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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Galvan S, Teixeira AP, Fussenegger M. Enhancing cell-based therapies with synthetic gene circuits responsive to molecular stimuli. Biotechnol Bioeng 2024. [PMID: 38867466 DOI: 10.1002/bit.28770] [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: 10/13/2023] [Revised: 04/21/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
Synthetic biology aims to contribute to the development of next-generation patient-specific cell-based therapies for chronic diseases especially through the construction of sophisticated synthetic gene switches to enhance the safety and spatiotemporal controllability of engineered cells. Indeed, switches that sense and process specific cues, which may be either externally administered triggers or endogenous disease-associated molecules, have emerged as powerful tools for programming and fine-tuning therapeutic outputs. Living engineered cells, often referred to as designer cells, incorporating such switches are delivered to patients either as encapsulated cell implants or by infusion, as in the case of the clinically approved CAR-T cell therapies. Here, we review recent developments in synthetic gene switches responsive to molecular stimuli, spanning regulatory mechanisms acting at the transcriptional, translational, and posttranslational levels. We also discuss current challenges facing clinical translation of cell-based therapies employing these devices.
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Affiliation(s)
- Silvia Galvan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ana P Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
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3
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Frankel NW, Deng H, Yucel G, Gainer M, Leemans N, Lam A, Li Y, Hung M, Lee D, Lee CT, Banicki A, Tian M, Almudhfar N, Naitmazi L, Roguev A, Lee S, Wong W, Gordley R, Lu TK, Garrison BS. Precision off-the-shelf natural killer cell therapies for oncology with logic-gated gene circuits. Cell Rep 2024; 43:114145. [PMID: 38669141 DOI: 10.1016/j.celrep.2024.114145] [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: 08/21/2023] [Revised: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive disease with a poor prognosis (5-year survival rate of 30.5% in the United States). Designing cell therapies to target AML is challenging because no single tumor-associated antigen (TAA) is highly expressed on all cancer subpopulations. Furthermore, TAAs are also expressed on healthy cells, leading to toxicity risk. To address these targeting challenges, we engineer natural killer (NK) cells with a multi-input gene circuit consisting of chimeric antigen receptors (CARs) controlled by OR and NOT logic gates. The OR gate kills a range of AML cells from leukemic stem cells to blasts using a bivalent CAR targeting FLT3 and/or CD33. The NOT gate protects healthy hematopoietic stem cells (HSCs) using an inhibitory CAR targeting endomucin, a protective antigen unique to healthy HSCs. NK cells with the combined OR-NOT gene circuit kill multiple AML subtypes and protect primary HSCs, and the circuit also works in vivo.
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MESH Headings
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Humans
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Animals
- Mice
- Receptors, Chimeric Antigen/metabolism
- Receptors, Chimeric Antigen/immunology
- Gene Regulatory Networks
- Hematopoietic Stem Cells/metabolism
- Cell Line, Tumor
- Precision Medicine/methods
- Cell- and Tissue-Based Therapy/methods
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Affiliation(s)
| | - Han Deng
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Gozde Yucel
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Marcus Gainer
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Nelia Leemans
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Alice Lam
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Yongshuai Li
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Michelle Hung
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Derrick Lee
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Chen-Ting Lee
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Andrew Banicki
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Mengxi Tian
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | | | | | - Assen Roguev
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | | | | | | | - Timothy K Lu
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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4
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Zhang X, Mille-Fragoso LS, Kaseniit KE, Call CC, Zhang M, Hu Y, Xie Y, Gao XJ. Post-Transcriptional Modular Synthetic Receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592453. [PMID: 38746461 PMCID: PMC11092781 DOI: 10.1101/2024.05.03.592453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Inspired by the power of transcriptional synthetic receptors and hoping to complement them to expand the toolbox for cell engineering, we establish LIDAR (Ligand-Induced Dimerization Activating RNA editing), a modular post-transcriptional synthetic receptor platform that harnesses RNA editing by ADAR. LIDAR is compatible with various receptor architectures in different cellular contexts, and enables the sensing of diverse ligands and the production of functional outputs. Furthermore, LIDAR can sense orthogonal signals in the same cell and produce synthetic spatial patterns, potentially enabling the programming of complex multicellular behaviors. Finally, LIDAR is compatible with compact encoding and can be delivered by synthetic mRNA. Thus, LIDAR expands the family of synthetic receptors, holding the promise to empower basic research and therapeutic applications.
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5
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Zhu B, Yin H, Zhang D, Zhang M, Chao X, Scimeca L, Wu MR. Synthetic biology approaches for improving the specificity and efficacy of cancer immunotherapy. Cell Mol Immunol 2024; 21:436-447. [PMID: 38605087 PMCID: PMC11061174 DOI: 10.1038/s41423-024-01153-x] [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: 09/10/2023] [Accepted: 03/03/2024] [Indexed: 04/13/2024] Open
Abstract
Immunotherapy has shown robust efficacy in treating a broad spectrum of hematological and solid cancers. Despite the transformative impact of immunotherapy on cancer treatment, several outstanding challenges remain. These challenges include on-target off-tumor toxicity, systemic toxicity, and the complexity of achieving potent and sustainable therapeutic efficacy. Synthetic biology has emerged as a promising approach to overcome these obstacles, offering innovative tools for engineering living cells with customized functions. This review provides an overview of the current landscape and future prospects of cancer immunotherapy, particularly emphasizing the role of synthetic biology in augmenting its specificity, controllability, and efficacy. We delineate and discuss two principal synthetic biology strategies: those targeting tumor surface antigens with engineered immune cells and those detecting intratumoral disease signatures with engineered gene circuits. This review concludes with a forward-looking perspective on the enduring challenges in cancer immunotherapy and the potential breakthroughs that synthetic biology may contribute to the field.
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Affiliation(s)
- Bo Zhu
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Hang Yin
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA
| | - Di Zhang
- Drug Safety Research & Evaluation, Takeda Pharmaceuticals International Company, Cambridge, MA, 02139, USA
| | - Meiling Zhang
- Medical Research Institute, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, 510080, China
| | - Xiaojuan Chao
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Luca Scimeca
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ming-Ru Wu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA.
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6
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Dolberg TB, Gunnels TF, Ling T, Sarnese KA, Crispino JD, Leonard JN. Building Synthetic Biosensors Using Red Blood Cell Proteins. ACS Synth Biol 2024; 13:1273-1289. [PMID: 38536408 DOI: 10.1021/acssynbio.3c00754] [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] [Indexed: 04/09/2024]
Abstract
As the use of engineered cell therapies expands from pioneering efforts in cancer immunotherapy to other applications, an attractive but less explored approach is the use of engineered red blood cells (RBCs). Compared to other cells, RBCs have a very long circulation time and reside in the blood compartment, so they could be ideally suited for applications as sentinel cells that enable in situ sensing and diagnostics. However, we largely lack tools for converting RBCs into biosensors. A unique challenge is that RBCs remodel their membranes during maturation, shedding many membrane components, suggesting that an RBC-specific approach may be needed. Toward addressing this need, here we develop a biosensing architecture built on RBC membrane proteins that are retained through erythropoiesis. This biosensor employs a mechanism in which extracellular ligand binding is transduced into intracellular reconstitution of a split output protein (including either a fluorophore or an enzyme). By comparatively evaluating a range of biosensor architectures, linker types, scaffold choices, and output signals, we identify biosensor designs and design features that confer substantial ligand-induced signal in vitro. Finally, we demonstrate that erythroid precursor cells engineered with our RBC-protein biosensors function in vivo. This study establishes a foundation for developing RBC-based biosensors that could ultimately address unmet needs including noninvasive monitoring of physiological signals for a range of diagnostic applications.
