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De Carluccio G, Fusco V, di Bernardo D. Engineering a synthetic gene circuit for high-performance inducible expression in mammalian systems. Nat Commun 2024; 15:3311. [PMID: 38632224 PMCID: PMC11024104 DOI: 10.1038/s41467-024-47592-y] [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: 09/28/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Inducible gene expression systems can be used to control the expression of a gene of interest by means of a small-molecule. One of the most common designs involves engineering a small-molecule responsive transcription factor (TF) and its cognate promoter, which often results in a compromise between minimal uninduced background expression (leakiness) and maximal induced expression. Here, we focus on an alternative strategy using quantitative synthetic biology to mitigate leakiness while maintaining high expression, without modifying neither the TF nor the promoter. Through mathematical modelling and experimental validations, we design the CASwitch, a mammalian synthetic gene circuit based on combining two well-known network motifs: the Coherent Feed-Forward Loop (CFFL) and the Mutual Inhibition (MI). The CASwitch combines the CRISPR-Cas endoribonuclease CasRx with the state-of-the-art Tet-On3G inducible gene system to achieve high performances. To demonstrate the potentialities of the CASwitch, we apply it to three different scenarios: enhancing a whole-cell biosensor, controlling expression of a toxic gene and inducible production of Adeno-Associated Virus (AAV) vectors.
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Affiliation(s)
- Giuliano De Carluccio
- Telethon Institute of Genetics and Medicine, Naples, Italy
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
| | - Virginia Fusco
- Telethon Institute of Genetics and Medicine, Naples, Italy
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine, Naples, Italy.
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy.
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Systems Biology Approaches for the Improvement of Oncolytic Virus-Based Immunotherapies. Cancers (Basel) 2023; 15:cancers15041297. [PMID: 36831638 PMCID: PMC9954314 DOI: 10.3390/cancers15041297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Oncolytic virus (OV)-based immunotherapy is mainly dependent on establishing an efficient cell-mediated antitumor immunity. OV-mediated antitumor immunity elicits a renewed antitumor reactivity, stimulating a T-cell response against tumor-associated antigens (TAAs) and recruiting natural killer cells within the tumor microenvironment (TME). Despite the fact that OVs are unspecific cancer vaccine platforms, to further enhance antitumor immunity, it is crucial to identify the potentially immunogenic T-cell restricted TAAs, the main key orchestrators in evoking a specific and durable cytotoxic T-cell response. Today, innovative approaches derived from systems biology are exploited to improve target discovery in several types of cancer and to identify the MHC-I and II restricted peptide repertoire recognized by T-cells. Using specific computation pipelines, it is possible to select the best tumor peptide candidates that can be efficiently vectorized and delivered by numerous OV-based platforms, in order to reinforce anticancer immune responses. Beyond the identification of TAAs, system biology can also support the engineering of OVs with improved oncotropism to reduce toxicity and maintain a sufficient portion of the wild-type virus virulence. Finally, these technologies can also pave the way towards a more rational design of armed OVs where a transgene of interest can be delivered to TME to develop an intratumoral gene therapy to enhance specific immune stimuli.
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Greenshpan Y, Sharabi O, Yegodayev KM, Novoplansky O, Elkabets M, Gazit R, Porgador A. The Contribution of the Minimal Promoter Element to the Activity of Synthetic Promoters Mediating CAR Expression in the Tumor Microenvironment. Int J Mol Sci 2022; 23:7431. [PMID: 35806439 PMCID: PMC9266962 DOI: 10.3390/ijms23137431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/01/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Harnessing immune effector cells to benefit cancer patients is becoming more and more prevalent in recent years. However, the increasing number of different therapeutic approaches, such as chimeric antigen receptors and armored chimeric antigen receptors, requires constant adjustments of the transgene expression levels. We have previously demonstrated it is possible to achieve spatial and temporal control of transgene expression as well as tailoring the inducing agents using the Chimeric Antigen Receptor Tumor Induced Vector (CARTIV) platform. Here we describe the next level of customization in our promoter platform. We have tested the functionality of three different minimal promoters, representing three different promoters' strengths, leading to varying levels of CAR expression and primary T cell function. This strategy shows yet another level of CARTIV gene regulation that can be easily integrated into existing CAR T systems.
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Affiliation(s)
- Yariv Greenshpan
- The Shraga Segal Department of Microbiology, Faculty of Health Sciences, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (Y.G.); (O.S.); (K.M.Y.); (O.N.); (M.E.)
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Omri Sharabi
- The Shraga Segal Department of Microbiology, Faculty of Health Sciences, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (Y.G.); (O.S.); (K.M.Y.); (O.N.); (M.E.)
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Ksenia M. Yegodayev
- The Shraga Segal Department of Microbiology, Faculty of Health Sciences, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (Y.G.); (O.S.); (K.M.Y.); (O.N.); (M.E.)
| | - Ofra Novoplansky
- The Shraga Segal Department of Microbiology, Faculty of Health Sciences, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (Y.G.); (O.S.); (K.M.Y.); (O.N.); (M.E.)
| | - Moshe Elkabets
- The Shraga Segal Department of Microbiology, Faculty of Health Sciences, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (Y.G.); (O.S.); (K.M.Y.); (O.N.); (M.E.)
| | - Roi Gazit
- The Shraga Segal Department of Microbiology, Faculty of Health Sciences, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (Y.G.); (O.S.); (K.M.Y.); (O.N.); (M.E.)
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Angel Porgador
- The Shraga Segal Department of Microbiology, Faculty of Health Sciences, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; (Y.G.); (O.S.); (K.M.Y.); (O.N.); (M.E.)
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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