1
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Lam C. Mathematical and In Silico Analysis of Synthetic Inhibitory Circuits That Program Self-Organizing Multicellular Structures. ACS Synth Biol 2024; 13:1925-1940. [PMID: 38781040 DOI: 10.1021/acssynbio.4c00230] [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: 05/25/2024]
Abstract
Bottom-up approaches are becoming increasingly popular for studying multicellular self-organization and development. In contrast to the classic top-down approach, where parts of the organization/developmental process are broken to understand the process, the goal is to build the process to understand it. For example, synthetic circuits have been built to understand how cell-cell communication and differential adhesion can drive multicellular development. The majority of current bottom-up efforts focus on using activatory circuits to engineer and understand development, but efforts with inhibitory circuits have been minimal. Yet, inhibitory circuits are ubiquitous and vital to native developmental processes. Thus, inhibitory circuits are a crucial yet poorly studied facet of bottom-up multicellular development. To demonstrate the potential of inhibitory circuits for building and developing multicellular structures, several synthetic inhibitory circuits that combine engineered cell-cell communication and differential adhesion were designed, and then examined for synthetic development capability using a previously validated in silico framework. These designed inhibitory circuits can build a variety of patterned, self-organized structures and even morphological oscillations. These results support that inhibitory circuits can be powerful tools for building, studying, and understanding developmental processes.
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Affiliation(s)
- Calvin Lam
- Independent Investigator, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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2
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Ramos R, Swedlund B, Ganesan AK, Morsut L, Maini PK, Monuki ES, Lander AD, Chuong CM, Plikus MV. Parsing patterns: Emerging roles of tissue self-organization in health and disease. Cell 2024; 187:3165-3186. [PMID: 38906093 DOI: 10.1016/j.cell.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/22/2024] [Accepted: 05/08/2024] [Indexed: 06/23/2024]
Abstract
Patterned morphologies, such as segments, spirals, stripes, and spots, frequently emerge during embryogenesis through self-organized coordination between cells. Yet, complex patterns also emerge in adults, suggesting that the capacity for spontaneous self-organization is a ubiquitous property of biological tissues. We review current knowledge on the principles and mechanisms of self-organized patterning in embryonic tissues and explore how these principles and mechanisms apply to adult tissues that exhibit features of patterning. We discuss how and why spontaneous pattern generation is integral to homeostasis and healing of tissues, illustrating it with examples from regenerative biology. We examine how aberrant self-organization underlies diverse pathological states, including inflammatory skin disorders and tumors. Lastly, we posit that based on such blueprints, targeted engineering of pattern-driving molecular circuits can be leveraged for synthetic biology and the generation of organoids with intricate patterns.
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Affiliation(s)
- Raul Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Benjamin Swedlund
- 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, USA
| | - Anand K Ganesan
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA; Department of Dermatology, University of California, Irvine, Irvine, CA, USA
| | - 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, USA; Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Philip K Maini
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Edwin S Monuki
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA; Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA
| | - Arthur D Lander
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
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3
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Shui S, Scheller L, Correia BE. Protein-based bandpass filters for controlling cellular signaling with chemical inputs. Nat Chem Biol 2024; 20:586-593. [PMID: 37957273 PMCID: PMC11062894 DOI: 10.1038/s41589-023-01463-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
Biological signal processing is vital for cellular function. Similar to electronic circuits, cells process signals via integrated mechanisms. In electronics, bandpass filters transmit frequencies with defined ranges, but protein-based counterparts for controlled responses are lacking in engineered biological systems. Here, we rationally design protein-based, chemically responsive bandpass filters (CBPs) showing OFF-ON-OFF patterns that respond to chemical concentrations within a specific range and reject concentrations outside that range. Employing structure-based strategies, we designed a heterodimeric construct that dimerizes in response to low concentrations of a small molecule (ON), and dissociates at high concentrations of the same molecule (OFF). The CBPs have a multidomain architecture in which we used known drug receptors, a computationally designed protein binder and small-molecule inhibitors. This modular system allows fine-tuning for optimal performance in terms of bandwidth, response, cutoff and fold changes. The CBPs were used to regulate cell surface receptor signaling pathways to control cellular activities in engineered cells.
