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Zhang T, Liu D, Zhang Y, Chen L, Zhang W, Sun T. Biomedical engineering utilizing living photosynthetic cyanobacteria and microalgae: Current status and future prospects. Mater Today Bio 2024; 27:101154. [PMID: 39113912 PMCID: PMC11304071 DOI: 10.1016/j.mtbio.2024.101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/24/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Cyanobacteria are the only prokaryotes capable of performing oxygenic photosynthesis on Earth. Besides their traditional roles serving as primary producers, cyanobacteria also synthesize abundant secondary metabolites including carotenoids, alkaloids, peptides, which have been reported to possess medicinal potentials. More importantly, the advancement of synthetic biology technology has further expanded their potential biomedical applications especially using living/engineered cyanobacteria, providing promising and attractive strategies for future disease treatments. To improve the understanding and to facilitate future applications, this review aims to discuss the current status and future prospects of cyanobacterial-based biomedical engineering. Firstly, specific properties of cyanobacteria related with biomedical applications like their natural products of bioactive compounds and heavy metal adsorption were concluded. Subsequently, based on these properties of cyanobacteria, we discussed the progress of their applications in various disease models like hypoxia microenvironment alleviation, wound healing, drug delivery, and so on. Finally, the future prospects including further exploration of cyanobacteria secondary metabolites, the integration of bioactive compounds synthesized by cyanobacteria in situ with medical diagnosis and treatment, and the optimization of in vivo application were critically presented. The review will promote the studies related with cyanobacteria-based biomedical engineering and its practical application in clinical trials in the future.
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Affiliation(s)
- Tong Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Dailin Liu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Yingying Zhang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
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2
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Gómez-Felipe A, Branchini E, Wang B, Marconi M, Bertrand-Rakusová H, Stan T, Burkiewicz J, de Folter S, Routier-Kierzkowska AL, Wabnik K, Kierzkowski D. Two orthogonal differentiation gradients locally coordinate fruit morphogenesis. Nat Commun 2024; 15:2912. [PMID: 38575617 PMCID: PMC10995178 DOI: 10.1038/s41467-024-47325-1] [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: 01/18/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Morphogenesis requires the coordination of cellular behaviors along developmental axes. In plants, gradients of growth and differentiation are typically established along a single longitudinal primordium axis to control global organ shape. Yet, it remains unclear how these gradients are locally adjusted to regulate the formation of complex organs that consist of diverse tissue types. Here we combine quantitative live imaging at cellular resolution with genetics, and chemical treatments to understand the formation of Arabidopsis thaliana female reproductive organ (gynoecium). We show that, contrary to other aerial organs, gynoecium shape is determined by two orthogonal, time-shifted differentiation gradients. An early mediolateral gradient controls valve morphogenesis while a late, longitudinal gradient regulates style differentiation. Local, tissue-dependent action of these gradients serves to fine-tune the common developmental program governing organ morphogenesis to ensure the specialized function of the gynoecium.
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Affiliation(s)
- Andrea Gómez-Felipe
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Elvis Branchini
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Binghan Wang
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Marco Marconi
- centro De Biotecnología Y Genómica De Plantas (Universidad Politécnica De Madrid (Upm), Instituto Nacional De Investigación Y Tecnología Agraria Y Alimentaria (Inia, Csic), Campus De Montegancedo, Pozuelo De Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Hana Bertrand-Rakusová
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Teodora Stan
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Jérôme Burkiewicz
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), CP, 36824, Irapuato, Mexico
| | - Anne-Lise Routier-Kierzkowska
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada
| | - Krzysztof Wabnik
- centro De Biotecnología Y Genómica De Plantas (Universidad Politécnica De Madrid (Upm), Instituto Nacional De Investigación Y Tecnología Agraria Y Alimentaria (Inia, Csic), Campus De Montegancedo, Pozuelo De Alarcón, 28223, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Daniel Kierzkowski
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montréal, QC, H1X 2B2, Canada.
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3
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McMillen P, Levin M. Collective intelligence: A unifying concept for integrating biology across scales and substrates. Commun Biol 2024; 7:378. [PMID: 38548821 PMCID: PMC10978875 DOI: 10.1038/s42003-024-06037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
A defining feature of biology is the use of a multiscale architecture, ranging from molecular networks to cells, tissues, organs, whole bodies, and swarms. Crucially however, biology is not only nested structurally, but also functionally: each level is able to solve problems in distinct problem spaces, such as physiological, morphological, and behavioral state space. Percolating adaptive functionality from one level of competent subunits to a higher functional level of organization requires collective dynamics: multiple components must work together to achieve specific outcomes. Here we overview a number of biological examples at different scales which highlight the ability of cellular material to make decisions that implement cooperation toward specific homeodynamic endpoints, and implement collective intelligence by solving problems at the cell, tissue, and whole-organism levels. We explore the hypothesis that collective intelligence is not only the province of groups of animals, and that an important symmetry exists between the behavioral science of swarms and the competencies of cells and other biological systems at different scales. We then briefly outline the implications of this approach, and the possible impact of tools from the field of diverse intelligence for regenerative medicine and synthetic bioengineering.
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Affiliation(s)
- Patrick McMillen
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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Glass DS, Bren A, Vaisbourd E, Mayo A, Alon U. A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover. Cell 2024; 187:931-944.e12. [PMID: 38320549 PMCID: PMC10882425 DOI: 10.1016/j.cell.2024.01.024] [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] [Received: 07/10/2023] [Revised: 11/27/2023] [Accepted: 01/16/2024] [Indexed: 02/08/2024]
Abstract
Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.