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Affiliation(s)
- Taylor B Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Taylor F Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Te Ling
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, United States
| | - Kelly A Sarnese
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - John D Crispino
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, United States
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
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7
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Kalogriopoulos NA, Tei R, Yan Y, Ravalin M, Li Y, Ting A. Synthetic G protein-coupled receptors for programmable sensing and control of cell behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589622. [PMID: 38659921 PMCID: PMC11042292 DOI: 10.1101/2024.04.15.589622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Synthetic receptors that mediate antigen-dependent cell responses are transforming therapeutics, drug discovery, and basic research. However, established technologies such as chimeric antigen receptors (CARs) can only detect immobilized antigens, have limited output scope, and lack built-in drug control. Here, we engineer synthetic G protein-coupled receptors (GPCRs) capable of driving a wide range of native or nonnative cellular processes in response to user-defined antigen. We achieve modular antigen gating by engineering and fusing a conditional auto-inhibitory domain onto GPCR scaffolds. Antigen binding to a fused nanobody relieves auto-inhibition and enables receptor activation by drug, thus generating Programmable Antigen-gated G protein-coupled Engineered Receptors (PAGERs). We create PAGERs responsive to more than a dozen biologically and therapeutically important soluble and cell surface antigens, in a single step, from corresponding nanobody binders. Different PAGER scaffolds permit antigen binding to drive transgene expression, real-time fluorescence, or endogenous G protein activation, enabling control of cytosolic Ca 2+ , lipid signaling, cAMP, and neuronal activity. Due to its modular design and generalizability, we expect PAGER to have broad utility in discovery and translational science.
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8
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Wang X, Kang L, Kong D, Wu X, Zhou Y, Yu G, Dai D, Ye H. A programmable protease-based protein secretion platform for therapeutic applications. Nat Chem Biol 2024; 20:432-442. [PMID: 37872400 DOI: 10.1038/s41589-023-01433-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 09/02/2023] [Indexed: 10/25/2023]
Abstract
Cell-based therapies represent potent enabling technologies in biomedical science. However, current genetic control systems for engineered-cell therapies are predominantly based on the transcription or translation of therapeutic outputs. Here we report a protease-based rapid protein secretion system (PASS) that regulates the secretion of pretranslated proteins retained in the endoplasmic reticulum (ER) owing to an ER-retrieval signal. Upon cleavage by inducible proteases, these proteins are secreted. Three PASS variants (chemPASS, antigenPASS and optoPASS) are developed. With chemPASS, we demonstrate the reversal of hyperglycemia in diabetic mice within minutes via drug-induced insulin secretion. AntigenPASS-equipped cells recognize the tumor antigen and secrete granzyme B and perforin, inducing targeted cell apoptosis. Finally, results from mouse models of diabetes, hypertension and inflammatory pain demonstrate light-induced, optoPASS-mediated therapeutic peptide secretion within minutes, conferring anticipated therapeutic benefits. PASS is a flexible platform for rapid delivery of therapeutic proteins that can facilitate the development and adoption of cell-based precision therapies.
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Affiliation(s)
- Xinyi Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Liping Kang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Deqiang Kong
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xin Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- Wuhu Hospital, Health Science Center, East China Normal University, Wuhu City, China
| | - Guiling Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Di Dai
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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9
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Stranford DM, Simons LM, Berman KE, Cheng L, DiBiase BN, Hung ME, Lucks JB, Hultquist JF, Leonard JN. Genetically encoding multiple functionalities into extracellular vesicles for the targeted delivery of biologics to T cells. Nat Biomed Eng 2024; 8:397-414. [PMID: 38012307 PMCID: PMC11088532 DOI: 10.1038/s41551-023-01142-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
The genetic modification of T cells has advanced cellular immunotherapies, yet the delivery of biologics specifically to T cells remains challenging. Here we report a suite of methods for the genetic engineering of cells to produce extracellular vesicles (EVs)-which naturally encapsulate and transfer proteins and nucleic acids between cells-for the targeted delivery of biologics to T cells without the need for chemical modifications. Specifically, the engineered cells secreted EVs that actively loaded protein cargo via a protein tag and that displayed high-affinity T-cell-targeting domains and fusogenic glycoproteins. We validated the methods by engineering EVs that delivered Cas9-single-guide-RNA complexes to ablate the gene encoding the C-X-C chemokine co-receptor type 4 in primary human CD4+ T cells. The strategy is amenable to the targeted delivery of biologics to other cell types.
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Affiliation(s)
- Devin M Stranford
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Katherine E Berman
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA
| | - Luyi Cheng
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA
| | - Beth N DiBiase
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Michelle E Hung
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, USA.
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10
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Recktenwald M, Hutt E, Davis L, MacAulay J, Daringer NM, Galie PA, Staehle MM, Vega SL. Engineering transcriptional regulation for cell-based therapies. SLAS Technol 2024; 29:100121. [PMID: 38340892 DOI: 10.1016/j.slast.2024.100121] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
A major aim in the field of synthetic biology is developing tools capable of responding to user-defined inputs by activating therapeutically relevant cellular functions. Gene transcription and regulation in response to external stimuli are some of the most powerful and versatile of these cellular functions being explored. Motivated by the success of chimeric antigen receptor (CAR) T-cell therapies, transmembrane receptor-based platforms have been embraced for their ability to sense extracellular ligands and to subsequently activate intracellular signal transduction. The integration of transmembrane receptors with transcriptional activation platforms has not yet achieved its full potential. Transient expression of plasmid DNA is often used to explore gene regulation platforms in vitro. However, applications capable of targeting therapeutically relevant endogenous or stably integrated genes are more clinically relevant. Gene regulation may allow for engineered cells to traffic into tissues of interest and secrete functional proteins into the extracellular space or to differentiate into functional cells. Transmembrane receptors that regulate transcription have the potential to revolutionize cell therapies in a myriad of applications, including cancer treatment and regenerative medicine. In this review, we will examine current engineering approaches to control transcription in mammalian cells with an emphasis on systems that can be selectively activated in response to extracellular signals. We will also speculate on the potential therapeutic applications of these technologies and examine promising approaches to expand their capabilities and tighten the control of gene regulation in cellular therapies.
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Affiliation(s)
- Matthias Recktenwald
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Evan Hutt
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Leah Davis
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - James MacAulay
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Nichole M Daringer
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Peter A Galie
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Mary M Staehle
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Sebastián L Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; Department of Orthopaedic Surgery, Cooper Medical School of Rowan University, Camden, NJ 08103, USA.
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11
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Mao Y, Wang S, Yu J, Li W. Engineering pluripotent stem cells with synthetic biology for regenerative medicine. MEDICAL REVIEW (2021) 2024; 4:90-109. [PMID: 38680679 PMCID: PMC11046572 DOI: 10.1515/mr-2023-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/14/2024] [Indexed: 05/01/2024]
Abstract
Pluripotent stem cells (PSCs), characterized by self-renewal and capacity of differentiating into three germ layers, are the programmable building blocks of life. PSC-derived cells and multicellular systems, particularly organoids, exhibit great potential for regenerative medicine. However, this field is still in its infancy, partly due to limited strategies to robustly and precisely control stem cell behaviors, which are tightly regulated by inner gene regulatory networks in response to stimuli from the extracellular environment. Synthetic receptors and genetic circuits are powerful tools to customize the cellular sense-and-response process, suggesting their underlying roles in precise control of cell fate decision and function reconstruction. Herein, we review the progress and challenges needed to be overcome in the fields of PSC-based cell therapy and multicellular system generation, respectively. Furthermore, we summarize several well-established synthetic biology tools and their applications in PSC engineering. Finally, we highlight the challenges and perspectives of harnessing synthetic biology to PSC engineering for regenerative medicine.
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Affiliation(s)
- Yihuan Mao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Siqi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Jiazhen Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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12
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Cui M, Lee S, Ban SH, Ryu JR, Shen M, Yang SH, Kim JY, Choi SK, Han J, Kim Y, Han K, Lee D, Sun W, Kwon HB, Lee D. A single-component, light-assisted uncaging switch for endoproteolytic release. Nat Chem Biol 2024; 20:353-364. [PMID: 37973890 DOI: 10.1038/s41589-023-01480-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Proteases function as pivotal molecular switches, initiating numerous biological events. Notably, potyviral protease, derived from plant viruses, has emerged as a trusted proteolytic switch in synthetic biological circuits. To harness their capabilities, we have developed a single-component photocleavable switch, termed LAUNCHER (Light-Assisted UNcaging switCH for Endoproteolytic Release), by employing a circularly permutated tobacco etch virus protease and a blue-light-gated substrate, which are connected by fine-tuned intermodular linkers. As a single-component system, LAUNCHER exhibits a superior signal-to-noise ratio compared with multi-component systems, enabling precise and user-controllable release of payloads. This characteristic renders LAUNCHER highly suitable for diverse cellular applications, including transgene expression, tailored subcellular translocation and optochemogenetics. Additionally, the plug-and-play integration of LAUNCHER into existing synthetic circuits facilitates the enhancement of circuit performance. The demonstrated efficacy of LAUNCHER in improving existing circuitry underscores its significant potential for expanding its utilization in various applications.