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Affiliation(s)
- Sailan Shui
- Laboratory of Protein Design and Immunoengineering (LPDI)-STI-EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Leo Scheller
- Laboratory of Protein Design and Immunoengineering (LPDI)-STI-EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering (LPDI)-STI-EPFL, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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4
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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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5
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Lam C. Design and mathematical analysis of activating transcriptional amplifiers that enable modular temporal control in synthetic juxtacrine circuits. Synth Syst Biotechnol 2023; 8:654-672. [PMID: 37868744 PMCID: PMC10587772 DOI: 10.1016/j.synbio.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/09/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
The ability to control mammalian cells such that they self-organize or enact therapeutic effects as desired has incredible implications. Not only would it further our understanding of native processes such as development and the immune response, but it would also have powerful applications in medical fields such as regenerative medicine and immunotherapy. This control is typically obtained by synthetic circuits that use synthetic receptors, but control remains incomplete. The synthetic juxtacrine receptors (SJRs) are widely used as they are fully modular and enable spatial control, but they have limited gene expression amplification and temporal control. As these are integral facets to cell control, I therefore designed transcription factor based amplifiers that amplify gene expression and enable unidirectional temporal control by prolonging duration of target gene expression. Using a validated in silico framework for SJR signaling, I combined these amplifiers with SJRs and show that these SJR amplifier circuits can direct spatiotemporal patterning and improve the quality of self-organization. I then show that these circuits can improve chimeric antigen receptor (CAR) T cell tumor killing against various heterogenous antigen expression tumors. These amplifiers are flexible tools that improve control over SJR based circuits with both basic and therapeutic applications.
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6
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Vazana-Netzarim R, Elmalem Y, Sofer S, Bruck H, Danino N, Sarig U. Distinct HAND2/HAND2-AS1 Expression Levels May Fine-Tune Mesenchymal and Epithelial Cell Plasticity of Human Mesenchymal Stem Cells. Int J Mol Sci 2023; 24:16546. [PMID: 38003736 PMCID: PMC10672054 DOI: 10.3390/ijms242216546] [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: 09/21/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
We previously developed several successful decellularization strategies that yielded porcine cardiac extracellular matrices (pcECMs) exhibiting tissue-specific bioactivity and bioinductive capacity when cultured with various pluripotent and multipotent stem cells. Here, we study the tissue-specific effects of the pcECM on seeded human mesenchymal stem cell (hMSC) phenotypes using reverse transcribed quantitative polymerase chain reaction (RT-qPCR) arrays for cardiovascular related gene expression. We further corroborated interesting findings at the protein level (flow cytometry and immunological stains) as well as bioinformatically using several mRNA sequencing and protein databases of normal and pathologic adult and embryonic (organogenesis stage) tissue expression. We discovered that upon the seeding of hMSCs on the pcECM, they displayed a partial mesenchymal-to-epithelial transition (MET) toward endothelial phenotypes (CD31+) and morphologies, which were preceded by an early spike (~Day 3 onward after seeding) in HAND2 expression at both the mRNA and protein levels compared to that in plate controls. The CRISPR-Cas9 knockout (KO) of HAND2 and its associated antisense long non-coding RNA (HAND2-AS1) regulatory region resulted in proliferation arrest, hypertrophy, and senescent-like morphology. Bioinformatic analyses revealed that HAND2 and HAND2-AS1 are highly correlated in expression and are expressed in many different tissue types albeit at distinct yet tightly regulated expression levels. Deviation (downregulation or upregulation) from these basal tissue expression levels is associated with a long list of pathologies. We thus suggest that HAND2 expression levels may possibly fine-tune hMSCs' plasticity through affecting senescence and mesenchymal-to-epithelial transition states, through yet unknown mechanisms. Targeting this pathway may open up a promising new therapeutic approach for a wide range of diseases, including cancer, degenerative disorders, and aging. Nevertheless, further investigation is required to validate these findings and better understand the molecular players involved, potential inducers and inhibitors of this pathway, and eventually potential therapeutic applications.
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Affiliation(s)
- Rachel Vazana-Netzarim
- The Dr. Miriam and Sheldon Adelson School of Medicine, Department of Morphological Sciences and Teratology, Ariel University, Ariel 4070000, Israel; (R.V.-N.); (N.D.)
| | - Yishay Elmalem
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, Ariel 4070000, Israel (S.S.); (H.B.)
| | - Shachar Sofer
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, Ariel 4070000, Israel (S.S.); (H.B.)
| | - Hod Bruck
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, Ariel 4070000, Israel (S.S.); (H.B.)
| | - Naama Danino
- The Dr. Miriam and Sheldon Adelson School of Medicine, Department of Morphological Sciences and Teratology, Ariel University, Ariel 4070000, Israel; (R.V.-N.); (N.D.)
| | - Udi Sarig
- The Dr. Miriam and Sheldon Adelson School of Medicine, Department of Morphological Sciences and Teratology, Ariel University, Ariel 4070000, Israel; (R.V.-N.); (N.D.)
