1
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Yun J, Huang Y, Miller ADC, Chang BL, Baldini L, Dhanabalan KM, Li E, Li H, Mukherjee A. Destabilized reporters for background-subtracted, chemically-gated, and multiplexed deep-tissue imaging. Chem Sci 2024; 15:11108-11121. [PMID: 39027298 PMCID: PMC11253201 DOI: 10.1039/d4sc00377b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/23/2024] [Indexed: 07/20/2024] Open
Abstract
Tracking gene expression in deep tissues requires genetic reporters that can be unambiguously detected using tissue penetrant techniques. Magnetic resonance imaging (MRI) is uniquely suited for this purpose; however, there is a dearth of reporters that can be reliably linked to gene expression with minimal interference from background tissue signals. Here, we present a conceptually new method for generating background-subtracted, drug-gated, multiplex images of gene expression using MRI. Specifically, we engineered chemically erasable reporters consisting of a water channel, aquaporin-1, fused to destabilizing domains, which are stabilized by binding to cell-permeable small-molecule ligands. We showed that this approach allows for highly specific detection of gene expression through differential imaging. In addition, by engineering destabilized aquaporin-1 variants with orthogonal ligand requirements, it is possible to distinguish distinct subpopulations of cells in mixed cultures. Finally, we demonstrated this approach in a mouse tumor model through differential imaging of gene expression with minimal background.
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Affiliation(s)
- Jason Yun
- Department of Chemistry, University of California Santa Barbara CA 93106 USA
| | - Yimeng Huang
- Department of Chemistry, University of California Santa Barbara CA 93106 USA
| | - Austin D C Miller
- Biomolecular Science and Engineering Graduate Program, University of California Santa Barbara CA 93106 USA
| | - Brandon L Chang
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Barbara CA 93106 USA
| | - Logan Baldini
- Department of Chemical Engineering, University of California Santa Barbara CA 93106 USA
| | - Kaamini M Dhanabalan
- Department of Chemical Engineering, University of California Santa Barbara CA 93106 USA
| | - Eugene Li
- Department of Chemical Engineering, University of California Santa Barbara CA 93106 USA
| | - Honghao Li
- Department of Chemistry, University of California Santa Barbara CA 93106 USA
| | - Arnab Mukherjee
- Department of Chemistry, University of California Santa Barbara CA 93106 USA
- Biomolecular Science and Engineering Graduate Program, University of California Santa Barbara CA 93106 USA
- Department of Chemical Engineering, University of California Santa Barbara CA 93106 USA
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2
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Utsugi Y, Nishimura K, Yamanaka S, Nishino K, Kosako H, Sawasaki T, Shigemori H, Wandless TJ, Miyamae Y. Ubiquitin-Derived Fragment as a Peptide Linker for the Efficient Cleavage of a Target Protein from a Degron. ACS Chem Biol 2024; 19:497-505. [PMID: 38270585 DOI: 10.1021/acschembio.3c00670] [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: 01/26/2024]
Abstract
The chemogenetic control of cellular protein stability using degron tags is a powerful experimental strategy in biomedical research. However, this technique requires permanent fusion of the degron to a target protein, which may interfere with the proper function of the protein. Here, we report a peptide fragment from the carboxyl terminus of ubiquitin as a cleavable linker that exhibits the slow but efficient cleavage of a degron tag via cellular deubiquitinating enzymes (DUBs). We designed a fusion protein consisting of a cleavable linker and a destabilizing domain (DD), which conditionally controls the expression and release of a target protein in a ligand-induced state, allowing the free unmodified protein to perform its function. Insertion of an AGIA epitope at the carboxyl terminus of the linker made space for the DUBs to access the site to assist the cleavage reaction when the amino terminus of the target protein caused steric hindrance. The developed system, termed a cleavable degron using ubiquitin-derived linkers (c-DUB), provides robust and tunable regulation of target proteins in their native forms. The c-DUB system is a useful tool for the regulation of proteins that have terminal sites that are essential for the proper localization and function. In addition, a mechanistic investigation using proximity labeling showed that DUBs associate with the refolded DD to reverse ubiquitination, suggesting a cellular surveillance system for distinguishing the refolded DD from misfolded proteins. The c-DUB method may benefit from this machinery so that DUBs subsequently cleave the neighboring linker.
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Affiliation(s)
- Yuki Utsugi
- Doctoral Program in Life Science Innovation, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Ken Nishimura
- Laboratory of Gene Regulation, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Satoshi Yamanaka
- Division of Proteo-Interactome, Proteo-Science Center, Ehime University, 3 Bunkyocho, Matsuyama, Ehime 790-8577, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyocho, Matsuyama, Ehime 790-8577, Japan
| | - Hideyuki Shigemori
- Institute of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Thomas J Wandless
- Department of Chemical & Systems Biology, Stanford University, 269 Campus Drive, Stanford, California 94305, United States
| | - Yusaku Miyamae
- Institute of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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3
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Ogawa Y, Ueda TP, Obara K, Nishimura K, Kamura T. Targeted Protein Degradation Systems: Controlling Protein Stability Using E3 Ubiquitin Ligases in Eukaryotic Species. Cells 2024; 13:175. [PMID: 38247866 PMCID: PMC10814424 DOI: 10.3390/cells13020175] [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: 12/12/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This review explores various methods for modulating protein stability to achieve target protein degradation, which is a crucial aspect in the study of biological processes and drug design. Thirty years have passed since the introduction of heat-inducible degron cells utilizing the N-end rule, and methods for controlling protein stability using the ubiquitin-proteasome system have moved from academia to industry. This review covers protein stability control methods, from the early days to recent advancements, and discusses the evolution of techniques in this field. This review also addresses the challenges and future directions of protein stability control techniques by tracing their development from the inception of protein stability control methods to the present day.
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Affiliation(s)
| | | | | | - Kohei Nishimura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan; (Y.O.); (T.P.U.); (K.O.)
| | - Takumi Kamura
- Department of Biological Science, Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan; (Y.O.); (T.P.U.); (K.O.)
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4
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Kishimoto T, Nishimura K, Morishita K, Fukuda A, Miyamae Y, Kumagai Y, Sumaru K, Nakanishi M, Hisatake K, Sano M. An engineered ligand-responsive Csy4 endoribonuclease controls transgene expression from Sendai virus vectors. J Biol Eng 2024; 18:9. [PMID: 38229076 DOI: 10.1186/s13036-024-00404-9] [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: 09/22/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Viral vectors are attractive gene delivery vehicles because of their broad tropism, high transduction efficiency, and durable expression. With no risk of integration into the host genome, the vectors developed from RNA viruses such as Sendai virus (SeV) are especially promising. However, RNA-based vectors have limited applicability because they lack a convenient method to control transgene expression by an external inducer. RESULTS We engineered a Csy4 switch in Sendai virus-based vectors by combining Csy4 endoribonuclease with mutant FKBP12 (DD: destabilizing domain) that becomes stabilized when a small chemical Shield1 is supplied. In this Shield1-responsive Csy4 (SrC) switch, Shield1 increases Csy4 fused with DD (DD-Csy4), which then cleaves and downregulates the transgene mRNA containing the Csy4 recognition sequence (Csy4RS). Moreover, when Csy4RS is inserted in the viral L gene, the SrC switch suppresses replication and transcription of the SeV vector in infected cells in a Shield1-dependent manner, thus enabling complete elimination of the vector from the cells. By temporally controlling BRN4 expression, a BRN4-expressing SeV vector equipped with the SrC switch achieves efficient, stepwise differentiation of embryonic stem cells into neural stem cells, and then into astrocytes. CONCLUSION SeV-based vectors with the SrC switch should find wide applications in stem cell research, regenerative medicine, and gene therapy, especially when precise control of reprogramming factor expression is desirable.