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Affiliation(s)
- David S Glass
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elizabeth Vaisbourd
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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Wang X, Liang Q, Luo Y, Ye J, Yu Y, Chen F. Engineering the next generation of theranostic biomaterials with synthetic biology. Bioact Mater 2024; 32:514-529. [PMID: 38026437 PMCID: PMC10660023 DOI: 10.1016/j.bioactmat.2023.10.018] [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: 07/19/2023] [Revised: 10/06/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Biomaterials have evolved from inert materials to responsive entities, playing a crucial role in disease diagnosis, treatment, and modeling. However, their advancement is hindered by limitations in chemical and mechanical approaches. Synthetic biology enabling the genetically reprograming of biological systems offers a new paradigm. It has achieved remarkable progresses in cell reprogramming, engineering designer cells for diverse applications. Synthetic biology also encompasses cell-free systems and rational design of biological molecules. This review focuses on the application of synthetic biology in theranostics, which boost rapid development of advanced biomaterials. We introduce key fundamental concepts of synthetic biology and highlight frontier applications thereof, aiming to explore the intersection of synthetic biology and biomaterials. This integration holds tremendous promise for advancing biomaterial engineering with programable complex functions.
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Affiliation(s)
- Xiang Wang
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qianyi Liang
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yixuan Luo
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jianwen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yin Yu
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fei Chen
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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6
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Zheng F, Kawabe Y, Kamihira M. RNA Aptamer-Mediated Gene Activation Systems for Inducible Transgene Expression in Animal Cells. ACS Synth Biol 2024; 13:230-241. [PMID: 38073086 DOI: 10.1021/acssynbio.3c00472] [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: 01/23/2024]
Abstract
RNA expression analyses can be used to obtain various information from inside cells, such as physical conditions, the chemical environment, and endogenous signals. For detecting RNA, the system regulating intracellular gene expression has the potential for monitoring RNA expression levels in real time within living cells. Synthetic biology provides powerful tools for detecting and analyzing RNA inside cells. Here, we devised an RNA aptamer-mediated gene activation system, RAMGA, to induce RNA-triggered gene expression activation by employing an inducible complex formation strategy grounded in synthetic biology. This methodology connects DNA-binding domains and transactivators through target RNA using RNA-binding domains, including phage coat proteins. MS2 bacteriophage coat protein fused with a transcriptional activator and PP7 bacteriophage coat protein fused with the tetracycline repressor (tetR) can be bridged by target RNA encoding MS2 and PP7 stem-loops, resulting in transcriptional activation. We generated recombinant CHO cells containing an inducible GFP expression module governed by a minimal promoter with a tetR-responsive element. Cells carrying the trigger RNA exhibited robust reporter gene expression, whereas cells lacking it exhibited no expression. GFP expression was upregulated over 200-fold compared with that in cells without a target RNA expression vector. Moreover, this system can detect the expression of mRNA tagged with aptamer tags and modulate reporter gene expression based on the target mRNA level without affecting the expression of the original mRNA-encoding gene. The RNA-triggered gene expression systems developed in this study have potential as a new platform for establishing gene circuits, evaluating endogenous gene expression, and developing novel RNA detectors.
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Affiliation(s)
- Feiyang Zheng
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshinori Kawabe
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masamichi Kamihira
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Gumuskaya G, Srivastava P, Cooper BG, Lesser H, Semegran B, Garnier S, Levin M. Motile Living Biobots Self-Construct from Adult Human Somatic Progenitor Seed Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303575. [PMID: 38032125 PMCID: PMC10811512 DOI: 10.1002/advs.202303575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/31/2023] [Indexed: 12/01/2023]
Abstract
Fundamental knowledge gaps exist about the plasticity of cells from adult soma and the potential diversity of body shape and behavior in living constructs derived from genetically wild-type cells. Here anthrobots are introduced, a spheroid-shaped multicellular biological robot (biobot) platform with diameters ranging from 30 to 500 microns and cilia-powered locomotive abilities. Each Anthrobot begins as a single cell, derived from the adult human lung, and self-constructs into a multicellular motile biobot after being cultured in extra cellular matrix for 2 weeks and transferred into a minimally viscous habitat. Anthrobots exhibit diverse behaviors with motility patterns ranging from tight loops to straight lines and speeds ranging from 5-50 microns s-1 . The anatomical investigations reveal that this behavioral diversity is significantly correlated with their morphological diversity. Anthrobots can assume morphologies with fully polarized or wholly ciliated bodies and spherical or ellipsoidal shapes, each related to a distinct movement type. Anthrobots are found to be capable of traversing, and inducing rapid repair of scratches in, cultured human neural cell sheets in vitro. By controlling microenvironmental cues in bulk, novel structures, with new and unexpected behavior and biomedically-relevant capabilities, can be discovered in morphogenetic processes without direct genetic editing or manual sculpting.
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Affiliation(s)
- Gizem Gumuskaya
- Allen Discovery Center at Tufts Universityand Department of BiologyTufts UniversityMedfordMA02155USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
| | - Pranjal Srivastava
- Allen Discovery Center at Tufts Universityand Department of BiologyTufts UniversityMedfordMA02155USA
| | - Ben G. Cooper
- Allen Discovery Center at Tufts Universityand Department of BiologyTufts UniversityMedfordMA02155USA
| | - Hannah Lesser
- Allen Discovery Center at Tufts Universityand Department of BiologyTufts UniversityMedfordMA02155USA
| | - Ben Semegran
- Allen Discovery Center at Tufts Universityand Department of BiologyTufts UniversityMedfordMA02155USA
| | - Simon Garnier
- Federated Department of Biological SciencesNew Jersey Institute of TechnologyNewarkNJ07102USA
| | - Michael Levin
- Allen Discovery Center at Tufts Universityand Department of BiologyTufts UniversityMedfordMA02155USA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
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Simpson K, L'Homme A, Keymer J, Federici F. Spatial biology of Ising-like synthetic genetic networks. BMC Biol 2023; 21:185. [PMID: 37667283 PMCID: PMC10478219 DOI: 10.1186/s12915-023-01681-4] [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: 12/20/2022] [Accepted: 08/11/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Understanding how spatial patterns of gene expression emerge from the interaction of individual gene networks is a fundamental challenge in biology. Developing a synthetic experimental system with a common theoretical framework that captures the emergence of short- and long-range spatial correlations (and anti-correlations) from interacting gene networks could serve to uncover generic scaling properties of these ubiquitous phenomena. RESULTS Here, we combine synthetic biology, statistical mechanics models, and computational simulations to study the spatial behavior of synthetic gene networks (SGNs) in Escherichia coli quasi-2D colonies growing on hard agar surfaces. Guided by the combined mechanisms of the contact process lattice simulation and two-dimensional Ising model (CPIM), we describe the spatial behavior of bi-stable and chemically coupled SGNs that self-organize into patterns of long-range correlations with power-law scaling or short-range anti-correlations. These patterns, resembling ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points, maintain their scaling properties upon changes in growth rate and cell shape. CONCLUSIONS Our findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia.