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Affiliation(s)
- Mingguang Cui
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seunghwan Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Hwan Ban
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jae Ryun Ryu
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Meiying Shen
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Hyun Yang
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Young Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seul Ki Choi
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaemin Han
- Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
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Teixeira AP, Fussenegger M. Synthetic Gene Circuits for Regulation of Next-Generation Cell-Based Therapeutics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309088. [PMID: 38126677 PMCID: PMC10885662 DOI: 10.1002/advs.202309088] [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: 11/24/2023] [Indexed: 12/23/2023]
Abstract
Arming human cells with synthetic gene circuits enables to expand their capacity to execute superior sensing and response actions, offering tremendous potential for innovative cellular therapeutics. This can be achieved by assembling components from an ever-expanding molecular toolkit, incorporating switches based on transcriptional, translational, or post-translational control mechanisms. This review provides examples from the three classes of switches, and discusses their advantages and limitations to regulate the activity of therapeutic cells in vivo. Genetic switches designed to recognize internal disease-associated signals often encode intricate actuation programs that orchestrate a reduction in the sensed signal, establishing a closed-loop architecture. Conversely, switches engineered to detect external molecular or physical cues operate in an open-loop fashion, switching on or off upon signal exposure. The integration of such synthetic gene circuits into the next generation of chimeric antigen receptor T-cells is already enabling precise calibration of immune responses in terms of magnitude and timing, thereby improving the potency and safety of therapeutic cells. Furthermore, pre-clinical engineered cells targeting other chronic diseases are gathering increasing attention, and this review discusses the path forward for achieving clinical success. With synthetic biology at the forefront, cellular therapeutics holds great promise for groundbreaking treatments.
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Affiliation(s)
- Ana P. Teixeira
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichKlingelbergstrasse 48BaselCH‐4056Switzerland
- Faculty of ScienceUniversity of BaselKlingelbergstrasse 48BaselCH‐4056Switzerland
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14
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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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15
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Weinberg ZY, Soliman SS, Kim MS, Chen IP, Ott M, El-Samad H. De novo-designed minibinders expand the synthetic biology sensing repertoire. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575267. [PMID: 38293112 PMCID: PMC10827046 DOI: 10.1101/2024.01.12.575267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Synthetic and chimeric receptors capable of recognizing and responding to user-defined antigens have enabled "smart" therapeutics based on engineered cells. These cell engineering tools depend on antigen sensors which are most often derived from antibodies. Advances in the de novo design of proteins have enabled the design of protein binders with the potential to target epitopes with unique properties and faster production timelines compared to antibodies. Building upon our previous work combining a de novo-designed minibinder of the Spike protein of SARS-CoV-2 with the synthetic receptor synNotch (SARSNotch), we investigated whether minibinders can be readily adapted to a diversity of cell engineering tools. We show that the Spike minibinder LCB1 easily generalizes to a next-generation proteolytic receptor SNIPR that performs similarly to our previously reported SARSNotch. LCB1-SNIPR successfully enables the detection of live SARS-CoV-2, an improvement over SARSNotch which can only detect cell-expressed Spike. To test the generalizability of minibinders to diverse applications, we tested LCB1 as an antigen sensor for a chimeric antigen receptor (CAR). LCB1-CAR enabled CD8+ T cells to cytotoxically target Spike-expressing cells. Our findings suggest that minibinders represent a novel class of antigen sensors that have the potential to dramatically expand the sensing repertoire of cell engineering tools.
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Affiliation(s)
| | | | - Matthew S. Kim
- Tetrad Gradudate Program, UCSF, San Francisco CA
- Cell Design Institute, San Francisco CA
| | - Irene P. Chen
- Gladstone Institutes, San Francisco CA
- Department of Medicine, UCSF, San Francisco CA
| | - Melanie Ott
- Gladstone Institutes, San Francisco CA
- Department of Medicine, UCSF, San Francisco CA
- Chan Zuckerberg Biohub–San Francisco, San Francisco CA
| | - Hana El-Samad
- Department of Biochemistry & Biophysics, UCSF, San Francisco CA
- Cell Design Institute, San Francisco CA
- Chan Zuckerberg Biohub–San Francisco, San Francisco CA
- Altos Labs, San Francisco CA
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16
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Teng F, Cui T, Zhou L, Gao Q, Zhou Q, Li W. Programmable synthetic receptors: the next-generation of cell and gene therapies. Signal Transduct Target Ther 2024; 9:7. [PMID: 38167329 PMCID: PMC10761793 DOI: 10.1038/s41392-023-01680-5] [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: 05/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024] Open
Abstract
Cell and gene therapies hold tremendous promise for treating a range of difficult-to-treat diseases. However, concerns over the safety and efficacy require to be further addressed in order to realize their full potential. Synthetic receptors, a synthetic biology tool that can precisely control the function of therapeutic cells and genetic modules, have been rapidly developed and applied as a powerful solution. Delicately designed and engineered, they can be applied to finetune the therapeutic activities, i.e., to regulate production of dosed, bioactive payloads by sensing and processing user-defined signals or biomarkers. This review provides an overview of diverse synthetic receptor systems being used to reprogram therapeutic cells and their wide applications in biomedical research. With a special focus on four synthetic receptor systems at the forefront, including chimeric antigen receptors (CARs) and synthetic Notch (synNotch) receptors, we address the generalized strategies to design, construct and improve synthetic receptors. Meanwhile, we also highlight the expanding landscape of therapeutic applications of the synthetic receptor systems as well as current challenges in their clinical translation.
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Affiliation(s)
- Fei Teng
- University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingqin Gao
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Wei Li
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
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Baronaite U, Cachat E. Preparation of Chromobodies for the Detection of Cell Surface Epitopes. Methods Mol Biol 2024; 2774:303-314. [PMID: 38441773 DOI: 10.1007/978-1-0716-3718-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Chromobodies are nanobodies genetically fused to fluorescent proteins, which were developed to visualize endogenous intracellular antigens. These versatile bioimaging nanotools can also be used to detect cell surface epitopes, and we describe here how we use them as an alternative to conjugated antibodies. This way, we routinely test the binding efficiency of nanobodies for their cognate cell surface antigens, before integrating them as sensing domains into complex synthetic receptor architectures.
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Affiliation(s)
- Ugne Baronaite
- Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- Institute for Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Elise Cachat
- Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
- Institute for Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
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18
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Malaguti M, Lebek T, Blin G, Lowell S. Enabling neighbour labelling: using synthetic biology to explore how cells influence their neighbours. Development 2024; 151:dev201955. [PMID: 38165174 PMCID: PMC10820747 DOI: 10.1242/dev.201955] [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: 09/08/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
Cell-cell interactions are central to development, but exploring how a change in any given cell relates to changes in the neighbour of that cell can be technically challenging. Here, we review recent developments in synthetic biology and image analysis that are helping overcome this problem. We highlight the opportunities presented by these advances and discuss opportunities and limitations in applying them to developmental model systems.