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Grants
- JP19H03203, JP19K22945, JP19K07343, JP21H02678, JP19K06501 Japan Society for the Promotion of Science
- JP19H03203, JP19K22945, JP19K07343, JP21H02678, JP19K06501 Japan Society for the Promotion of Science
- JP19H03203, JP19K22945, JP19K07343, JP21H02678, JP19K06501 Japan Society for the Promotion of Science
- JP19H03203, JP19K22945, JP19K07343, JP21H02678, JP19K06501 Japan Society for the Promotion of Science
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Affiliation(s)
- Takumi Kishimoto
- Laboratory of Gene Regulation, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Ken Nishimura
- Laboratory of Gene Regulation, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Kana Morishita
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Aya Fukuda
- Laboratory of Gene Regulation, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yusaku Miyamae
- Institute of Life and Environment Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yutaro Kumagai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Kimio Sumaru
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Mahito Nakanishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
- TOKIWA-Bio, Inc, 2-1-6 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
| | - Koji Hisatake
- Laboratory of Gene Regulation, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Masayuki Sano
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
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5
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Layden HM, Johnson AE, Hiebert SW. Chemical-genetics refines transcription factor regulatory circuits. Trends Cancer 2024; 10:65-75. [PMID: 37722945 PMCID: PMC10840957 DOI: 10.1016/j.trecan.2023.08.012] [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: 04/27/2023] [Revised: 08/14/2023] [Accepted: 08/25/2023] [Indexed: 09/20/2023]
Abstract
Transcriptional dysregulation is a key step in oncogenesis, but our understanding of transcriptional control has relied on genetic approaches that are slow and allow for compensation. Chemical-genetic approaches have shortened the time frame for the analysis of transcription factors from days or weeks to minutes. These studies show that while DNA-binding proteins bind to thousands of sites, they are directly required to regulate only a small cadre of genes. Moreover, these transcriptional control networks are far more distinct, with much less overlap and interconnectivity than predicted from DNA binding. The identified direct targets can then be used to dissect the mechanism of action of these factors, which could identify ways to therapeutically manipulate these oncogenic transcriptional control networks.
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Affiliation(s)
- Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Anna E Johnson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37027, USA.
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6
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Etersque JM, Lee IK, Sharma N, Xu K, Ruff A, Northrup JD, Sarkar S, Nguyen T, Lauman R, Burslem GM, Sellmyer MA. Regulation of eDHFR-tagged proteins with trimethoprim PROTACs. Nat Commun 2023; 14:7071. [PMID: 37923771 PMCID: PMC10624689 DOI: 10.1038/s41467-023-42820-3] [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: 02/07/2023] [Accepted: 10/22/2023] [Indexed: 11/06/2023] Open
Abstract
Temporal control of protein levels in cells and living animals can be used to improve our understanding of protein function. In addition, control of engineered proteins could be used in therapeutic applications. PRoteolysis-TArgeting Chimeras (PROTACs) have emerged as a small-molecule-driven strategy to achieve rapid, post-translational regulation of protein abundance via recruitment of an E3 ligase to the target protein of interest. Here, we develop several PROTAC molecules by covalently linking the antibiotic trimethoprim (TMP) to pomalidomide, a ligand for the E3 ligase, Cereblon. These molecules induce degradation of proteins of interest (POIs) genetically fused to a small protein domain, E. coli dihydrofolate reductase (eDHFR), the molecular target of TMP. We show that various eDHFR-tagged proteins can be robustly degraded to 95% of maximum expression with PROTAC molecule 7c. Moreover, TMP-based PROTACs minimally affect the expression of immunomodulatory imide drug (IMiD)-sensitive neosubstrates using proteomic and biochemical assays. Finally, we show multiplexed regulation with another known degron-PROTAC pair, as well as reversible protein regulation in a rodent model of metastatic cancer, demonstrating the formidable strength of this system. Altogether, TMP PROTACs are a robust approach for selective and reversible degradation of eDHFR-tagged proteins in vitro and in vivo.
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Affiliation(s)
- Jean M Etersque
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iris K Lee
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nitika Sharma
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kexiang Xu
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Ruff
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Justin D Northrup
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Swarbhanu Sarkar
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tommy Nguyen
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard Lauman
- The Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - George M Burslem
- The Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark A Sellmyer
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- The Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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7
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Giordano Attianese GMP, Ash S, Irving M. Coengineering specificity, safety, and function into T cells for cancer immunotherapy. Immunol Rev 2023; 320:166-198. [PMID: 37548063 DOI: 10.1111/imr.13252] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023]
Abstract
Adoptive T-cell transfer (ACT) therapies, including of tumor infiltrating lymphocytes (TILs) and T cells gene-modified to express either a T cell receptor (TCR) or a chimeric antigen receptor (CAR), have demonstrated clinical efficacy for a proportion of patients and cancer-types. The field of ACT has been driven forward by the clinical success of CD19-CAR therapy against various advanced B-cell malignancies, including curative responses for some leukemia patients. However, relapse remains problematic, in particular for lymphoma. Moreover, for a variety of reasons, relative limited efficacy has been demonstrated for ACT of non-hematological solid tumors. Indeed, in addition to pre-infusion challenges including lymphocyte collection and manufacturing, ACT failure can be attributed to several biological processes post-transfer including, (i) inefficient tumor trafficking, infiltration, expansion and retention, (ii) chronic antigen exposure coupled with insufficient costimulation resulting in T-cell exhaustion, (iii) a range of barriers in the tumor microenvironment (TME) mediated by both tumor cells and suppressive immune infiltrate, (iv) tumor antigen heterogeneity and loss, or down-regulation of antigen presentation machinery, (v) gain of tumor intrinsic mechanisms of resistance such as to apoptosis, and (vi) various forms of toxicity and other adverse events in patients. Affinity-optimized TCRs can improve T-cell function and innovative CAR designs as well as gene-modification strategies can be used to coengineer specificity, safety, and function into T cells. Coengineering strategies can be designed not only to directly support the transferred T cells, but also to block suppressive barriers in the TME and harness endogenous innate and adaptive immunity. Here, we review a selection of the remarkable T-cell coengineering strategies, including of tools, receptors, and gene-cargo, that have been developed in recent years to augment tumor control by ACT, more and more of which are advancing to the clinic.