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Affiliation(s)
- Kevin Simpson
- ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Alfredo L'Homme
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan Keymer
- Institute for Advanced Studies, Shenzhen X-Institute, Shenzhen, China.
- Schools of Physics and Biology, Pontificia Universidad Católica de Chile, Santiago, Chile.
- Department of Natural Sciences and Technology, Universidad de Aysén, Coyhaique, Chile.
| | - Fernán Federici
- ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
- FONDAP Center for Genome Regulation - Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Yang JS, Reyna-Llorens I. Plant synthetic biology: exploring the frontiers of sustainable agriculture and fundamental plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3787-3790. [PMID: 37462736 DOI: 10.1093/jxb/erad220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Affiliation(s)
- Jae-Seong Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Ivan Reyna-Llorens
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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Kocaoglan EG, Radhakrishnan D, Nakayama N. Synthetic developmental biology: molecular tools to re-design plant shoots and roots. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3864-3876. [PMID: 37155965 PMCID: PMC10826796 DOI: 10.1093/jxb/erad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
Plant morphology and anatomy strongly influence agricultural yield. Crop domestication has strived for desirable growth and developmental traits, such as larger and more fruits and semi-dwarf architecture. Genetic engineering has accelerated rational, purpose-driven engineering of plant development, but it can be unpredictable. Developmental pathways are complex and riddled with environmental and hormonal inputs, as well as feedback and feedforward interactions, which occur at specific times and places in a growing multicellular organism. Rational modification of plant development would probably benefit from precision engineering based on synthetic biology approaches. This review outlines recently developed synthetic biology technologies for plant systems and highlights their potential for engineering plant growth and development. Streamlined and high-capacity genetic construction methods (Golden Gate DNA Assembly frameworks and toolkits) allow fast and variation-series cloning of multigene transgene constructs. This, together with a suite of gene regulation tools (e.g. cell type-specific promoters, logic gates, and multiplex regulation systems), is starting to enable developmental pathway engineering with predictable outcomes in model plant and crop species.
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Affiliation(s)
- Elif Gediz Kocaoglan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Dhanya Radhakrishnan
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Naomi Nakayama
- Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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Bongard J, Levin M. There’s Plenty of Room Right Here: Biological Systems as Evolved, Overloaded, Multi-Scale Machines. Biomimetics (Basel) 2023; 8:biomimetics8010110. [PMID: 36975340 PMCID: PMC10046700 DOI: 10.3390/biomimetics8010110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic view. Such a view dissolves the contingent dichotomies driven by human cognitive biases (e.g., a tendency to oversimplify) and prior technological limitations in favor of a more continuous view, necessitated by the study of evolution, developmental biology, and intelligent machines. Form and function are tightly entwined in nature, and in some cases, in robotics as well. Thus, efforts to re-shape living systems for biomedical or bioengineering purposes require prediction and control of their function at multiple scales. This is challenging for many reasons, one of which is that living systems perform multiple functions in the same place at the same time. We refer to this as “polycomputing”—the ability of the same substrate to simultaneously compute different things, and make those computational results available to different observers. This ability is an important way in which living things are a kind of computer, but not the familiar, linear, deterministic kind; rather, living things are computers in the broad sense of their computational materials, as reported in the rapidly growing physical computing literature. We argue that an observer-centered framework for the computations performed by evolved and designed systems will improve the understanding of mesoscale events, as it has already done at quantum and relativistic scales. To develop our understanding of how life performs polycomputing, and how it can be convinced to alter one or more of those functions, we can first create technologies that polycompute and learn how to alter their functions. Here, we review examples of biological and technological polycomputing, and develop the idea that the overloading of different functions on the same hardware is an important design principle that helps to understand and build both evolved and designed systems. Learning to hack existing polycomputing substrates, as well as to evolve and design new ones, will have massive impacts on regenerative medicine, robotics, and computer engineering.
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Affiliation(s)
- Joshua Bongard
- Department of Computer Science, University of Vermont, Burlington, VT 05405, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Ave., Suite 4600, Medford, MA 02155, USA
- Correspondence: ; Tel.: +(617)-627-6161
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Wang S, Garcia-Ojalvo J, Elowitz MB. Periodic spatial patterning with a single morphogen. Cell Syst 2022; 13:1033-1047.e7. [PMID: 36435178 DOI: 10.1016/j.cels.2022.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/13/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022]
Abstract
During multicellular development, periodic spatial patterning systems generate repetitive structures, such as digits, vertebrae, and teeth. Turing patterning provides a foundational paradigm for understanding such systems. The simplest Turing systems are believed to require at least two morphogens to generate periodic patterns. Here, using mathematical modeling, we show that a simpler circuit, including only a single diffusible morphogen, is sufficient to generate long-range, spatially periodic patterns that propagate outward from transient initiating perturbations and remain stable after the perturbation is removed. Furthermore, an additional bistable intracellular feedback or operation on a growing cell lattice can make patterning robust to noise. Together, these results show that a single morphogen can be sufficient for robust spatial pattern formation and should provide a foundation for engineering pattern formation in the emerging field of synthetic developmental biology.