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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
| | - Tamina Lebek
- 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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19
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Dolberg TB, Gunnels TF, Ling T, Sarnese KA, Crispino JD, Leonard JN. Building synthetic biosensors using red blood cell proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.16.571988. [PMID: 38168174 PMCID: PMC10760168 DOI: 10.1101/2023.12.16.571988] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
As the use of engineered cell therapies expands from pioneering efforts in cancer immunotherapy to other applications, an attractive but less explored approach is the use of engineered red blood cells (RBCs). Compared to other cells, RBCs have a very long circulation time and reside in the blood compartment, so they could be ideally suited for applications as sentinel cells that enable in situ sensing and diagnostics. However, we largely lack tools for converting RBCs into biosensors. A unique challenge is that RBCs remodel their membranes during maturation, shedding many membrane components, suggesting that an RBC-specific approach may be needed. Towards addressing this need, here we develop a biosensing architecture built on RBC membrane proteins that are retained through erythropoiesis. This biosensor employs a mechanism in which extracellular ligand binding is transduced into intracellular reconstitution of a split output protein (including either a fluorophore or an enzyme). By comparatively evaluating a range of biosensor architectures, linker types, scaffold choices, and output signals, we identify biosensor designs and design features that confer substantial ligand-induced signal in vitro. Finally, we demonstrate that erythroid precursor cells engineered with our RBC protein biosensors function in vivo. This study establishes a foundation for developing RBC-based biosensors that could ultimately address unmet needs including non-invasive monitoring of physiological signals for a range of diagnostic applications.
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Affiliation(s)
- Taylor B. Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Taylor F. Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Te Ling
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kelly A. Sarnese
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - John D. Crispino
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Joshua N. Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 60208, USA
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20
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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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21
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Makri Pistikou AM, Cremers GAO, Nathalia BL, Meuleman TJ, Bögels BWA, Eijkens BV, de Dreu A, Bezembinder MTH, Stassen OMJA, Bouten CCV, Merkx M, Jerala R, de Greef TFA. Engineering a scalable and orthogonal platform for synthetic communication in mammalian cells. Nat Commun 2023; 14:7001. [PMID: 37919273 PMCID: PMC10622552 DOI: 10.1038/s41467-023-42810-5] [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: 11/18/2022] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
The rational design and implementation of synthetic mammalian communication systems can unravel fundamental design principles of cell communication circuits and offer a framework for engineering of designer cell consortia with potential applications in cell therapeutics. Here, we develop the foundations of an orthogonal, and scalable mammalian synthetic communication platform that exploits the programmability of synthetic receptors and selective affinity and tunability of diffusing coiled-coil peptides. Leveraging the ability of coiled-coils to exclusively bind to a cognate receptor, we demonstrate orthogonal receptor activation and Boolean logic operations at the receptor level. We show intercellular communication based on synthetic receptors and secreted multidomain coiled-coils and demonstrate a three-cell population system that can perform AND gate logic. Finally, we show CC-GEMS receptor-dependent therapeutic protein expression. Our work provides a modular and scalable framework for the engineering of complex cell consortia, with the potential to expand the aptitude of cell therapeutics and diagnostics.
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Affiliation(s)
- Anna-Maria Makri Pistikou
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Glenn A O Cremers
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bryan L Nathalia
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Theodorus J Meuleman
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bruno V Eijkens
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Anne de Dreu
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten T H Bezembinder
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Oscar M J A Stassen
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Carlijn C V Bouten
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Laboratory for Cell and Tissue Engineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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22
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Vlahos AE, Call CC, Kadaba SE, Guo S, Gao XJ. Compact Programmable Control of Protein Secretion in Mammalian Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560774. [PMID: 37873144 PMCID: PMC10592972 DOI: 10.1101/2023.10.04.560774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Synthetic biology currently holds immense potential to engineer the spatiotemporal control of intercellular signals for biomedicine. Programming behaviors using protein-based circuits has advantages over traditional gene circuits such as compact delivery and direct interactions with signaling proteins. Previously, we described a generalizable platform called RELEASE to enable the control of intercellular signaling through the proteolytic removal of ER-retention motifs compatible with pre-existing protease-based circuits. However, these tools lacked the ability to reliably program complex expression profiles and required numerous proteases, limiting delivery options. Here, we harness the recruitment and antagonistic behavior of endogenous 14-3-3 proteins to create RELEASE-NOT to turn off protein secretion in response to protease activity. By combining RELEASE and RELEASE-NOT, we establish a suite of protein-level processing and output modules called Compact RELEASE (compRELEASE). This innovation enables functions such as logic processing and analog signal filtering using a single input protease. Furthermore, we demonstrate the compactness of the post-translational design by using polycistronic single transcripts to engineer cells to control protein secretion via lentiviral integration and leverage mRNA delivery to selectively express cell surface proteins only in engineered cells harboring inducible proteases. CompRELEASE enables complex control of protein secretion and enhances the potential of synthetic protein circuits for therapeutic applications, while minimizing the overall genetic payload.
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Affiliation(s)
- Alexander E. Vlahos
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Connor C. Call
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Samarth E. Kadaba
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Siqi Guo
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
- The Chinese Undergraduate Visiting Research (UGVR) Program, Stanford, CA, 94305, USA
| | - Xiaojing J. Gao
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
- Neurosciences Interdepartmental Program, Stanford University, Stanford, CA, 94305, USA
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23
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Page A, Delles M, Nègre D, Costa C, Fusil F, Cosset FL. Engineering B cells with customized therapeutic responses using a synthetic circuit. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:1-14. [PMID: 37359346 PMCID: PMC10285500 DOI: 10.1016/j.omtn.2023.05.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
The expansion of genetic engineering has brought a new dimension for synthetic immunology. Immune cells are perfect candidates because of their ability to patrol the body, interact with many cell types, proliferate upon activation, and differentiate in memory cells. This study aimed at implementing a new synthetic circuit in B cells, allowing the expression of therapeutic molecules in a temporally and spatially restricted manner that is induced by the presence of specific antigens. This should enhance endogenous B cell functions in terms of recognition and effector properties. We developed a synthetic circuit encoding a sensor (a membrane-anchored B cell receptor targeting a model antigen), a transducer (a minimal promoter induced by the activated sensor), and effector molecules. We isolated a 734-bp-long fragment of the NR4A1 promoter, specifically activated by the sensor signaling cascade in a fully reversible manner. We demonstrate full antigen-specific circuit activation as its recognition by the sensor induced the activation of the NR4A1 promoter and the expression of the effector. Overall, such novel synthetic circuits offer huge possibilities for the treatment of many pathologies, as they are completely programmable; thus, the signal-specific sensors and effector molecules can be adapted to each disease.
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Affiliation(s)
- Audrey Page
- CIRI - Centre International de Recherche en Infectiologie, University Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 Allée d’Italie, 69007 Lyon, France
| | - Marie Delles
- CIRI - Centre International de Recherche en Infectiologie, University Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 Allée d’Italie, 69007 Lyon, France
| | - Didier Nègre
- CIRI - Centre International de Recherche en Infectiologie, University Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 Allée d’Italie, 69007 Lyon, France
| | - Caroline Costa
- CIRI - Centre International de Recherche en Infectiologie, University Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 Allée d’Italie, 69007 Lyon, France
| | - Floriane Fusil
- CIRI - Centre International de Recherche en Infectiologie, University Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 Allée d’Italie, 69007 Lyon, France
| | - François-Loïc Cosset
- CIRI - Centre International de Recherche en Infectiologie, University Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 Allée d’Italie, 69007 Lyon, France
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Zhu I, Piraner DI, Roybal KT. Synthesizing a Smarter CAR T Cell: Advanced Engineering of T-cell Immunotherapies. Cancer Immunol Res 2023; 11:1030-1043. [PMID: 37429007 PMCID: PMC10527511 DOI: 10.1158/2326-6066.cir-22-0962] [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: 12/11/2022] [Revised: 03/15/2023] [Accepted: 06/02/2023] [Indexed: 07/12/2023]
Abstract
The immune system includes an array of specialized cells that keep us healthy by responding to pathogenic cues. Investigations into the mechanisms behind immune cell behavior have led to the development of powerful immunotherapies, including chimeric-antigen receptor (CAR) T cells. Although CAR T cells have demonstrated efficacy in treating blood cancers, issues regarding their safety and potency have hindered the use of immunotherapies in a wider spectrum of diseases. Efforts to integrate developments in synthetic biology into immunotherapy have led to several advancements with the potential to expand the range of treatable diseases, fine-tune the desired immune response, and improve therapeutic cell potency. Here, we examine current synthetic biology advances that aim to improve on existing technologies and discuss the promise of the next generation of engineered immune cell therapies.