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Affiliation(s)
- Greta Maria Paola Giordano Attianese
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sarah Ash
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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8
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Yun J, Baldini L, Huang Y, Li E, Li H, Chacko AN, Miller AD, Wan J, Mukherjee A. Engineering ligand stabilized aquaporin reporters for magnetic resonance imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543364. [PMID: 37333371 PMCID: PMC10274688 DOI: 10.1101/2023.06.02.543364] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Imaging transgene expression in live tissues requires reporters that are detectable with deeply penetrant modalities, such as magnetic resonance imaging (MRI). Here, we show that LSAqp1, a water channel engineered from aquaporin-1, can be used to create background-free, drug-gated, and multiplex images of gene expression using MRI. LSAqp1 is a fusion protein composed of aquaporin-1 and a degradation tag that is sensitive to a cell-permeable ligand, which allows for dynamic small molecule modulation of MRI signals. LSAqp1 improves specificity for imaging gene expression by allowing reporter signals to be conditionally activated and distinguished from the tissue background by difference imaging. In addition, by engineering destabilized aquaporin-1 variants with different ligand requirements, it is possible to image distinct cell types simultaneously. Finally, we expressed LSAqp1 in a tumor model and showed successful in vivo imaging of gene expression without background activity. LSAqp1 provides a conceptually unique approach to accurately measure gene expression in living organisms by combining the physics of water diffusion and biotechnology tools to control protein stability.
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Affiliation(s)
- Jason Yun
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Logan Baldini
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Yimeng Huang
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Eugene Li
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Honghao Li
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Asish N. Chacko
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Austin D.C. Miller
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Jinyang Wan
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Arnab Mukherjee
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
- Biological Engineering, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
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9
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Phanindhar K, Mishra RK. Auxin-inducible degron system: an efficient protein degradation tool to study protein function. Biotechniques 2023; 74:186-198. [PMID: 37191015 DOI: 10.2144/btn-2022-0108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Targeted protein degradation, with its rapid protein depletion kinetics, allows the measurement of acute changes in the cell. The auxin-inducible degron (AID) system, rapidly degrades AID-tagged proteins only in the presence of auxin. The AID system being inducible makes the study of essential genes and dynamic processes like cell differentiation, cell cycle and genome organization feasible. The AID degradation system has been adapted to yeast, protozoans, C. elegans, Drosophila, zebrafish, mouse and mammalian cell lines. Using the AID system, researchers have unveiled novel functions for essential proteins at developmental stages that were previously difficult to investigate due to early lethality. This comprehensive review discusses the development, advancements, applications and drawbacks of the AID system and compares it with other available protein degradation systems.
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Affiliation(s)
- Kundurthi Phanindhar
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular & Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- Tata Institute for Genetics & Society (TIGS), Bangalore, 560065, India
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10
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Shen J, Geng L, Li X, Emery C, Kroning K, Shingles G, Lee K, Heyden M, Li P, Wang W. A general method for chemogenetic control of peptide function. Nat Methods 2023; 20:112-122. [PMID: 36481965 PMCID: PMC10069916 DOI: 10.1038/s41592-022-01697-8] [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: 01/03/2021] [Accepted: 10/21/2022] [Indexed: 12/13/2022]
Abstract
Natural or engineered peptides serve important biological functions. A general approach to achieve chemical-dependent activation of short peptides will be valuable for spatial and temporal control of cellular processes. Here we present a pair of chemically activated protein domains (CAPs) for controlling the accessibility of both the N- and C-terminal portion of a peptide. CAPs were developed through directed evolution of an FK506-binding protein. By fusing a peptide to one or both CAPs, the function of the peptide is blocked until a small molecule displaces them from the FK506-binding protein ligand-binding site. We demonstrate that CAPs are generally applicable to a range of short peptides, including a protease cleavage site, a dimerization-inducing heptapeptide, a nuclear localization signal peptide, and an opioid peptide, with a chemical dependence up to 156-fold. We show that the CAPs system can be utilized in cell cultures and multiple organs in living animals.
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Affiliation(s)
- Jiaqi Shen
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Lequn Geng
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Xingyu Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Catherine Emery
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Kayla Kroning
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Gwendolyn Shingles
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Kerry Lee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Peng Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.
| | - Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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11
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Birocchi F, Cusimano M, Rossari F, Beretta S, Rancoita PMV, Ranghetti A, Colombo S, Costa B, Angel P, Sanvito F, Callea M, Norata R, Chaabane L, Canu T, Spinelli A, Genua M, Ostuni R, Merelli I, Coltella N, Naldini L. Targeted inducible delivery of immunoactivating cytokines reprograms glioblastoma microenvironment and inhibits growth in mouse models. Sci Transl Med 2022; 14:eabl4106. [DOI: 10.1126/scitranslmed.abl4106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Glioblastoma multiforme (GBM) is the most common and lethal brain tumor characterized by a strongly immunosuppressive tumor microenvironment (TME) that represents a barrier also for the development of effective immunotherapies. The possibility to revert this hostile TME by immunoactivating cytokines is hampered by the severe toxicity associated with their systemic administration. Here, we exploited a lentiviral vector–based platform to engineer hematopoietic stem cells ex vivo with the aim of releasing, via their tumor-infiltrating monocyte/macrophage progeny, interferon-α (IFN-α) or interleukin-12 (IL-12) at the tumor site with spatial and temporal selectivity. Taking advantage of a syngeneic GBM mouse model, we showed that inducible release of IFN-α within the TME achieved robust tumor inhibition up to eradication and outperformed systemic treatment with the recombinant protein in terms of efficacy, tolerability, and specificity. Single-cell RNA sequencing of the tumor immune infiltrate revealed reprogramming of the immune microenvironment toward a proinflammatory and antitumoral state associated with loss of a macrophage subpopulation shown to be associated with poor prognosis in human GBM. The spatial and temporal control of IL-12 release was critical to overcome an otherwise lethal hematopoietic toxicity while allowing to fully exploit its antitumor activity. Overall, our findings demonstrate a potential therapeutic approach for GBM and set the bases for a recently launched first-in-human clinical trial in patients with GBM.
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Affiliation(s)
- Filippo Birocchi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Melania Cusimano
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Federico Rossari
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Paola M. V. Rancoita
- CUSSB-University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Anna Ranghetti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Stefano Colombo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Barbara Costa
- Division of Signal Transduction and Growth Control, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Peter Angel
- Division of Signal Transduction and Growth Control, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Francesca Sanvito
- Pathology Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Marcella Callea
- Pathology Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Rossana Norata
- GLP Test Facility, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Linda Chaabane
- Experimental Imaging Center, Preclinical Imaging Facility, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Tamara Canu
- Experimental Imaging Center, Preclinical Imaging Facility, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Antonello Spinelli
- Experimental Imaging Center, Preclinical Imaging Facility, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Marco Genua
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Renato Ostuni
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- National Research Council, Institute for Biomedical Technologies, 20054 Segrate, Italy
| | - Nadia Coltella
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
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12
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Abstract
The steadfast advance of the synthetic biology field has enabled scientists to use genetically engineered cells, instead of small molecules or biologics, as the basis for the development of novel therapeutics. Cells endowed with synthetic gene circuits can control the localization, timing and dosage of therapeutic activities in response to specific disease biomarkers and thus represent a powerful new weapon in the fight against disease. Here, we conceptualize how synthetic biology approaches can be applied to programme living cells with therapeutic functions and discuss the advantages that they offer over conventional therapies in terms of flexibility, specificity and predictability, as well as challenges for their development. We present notable advances in the creation of engineered cells that harbour synthetic gene circuits capable of biological sensing and computation of signals derived from intracellular or extracellular biomarkers. We categorize and describe these developments based on the cell scaffold (human or microbial) and the site at which the engineered cell exerts its therapeutic function within its human host. The design of cell-based therapeutics with synthetic biology is a rapidly growing strategy in medicine that holds great promise for the development of effective treatments for a wide variety of human diseases.