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Affiliation(s)
- Sheng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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13
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Hazan H, Levin M. Exploring the Behavior of Bioelectric Circuits Using Evolution Heuristic Search. Bioelectricity 2022. [DOI: 10.1089/bioe.2022.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hananel Hazan
- Allen Discovery Center at Tufts University, Medford, Massachusetts, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts, USA
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14
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Martínez-Ara G, Stapornwongkul KS, Ebisuya M. Scaling up complexity in synthetic developmental biology. Science 2022; 378:864-868. [DOI: 10.1126/science.add9666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The application of synthetic biology approaches to study development opens the possibility to build and manipulate developmental processes to understand them better. Researchers have reconstituted fundamental developmental processes, such as cell patterning and sorting, by engineering gene circuits in vitro. Moreover, new tools have been created that allow for the control of developmental processes in more complex organoids and embryos. Synthetic approaches allow testing of which components are sufficient to reproduce a developmental process and under which conditions as well as what effect perturbations have on other processes. We envision that the future of synthetic developmental biology requires an increase in the diversity of available tools and further efforts to combine multiple developmental processes into one system.
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Affiliation(s)
| | | | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, 08003 Barcelona, Spain
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15
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Bao M, Cornwall-Scoones J, Zernicka-Goetz M. Stem-cell-based human and mouse embryo models. Curr Opin Genet Dev 2022; 76:101970. [PMID: 35988317 PMCID: PMC10309046 DOI: 10.1016/j.gde.2022.101970] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
Abstract
Synthetic embryology aims to develop embryo-like structures from stem cells to provide new insight into early stages of mammalian development. Recent advances in synthetic embryology have highlighted the remarkable capacity of stem cells to self-organize under certain biochemical or biophysical stimulations, generating structures that recapitulate the fate and form of early mouse/human embryos, in which symmetry breaking, pattern formation, or proper morphogenesis can be observed spontaneously. Here we review recent progress on the design principles for different types of embryoids and discuss the impact of different biochemical and biophysical factors on the process of stem-cell self-organization. We also offer our thoughts about the principal future challenges.
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Affiliation(s)
- Min Bao
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK. https://twitter.com/@Min_Bao_
| | - Jake Cornwall-Scoones
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA; The Francis Crick Institute, London NW1 1AT, UK. https://twitter.com/@jake_cs_
| | - Magdalena Zernicka-Goetz
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK.
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16
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Optogenetic control of apical constriction induces synthetic morphogenesis in mammalian tissues. Nat Commun 2022; 13:5400. [PMID: 36104355 PMCID: PMC9474505 DOI: 10.1038/s41467-022-33115-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/02/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThe emerging field of synthetic developmental biology proposes bottom-up approaches to examine the contribution of each cellular process to complex morphogenesis. However, the shortage of tools to manipulate three-dimensional (3D) shapes of mammalian tissues hinders the progress of the field. Here we report the development of OptoShroom3, an optogenetic tool that achieves fast spatiotemporal control of apical constriction in mammalian epithelia. Activation of OptoShroom3 through illumination in an epithelial Madin-Darby Canine Kidney (MDCK) cell sheet reduces the apical surface of the stimulated cells and causes displacements in the adjacent regions. Light-induced apical constriction provokes the folding of epithelial cell colonies on soft gels. Its application to murine and human neural organoids leads to thickening of neuroepithelia, apical lumen reduction in optic vesicles, and flattening in neuroectodermal tissues. These results show that spatiotemporal control of apical constriction can trigger several types of 3D deformation depending on the initial tissue context.
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17
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Malaguti M, Portero Migueles R, Annoh J, Sadurska D, Blin G, Lowell S. SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo. Development 2022; 149:275525. [PMID: 35616331 PMCID: PMC9270970 DOI: 10.1242/dev.200226] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/13/2022] [Indexed: 12/11/2022]
Abstract
Cell-cell interactions govern differentiation and cell competition in pluripotent cells during early development, but the investigation of such processes is hindered by a lack of efficient analysis tools. Here, we introduce SyNPL: clonal pluripotent stem cell lines that employ optimised Synthetic Notch (SynNotch) technology to report cell-cell interactions between engineered ‘sender’ and ‘receiver’ cells in cultured pluripotent cells and chimaeric mouse embryos. A modular design makes it straightforward to adapt the system for programming differentiation decisions non-cell-autonomously in receiver cells in response to direct contact with sender cells. We demonstrate the utility of this system by enforcing neuronal differentiation at the boundary between two cell populations. In summary, we provide a new adaptation of SynNotch technology that could be used to identify cell interactions and to profile changes in gene or protein expression that result from direct cell-cell contact with defined cell populations in culture and in early embryos, and that can be customised to generate synthetic patterning of cell fate decisions. Summary: Optimised Synthetic Notch circuitry in mouse pluripotent stem cells provides a modular tool with which to monitor cell-cell interactions and program synthetic patterning of cell fates in culture and in embryos.