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Affiliation(s)
- Iowis Zhu
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
- These authors contributed equally
| | - Dan I. Piraner
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
- These authors contributed equally
| | - Kole T. Roybal
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA 8Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Gladstone UCSF Institute for Genetic Immunology, San Francisco, CA 94107, USA
- UCSF Cell Design Institute, San Francisco, CA 94158, USA
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25
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Lee JC, Brien HJ, Walton BL, Eidman ZM, Toda S, Lim WA, Brunger JM. Instructional materials that control cellular activity through synthetic Notch receptors. Biomaterials 2023; 297:122099. [PMID: 37023529 PMCID: PMC10320837 DOI: 10.1016/j.biomaterials.2023.122099] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/13/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023]
Abstract
The field of regenerative engineering relies primarily on the dual technical platforms of cell selection/conditioning and biomaterial fabrication to support directed cell differentiation. As the field has matured, an appreciation for the influence of biomaterials on cell behaviors has resulted in engineered matrices that meet biomechanical and biochemical demands of target pathologies. Yet, despite advances in methods to produce designer matrices, regenerative engineers remain unable to reliably orchestrate behaviors of therapeutic cells in situ. Here, we present a platform named MATRIX whereby cellular responses to biomaterials can be custom defined by combining engineered materials with cells expressing cognate synthetic biology control modules. Such privileged channels of material-to-cell communication can activate synthetic Notch receptors and govern activities as diverse as transcriptome engineering, inflammation attenuation, and pluripotent stem cell differentiation, all in response to materials decorated with otherwise bioinert ligands. Further, we show that engineered cellular behaviors are confined to programmed biomaterial surfaces, highlighting the potential to use this platform to spatially organize cellular responses to bulk, soluble factors. This integrated approach of co-engineering cells and biomaterials for orthogonal interactions opens new avenues for reproducible control of cell-based therapies and tissue replacements.
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Affiliation(s)
- Joanne C Lee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37212, USA
| | - Hannah J Brien
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37212, USA
| | - Bonnie L Walton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37212, USA
| | - Zachary M Eidman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37212, USA
| | - Satoshi Toda
- WPI Nano Life Science Institute (NanoLSI), Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Wendell A Lim
- Cell Design Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Jonathan M Brunger
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37212, USA; Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, 37212, USA.
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McNamara HM, Ramm B, Toettcher JE. Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems. Semin Cell Dev Biol 2023; 141:33-42. [PMID: 35484026 PMCID: PMC10332110 DOI: 10.1016/j.semcdb.2022.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022]
Abstract
Technological advances have driven many recent advances in developmental biology. Light sheet imaging can reveal single-cell dynamics in living three-dimensional tissues, whereas single-cell genomic methods open the door to a complete catalogue of cell types and gene expression states. An equally powerful but complementary set of approaches are also becoming available to define development processes from the bottom up. These synthetic approaches aim to reconstruct the minimal developmental patterns, signaling processes, and gene networks that produce the basic set of developmental operations: spatial polarization, morphogen interpretation, tissue movement, and cellular memory. In this review we discuss recent approaches at the intersection of synthetic biology and development, including synthetic circuits to deliver and record signaling stimuli and synthetic reconstitution of pattern formation on multicellular scales.
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Affiliation(s)
- Harold M McNamara
- Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA; Department of Physics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Beatrice Ramm
- Department of Physics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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Liu H, Baeumler TA, Nakamura K, Okada Y, Cho S, Eguchi A, Kuroda D, Tsumoto K, Ueki R, Sando S. An Engineered Synthetic Receptor-Aptamer Pair for an Artificial Signal Transduction System. ACS NANO 2023; 17:9039-9048. [PMID: 37154259 DOI: 10.1021/acsnano.2c11744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cell membrane receptors regulate cellular responses through sensing extracellular environmental signals and subsequently transducing them. Receptor engineering provides a means of directing cells to react to a designated external cue and exert programmed functions. However, rational design and precise modulation of receptor signaling activity remain challenging. Here, we report an aptamer-based signal transduction system and its applications in controlling and customizing the functions of engineered receptors. A previously reported membrane receptor-aptamer pair was used to design a synthetic receptor system that transduces cell signaling depending on exogenous aptamer input. To eliminate the cross-reactivity of the receptor with its native ligand, the extracellular domain of the receptor was engineered to ensure that the receptor was solely activated by the DNA aptamer. The present system features tunability in the signaling output level using aptamer ligands with different receptor dimerization propensities. In addition, the functional programmability of DNA aptamers enables the modular sensing of extracellular molecules without the need for genetic engineering of the receptor.
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Affiliation(s)
| | | | | | | | | | | | - Daisuke Kuroda
- Research Center for Drug and Vaccine Development National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Kouhei Tsumoto
- The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
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Zhou J, Ge Q, Wang D, Guo Q, Tao Y. Engineering a modular double-transmembrane synthetic receptor system for customizing cellular programs. Cell Rep 2023; 42:112385. [PMID: 37043348 DOI: 10.1016/j.celrep.2023.112385] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/21/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
Implementation of designer receptors in engineered cells confers them to sense a particular physiological or disease state and respond with user-defined programs. To expand the therapeutic application scope of engineered cells, synthetic receptors realized through different strategies are in great demand. Here, we develop a synthetic receptor system that exerts dual control by incorporating two transmembrane helices for the signal chain. Together with a sensor-actuator device with minimal background signals and a positive loop circuit, this receptor system can sensitively respond to extracellular protein signals. We demonstrate that this synthetic receptor system can be readily adapted to respond to various inputs, such as interleukin-1 (IL-1), programmed death ligand 1 (PD-L1), and HER2, and release customized outputs, including fluorescence signals and the therapeutic molecule IL-2. The robust signaling ability and generality of this receptor system promise it to be a useful tool in the field of cell engineering for fundamental research and translational applications.
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Affiliation(s)
- Jingru Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Qiangqiang Ge
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Dandan Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Qiong Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China.
| | - Yuyong Tao
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China.
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30
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Lee E, Shrestha KL, Kang S, Ramakrishnan N, Kwon Y. Cell-Based Sensors for the Detection of EGF and EGF-Stimulated Ca 2+ Signaling. BIOSENSORS 2023; 13:383. [PMID: 36979595 PMCID: PMC10045995 DOI: 10.3390/bios13030383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Epidermal growth factor (EGF)-mediated activation of EGF receptors (EGFRs) has become an important target in drug development due to the implication of EGFR-mediated cellular signaling in cancer development. While various in vitro approaches are developed for monitoring EGF-EGFR interactions, they have several limitations. Herein, we describe a live cell-based sensor system that can be used to monitor the interaction of EGF and EGFR as well as the subsequent signaling events. The design of the EGF-detecting sensor cells is based on the split-intein-mediated conditional protein trans-cleavage reaction (CPC). CPC is triggered by the presence of the target (EGF) to activate a signal peptide that translocates the fluorescent cargo to the target cellular location (mitochondria). The developed sensor cell demonstrated excellent sensitivity with a fast response time. It was also successfully used to detect an agonist and antagonist of EGFR (transforming growth factor-α and Cetuximab, respectively), demonstrating excellent specificity and capability of screening the analytes based on their function. The usage of sensor cells was then expanded from merely detecting the presence of target to monitoring the target-mediated signaling cascade, by exploiting previously developed Ca2+-detecting sensor cells. These sensor cells provide a useful platform for monitoring EGF-EGFR interaction, for screening EGFR effectors, and for studying downstream cellular signaling cascades.
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Affiliation(s)
- Euiyeon Lee
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Keshab Lal Shrestha
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
| | - Seonhye Kang
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
| | - Neethu Ramakrishnan
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
| | - Youngeun Kwon
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
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31
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Li S, Tang H, Li C, Ma J, Ali M, Dong Q, Wu J, Hui Y, Sun C. Synthetic Biology Technologies And Genetically Engineering Strategies For Enhanced Cell Therapeutics. Stem Cell Rev Rep 2023; 19:309-321. [PMID: 36166137 PMCID: PMC9514184 DOI: 10.1007/s12015-022-10454-5] [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] [Accepted: 09/13/2022] [Indexed: 02/07/2023]
Abstract
Stem cell therapy mainly uses natural stem cells for transplantation, and the use of genetic engineering to optimize stem cell products is a very important process. This article reviews successful gene modification methods in the field of immune cell therapy and summarizes some attempts at stem cell gene editing in current research. Cell bridging is an innovative cutting-edge strategy that includes the specific recognition and signal transduction of artificial receptors. The "off-the-shelf" cell strategies mainly introduce the advantages of allogeneic cell therapy and how to overcome issues such as immunogenicity. Gene regulatory systems allow us to manipulate cells with small molecules to control cellular phenotypes. In addition, we also summarize some important genes that can provide a reference for cell genetic engineering. In conclusion, we summarize a variety of technical strategies for gene editing cells to provide useful ideas and experiences for future stem cell therapy research.