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13
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Kolesov DV, Sokolinskaya EL, Lukyanov KA, Bogdanov AM. Molecular Tools for Targeted Control of Nerve Cell Electrical Activity. Part II. Acta Naturae 2021; 13:17-32. [PMID: 35127143 PMCID: PMC8807539 DOI: 10.32607/actanaturae.11415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/14/2021] [Indexed: 01/01/2023] Open
Abstract
In modern life sciences, the issue of a specific, exogenously directed manipulation of a cell's biochemistry is a highly topical one. In the case of electrically excitable cells, the aim of the manipulation is to control the cells' electrical activity, with the result being either excitation with subsequent generation of an action potential or inhibition and suppression of the excitatory currents. The techniques of electrical activity stimulation are of particular significance in tackling the most challenging basic problem: figuring out how the nervous system of higher multicellular organisms functions. At this juncture, when neuroscience is gradually abandoning the reductionist approach in favor of the direct investigation of complex neuronal systems, minimally invasive methods for brain tissue stimulation are becoming the basic element in the toolbox of those involved in the field. In this review, we describe three approaches that are based on the delivery of exogenous, genetically encoded molecules sensitive to external stimuli into the nervous tissue. These approaches include optogenetics (overviewed in Part I), as well as chemogenetics and thermogenetics (described here, in Part II), which is significantly different not only in the nature of the stimuli and structure of the appropriate effector proteins, but also in the details of experimental applications. The latter circumstance is an indication that these are rather complementary than competing techniques.
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Affiliation(s)
- D. V. Kolesov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - E. L. Sokolinskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - K. A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - A. M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
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14
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López Del Amo V, Leger BS, Cox KJ, Gill S, Bishop AL, Scanlon GD, Walker JA, Gantz VM, Choudhary A. Small-Molecule Control of Super-Mendelian Inheritance in Gene Drives. Cell Rep 2021; 31:107841. [PMID: 32610142 PMCID: PMC7587219 DOI: 10.1016/j.celrep.2020.107841] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/20/2020] [Accepted: 06/09/2020] [Indexed: 11/29/2022] Open
Abstract
Synthetic CRISPR-based gene-drive systems have tremendous potential in public health and agriculture, such as for fighting vector-borne diseases or suppressing crop pest populations. These elements can rapidly spread in a population by breaching the inheritance limit of 50% dictated by Mendel's law of gene segregation, making them a promising tool for population engineering. However, current technologies lack control over their propagation capacity, and there are important concerns about potential unchecked spreading. Here, we describe a gene-drive system in Drosophila that generates an analog inheritance output that can be tightly and conditionally controlled to between 50% and 100%. This technology uses a modified SpCas9 that responds to a synthetic, orally available small molecule, fine-tuning the inheritance probability. This system opens a new avenue to feasibility studies for spatial and temporal control of gene drives using small molecules.
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Affiliation(s)
- Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Brittany S Leger
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kurt J Cox
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Shubhroz Gill
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Garrett D Scanlon
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James A Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA.
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15
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Chang L, Ruiz P, Ito T, Sellers WR. Targeting pan-essential genes in cancer: Challenges and opportunities. Cancer Cell 2021; 39:466-479. [PMID: 33450197 PMCID: PMC8157671 DOI: 10.1016/j.ccell.2020.12.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
Despite remarkable successes in the clinic, cancer targeted therapy development remains challenging and the failure rate is disappointingly high. This problem is partly due to the misapplication of the targeted therapy paradigm to therapeutics targeting pan-essential genes, which can result in therapeutics whereby efficacy is attenuated by dose-limiting toxicity. Here we summarize the key features of successful chemotherapy and targeted therapy agents, and use case studies to outline recurrent challenges to drug development efforts targeting pan-essential genes. Finally, we suggest strategies to avoid previous pitfalls for ongoing and future development of pan-essential therapeutics.
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Affiliation(s)
- Liang Chang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Ruiz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Takahiro Ito
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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16
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Weber EW, Parker KR, Sotillo E, Lynn RC, Anbunathan H, Lattin J, Good Z, Belk JA, Daniel B, Klysz D, Malipatlolla M, Xu P, Bashti M, Heitzeneder S, Labanieh L, Vandris P, Majzner RG, Qi Y, Sandor K, Chen LC, Prabhu S, Gentles AJ, Wandless TJ, Satpathy AT, Chang HY, Mackall CL. Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling. Science 2021; 372:eaba1786. [PMID: 33795428 PMCID: PMC8049103 DOI: 10.1126/science.aba1786] [Citation(s) in RCA: 315] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/07/2020] [Accepted: 02/11/2021] [Indexed: 12/30/2022]
Abstract
T cell exhaustion limits immune responses against cancer and is a major cause of resistance to chimeric antigen receptor (CAR)-T cell therapeutics. Using murine xenograft models and an in vitro model wherein tonic CAR signaling induces hallmark features of exhaustion, we tested the effect of transient cessation of receptor signaling, or rest, on the development and maintenance of exhaustion. Induction of rest through enforced down-regulation of the CAR protein using a drug-regulatable system or treatment with the multikinase inhibitor dasatinib resulted in the acquisition of a memory-like phenotype, global transcriptional and epigenetic reprogramming, and restored antitumor functionality in exhausted CAR-T cells. This work demonstrates that rest can enhance CAR-T cell efficacy by preventing or reversing exhaustion, and it challenges the notion that exhaustion is an epigenetically fixed state.