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Affiliation(s)
- Mattias Malaguti
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Rosa Portero Migueles
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Jennifer Annoh
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Daina Sadurska
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Guillaume Blin
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Sally Lowell
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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18
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Barbier I, Kusumawardhani H, Schaerli Y. Engineering synthetic spatial patterns in microbial populations and communities. Curr Opin Microbiol 2022; 67:102149. [DOI: 10.1016/j.mib.2022.102149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 02/03/2023]
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19
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Lam C, Saluja S, Courcoubetis G, Yu D, Chung C, Courte J, Morsut L. Parameterized Computational Framework for the Description and Design of Genetic Circuits of Morphogenesis Based on Contact-Dependent Signaling and Changes in Cell-Cell Adhesion. ACS Synth Biol 2022; 11:1417-1439. [PMID: 35363477 PMCID: PMC10389258 DOI: 10.1021/acssynbio.0c00369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Synthetic development is a nascent field of research that uses the tools of synthetic biology to design genetic programs directing cellular patterning and morphogenesis in higher eukaryotic cells, such as mammalian cells. One specific example of such synthetic genetic programs was based on cell-cell contact-dependent signaling using synthetic Notch pathways and was shown to drive the formation of multilayered spheroids by modulating cell-cell adhesion via differential expression of cadherin family proteins in a mouse fibroblast cell line (L929). The design method for these genetic programs relied on trial and error, which limited the number of possible circuits and parameter ranges that could be explored. Here, we build a parameterized computational framework that, given a cell-cell communication network driving changes in cell adhesion and initial conditions as inputs, predicts developmental trajectories. We first built a general computational framework where contact-dependent cell-cell signaling networks and changes in cell-cell adhesion could be designed in a modular fashion. We then used a set of available in vitro results (that we call the "training set" in analogy to similar pipelines in the machine learning field) to parameterize the computational model with values for adhesion and signaling. We then show that this parameterized model can qualitatively predict experimental results from a "testing set" of available in vitro data that varied the genetic network in terms of adhesion combinations, initial number of cells, and even changes to the network architecture. Finally, this parameterized model is used to recommend novel network implementation for the formation of a four-layered structure that has not been reported previously. The framework that we develop here could function as a testing ground to identify the reachable space of morphologies that can be obtained by controlling contact-dependent cell-cell communications and adhesion with these molecular tools and in this cellular system. Additionally, we discuss how the model could be expanded to include other forms of communication or effectors for the computational design of the next generation of synthetic developmental trajectories.
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Affiliation(s)
- Calvin Lam
- Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033-9080, United States
| | - Sajeev Saluja
- Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033-9080, United States
| | - George Courcoubetis
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, United States
| | - Dottie Yu
- Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033-9080, United States
| | - Christian Chung
- Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033-9080, United States
| | - Josquin Courte
- Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033-9080, United States
| | - 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, California 90033-9080, United States
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089-1111, United States
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20
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Synthetic developmental biology: Engineering approaches to guide multicellular organization. Stem Cell Reports 2022; 17:715-733. [PMID: 35276092 PMCID: PMC9023767 DOI: 10.1016/j.stemcr.2022.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Multicellular organisms of various complexities self-organize in nature. Organoids are in vitro 3D structures that display important aspects of the anatomy and physiology of their in vivo counterparts and that develop from pluripotent or tissue-specific stem cells through a self-organization process. In this review, we describe the multidisciplinary concept of “synthetic developmental biology” where engineering approaches are employed to guide multicellular organization in an experimental setting. We introduce a novel classification of engineering approaches based on the extent of microenvironmental manipulation applied to organoids. In the final section, we discuss how engineering tools might help overcome current limitations in organoid construction.
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21
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Guiziou S, Chu JC, Nemhauser JL. Decoding and recoding plant development. PLANT PHYSIOLOGY 2021; 187:515-526. [PMID: 35237818 PMCID: PMC8491033 DOI: 10.1093/plphys/kiab336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/26/2021] [Indexed: 05/04/2023]
Abstract
The development of multicellular organisms has been studied for centuries, yet many critical events and mechanisms of regulation remain challenging to observe directly. Early research focused on detailed observational and comparative studies. Molecular biology has generated insights into regulatory mechanisms, but only for a limited number of species. Now, synthetic biology is bringing these two approaches together, and by adding the possibility of sculpting novel morphologies, opening another path to understanding biology. Here, we review a variety of recently invented techniques that use CRISPR/Cas9 and phage integrases to trace the differentiation of cells over various timescales, as well as to decode the molecular states of cells in high spatiotemporal resolution. Most of these tools have been implemented in animals. The time is ripe for plant biologists to adopt and expand these approaches. Here, we describe how these tools could be used to monitor development in diverse plant species, as well as how they could guide efforts to recode programs of interest.