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Affiliation(s)
- Siyu Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Hao Tang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
| | - Cheng Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Jiajia Ma
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Maqsood Ali
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Qi Dong
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Jiajia Wu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China
| | - Yang Hui
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 157 BaoJian Road Nangang Dist, Harbin, 150086, People's Republic of China.
- Basic Medical Institute of Heilongjiang Medical Science Academy, Harbin, China.
| | - Chongran Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, 866 Yuhangtang Road, Hangzhou City, Xihu District, 310058, People's Republic of China.
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Trentesaux C, Yamada T, Klein OD, Lim WA. Harnessing synthetic biology to engineer organoids and tissues. Cell Stem Cell 2023; 30:10-19. [PMID: 36608674 DOI: 10.1016/j.stem.2022.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023]
Abstract
The development of an organism depends on intrinsic genetic programs of progenitor cells and their spatiotemporally complex extrinsic environment. Ex vivo generation of organoids from progenitor cells provides a platform for recapitulating and exploring development. Current approaches rely largely on soluble morphogens or engineered biomaterials to manipulate the physical environment, but the emerging field of synthetic biology provides a powerful toolbox to genetically manipulate cell communication, adhesion, and even cell fate. Applying these modular tools to organoids should lead to a deeper understanding of developmental principles, improved organoid models, and an enhanced capability to design tissues for regenerative purposes.
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Affiliation(s)
- Coralie Trentesaux
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Toshimichi Yamada
- Cell Design Institute, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - Wendell A Lim
- Cell Design Institute, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA.
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de Rossi J, Arefeayne Y, Robinson A, Segatori L. Emerging technologies for genetic control systems in cellular therapies. Curr Opin Biotechnol 2022; 78:102833. [PMID: 36334445 PMCID: PMC10091305 DOI: 10.1016/j.copbio.2022.102833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/23/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022]
Abstract
Progress in synthetic biology has enabled the construction of designer cells that sense biological inputs, and, in response, activate user-defined biomolecular programs. Such engineered cells provide unique opportunities for treating a wide variety of diseases. Current strategies mostly rely on cell-surface receptor systems engineered to convert binding interactions into activation of a transcriptional program. Genetic control systems are emerging as an appealing alternative to receptor-based sensors as they overcome the need for receptor engineering and result in cellular behaviors that operate over therapeutically relevant timescales. Genetic control systems include synthetic gene networks, RNA-based sensors, and post-translational tools. These technologies present fundamental challenges, including the requirement for precise integration with innate pathways, the need for parts orthogonal to existing circuitries, and the metabolic burden induced by such complex cell engineering endeavors. This review discusses the challenges in the design of genetic control systems for cellular therapies and their translational applications.
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Affiliation(s)
- Jacopo de Rossi
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Yafet Arefeayne
- Department of Bioengineering, Rice University, Houston, United States
| | - Ashley Robinson
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Laura Segatori
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States; Department of Bioengineering, Rice University, Houston, United States; Department of Chemical and Biomolecular Engineering, Rice University, Houston, United States; Department of Biosciences, Rice University, Houston, United States.
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Donaldson J, Kleinjan DJ, Rosser S. Synthetic biology approaches for dynamic CHO cell engineering. Curr Opin Biotechnol 2022; 78:102806. [PMID: 36194920 DOI: 10.1016/j.copbio.2022.102806] [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: 05/31/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022]
Abstract
Fed-batch culture of Chinese hamster ovary (CHO) cells remains the most commonly used method for producing biopharmaceuticals. Static CHO cell-line engineering approaches have incrementally improved productivity, growth and product quality through permanent knockout of genes with a negative impact on production, or constitutive overexpression of genes with a positive impact. However, during fed-batch culture, conditions (such as nutrient availability) are continually changing. Therefore, traits that are most beneficial during early-phase culture (such as high growth rate) may be less desirable in late phase. Unlike with static approaches, dynamic cell line engineering strategies can optimise such traits by implementing synthetic sense-and-respond programmes. Here, we review emerging synthetic biology tools that can be used to build dynamic, self-regulating CHO cells, capable of detecting intra-/extracellular cues and generating user-defined responses tailored to the stage-specific needs of the production process.
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Affiliation(s)
- James Donaldson
- UK Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Dirk-Jan Kleinjan
- UK Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan Rosser
- UK Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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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. [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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Abstract
Regulatory processes in biology can be re-conceptualized in terms of logic gates, analogous to those in computer science. Frequently, biological systems need to respond to multiple, sometimes conflicting, inputs to provide the correct output. The language of logic gates can then be used to model complex signal transduction and metabolic processes. Advances in synthetic biology in turn can be used to construct new logic gates, which find a variety of biotechnology applications including in the production of high value chemicals, biosensing, and drug delivery. In this review, we focus on advances in the construction of logic gates that take advantage of biological catalysts, including both protein-based and nucleic acid-based enzymes. These catalyst-based biomolecular logic gates can read a variety of molecular inputs and provide chemical, optical, and electrical outputs, allowing them to interface with other types of biomolecular logic gates or even extend to inorganic systems. Continued advances in molecular modeling and engineering will facilitate the construction of new logic gates, further expanding the utility of biomolecular computing.
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Fink T, Jerala R. Designed protease-based signaling networks. Curr Opin Chem Biol 2022; 68:102146. [DOI: 10.1016/j.cbpa.2022.102146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/09/2022] [Accepted: 03/14/2022] [Indexed: 12/27/2022]
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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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Sowlati-Hashjin S, Gandhi A, Garton M. Dawn of a New Era for Membrane Protein Design. BIODESIGN RESEARCH 2022; 2022:9791435. [PMID: 37850134 PMCID: PMC10521746 DOI: 10.34133/2022/9791435] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/20/2022] [Indexed: 10/19/2023] Open
Abstract
A major advancement has recently occurred in the ability to predict protein secondary structure from sequence using artificial neural networks. This new accessibility to high-quality predicted structures provides a big opportunity for the protein design community. It is particularly welcome for membrane protein design, where the scarcity of solved structures has been a major limitation of the field for decades. Here, we review the work done to date on the membrane protein design and set out established and emerging tools that can be used to most effectively exploit this new access to structures.
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Affiliation(s)
- Shahin Sowlati-Hashjin
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Aanshi Gandhi
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Michael Garton
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
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Zhu I, Liu R, Garcia JM, Hyrenius-Wittsten A, Piraner DI, Alavi J, Israni DV, Liu B, Khalil AS, Roybal KT. Modular design of synthetic receptors for programmed gene regulation in cell therapies. Cell 2022; 185:1431-1443.e16. [PMID: 35427499 PMCID: PMC9108009 DOI: 10.1016/j.cell.2022.03.023] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 01/20/2022] [Accepted: 03/15/2022] [Indexed: 01/01/2023]
Abstract
Synthetic biology has established powerful tools to precisely control cell function. Engineering these systems to meet clinical requirements has enormous medical implications. Here, we adopted a clinically driven design process to build receptors for the autonomous control of therapeutic cells. We examined the function of key domains involved in regulated intramembrane proteolysis and showed that systematic modular engineering can generate a class of receptors that we call synthetic intramembrane proteolysis receptors (SNIPRs) that have tunable sensing and transcriptional response abilities. We demonstrate the therapeutic potential of the receptor platform by engineering human primary T cells for multi-antigen recognition and production of dosed, bioactive payloads relevant to the treatment of disease. Our design framework enables the development of fully humanized and customizable transcriptional receptors for the programming of therapeutic cells suitable for clinical translation.
