more appreciative of the fundamental role of intercellular communication in natural systems spanning prokaryotic biofilms to eukaryotic developmental systems and neurological networks. From an engineering perspective, the use of cell-cell communication provides an opportunity to engineer more complex and robust functions using cellular components. Indeed, this strategy has been adopted in synthetic biology in the creation of diverse gene circuits that program spatiotemporal dynamics in one or multiple populations. Gene circuits such as these may offer insights regarding basic biological questions and motifs or serve as a basis for novel applications.
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32
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33
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Neves J, Abelló G, Petrovic J, Giraldez F. Patterning and cell fate in the inner ear: a case for Notch in the chicken embryo. Dev Growth Differ 2012; 55:96-112. [PMID: 23252974 DOI: 10.1111/dgd.12016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 10/09/2012] [Accepted: 10/09/2012] [Indexed: 01/08/2023]
Abstract
The development of the inner ear provides a beautiful example of one basic problem in development, that is, to understand how different cell types are generated at specific times and domains throughout embryonic life. The functional unit of the inner ear consists of hair cells, supporting cells and neurons, all deriving from progenitor cells located in the neurosensory competent domain of the otic placode. Throughout development, the otic placode resolves into the complex inner ear labyrinth, which holds the auditory and vestibular sensory organs that are innervated in a highly specific manner. How does the early competent domain of the otic placode give rise to the diverse specialized cell types of the different sensory organs of the inner ear? We review here our current understanding on the role of Notch signaling in coupling patterning and cell fate determination during inner ear development, with a particular emphasis on contributions from the chicken embryo as a model organism. We discuss further the question of how these two processes rely on two modes of operation of the Notch signaling pathway named lateral induction and lateral inhibition.
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Affiliation(s)
- Joana Neves
- CEXS, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
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34
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Abstract
Tissue-scale organization emerges from the action of sophisticated multiscale developmental programs. But the design rules for composing elementary signaling and information processing modules into such functional systems and for integrating them into the noisy and convoluted living context remain incompletely addressed. The construction of a synthetic gene circuit encoding contact-dependent signal propagation demonstrates one broadly applicable approach to this problem. The circuit comprises orthogonal signaling through the Delta ligand and the Notch receptor, multicellular positive feedback, and transcriptional signal amplification. Positive feedback and contact signaling proved sufficient for bistability and signal propagation across a population of mammalian cells, but only when combined with signal amplification. Thus, construction and characterization of synthetic gene circuits have made it possible to establish mechanistic sufficiency and the minimal requirements for the phenotype of interest.
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Affiliation(s)
- Adrian L Slusarczyk
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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