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Affiliation(s)
- Sarah Guiziou
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | - Jonah C. Chu
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | - Jennifer L. Nemhauser
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
- Author for communication:
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22
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Pereira Daoud AM, Popovic M, Dondorp WJ, Trani Bustos M, Bredenoord AL, Chuva de Sousa Lopes SM, van den Brink SC, Roelen BAJ, de Wert GMWR, Heindryckx B. Modelling human embryogenesis: embryo-like structures spark ethical and policy debate. Hum Reprod Update 2021; 26:779-798. [PMID: 32712668 DOI: 10.1093/humupd/dmaa027] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Studying the human peri-implantation period remains hindered by the limited accessibility of the in vivo environment and scarcity of research material. As such, continuing efforts have been directed towards developing embryo-like structures (ELS) from pluripotent stem cells (PSCs) that recapitulate aspects of embryogenesis in vitro. While the creation of such models offers immense potential for studying fundamental processes in both pre- and early post-implantation development, it also proves ethically contentious due to wide-ranging views on the moral and legal reverence due to human embryos. Lack of clarity on how to qualify and regulate research with ELS thus presents a challenge in that it may either limit this new field of research without valid grounds or allow it to develop without policies that reflect justified ethical concerns. OBJECTIVE AND RATIONALE The aim of this article is to provide a comprehensive overview of the existing scientific approaches to generate ELS from mouse and human PSCs, as well as discuss future strategies towards innovation in the context of human development. Concurrently, we aim to set the agenda for the ethical and policy issues surrounding research on human ELS. SEARCH METHODS The PubMed database was used to search peer-reviewed articles and reviews using the following terms: 'stem cells', 'pluripotency', 'implantation', 'preimplantation', 'post-implantation', 'blastocyst', 'embryoid bodies', 'synthetic embryos', 'embryo models', 'self-assembly', 'human embryo-like structures', 'artificial embryos' in combination with other keywords related to the subject area. The PubMed and Web of Science databases were also used to systematically search publications on the ethics of ELS and human embryo research by using the aforementioned keywords in combination with 'ethics', 'law', 'regulation' and equivalent terms. All relevant publications until December 2019 were critically evaluated and discussed. OUTCOMES In vitro systems provide a promising way forward for uncovering early human development. Current platforms utilize PSCs in both two- and three-dimensional settings to mimic various early developmental stages, including epiblast, trophoblast and amniotic cavity formation, in addition to axis development and gastrulation. Nevertheless, much hinges on the term 'embryo-like'. Extension of traditional embryo frameworks to research with ELS reveals that (i) current embryo definitions require reconsideration, (ii) cellular convertibility challenges the attribution of moral standing on the basis of 'active potentiality' and (iii) meaningful application of embryo protective directives will require rethinking of the 14-day culture limit and moral weight attributed to (non-)viability. Many conceptual and normative (dis)similarities between ELS and embryos thus remain to be thoroughly elucidated. WIDER IMPLICATIONS Modelling embryogenesis holds vast potential for both human developmental biology and understanding various etiologies associated with infertility. To date, ELS have been shown to recapitulate several aspects of peri-implantation development, but critically, cannot develop into a fetus. Yet, concurrent to scientific innovation, considering the extent to which the use of ELS may raise moral concerns typical of human embryo research remains paramount. This will be crucial for harnessing the potential of ELS as a valuable research tool, whilst remaining within a robust moral and legal framework of professionally acceptable practices.
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Affiliation(s)
- Ana M Pereira Daoud
- Department of Health Ethics and Society, Maastricht University, Maastricht, The Netherlands.,Department of Medical Humanities, Utrecht University Medical Center, Utrecht, The Netherlands.,School for Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Mina Popovic
- Ghent-Fertility And Stem cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Wybo J Dondorp
- Department of Health Ethics and Society, Maastricht University, Maastricht, The Netherlands.,School for Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.,School for Care and Public Health Research (CAPHRI), Maastricht University, Maastricht, The Netherlands.,Socrates chair Ethics of Reproductive Genetics endowed by the Dutch Humanist Association, Amsterdam, The Netherlands
| | - Marc Trani Bustos
- Ghent-Fertility And Stem cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium.,Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Annelien L Bredenoord
- Department of Medical Humanities, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Susana M Chuva de Sousa Lopes
- Ghent-Fertility And Stem cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Susanne C van den Brink
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bernard A J Roelen
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Guido M W R de Wert
- Department of Health Ethics and Society, Maastricht University, Maastricht, The Netherlands.,School for Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.,School for Care and Public Health Research (CAPHRI), Maastricht University, Maastricht, The Netherlands
| | - Björn Heindryckx
- Ghent-Fertility And Stem cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
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23
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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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24
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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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25
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Gough A, Soto-Gutierrez A, Vernetti L, Ebrahimkhani MR, Stern AM, Taylor DL. Human biomimetic liver microphysiology systems in drug development and precision medicine. Nat Rev Gastroenterol Hepatol 2021; 18:252-268. [PMID: 33335282 PMCID: PMC9106093 DOI: 10.1038/s41575-020-00386-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 02/07/2023]
Abstract
Microphysiology systems (MPS), also called organs-on-chips and tissue chips, are miniaturized functional units of organs constructed with multiple cell types under a variety of physical and biochemical environmental cues that complement animal models as part of a new paradigm of drug discovery and development. Biomimetic human liver MPS have evolved from simpler 2D cell models, spheroids and organoids to address the increasing need to understand patient-specific mechanisms of complex and rare diseases, the response to therapeutic treatments, and the absorption, distribution, metabolism, excretion and toxicity of potential therapeutics. The parallel development and application of transdisciplinary technologies, including microfluidic devices, bioprinting, engineered matrix materials, defined physiological and pathophysiological media, patient-derived primary cells, and pluripotent stem cells as well as synthetic biology to engineer cell genes and functions, have created the potential to produce patient-specific, biomimetic MPS for detailed mechanistic studies. It is projected that success in the development and maturation of patient-derived MPS with known genotypes and fully matured adult phenotypes will lead to advanced applications in precision medicine. In this Review, we examine human biomimetic liver MPS that are designed to recapitulate the liver acinus structure and functions to enhance our knowledge of the mechanisms of disease progression and of the absorption, distribution, metabolism, excretion and toxicity of therapeutic candidates and drugs as well as to evaluate their mechanisms of action and their application in precision medicine and preclinical trials.
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Affiliation(s)
- Albert Gough
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alejandro Soto-Gutierrez
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lawrence Vernetti
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mo R Ebrahimkhani
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew M Stern
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - D Lansing Taylor
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA.
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26
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Stapornwongkul KS, Vincent JP. Generation of extracellular morphogen gradients: the case for diffusion. Nat Rev Genet 2021; 22:393-411. [PMID: 33767424 DOI: 10.1038/s41576-021-00342-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Cells within developing tissues rely on morphogens to assess positional information. Passive diffusion is the most parsimonious transport model for long-range morphogen gradient formation but does not, on its own, readily explain scaling, robustness and planar transport. Here, we argue that diffusion is sufficient to ensure robust morphogen gradient formation in a variety of tissues if the interactions between morphogens and their extracellular binders are considered. A current challenge is to assess how the affinity for extracellular binders, as well as other biophysical and cell biological parameters, determines gradient dynamics and shape in a diffusion-based transport system. Technological advances in genome editing, tissue engineering, live imaging and in vivo biophysics are now facilitating measurement of these parameters, paving the way for mathematical modelling and a quantitative understanding of morphogen gradient formation and modulation.