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Affiliation(s)
- Evan W Weber
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin R Parker
- Department of Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rachel C Lynn
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hima Anbunathan
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John Lattin
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zinaida Good
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Dorota Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meena Malipatlolla
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Xu
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Malek Bashti
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sabine Heitzeneder
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Panayiotis Vandris
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robbie G Majzner
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yanyan Qi
- Department of Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ling-Chun Chen
- Department of Chemical and Systems Biology, Stanford University, CA 94305, USA
| | - Snehit Prabhu
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew J Gentles
- Department of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas J Wandless
- Department of Chemical and Systems Biology, Stanford University, CA 94305, USA
| | - Ansuman T Satpathy
- Department of Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Department of Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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17
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Functional Imaging Using Bioluminescent Reporter Genes in Living Subjects. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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18
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Nishimura K, Yamada R, Hagihara S, Iwasaki R, Uchida N, Kamura T, Takahashi K, Torii KU, Fukagawa T. A super-sensitive auxin-inducible degron system with an engineered auxin-TIR1 pair. Nucleic Acids Res 2020; 48:e108. [PMID: 32941625 PMCID: PMC7544234 DOI: 10.1093/nar/gkaa748] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/19/2020] [Accepted: 08/28/2020] [Indexed: 01/27/2023] Open
Abstract
The auxin-inducible degron (AID) system enables rapid depletion of target proteins within the cell by applying the natural auxin IAA. The AID system is useful for investigating the physiological functions of essential proteins; however, this system generally requires high dose of auxin to achieve effective depletion in vertebrate cells. Here, we describe a super-sensitive AID system that incorporates the synthetic auxin derivative 5-Ad-IAA and its high-affinity-binding partner OsTIR1F74A. The super-sensitive AID system enabled more than a 1000-fold reduction of the AID inducer concentrations in chicken DT40 cells. To apply this system to various mammalian cell lines including cancer cells containing multiple sets of chromosomes, we utilized a single-step method where CRISPR/Cas9-based gene knockout is combined with insertion of a pAID plasmid. The single-step method coupled with the super-sensitive AID system enables us to easily and rapidly generate AID-based conditional knockout cells in a wide range of vertebrate cell lines. Our improved method that incorporates the super-sensitive AID system and the single-step method provides a powerful tool for elucidating the roles of essential genes.
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Affiliation(s)
- Kohei Nishimura
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan.,Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Ryotaro Yamada
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan.,RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shinya Hagihara
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan.,RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Rie Iwasaki
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan
| | - Naoyuki Uchida
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan.,Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Takumi Kamura
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Koji Takahashi
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.,Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan
| | - Keiko U Torii
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan.,Department of Molecular Biosciences, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA.,Howard Hughes Medical Institute, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
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19
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Ineichen BV, Di Palma S, Laczko E, Liddelow SA, Neumann S, Schwab ME, Mosberger AC. Regional Differences in Penetration of the Protein Stabilizer Trimethoprim (TMP) in the Rat Central Nervous System. Front Mol Neurosci 2020; 13:167. [PMID: 33013318 PMCID: PMC7496896 DOI: 10.3389/fnmol.2020.00167] [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: 06/17/2020] [Accepted: 08/11/2020] [Indexed: 12/04/2022] Open
Abstract
Regulating gene expression at the protein level is becoming increasingly important for answering basic questions in neurobiology. Several techniques using destabilizing domains (DD) on transgenes, which can be activated or deactivated by specific drugs, have been developed to achieve this goal. A DD from bacterial dihydrofolate reductase bound and stabilized by trimethoprim (TMP) represents such a tool. To control transgenic protein levels in the brain, the DD-regulating drugs need to have sufficient penetration into the central nervous system (CNS). Yet, very limited information is available on TMP pharmacokinetics in the CNS following systemic injection. Here, we performed a pharmacokinetic study on the penetration of TMP into different CNS compartments in the rat. We used mass spectrometry to measure TMP concentrations in serum, cerebrospinal fluid (CSF) and tissue samples of different CNS regions upon intraperitoneal TMP injection. We show that TMP quickly (within 10 min) penetrates from serum to CSF through the blood-CSF barrier. TMP also shows quick penetration into brain tissue but concentrations were an order of magnitude lower compared to serum or CSF. TMP concentration in spinal cord was lower than in any other analyzed CNS area. Nevertheless, effective levels of TMP to stabilize DDs can be reached in the CNS with half-lives around 2 h. These data show that TMP has good and fast penetration properties into the CNS and is therefore a valuable ligand for precisely controlling protein expression in the CNS in rodents.
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Affiliation(s)
- Benjamin V Ineichen
- Department of Health Sciences and Technology, Brain Research Institute, University of Zurich, ETH Zürich, Zurich, Switzerland
| | - Serena Di Palma
- Functional Genomics Center Zurich, University of Zurich, ETH Zürich, Zurich, Switzerland
| | - Endre Laczko
- Functional Genomics Center Zurich, University of Zurich, ETH Zürich, Zurich, Switzerland
| | - Shane A Liddelow
- Neuroscience Institute, NYU School of Medicine, New York, NY, United States.,Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY, United States.,Department of Ophthalmology, NYU School of Medicine, New York, NY, United States
| | - Susanne Neumann
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Martin E Schwab
- Department of Health Sciences and Technology, Brain Research Institute, University of Zurich, ETH Zürich, Zurich, Switzerland
| | - Alice C Mosberger
- Department of Health Sciences and Technology, Brain Research Institute, University of Zurich, ETH Zürich, Zurich, Switzerland
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20
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Miyamae Y, Chen LC, Utsugi Y, Farrants H, Wandless TJ. A Method for Conditional Regulation of Protein Stability in Native or Near-Native Form. Cell Chem Biol 2020; 27:1573-1581.e3. [PMID: 33007216 PMCID: PMC7749034 DOI: 10.1016/j.chembiol.2020.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/17/2020] [Accepted: 09/09/2020] [Indexed: 01/10/2023]
Abstract
Here, we report a method to regulate cellular protein levels by introducing a ubiquitin variant between a destabilizing domain (DD) and the regulated protein. When produced in the absence of a stabilizing ligand the DD dominates and the entire fusion protein is processively degraded by the proteasome. In the presence of the stabilizing ligand the fusion protein is metabolically stable and becomes a substrate for abundant ubiquitin-specific proteases, liberating a native, or a near-native protein-of-interest. This technique is thus particularly useful for the study of proteins whose free N terminus is required for proper function. In addition, removal of the DD in the presence of stabilizing ligand leads to higher expression levels of regulated protein when cells experience transient exposure to a stabilizing ligand, such as in a living animal receiving a single dose of a pharmacological agent as the stabilizing ligand.
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Affiliation(s)
- Yusaku Miyamae
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, U.S.A; Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Ling-Chun Chen
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Yuki Utsugi
- Master's/Doctoral Program in Life Science Innovation, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Helen Farrants
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Thomas J Wandless
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA 94305, U.S.A.
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21
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Ramadurgum P, Daniel S, Hulleman JD. Protocol for In Vivo Evaluation and Use of Destabilizing Domains in the Eye, Liver, and Beyond. STAR Protoc 2020; 1. [PMID: 32995756 PMCID: PMC7521670 DOI: 10.1016/j.xpro.2020.100094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Destabilizing domains (DDs) have been used successfully to conditionally control the abundance of proteins of interest (POIs) in a small-molecule-dependent manner in mice, worms (Caenorhabditis elegans), and Drosophila. However, development of such systems must account for delivery of the DD-POIs to the target tissue, accessibility of the target tissue to the small molecule, and quantification of stabilization. Here, we describe the considerations and steps to take in order to effectively implement a DD-POI in mouse ocular and hepatic tissue. For complete details on the use and execution of this protocol, please refer to Datta et al. (2018), Ramadurgum and Hulleman (2020), and Ramadurgum et al. (2020).