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, Ariel 4070000, Israel (S.S.); (H.B.)
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7
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Wauford N, Patel A, Tordoff J, Enghuus C, Jin A, Toppen J, Kemp ML, Weiss R. Synthetic symmetry breaking and programmable multicellular structure formation. Cell Syst 2023; 14:806-818.e5. [PMID: 37689062 PMCID: PMC10919224 DOI: 10.1016/j.cels.2023.08.001] [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: 10/17/2022] [Revised: 04/14/2023] [Accepted: 08/02/2023] [Indexed: 09/11/2023]
Abstract
During development, cells undergo symmetry breaking into differentiated subpopulations that self-organize into complex structures.1,2,3,4,5 However, few tools exist to recapitulate these behaviors in a controllable and coupled manner.6,7,8,9 Here, we engineer a stochastic recombinase genetic switch tunable by small molecules to induce programmable symmetry breaking, commitment to downstream cell fates, and morphological self-organization. Inducers determine commitment probabilities, generating tunable subpopulations as a function of inducer dosage. We use this switch to control the cell-cell adhesion properties of cells committed to each fate.10,11 We generate a wide variety of 3D morphologies from a monoclonal population and develop a computational model showing high concordance with experimental results, yielding new quantitative insights into the relationship between cell-cell adhesion strengths and downstream morphologies. We expect that programmable symmetry breaking, generating precise and tunable subpopulation ratios and coupled to structure formation, will serve as an integral component of the toolbox for complex tissue and organoid engineering.
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Affiliation(s)
- Noreen Wauford
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshay Patel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jesse Tordoff
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Casper Enghuus
- Department of Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew Jin
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jack Toppen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Melissa L Kemp
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Fernandes TG. Organoids as complex (bio)systems. Front Cell Dev Biol 2023; 11:1268540. [PMID: 37691827 PMCID: PMC10485618 DOI: 10.3389/fcell.2023.1268540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023] Open
Abstract
Organoids are three-dimensional structures derived from stem cells that mimic the organization and function of specific organs, making them valuable tools for studying complex systems in biology. This paper explores the application of complex systems theory to understand and characterize organoids as exemplars of intricate biological systems. By identifying and analyzing common design principles observed across diverse natural, technological, and social complex systems, we can gain insights into the underlying mechanisms governing organoid behavior and function. This review outlines general design principles found in complex systems and demonstrates how these principles manifest within organoids. By acknowledging organoids as representations of complex systems, we can illuminate our understanding of their normal physiological behavior and gain valuable insights into the alterations that can lead to disease. Therefore, incorporating complex systems theory into the study of organoids may foster novel perspectives in biology and pave the way for new avenues of research and therapeutic interventions to improve human health and wellbeing.
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Affiliation(s)
- Tiago G. Fernandes
- Department of Bioengineering and iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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9
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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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10
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Tang MG, Zhang S, Xiong LG, Zhou JH, Huang JA, Zhao AQ, Liu ZH, Liu AL. A comprehensive review of polyphenol oxidase in tea (Camellia sinensis): Physiological characteristics, oxidation manufacturing, and biosynthesis of functional constituents. Compr Rev Food Sci Food Saf 2023; 22:2267-2291. [PMID: 37043598 DOI: 10.1111/1541-4337.13146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 04/14/2023]
Abstract
Polyphenol oxidase (PPO) is a metalloenzyme with a type III copper core that is abundant in nature. As one of the most essential enzymes in the tea plant (Camellia sinensis), the further regulation of PPO is critical for enhancing defensive responses, cultivating high-quality germplasm resources of tea plants, and producing tea products that are both functional and sensory qualities. Due to their physiological and pharmacological values, the constituents from the oxidative polymerization of PPO in tea manufacturing may serve as functional foods to prevent and treat chronic non-communicable diseases. However, current knowledge of the utilization of PPO in the tea industry is only available from scattered sources, and a more comprehensive study is required to reveal the relationship between PPO and tea obviously. A more comprehensive review of the role of PPO in tea was reported for the first time, as its classification, catalytic mechanism, and utilization in modulating tea flavors, compositions, and nutrition, along with the relationships between PPO-mediated enzymatic reactions and the formation of functional constituents in tea, and the techniques for the modification and application of PPO based on modern enzymology and synthetic biology are summarized and suggested in this article.