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27
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Duran-Nebreda S, Pla J, Vidiella B, Piñero J, Conde-Pueyo N, Solé R. Synthetic Lateral Inhibition in Periodic Pattern Forming Microbial Colonies. ACS Synth Biol 2021; 10:277-285. [PMID: 33449631 PMCID: PMC8486170 DOI: 10.1021/acssynbio.0c00318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multicellular entities are characterized by intricate spatial patterns, intimately related to the functions they perform. These patterns are often created from isotropic embryonic structures, without external information cues guiding the symmetry breaking process. Mature biological structures also display characteristic scales with repeating distributions of signals or chemical species across space. Many candidate patterning modules have been used to explain processes during development and typically include a set of interacting and diffusing chemicals or agents known as morphogens. Great effort has been put forward to better understand the conditions in which pattern-forming processes can occur in the biological domain. However, evidence and practical knowledge allowing us to engineer symmetry-breaking is still lacking. Here we follow a different approach by designing a synthetic gene circuit in E. coli that implements a local activation long-range inhibition mechanism. The synthetic gene network implements an artificial differentiation process that changes the physicochemical properties of the agents. Using both experimental results and modeling, we show that the proposed system is capable of symmetry-breaking leading to regular spatial patterns during colony growth. Studying how these patterns emerge is fundamental to further our understanding of the evolution of biocomplexity and the role played by self-organization. The artificial system studied here and the engineering perspective on embryogenic processes can help validate developmental theories and identify universal properties underpinning biological pattern formation, with special interest for the area of synthetic developmental biology.
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Affiliation(s)
- Salva Duran-Nebreda
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Evolution of Technology Lab, Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
| | - Jordi Pla
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Blai Vidiella
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Jordi Piñero
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Nuria Conde-Pueyo
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Ricard Solé
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, United States
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28
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Velazquez JJ, LeGraw R, Moghadam F, Tan Y, Kilbourne J, Maggiore JC, Hislop J, Liu S, Cats D, Chuva de Sousa Lopes SM, Plaisier C, Cahan P, Kiani S, Ebrahimkhani MR. Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids. Cell Syst 2020; 12:41-55.e11. [PMID: 33290741 PMCID: PMC8164844 DOI: 10.1016/j.cels.2020.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/13/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022]
Abstract
Pluripotent stem cell (PSC)-derived organoids have emerged as novel multicellular models of human tissue development but display immature phenotypes, aberrant tissue fates, and a limited subset of cells. Here, we demonstrate that integrated analysis and engineering of gene regulatory networks (GRNs) in PSC-derived multilineage human liver organoids direct maturation and vascular morphogenesis in vitro. Overexpression of PROX1 and ATF5, combined with targeted CRISPR-based transcriptional activation of endogenous CYP3A4, reprograms tissue GRNs and improves native liver functions, such as FXR signaling, CYP3A4 enzymatic activity, and stromal cell reactivity. The engineered tissues possess superior liver identity when compared with other PSC-derived liver organoids and show the presence of hepatocyte, biliary, endothelial, and stellate-like cell populations in single-cell RNA-seq analysis. Finally, they show hepatic functions when studied in vivo. Collectively, our approach provides an experimental framework to direct organogenesis in vitro by systematically probing molecular pathways and transcriptional networks that promote tissue development.
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Affiliation(s)
- Jeremy J Velazquez
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Ryan LeGraw
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Farzaneh Moghadam
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Yuqi Tan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Joseph C Maggiore
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Joshua Hislop
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Silvia Liu
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Davy Cats
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Einthovenweg, 2333 ZC Leiden, the Netherlands
| | - Susana M Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg, 2333 ZC Leiden, the Netherlands
| | - Christopher Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Patrick Cahan
- Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Samira Kiani
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Mo R Ebrahimkhani
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA; Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Phoenix, AZ 85054, USA; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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29
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Mumford TR, Roth L, Bugaj LJ. Reverse and Forward Engineering Multicellular Structures with Optogenetics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020; 16:61-71. [PMID: 33718689 PMCID: PMC7945718 DOI: 10.1016/j.cobme.2020.100250] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding how cells self-organize into functional higher-order structures is of great interest, both towards deciphering animal development, as well as for our ability to predictably build custom tissues to meet research and therapeutic needs. The proper organization of cells across length-scales results from interconnected and dynamic networks of molecules and cells. Optogenetic probes provide dynamic and tunable control over molecular events within cells, and thus represent a powerful approach to both dissect and control collective cell behaviors. Here we emphasize the breadth of the optogenetic toolkit and discuss how these methods have already been used to reverse-engineer the design rules of developing organisms. We also offer our perspective on the rich potential for optogenetics to power forward-engineering of tissue assembly towards the generation of bespoke tissues with user-defined properties.
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Affiliation(s)
- Thomas R. Mumford
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lee Roth
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lukasz J. Bugaj
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
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30
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Toda S. Synthetic tissue engineering: Programming multicellular self-organization by designing customized cell-cell communication. Biophys Physicobiol 2020; 17:42-50. [PMID: 33173713 PMCID: PMC7593132 DOI: 10.2142/biophysico.bsj-2020002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/27/2020] [Indexed: 12/02/2022] Open
Abstract
Cells communicate with each other to organize multicellular collective systems and assemble complex, elaborate tissue structures by themselves during development. Despite intensive biological studies, what kind of cell-cell communication can sufficiently drive self-organization of specific tissue architectures remain unclear. Thanks to recent advances on genetic engineering technologies, synthetic biologists start to build customized cell-cell communication with user-defined signal input and gene expression output to program multicellular behaviors using mammalian systems. This review article introduces how we can design and engineer customized cell-cell communication to program synthetic self-organizing multicellular structures. Creating tissue formation processes with synthetic genetic programs will help understanding of fundamental principles of how genetic programs drive tissue self-organization and provide new capabilities on tissue engineering for cell-based regenerative therapy applications.