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Affiliation(s)
- Prerana Ramadurgum
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Steffi Daniel
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - John D Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.,Technical Contact
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22
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Prey for the Proteasome: Targeted Protein Degradation-A Medicinal Chemist's Perspective. Angew Chem Int Ed Engl 2020; 59:15448-15466. [PMID: 32428344 PMCID: PMC7496094 DOI: 10.1002/anie.202004310] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Targeted protein degradation (TPD), the ability to control a proteins fate by triggering its degradation in a highly selective and effective manner, has created tremendous excitement in chemical biology and drug discovery within the past decades. The TPD field is spearheaded by small molecule induced protein degradation with molecular glues and proteolysis targeting chimeras (PROTACs) paving the way to expand the druggable space and to create a new paradigm in drug discovery. However, besides the therapeutic angle of TPD a plethora of novel techniques to modulate and control protein levels have been developed. This enables chemical biologists to better understand protein function and to discover and verify new therapeutic targets. This Review gives a comprehensive overview of chemical biology techniques inducing TPD. It explains the strengths and weaknesses of these methods in the context of drug discovery and discusses their future potential from a medicinal chemist's perspective.
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Affiliation(s)
- Laura M. Luh
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Ulrike Scheib
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Katrin Juenemann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Lars Wortmann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Michael Brands
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Philipp M. Cromm
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
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23
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Hu PY, Fan XM, Zhang YN, Wang SB, Wan WJ, Pan HY, Mou XZ. The limiting factors of oncolytic virus immunotherapy and the approaches to overcome them. Appl Microbiol Biotechnol 2020; 104:8231-8242. [PMID: 32816087 DOI: 10.1007/s00253-020-10802-w] [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: 06/22/2020] [Revised: 06/22/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Oncolytic virus (OV) immunotherapy is characterized by viruses which specifically target cancer cells and cause their cytolysis. They provide a unique and promising new tool for the eradication of cancer as they interact with and affect the tumor microenvironment (TME), vasculature, and immune system. Advancements of genetic engineering have allowed for these viruses to be armed in such a way to have enhanced targeting, strong immunomodulation properties, and an ability to modify the TME. However, there are still major limitations in their use, mostly due to difficulties in delivering the viral particles to the tumors and in ensuring that the immunomodulatory properties are able to stimulate the host immune response to mount a complete response. Using novel delivery systems and using OVs as a complementary therapy in a combinatorial treatment have shown some significant successes. In this review, we discuss the major issues and difficulties in using OVs as anti-tumor agents and some of the strategies put in place so far to overcome these limitations. KEY POINTS: • Oncolytic viruses (OVs) infect cancer cells and cause their cytolysis. • The major limitations in using OVs as anti-tumor therapy were discussed. • The potential strategies to overcome these limitations were summarized.
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Affiliation(s)
- Pei-Yang Hu
- Department of Traumatology, Tiantai People's Hospital of Zhejiang Province (Tiantai Branch of Zhejiang People's Hospital), Taizhou, 317200, China
| | - Xiao-Ming Fan
- Department of Ultrasound, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China
| | - You-Ni Zhang
- Department of Traumatology, Tiantai People's Hospital of Zhejiang Province (Tiantai Branch of Zhejiang People's Hospital), Taizhou, 317200, China.,Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.,Clinical Research Institute, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China
| | - Shi-Bing Wang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.,Clinical Research Institute, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China
| | - Wei-Jie Wan
- Shandong Xiandai University, Jinan, 250104, China
| | - Hong-Ying Pan
- Department of Infectious Diseases, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
| | - Xiao-Zhou Mou
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China. .,Clinical Research Institute, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
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24
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Beute für das Proteasom: Gezielter Proteinabbau aus medizinalchemischer Perspektive. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Laura M. Luh
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Ulrike Scheib
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Katrin Juenemann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Lars Wortmann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Michael Brands
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Philipp M. Cromm
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
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25
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Richman SA, Wang LC, Moon EK, Khire UR, Albelda SM, Milone MC. Ligand-Induced Degradation of a CAR Permits Reversible Remote Control of CAR T Cell Activity In Vitro and In Vivo. Mol Ther 2020; 28:1600-1613. [PMID: 32559430 DOI: 10.1016/j.ymthe.2020.06.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/03/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
Chimeric antigen receptor (CAR)-modified T cells are endowed with novel antigen specificity and are most often administered to patients without an engineered mechanism to control the CAR T cells once infused. "Suicide switches" such as the small molecule-controlled, inducible caspase-9 (iCas9) system afford the ability to selectively eliminate engineered T cells; however, these approaches are designed for all-or-none, irreversible termination of an ongoing immune response. In order to permit reversible and adjustable modulation, we have created a CAR that is capable of on-demand downregulation by fusing the CAR to a previously developed ligand-induced degradation (LID) domain. Addition of a small molecule ligand triggers exposure of a cryptic degron within the LID domain, resulting in proteasomal degradation of the CAR-LID fusion protein and loss of CAR on the surface of T cells. This fusion construct allowed for reversible and "tunable" inhibition of CAR T cell activity in vitro. Delivery of the triggering molecule in CAR-LID-treated tumor-bearing mice temporarily reduced CAR activity through modulation of CAR surface expression. The ability to more flexibly modulate CAR T cell expression through a small molecule provides a platform for controlling possible adverse side effects, as well as preclinical investigations of CAR T cell biology.
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Affiliation(s)
- Sarah A Richman
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Liang-Chuan Wang
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Edmund K Moon
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Uday R Khire
- Cheminpharma LLC, 4 Research Drive, Woodbridge, CT 06525, USA
| | - Steven M Albelda
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Milone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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26
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Madsen D, Jørgensen FP, Palmer D, Roux ME, Olsen JV, Bols M, Schoffelen S, Diness F, Meldal M. Design and Combinatorial Development of Shield-1 Peptide Mimetics Binding to Destabilized FKBP12. ACS COMBINATORIAL SCIENCE 2020; 22:156-164. [PMID: 32027120 DOI: 10.1021/acscombsci.9b00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of computational design, a focused one-bead one-compound library has been prepared on microparticle-encoded PEGA1900 beads consisting of small tripeptides with a triazole-capped N-terminal. The library was screened towards a double point-mutated version of the human FKBP12 protein, known as the destabilizing domain (DD). Inspired by the decoded library hits, unnatural peptide structures were screened in a novel on-bead assay, which was useful for a rapid structure evaluation prior to off-bead resynthesis. Subsequently, a series of 19 compounds were prepared and tested using a competitive fluorescence polarization assay, which led to the discovery of peptide ligands with low micromolar binding affinity towards the DD. The methodology represents a rapid approach for identification of a novel structure scaffold, where the screening and initial structure refinement was accomplished using small quantities of library building blocks.
