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Santorelli M, Bhamidipati PS, Courte J, Swedlund B, Jain N, Poon K, Schildknecht D, Kavanagh A, MacKrell VA, Sondkar T, Malaguti M, Quadrato G, Lowell S, Thomson M, Morsut L. Control of spatio-temporal patterning via cell growth in a multicellular synthetic gene circuit. Nat Commun 2024; 15:9867. [PMID: 39562554 PMCID: PMC11577002 DOI: 10.1038/s41467-024-53078-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 10/01/2024] [Indexed: 11/21/2024] Open
Abstract
A major goal in synthetic development is to build gene regulatory circuits that control patterning. In natural development, an interplay between mechanical and chemical communication shapes the dynamics of multicellular gene regulatory circuits. For synthetic circuits, how non-genetic properties of the growth environment impact circuit behavior remains poorly explored. Here, we first describe an occurrence of mechano-chemical coupling in synthetic Notch (synNotch) patterning circuits: high cell density decreases synNotch-gated gene expression in different cellular systems in vitro. We then construct, both in vitro and in silico, a synNotch-based signal propagation circuit whose outcome can be regulated by cell density. Spatial and temporal patterning outcomes of this circuit can be predicted and controlled via modulation of cell proliferation, initial cell density, and/or spatial distribution of cell density. Our work demonstrates that synthetic patterning circuit outcome can be controlled via cellular growth, providing a means for programming multicellular circuit patterning outcomes.
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Affiliation(s)
- Marco Santorelli
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Pranav S Bhamidipati
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Josquin Courte
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Benjamin Swedlund
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Naisargee Jain
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kyle Poon
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Dominik Schildknecht
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andriu Kavanagh
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Victoria A MacKrell
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Trusha Sondkar
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mattias Malaguti
- Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Giorgia Quadrato
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sally Lowell
- Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
- Beckman Center for Single-Cell Profiling and Engineering, Pasadena, CA, USA.
| | - Leonardo Morsut
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
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Appleton E, Mehdipour N, Daifuku T, Briers D, Haghighi I, Moret M, Chao G, Wannier T, Chiappino-Pepe A, Huang J, Belta C, Church GM. Algorithms for Autonomous Formation of Multicellular Shapes from Single Cells. ACS Synth Biol 2024; 13:2753-2763. [PMID: 39194023 DOI: 10.1021/acssynbio.4c00037] [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: 08/29/2024]
Abstract
Multicellular organisms originate from a single cell, ultimately giving rise to mature organisms of heterogeneous cell type composition in complex structures. Recent work in the areas of stem cell biology and tissue engineering has laid major groundwork in the ability to convert certain types of cells into other types, but there has been limited progress in the ability to control the morphology of cellular masses as they grow. Contemporary approaches to this problem have included the use of artificial scaffolds, 3D bioprinting, and complex media formulations; however, there are no existing approaches to controlling this process purely through genetics and from a single-cell starting point. Here we describe a computer-aided design approach, called CellArchitect, for designing recombinase-based genetic circuits for controlling the formation of multicellular masses into arbitrary shapes in human cells.
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Affiliation(s)
- Evan Appleton
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Noushin Mehdipour
- Department of Systems Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Tristan Daifuku
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Demarcus Briers
- Department of Systems Engineering, Boston University, Boston, Massachusetts 02215, United States
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, United States
| | - Iman Haghighi
- Department of Systems Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Michaël Moret
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - George Chao
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Timothy Wannier
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Anush Chiappino-Pepe
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jeremy Huang
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Calin Belta
- Department of Systems Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
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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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Lam C, Morsut L. Programming Juxtacrine-Based Synthetic Signaling Networks in a Cellular Potts Framework. Methods Mol Biol 2024; 2760:283-307. [PMID: 38468095 DOI: 10.1007/978-1-0716-3658-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Synthetic development is a synthetic biology subfield aiming to reprogram higher-order eukaryotic cells for tissue formation and morphogenesis. Reprogramming efforts commonly rely upon implementing custom signaling networks into these cells, but the efficient design of these signaling networks is a substantial challenge. It is difficult to predict the tissue/morphogenic outcome of these networks, and in vitro testing of many networks is both costly and time-consuming. We therefore developed a computational framework with an in silico cell line (ISCL) that sports basic but modifiable features such as adhesion, motility, growth, and division. More importantly, ISCL can be quickly engineered with custom genetic circuits to test, improve, and explore different signaling network designs. We implemented this framework in a free cellular Potts modeling software CompuCell3D. In this chapter, we briefly discuss how to start with CompuCell3D and then go through the steps of how to make and modify ISCL. We then go through the steps of programming custom genetic circuits into ISCL to generate an example signaling network.
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Affiliation(s)
- Calvin Lam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Leonardo Morsut
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
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Almeida‐Pinto J, Lagarto MR, Lavrador P, Mano JF, Gaspar VM. Cell Surface Engineering Tools for Programming Living Assemblies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304040. [PMID: 37823678 PMCID: PMC10700290 DOI: 10.1002/advs.202304040] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/10/2023] [Indexed: 10/13/2023]
Abstract
Breakthroughs in precision cell surface engineering tools are supporting the rapid development of programmable living assemblies with valuable features for tackling complex biological problems. Herein, the authors overview the most recent technological advances in chemically- and biologically-driven toolboxes for engineering mammalian cell surfaces and triggering their assembly into living architectures. A particular focus is given to surface engineering technologies for enabling biomimetic cell-cell social interactions and multicellular cell-sorting events. Further advancements in cell surface modification technologies may expand the currently available bioengineering toolset and unlock a new generation of personalized cell therapeutics with clinically relevant biofunctionalities. The combination of state-of-the-art cell surface modifications with advanced biofabrication technologies is envisioned to contribute toward generating living materials with increasing tissue/organ-mimetic bioactivities and therapeutic potential.
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Affiliation(s)
- José Almeida‐Pinto
- Department of ChemistryCICECO‐Aveiro Institute of Materials University of Aveiro Campus Universitário de SantiagoAveiro3810‐193Portugal
| | - Matilde R. Lagarto
- Department of ChemistryCICECO‐Aveiro Institute of Materials University of Aveiro Campus Universitário de SantiagoAveiro3810‐193Portugal
| | - Pedro Lavrador
- Department of ChemistryCICECO‐Aveiro Institute of Materials University of Aveiro Campus Universitário de SantiagoAveiro3810‐193Portugal
| | - João F. Mano
- Department of ChemistryCICECO‐Aveiro Institute of Materials University of Aveiro Campus Universitário de SantiagoAveiro3810‐193Portugal
| | - Vítor M. Gaspar
- Department of ChemistryCICECO‐Aveiro Institute of Materials University of Aveiro Campus Universitário de SantiagoAveiro3810‐193Portugal
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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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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: 5] [Impact Index Per Article: 2.5] [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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Lam CK, Hyde RK, Patel SA. Synthetic Immunotherapy: Programming Immune Cells with Novel and Sophisticated Logic Capabilities. Transplant Cell Ther 2022; 28:560-571. [PMID: 35691572 DOI: 10.1016/j.jtct.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/23/2022] [Accepted: 06/06/2022] [Indexed: 10/18/2022]
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