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Affiliation(s)
- Satoshi Toda
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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31
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Abstract
Reconstitution is an experimental strategy that seeks to recapitulate biological events outside their natural contexts using a reduced set of components. Classically, biochemical reconstitution has been extensively applied to identify the minimal set of molecules sufficient for recreating the basic chemistry of life. By analogy, reconstitution approaches to developmental biology recapitulate aspects of developmental events outside an embryo, with the goal of revealing the basic genetic circuits or physical cues sufficient for recreating developmental decisions. The rapidly growing repertoire of genetic, molecular, microscopic, and bioengineering tools is expanding the complexity and precision of reconstitution experiments. We review the emerging field of synthetic developmental biology, with a focus on the ways in which reconstitution strategies and new biological tools have enhanced our modern understanding of fundamental questions in developmental biology.
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Affiliation(s)
- Gavin Schlissel
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Pulin Li
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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32
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Direct Readout of Neural Stem Cell Transgenesis with an Integration-Coupled Gene Expression Switch. Neuron 2020; 107:617-630.e6. [PMID: 32559415 PMCID: PMC7447981 DOI: 10.1016/j.neuron.2020.05.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 04/22/2020] [Accepted: 05/26/2020] [Indexed: 12/29/2022]
Abstract
Stable genomic integration of exogenous transgenes is essential in neurodevelopmental and stem cell studies. Despite tools driving increasingly efficient genomic insertion with DNA vectors, transgenesis remains fundamentally hindered by the impossibility of distinguishing integrated from episomal transgenes. Here, we introduce an integration-coupled On genetic switch, iOn, which triggers gene expression upon incorporation into the host genome through transposition, thus enabling rapid and accurate identification of integration events following transfection with naked plasmids. In vitro, iOn permits rapid drug-free stable transgenesis of mouse and human pluripotent stem cells with multiple vectors. In vivo, we demonstrate faithful cell lineage tracing, assessment of regulatory elements, and mosaic analysis of gene function in somatic transgenesis experiments that reveal neural progenitor potentialities and interaction. These results establish iOn as a universally applicable strategy to accelerate and simplify genetic engineering in cultured systems and model organisms by conditioning transgene activation to genomic integration. A gene expression switch powered by genomic integration Accelerated readout of additive transgenesis with one or multiple vectors Faithful lineage tracing and mosaic analysis by somatic transfection Near-universal applicability in cultured cells and animal models
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33
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Barbier I, Perez‐Carrasco R, Schaerli Y. Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch. Mol Syst Biol 2020; 16:e9361. [PMID: 32529808 PMCID: PMC7290156 DOI: 10.15252/msb.20199361] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 04/29/2020] [Accepted: 05/08/2020] [Indexed: 11/20/2022] Open
Abstract
The formation of spatiotemporal patterns of gene expression is frequently guided by gradients of diffusible signaling molecules. The toggle switch subnetwork, composed of two cross-repressing transcription factors, is a common component of gene regulatory networks in charge of patterning, converting the continuous information provided by the gradient into discrete abutting stripes of gene expression. We present a synthetic biology framework to understand and characterize the spatiotemporal patterning properties of the toggle switch. To this end, we built a synthetic toggle switch controllable by diffusible molecules in Escherichia coli. We analyzed the patterning capabilities of the circuit by combining quantitative measurements with a mathematical reconstruction of the underlying dynamical system. The toggle switch can produce robust patterns with sharp boundaries, governed by bistability and hysteresis. We further demonstrate how the hysteresis, position, timing, and precision of the boundary can be controlled, highlighting the dynamical flexibility of the circuit.
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Affiliation(s)
- Içvara Barbier
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Rubén Perez‐Carrasco
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
- Department of MathematicsUniversity College LondonLondonUK
| | - Yolanda Schaerli
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
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34
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Perkins ML, Benzinger D, Arcak M, Khammash M. Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling. Nat Commun 2020; 11:1355. [PMID: 32170129 PMCID: PMC7069979 DOI: 10.1038/s41467-020-15166-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/11/2020] [Indexed: 12/22/2022] Open
Abstract
Designing and implementing synthetic biological pattern formation remains challenging due to underlying theoretical complexity as well as the difficulty of engineering multicellular networks biochemically. Here, we introduce a cell-in-the-loop approach where living cells interact through in silico signaling, establishing a new testbed to interrogate theoretical principles when internal cell dynamics are incorporated rather than modeled. We present an easy-to-use theoretical test to predict the emergence of contrasting patterns in gene expression among laterally inhibiting cells. Guided by the theory, we experimentally demonstrate spontaneous checkerboard patterning in an optogenetic setup, where cell-to-cell signaling is emulated with light inputs calculated in silico from real-time gene expression measurements. The scheme successfully produces spontaneous, persistent checkerboard patterns for systems of sixteen patches, in quantitative agreement with theoretical predictions. Our research highlights how tools from dynamical systems theory may inform our understanding of patterning, and illustrates the potential of cell-in-the-loop for engineering synthetic multicellular systems.
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Affiliation(s)
- Melinda Liu Perkins
- Department of Electrical Engineering, University of California, Berkeley, CA, USA.
| | - Dirk Benzinger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Murat Arcak
- Department of Electrical Engineering, University of California, Berkeley, CA, USA
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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