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27
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Mills EM, Barlow VL, Luk LYP, Tsai YH. Applying switchable Cas9 variants to in vivo gene editing for therapeutic applications. Cell Biol Toxicol 2019; 36:17-29. [PMID: 31418127 PMCID: PMC7051928 DOI: 10.1007/s10565-019-09488-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Progress in targeted gene editing by programmable endonucleases has paved the way for their use in gene therapy. Particularly, Cas9 is an endonuclease with high activity and flexibility, rendering it an attractive option for therapeutic applications in clinical settings. Many disease-causing mutations could potentially be corrected by this versatile new technology. In addition, recently developed switchable Cas9 variants, whose activity can be controlled by an external stimulus, provide an extra level of spatiotemporal control on gene editing and are particularly desirable for certain applications. Here, we discuss the considerations and difficulties for implementing Cas9 to in vivo gene therapy. We put particular emphasis on how switchable Cas9 variants may resolve some of these barriers and advance gene therapy in the clinical setting.
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Affiliation(s)
- Emily M Mills
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | | | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
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28
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Zhang J, Chen L, Zhang J, Wang Y. Drug Inducible CRISPR/Cas Systems. Comput Struct Biotechnol J 2019; 17:1171-1177. [PMID: 31462973 PMCID: PMC6709367 DOI: 10.1016/j.csbj.2019.07.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 06/18/2019] [Accepted: 07/26/2019] [Indexed: 11/24/2022] Open
Abstract
Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems have been employed as a powerful versatile technology for programmable gene editing, transcriptional modulation, epigenetic modulation, and genome labeling, etc. Yet better control of their activity is important to accomplish greater precision and to reduce undesired outcomes such as off-target events. The use of small molecules to control CRISPR/Cas activity represents a promising direction. Here, we provide an updated review on multiple drug inducible CRISPR/Cas systems and discuss their distinct properties. We arbitrarily divided the emerging drug inducible CRISPR/Cas systems into two categories based on whether at transcription or protein level does chemical control occurs. The first category includes Tet-On/Off system and Cre-dependent system. The second category includes chemically induced proximity systems, intein splicing system, 4-Hydroxytamoxifen-Estrogen Receptor based nuclear localization systems, allosterically regulated Cas9 system, and destabilizing domain mediated protein degradation systems. Finally, the advantages and limitations of each system were summarized.
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Key Words
- 4-OHT, 4-Hydroxytamoxifen
- ABA, abscisic acid
- ADs, activation domains
- CIP, chemically induced proximity
- CRISPR, clustered, regularly interspaced, short palindromic repeats
- Cas, CRISPR-associated protein
- CrRNA, CRISPR RNA
- DD, destabilizing domain
- DHFR, dihydrofolate reductase
- ER, Estrogen Receptor
- FKBP, FK506-binding protein
- FRB, FKBP-rapamycin-binding domain
- GA, gibberellin
- HIT, Hybrid drug Inducible CRISPR/Cas9 Technologies
- Hsp90, heat shock protein 90
- LBD, ligand binding domain
- LSL, loxP-stop-loxP
- MST, multiplex single transcript
- NES, nuclear export sequence
- NLS, nuclear localization sequence
- Ptet, tetO-containing promoter
- Sa, Staphylococcus areus
- Sp, Streptococcus pyogenes
- TMP, trimethoprim
- TRE, tetracycline response element
- TRE3G, Tet-On 3G protein
- TetO, tet operator
- TetR, Tet repressor protein
- VPR, VP64-P65-Rta
- arC9, allosterically regulated Cas9
- dCas9, dead Cas9
- dCpf1, dead Cpf1
- dLbCpf1, Lachnospiraceae bacterium dCpf1
- dox, doxycycline
- iPSCs, induced pluripotent stem cells
- rtTA, reverse-tTA
- sgRNA, single guide RNA
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Affiliation(s)
- Jingfang Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Li Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ju Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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29
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Scheepstra M, Hekking KF, van Hijfte L, Folmer RH. Bivalent Ligands for Protein Degradation in Drug Discovery. Comput Struct Biotechnol J 2019; 17:160-176. [PMID: 30788082 PMCID: PMC6369262 DOI: 10.1016/j.csbj.2019.01.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 01/19/2023] Open
Abstract
Targeting the "undruggable" proteome remains one of the big challenges in drug discovery. Recent innovations in the field of targeted protein degradation and manipulation of the ubiquitin-proteasome system open up new therapeutic approaches for disorders that cannot be targeted with conventional inhibitor paradigms. Proteolysis targeting chimeras (PROTACs) are bivalent ligands in which a compound that binds to the protein target of interest is connected to a second molecule that binds an E3 ligase via a linker. The E3 protein is usually either Cereblon or Von Hippel-Lindau. Several examples of selective PROTAC molecules with potent effect in cells and in vivo models have been reported. The degradation of specific proteins via these bivalent molecules is already allowing for the study of biochemical pathways and cell biology with more specificity than was possible with inhibitor compounds. In this review, we provide a comprehensive overview of recent developments in the field of small molecule mediated protein degradation, including transcription factors, kinases and nuclear receptors. We discuss the potential benefits of protein degradation over inhibition as well as the challenges that need to be overcome.
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Key Words
- ABCB1, ATP-binding cassette sub-family B member 1
- AD, Alzheimer's disease
- AHR, aryl hydrogen receptor
- ALK, anaplastic lymphoma kinase
- Aβ, amyloid-β
- BET, bromodomain and extra-terminal
- BTK, Bruton's tyrosine kinase
- Bcl6, B-cell lymphoma 6
- Bivalent ligand
- Brd4, bromodomain 4
- CDK9, cyclin dependent kinase 9
- CK2, Casein kinase 2
- CLIPTAC, click-formed proteolysis targeting chimera
- CRBN, Cereblon
- Chimera
- DC50, the compound concentration that results in 50% target protein degradation
- DHODH, Dihydroorotate dehydrogenase
- Degrader
- ERK1, extracellular signal-regulated kinase 1
- ERRα, estrogen-related receptor alpha
- ERα, estrogen receptor alpha
- EZH2, enhancer of zeste homolog 2
- FLT3, FMS-like tyrosine kinase-3
- FRS2, fibroblast growth factor receptor substrate 2
- GCN5, general control nonderepressible 5
- GPCR, G-protein coupled receptor
- GST, glutathione S-transferase
- HDAC, histone deacetylase
- HTS, high-throughput screening
- MDM2, mouse double-minute 2 homolog
- MetAP-2, methionine aminopeptidase-2
- PCAF, P300/CBP-associated factor
- PEG, polyethylene glycol
- PI3K, phosphatidylinositol-3-kinase
- PLK-1, polo-like kinase 1
- POI, protein of interest
- PROTAC
- PROTAC, proteolysis targeting chimeras
- Proteasome
- Protein degradation
- RAR, retinoic acid receptor
- RIPK2, receptor-interacting serine/threonine-protein kinase 2
- RTK, receptor tyrosine kinase
- SARM, selective androgen receptor modulator
- SNIPER, specific and non-genetic IAP-dependent protein eraser
- TBK1, TANK-Binding kinase 1
- TRIM24, tripartite motif-containing 24 (also known as TIF1α)
- VHL, Von Hippel-Lindau
- cIAP1, cellular inhibitor of apoptosis protein
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30
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Yesbolatova A, Tominari Y, Kanemaki MT. Ligand-induced genetic degradation as a tool for target validation. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 31:91-98. [PMID: 31200864 DOI: 10.1016/j.ddtec.2018.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 01/02/2023]
Abstract
Targeted protein degraders, known as proteolysis targeting chimeras (PROTACs), are drawing more attention as next-generation drugs to target currently undruggable proteins. As drug discovery of functional degraders involves time- and cost-consuming laborious processes, we propose employing a ligand-induced genetic degradation system to validate candidate proteins before degrader development. Genetic degradation mimics degrader treatment by depleting a degron-fused protein in the presence of a defined ligand. All genetic systems use a combination of a degron and defined ligand that enables a protein of interest fused with the degron to be recruited to an E3 ubiquitin ligase for ubiquitylation and subsequent degradation by the proteasome. However, these events are based on different principles and have different features. We review the dTAG, HaloTag-based, auxin-inducible degron (AID), and destabilizing domain (DD) systems and discuss a strategy for degrader discovery against novel target proteins.
