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Liang Z, Hu Y, Li CY, Yau WL, Tan K, Kuang Y. VPg-based bidirectional synthetic mRNA circuits enable orthogonal protein regulation for high-resolution cell separation. Chem Commun (Camb) 2024; 60:5427-5430. [PMID: 38685869 DOI: 10.1039/d4cc01725k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Synthetic mRNA circuits commonly sense input to produce binary output signals for cell separation. Based on virus-origin cap-independent translation initiation machinery and RBP-aptamer interaction, we designed smart synthetic mRNA-based circuits that sense single input molecules to bidirectionally tune output signals in an orthogonal manner, enabling high-resolution separation of cell populations.
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Affiliation(s)
- Zhenghua Liang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Yaxin Hu
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Wai Laam Yau
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Kaixin Tan
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
| | - Yi Kuang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Room 5578, Academic Bldg, Clear Water Bay, Kowloon, Hong Kong.
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Shao J, Li S, Qiu X, Jiang J, Zhang L, Wang P, Si Y, Wu Y, He M, Xiong Q, Zhao L, Li Y, Fan Y, Viviani M, Fu Y, Wu C, Gao T, Zhu L, Fussenegger M, Wang H, Xie M. Engineered poly(A)-surrogates for translational regulation and therapeutic biocomputation in mammalian cells. Cell Res 2024; 34:31-46. [PMID: 38172533 PMCID: PMC10770082 DOI: 10.1038/s41422-023-00896-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/27/2023] [Indexed: 01/05/2024] Open
Abstract
Here, we present a gene regulation strategy enabling programmable control over eukaryotic translational initiation. By excising the natural poly-adenylation (poly-A) signal of target genes and replacing it with a synthetic control region harboring RNA-binding protein (RBP)-specific aptamers, cap-dependent translation is rendered exclusively dependent on synthetic translation initiation factors (STIFs) containing different RBPs engineered to conditionally associate with different eIF4F-binding proteins (eIFBPs). This modular design framework facilitates the engineering of various gene switches and intracellular sensors responding to many user-defined trigger signals of interest, demonstrating tightly controlled, rapid and reversible regulation of transgene expression in mammalian cells as well as compatibility with various clinically applicable delivery routes of in vivo gene therapy. Therapeutic efficacy was demonstrated in two animal models. To exemplify disease treatments that require on-demand drug secretion, we show that a custom-designed gene switch triggered by the FDA-approved drug grazoprevir can effectively control insulin expression and restore glucose homeostasis in diabetic mice. For diseases that require instantaneous sense-and-response treatment programs, we create highly specific sensors for various subcellularly (mis)localized protein markers (such as cancer-related fusion proteins) and show that translation-based protein sensors can be used either alone or in combination with other cell-state classification strategies to create therapeutic biocomputers driving self-sufficient elimination of tumor cells in mice. This design strategy demonstrates unprecedented flexibility for translational regulation and could form the basis for a novel class of programmable gene therapies in vivo.
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Affiliation(s)
- Jiawei Shao
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Shichao Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinyuan Qiu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, Hunan, China
| | - Jian Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Lihang Zhang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Research Center of Biological Computation, Zhejiang Laboratory, Hangzhou, Zhejiang, China
| | - Pengli Wang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Yaqing Si
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Yuhang Wu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Minghui He
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Qiqi Xiong
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Liuqi Zhao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yilin Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuxuan Fan
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mirta Viviani
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Yu Fu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Chaohua Wu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Ting Gao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, Hunan, China
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
- Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Hui Wang
- Research Center of Biological Computation, Zhejiang Laboratory, Hangzhou, Zhejiang, China.
| | - Mingqi Xie
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
- School of Engineering, Westlake University, Hangzhou, Zhejiang, China.
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Komatsu S, Ohno H, Saito H. Target-dependent RNA polymerase as universal platform for gene expression control in response to intracellular molecules. Nat Commun 2023; 14:7256. [PMID: 37978180 PMCID: PMC10656481 DOI: 10.1038/s41467-023-42802-5] [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: 06/21/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023] Open
Abstract
Controlling gene expression in response to specific molecules is an essential technique for regulating cellular functions. However, current platforms with transcription and translation regulators have a limited number of detectable molecules to induce gene expression. Here to address these issues, we present a Target-dependent RNA polymerase (TdRNAP) that can induce RNA transcription in response to the intracellular target specifically recognized by single antibody. By substituting the fused antibody, we demonstrate that TdRNAPs respond to a wide variety of molecules, including peptides, proteins, RNA, and small molecules, and produce desired transcripts in human cells. Furthermore, we show that multiple TdRNAPs can construct orthogonal and multilayer genetic circuits. Finally, we apply TdRNAP to achieve cell-specific genome editing that is autonomously triggered by detecting the target gene product. TdRNAP can expand the molecular variety for controlling gene expression and provide the genetic toolbox for bioengineering and future therapeutic applications.
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Affiliation(s)
- Shodai Komatsu
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hirohisa Ohno
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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Deng Z, Yang H, Tian Y, Liu Z, Sun F, Yang P. An OX40L mRNA vaccine inhibits the growth of hepatocellular carcinoma. Front Oncol 2022; 12:975408. [PMID: 36313716 PMCID: PMC9606466 DOI: 10.3389/fonc.2022.975408] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
mRNA cancer vaccines show therapeutic potential for malignant tumors, including hepatocellular carcinoma (HCC). We optimized and synthesized stable mRNA encoding costimulator Oxford 40 ligand (OX40L). For systemic delivery, OX40L mRNAs were loaded into lipid nanoparticles (LNPs). The expression and costimulatory effects of OX40L were investigated in vitro. OX40L was expressed on the cell surface and costimulated T cells. In vivo, intratumoral injection of LNPs encapsulating OX40L mRNAs significantly reduced tumor growth and increased the survival of mice bearing H22 tumors. Importantly, CD4+ and CD8+ T cells were significantly increased in the OX40L mRNA group in vivo. Taken together, our findings provide a promising clinical strategy for immunotherapy for HCC using mRNA vaccines.
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Affiliation(s)
- Zhuoya Deng
- Medical School of Chinese PLA, Beijing, China,Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hao Yang
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yuying Tian
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zherui Liu
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China,Peking University 302 Clinical Medical School, Peking University, Beijing, China
| | - Fang Sun
- Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Penghui Yang
- Medical School of Chinese PLA, Beijing, China,Faculty of Hepato-Pancreato-Biliary Surgery, Institute of Hepatobiliary Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China,*Correspondence: Penghui Yang,
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