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Affiliation(s)
- Iowis Zhu
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
| | - Raymond Liu
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
| | - Julie M Garcia
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
| | - Axel Hyrenius-Wittsten
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 221 84, Sweden
| | - Dan I Piraner
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
| | - Josef Alavi
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
| | - Divya V Israni
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Bin Liu
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA; Department of Anesthesia, University of California, San Francisco, San Francisco, CA 94110, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Kole T Roybal
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Gladstone UCSF Institute for Genetic Immunology, San Francisco, CA 94107, USA; UCSF Cell Design Institute, San Francisco, CA 94158, USA.
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Ma Y, Budde MW, Mayalu MN, Zhu J, Lu AC, Murray RM, Elowitz MB. Synthetic mammalian signaling circuits for robust cell population control. Cell 2022; 185:967-979.e12. [PMID: 35235768 PMCID: PMC8995209 DOI: 10.1016/j.cell.2022.01.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/18/2021] [Accepted: 01/28/2022] [Indexed: 01/23/2023]
Abstract
In multicellular organisms, cells actively sense and control their own population density. Synthetic mammalian quorum-sensing circuits could provide insight into principles of population control and extend cell therapies. However, a key challenge is reducing their inherent sensitivity to "cheater" mutations that evade control. Here, we repurposed the plant hormone auxin to enable orthogonal mammalian cell-cell communication and quorum sensing. We designed a paradoxical population control circuit, termed "Paradaux," in which auxin stimulates and inhibits net cell growth at different concentrations. This circuit limited population size over extended timescales of up to 42 days of continuous culture. By contrast, when operating in a non-paradoxical regime, population control became more susceptible to mutational escape. These results establish auxin as a versatile "private" communication system and demonstrate that paradoxical circuit architectures can provide robust population control.
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Affiliation(s)
- Yitong Ma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark W Budde
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Primordium Labs, Arcadia, CA 91006, USA
| | - Michaëlle N Mayalu
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Junqin Zhu
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Andrew C Lu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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42
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Chen M, Tian X, Xu L, Wu R, He H, Zhu H, Xu W, Wei CJ. Membrane tethering of CreER decreases uninduced cell labeling and cytotoxicity while maintaining recombination efficiency. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:1078-1091. [PMID: 35228901 PMCID: PMC8851158 DOI: 10.1016/j.omtn.2022.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 01/28/2022] [Indexed: 02/05/2023]
Abstract
Genetic lineage tracing is indispensable to unraveling the origin, fate, and plasticity of cells. However, the intrinsic leakiness in the CreER-loxP system raises concerns on data interpretation. Here, we reported the generation of a novel dual inducible CreER-loxP system with superior labeling characteristics. This two-component system consists of membrane localized CreER (mCreER: CD8α-FRB-CS-CreER) and TEV protease (mTEVp: CD8α-FKBP-TEVp), which are fusion proteins incorporated with the chemically induced dimerization machinery. Rapamycin and tamoxifen induce sequential dimerization of FKBP and FRB, cleavage of CreER from the membrane, and translocation into the nucleus. The labeling leakiness in Ad293 cells reduced dramatically from more than 70% to less than 5%. This tight labeling feature depends largely on the association of mCreER with HSP90, which conceals the TEV protease cutting site between FRB and CreER and thus preventing uninduced cleavage of the membrane-tethering CreER. Membrane-bound CreER also diminished significantly cytotoxicity. Our studies showed mCreER under the control of the rat insulin promoter increased labeling specificity in MIN6 islet beta-cells. Viability and insulin secretion of MIN6 cells remained intact. Our results demonstrate that this novel system can provide more stringent temporal and spatial control of gene expression and will be useful in cell fate probing.
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Affiliation(s)
- Mianqiao Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China
| | - Xiong Tian
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China
| | - Liqun Xu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China
| | - Ruolan Wu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China
| | - Haoming He
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China
| | - Haibao Zhu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China
| | - Wencan Xu
- Department of Endocrinology, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Chi-ju Wei
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China
- Multidisciplinary Research Center, Shantou University, Shantou, Guangdong 515063, China
- Corresponding author Chi-ju Wei, PhD, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China.
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43
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Manhas J, Edelstein HI, Leonard JN, Morsut L. The evolution of synthetic receptor systems. Nat Chem Biol 2022; 18:244-255. [PMID: 35058646 PMCID: PMC9041813 DOI: 10.1038/s41589-021-00926-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/18/2021] [Indexed: 12/15/2022]
Abstract
Receptors enable cells to detect, process and respond to information about their environments. Over the past two decades, synthetic biologists have repurposed physical parts and concepts from natural receptors to engineer synthetic receptors. These technologies implement customized sense-and-respond programs that link a cell's interaction with extracellular and intracellular cues to user-defined responses. When combined with tools for information processing, these advances enable programming of sophisticated customized functions. In recent years, the library of synthetic receptors and their capabilities has substantially evolved-a term we employ here to mean systematic improvement and expansion. Here, we survey the existing mammalian synthetic biology toolkit of protein-based receptors and signal-processing components, highlighting efforts to evolve and integrate some of the foundational synthetic receptor systems. We then propose a generalized strategy for engineering and improving receptor systems to meet defined functional objectives called a 'metric-enabled approach for synthetic receptor engineering' (MEASRE).
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Affiliation(s)
- Janvie Manhas
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- 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
| | - Hailey I Edelstein
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 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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44
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Protease-controlled secretion and display of intercellular signals. Nat Commun 2022; 13:912. [PMID: 35177637 PMCID: PMC8854555 DOI: 10.1038/s41467-022-28623-y] [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: 10/07/2021] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
To program intercellular communication for biomedicine, it is crucial to regulate the secretion and surface display of signaling proteins. If such regulations are at the protein level, there are additional advantages, including compact delivery and direct interactions with endogenous signaling pathways. Here we create a modular, generalizable design called Retained Endoplasmic Cleavable Secretion (RELEASE), with engineered proteins retained in the endoplasmic reticulum and displayed/secreted in response to specific proteases. The design allows functional regulation of multiple synthetic and natural proteins by synthetic protease circuits to realize diverse signal processing capabilities, including logic operation and threshold tuning. By linking RELEASE to additional sensing and processing circuits, we can achieve elevated protein secretion in response to "undruggable" oncogene KRAS mutants. RELEASE should enable the local, programmable delivery of intercellular cues for a broad variety of fields such as neurobiology, cancer immunotherapy and cell transplantation.
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45
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Javdan SB, Deans TL. Design and development of engineered receptors for cell and tissue engineering. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100363. [PMID: 34527831 PMCID: PMC8437148 DOI: 10.1016/j.coisb.2021.100363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Advances in synthetic biology have provided genetic tools to reprogram cells to obtain desired cellular functions that include tools to enable the customization of cells to sense an extracellular signal and respond with a desired output. These include a variety of engineered receptors capable of transmembrane signaling that transmit information from outside of the cell to inside when specific ligands bind to them. Recent advances in synthetic receptor engineering have enabled the reprogramming of cell and tissue behavior, controlling cell fate decisions, and providing new vehicles for therapeutic delivery.
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Affiliation(s)
- Shwan B. Javdan
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT
| | - Tara L. Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT
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46
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Cable J, Leonard JN, Lu TK, Xie Z, Chang MW, Fernández LÁ, Lora JM, Kaufman HL, Quintana FJ, Geiger R, F Lesser C, Lynch JP, Hava DL, Cornish VW, Lee GK, DiAndreth B, Fero M, Srivastava R, De Coster T, Roybal KT, Rackham OJL, Kiani S, Zhu I, Hernandez-Lopez RA, Guo T, Chen WCW. Synthetic biology: at the crossroads of genetic engineering and human therapeutics-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:98-117. [PMID: 34786712 DOI: 10.1111/nyas.14710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/12/2022]
Abstract
Synthetic biology has the potential to transform cell- and gene-based therapies for a variety of diseases. Sophisticated tools are now available for both eukaryotic and prokaryotic cells to engineer cells to selectively achieve therapeutic effects in response to one or more disease-related signals, thus sparing healthy tissue from potentially cytotoxic effects. This report summarizes the Keystone eSymposium "Synthetic Biology: At the Crossroads of Genetic Engineering and Human Therapeutics," which took place on May 3 and 4, 2021. Given that several therapies engineered using synthetic biology have entered clinical trials, there was a clear need for a synthetic biology symposium that emphasizes the therapeutic applications of synthetic biology as opposed to the technical aspects. Presenters discussed the use of synthetic biology to improve T cell, gene, and viral therapies, to engineer probiotics, and to expand upon existing modalities and functions of cell-based therapies.