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Affiliation(s)
- Meng-Ge Tang
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Co-Innovation Centre of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, and Shaanxi Key Laboratory for Hazard Factors Assessment in Processing and Storage of Agricultural Products, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Sheng Zhang
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Co-Innovation Centre of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Co-Innovation Centre of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China
| | - Jing-Hui Zhou
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Co-Innovation Centre of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Co-Innovation Centre of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China
| | - Ai-Qing Zhao
- Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, and Shaanxi Key Laboratory for Hazard Factors Assessment in Processing and Storage of Agricultural Products, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Zhong-Hua Liu
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Co-Innovation Centre of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China
| | - Ai-Ling Liu
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Co-Innovation Centre of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
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11
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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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12
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Jiang Z, Xu Y, Fu M, Zhu D, Li N, Yang G. Genetically modified cell spheroids for tissue engineering and regenerative medicine. J Control Release 2023; 354:588-605. [PMID: 36657601 DOI: 10.1016/j.jconrel.2023.01.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/21/2023]
Abstract
Cell spheroids offer cell-to-cell interactions and show advantages in survival rate and paracrine effect to solve clinical and biomedical inquiries ranging from tissue engineering and regenerative medicine to disease pathophysiology. Therefore, cell spheroids are ideal vehicles for gene delivery. Genetically modified spheroids can enhance specific gene expression to promote tissue regeneration. Gene deliveries to cell spheroids are via viral vectors or non-viral vectors. Some new technologies like CRISPR/Cas9 also have been used in genetically modified methods to deliver exogenous gene to the host chromosome. It has been shown that genetically modified cell spheroids had the potential to differentiate into bone, cartilage, vascular, nerve, cardiomyocytes, skin, and skeletal muscle as well as organs like the liver to replace the diseased organ in the animal and pre-clinical trials. This article reviews the recent articles about genetically modified spheroid cells and explains the fabrication, applications, development timeline, limitations, and future directions of genetically modified cell spheroid.
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Affiliation(s)
- Zhiwei Jiang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Yi Xu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Mengdie Fu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Danji Zhu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Na Li
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Guoli Yang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China.
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13
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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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14
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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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15
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Shaffer JM, Greenwald I. SALSA, a genetically encoded biosensor for spatiotemporal quantification of Notch signal transduction in vivo. Dev Cell 2022; 57:930-944.e6. [PMID: 35413239 PMCID: PMC9473748 DOI: 10.1016/j.devcel.2022.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/14/2022] [Accepted: 03/14/2022] [Indexed: 12/26/2022]
Abstract
Notch-mediated lateral specification is a fundamental mechanism to resolve stochastic cell fate choices by amplifying initial differences between equivalent cells. To study how stochastic events impact Notch activity, we developed a biosensor, SALSA (sensor able to detect lateral signaling activity), consisting of an amplifying "switch"-Notch tagged with TEV protease-and a "reporter"-GFP fused to a nuclearly localized red fluorescent protein, separated by a TEVp cut site. When ligand activates Notch, TEVp enters the nucleus and releases GFP from its nuclear tether, allowing Notch activation to be quantified based on the changes in GFP subcellular localization. We show that SALSA accurately reports Notch activity in different signaling paradigms in Caenorhabditis elegans and use time-lapse imaging to test hypotheses about how stochastic elements ensure a reproducible and robust outcome in a canonical lin-12/Notch-mediated lateral signaling paradigm. SALSA should be generalizable to other experimental systems and be adaptable to increase options for bespoke "SynNotch" applications.
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Affiliation(s)
- Justin M Shaffer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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16
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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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17
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Signalling dynamics in embryonic development. Biochem J 2021; 478:4045-4070. [PMID: 34871368 PMCID: PMC8718268 DOI: 10.1042/bcj20210043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 02/08/2023]
Abstract
In multicellular organisms, cellular behaviour is tightly regulated to allow proper embryonic development and maintenance of adult tissue. A critical component in this control is the communication between cells via signalling pathways, as errors in intercellular communication can induce developmental defects or diseases such as cancer. It has become clear over the last years that signalling is not static but varies in activity over time. Feedback mechanisms present in every signalling pathway lead to diverse dynamic phenotypes, such as transient activation, signal ramping or oscillations, occurring in a cell type- and stage-dependent manner. In cells, such dynamics can exert various functions that allow organisms to develop in a robust and reproducible way. Here, we focus on Erk, Wnt and Notch signalling pathways, which are dynamic in several tissue types and organisms, including the periodic segmentation of vertebrate embryos, and are often dysregulated in cancer. We will discuss how biochemical processes influence their dynamics and how these impact on cellular behaviour within multicellular systems.
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