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Affiliation(s)
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Interdisciplinary Biological Sciences Program, Chemistry of Life Processes Institute; and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois
| | - Timothy K Lu
- Research Lab of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Senti Biosciences, South San Francisco, California
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Matthew Wook Chang
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - José M Lora
- Intergalactic Therapeutics, Cambridge, Massachusetts
| | - Howard L Kaufman
- Division of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston and The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Roger Geiger
- Institute for Research in Biomedicine, and Institute of Oncology Research, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Cammie F Lesser
- Department of Microbiology, Blavatnik Institute, Harvard Medical School and Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jason P Lynch
- Department of Microbiology, Blavatnik Institute, Harvard Medical School and Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - David L Hava
- Research Lab of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Gary K Lee
- Senti Biosciences, South San Francisco, California
| | | | - Michael Fero
- TeselaGen Biotechnology, San Francisco, California
| | - Rajkamal Srivastava
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Kolkata, India
| | - Tim De Coster
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kole T Roybal
- Department of Microbiology and Immunology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.,Chan Zuckerberg Biohub; Parker Institute for Cancer Immunotherapy, Gladstone-UCSF Institute for Genomic Immunology; and UCSF Cell Design Institute, San Francisco, California
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore
| | - Samira Kiani
- Division of Experimental Pathology, Department of Pathology, School of Medicine; and Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Iowis Zhu
- University of California, San Francisco, San Francisco, California
| | - Rogelio A Hernandez-Lopez
- Cell Design Institute, Department of Cellular and Molecular Pharmacology; and Center for Cellular Construction, University of California San Francisco, San Francisco, California
| | - Tingxi Guo
- Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - William C W Chen
- Research Laboratory of Electronics and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge; and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
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47
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Page A, Hubert J, Fusil F, Cosset FL. Exploiting B Cell Transfer for Cancer Therapy: Engineered B Cells to Eradicate Tumors. Int J Mol Sci 2021; 22:9991. [PMID: 34576154 PMCID: PMC8468294 DOI: 10.3390/ijms22189991] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/22/2023] Open
Abstract
Nowadays, cancers still represent a significant health burden, accounting for around 10 million deaths per year, due to ageing populations and inefficient treatments for some refractory cancers. Immunotherapy strategies that modulate the patient's immune system have emerged as good treatment options. Among them, the adoptive transfer of B cells selected ex vivo showed promising results, with a reduction in tumor growth in several cancer mouse models, often associated with antitumoral immune responses. Aside from the benefits of their intrinsic properties, including antigen presentation, antibody secretion, homing and long-term persistence, B cells can be modified prior to reinfusion to increase their therapeutic role. For instance, B cells have been modified mainly to boost their immuno-stimulatory activation potential by forcing the expression of costimulatory ligands using defined culture conditions or gene insertion. Moreover, tumor-specific antigen presentation by infused B cells has been increased by ex vivo antigen loading (peptides, RNA, DNA, virus) or by the sorting/ engineering of B cells with a B cell receptor specific to tumor antigens. Editing of the BCR also rewires B cell specificity toward tumor antigens, and may trigger, upon antigen recognition, the secretion of antitumor antibodies by differentiated plasma cells that can then be recognized by other immune components or cells involved in tumor clearance by antibody-dependent cell cytotoxicity or complement-dependent cytotoxicity for example. With the expansion of gene editing methodologies, new strategies to reprogram immune cells with whole synthetic circuits are being explored: modified B cells can sense disease-specific biomarkers and, in response, trigger the expression of therapeutic molecules, such as molecules that counteract the tumoral immunosuppressive microenvironment. Such strategies remain in their infancy for implementation in B cells, but are likely to expand in the coming years.
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Affiliation(s)
| | | | | | - François-Loïc Cosset
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 Allée d’Italie, F-69007 Lyon, France; (A.P.); (J.H.); (F.F.)
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48
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Beitz AM, Oakes CG, Galloway KE. Synthetic gene circuits as tools for drug discovery. Trends Biotechnol 2021; 40:210-225. [PMID: 34364685 DOI: 10.1016/j.tibtech.2021.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022]
Abstract
Within mammalian systems, there exists enormous opportunity to use synthetic gene circuits to enhance phenotype-based drug discovery, to map the molecular origins of disease, and to validate therapeutics in complex cellular systems. While drug discovery has relied on marker staining and high-content imaging in cell-based assays, synthetic gene circuits expand the potential for precision and speed. Here we present a vision of how circuits can improve the speed and accuracy of drug discovery by enhancing the efficiency of hit triage, capturing disease-relevant dynamics in cell-based assays, and simplifying validation and readouts from organoids and microphysiological systems (MPS). By tracking events and cellular states across multiple length and time scales, circuits will transform how we decipher the causal link between molecular events and phenotypes to improve the selectivity and sensitivity of cell-based assays.
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Affiliation(s)
- Adam M Beitz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Conrad G Oakes
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Mishra D, Bepler T, Teague B, Berger B, Broach J, Weiss R. An engineered protein-phosphorylation toggle network with implications for endogenous network discovery. Science 2021; 373:eaav0780. [PMID: 34210851 PMCID: PMC11203391 DOI: 10.1126/science.aav0780] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 04/29/2021] [Indexed: 12/23/2022]
Abstract
Synthetic biological networks comprising fast, reversible reactions could enable engineering of new cellular behaviors that are not possible with slower regulation. Here, we created a bistable toggle switch in Saccharomyces cerevisiae using a cross-repression topology comprising 11 protein-protein phosphorylation elements. The toggle is ultrasensitive, can be induced to switch states in seconds, and exhibits long-term bistability. Motivated by our toggle's architecture and size, we developed a computational framework to search endogenous protein pathways for other large and similar bistable networks. Our framework helped us to identify and experimentally verify five formerly unreported endogenous networks that exhibit bistability. Building synthetic protein-protein networks will enable bioengineers to design fast sensing and processing systems, allow sophisticated regulation of cellular processes, and aid discovery of endogenous networks with particular functions.
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Affiliation(s)
- Deepak Mishra
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tristan Bepler
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Brian Teague
- Department of Biology, University of Wisconsin, Stout, WI, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jim Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
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Pandelakis M, Delgado E, Ebrahimkhani MR. CRISPR-Based Synthetic Transcription Factors In Vivo: The Future of Therapeutic Cellular Programming. Cell Syst 2021; 10:1-14. [PMID: 31972154 DOI: 10.1016/j.cels.2019.10.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/14/2019] [Accepted: 10/09/2019] [Indexed: 01/04/2023]
Abstract
Pinpoint control over endogenous gene expression in vivo has long been a fevered dream for clinicians and researchers alike. With the recent repurposing of programmable, RNA-guided DNA endonucleases from the CRISPR bacterial immune system, this dream is becoming a powerful reality. Engineered CRISPR/Cas9-based transcriptional regulators and epigenome editors have enabled researchers to perturb endogenous gene expression in vivo, allowing for the therapeutic reprogramming of cell and tissue behavior. For this technology to be of maximal use, a variety of technological hurdles still need to be addressed. Better understanding of the design principle controlling gene expression together with technologies that enable spatiotemporal control of transcriptional engineering are fundamental for rational design, improved efficacy, and ultimately safe translation to humans. In this review, we will discuss recent advances and integrative strategies that can help pave the path toward a new class of transcriptional therapeutics.
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Affiliation(s)
- Matthew Pandelakis
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA
| | - Elizabeth Delgado
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA
| | - Mo R Ebrahimkhani
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA; Department of Pathology, Division of Experimental Pathology, University of Pittsburgh, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA.
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