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Affiliation(s)
- Aisha Yesbolatova
- National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yusuke Tominari
- FIMECS, Inc., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Masato T Kanemaki
- National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan.
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31
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Cella F, Wroblewska L, Weiss R, Siciliano V. Engineering protein-protein devices for multilayered regulation of mRNA translation using orthogonal proteases in mammalian cells. Nat Commun 2018; 9:4392. [PMID: 30349044 PMCID: PMC6197189 DOI: 10.1038/s41467-018-06825-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022] Open
Abstract
The development of RNA-encoded regulatory circuits relying on RNA-binding proteins (RBPs) has enhanced the applicability and prospects of post-transcriptional synthetic network for reprogramming cellular functions. However, the construction of RNA-encoded multilayer networks is still limited by the availability of composable and orthogonal regulatory devices. Here, we report on control of mRNA translation with newly engineered RBPs regulated by viral proteases in mammalian cells. By combining post-transcriptional and post-translational control, we expand the operational landscape of RNA-encoded genetic circuits with a set of regulatory devices including: i) RBP-protease, ii) protease-RBP, iii) protease–protease, iv) protein sensor protease-RBP, and v) miRNA-protease/RBP interactions. The rational design of protease-regulated proteins provides a diverse toolbox for synthetic circuit regulation that enhances multi-input information processing-actuation of cellular responses. Our approach enables design of artificial circuits that can reprogram cellular function with potential benefits as research tools and for future in vivo therapeutics and biotechnological applications. RNA-encoded regulatory circuits are desirable because they do not integrate in the host and are less immunogenic, but the availability of regulatory devices is limited. Here the authors develop viral protease RNA-binding proteins and protease–protease genetic circuits that ultimately regulate mRNA translation.
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Affiliation(s)
- Federica Cella
- Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, 80125, Naples, Italy.,University of Genoa, 16132, Genoa, Italy
| | | | - Ron Weiss
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, 02139, Cambridge, MA, USA
| | - Velia Siciliano
- Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, 80125, Naples, Italy.
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32
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Abstract
Chemogenetic technologies enable selective pharmacological control of specific cell populations. An increasing number of approaches have been developed that modulate different signaling pathways. Selective pharmacological control over G protein-coupled receptor signaling, ion channel conductances, protein association, protein stability, and small molecule targeting allows modulation of cellular processes in distinct cell types. Here, we review these chemogenetic technologies and instances of their applications in complex tissues in vivo and ex vivo.
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Affiliation(s)
- Deniz Atasoy
- Department of Physiology, School of Medicine and Regenerative-Restorative Medicine Research Center (REMER), Istanbul Medipol University , Istanbul , Turkey ; and Janelia Research Campus, Howard Hughes Medical Institute , Ashburn, Virginia
| | - Scott M Sternson
- Department of Physiology, School of Medicine and Regenerative-Restorative Medicine Research Center (REMER), Istanbul Medipol University , Istanbul , Turkey ; and Janelia Research Campus, Howard Hughes Medical Institute , Ashburn, Virginia
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33
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Kim J, Heo WD. Synergistic Ensemble of Optogenetic Actuators and Dynamic Indicators in Cell Biology. Mol Cells 2018; 41:809-817. [PMID: 30157546 PMCID: PMC6182222 DOI: 10.14348/molcells.2018.0295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022] Open
Abstract
Discovery of the naturally evolved fluorescent proteins and their genetically engineered biosensors have enormously contributed to current bioimaging techniques. These reporters to trace dynamic changes of intracellular protein activities have continuously transformed according to the various demands in biological studies. Along with that, light-inducible optogenetic technologies have offered scientists to perturb, control and analyze the function of intracellular machineries in spatiotemporal manner. In this review, we present an overview of the molecular strategies that have been exploited for producing genetically encoded protein reporters and various optogenetic modules. Finally, in particular, we discuss the current efforts for combined use of these reporters and optogenetic modules as a powerful tactic for the control and imaging of signaling events in cells and tissues.
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Affiliation(s)
- Jihoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon 34141,
Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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34
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Natsume T, Kanemaki MT. Conditional Degrons for Controlling Protein Expression at the Protein Level. Annu Rev Genet 2018; 51:83-102. [PMID: 29178817 DOI: 10.1146/annurev-genet-120116-024656] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein depletion. Compared with technologies targeting the pretranslation steps, direct protein depletion (or protein knockdown approaches) is advantageous in terms of specificity, reversibility, and time required for depletion, which can be achieved by fusing a POI with a protein domain called a degron that induces rapid proteolysis of the fusion protein. Conditional degrons can be activated or inhibited by temperature, small molecules, light, or the expression of another protein. The conditional degron-based technologies currently available are described and discussed.
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Affiliation(s)
- Toyoaki Natsume
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
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35
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Moggs J, Terranova R. Chromatin dynamics underlying latent responses to xenobiotics. Toxicol Res (Camb) 2018; 7:606-617. [PMID: 30090610 PMCID: PMC6062062 DOI: 10.1039/c7tx00317j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/26/2018] [Indexed: 11/21/2022] Open
Abstract
Pleiotropic xenobiotics can trigger dynamic alterations in mammalian chromatin structure and function but many of these are likely non-adverse and simply reflect short-term changes in DNA transactions underlying normal homeostatic, adaptive and protective cellular responses. However, it is plausible that a subset of xenobiotic-induced perturbations of somatic tissue or germline epigenomes result in delayed-onset and long-lasting adverse effects, in particular if they occur during critical stages of growth and development. These could include reprogramming, dedifferentiation, uncontrolled growth, and cumulative toxicity effects through molecular memory of prior xenobiotic exposures or altered susceptibility to subsequent xenobiotic exposures. Here we discuss the current evidence for epigenetic mechanisms underlying latent responses to xenobiotics, and the potential for identifying molecular epigenetic changes that are prodromal to overt morphologic or functional toxicity phenotypes.
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Affiliation(s)
- Jonathan Moggs
- Preclinical Safety , Translational Medicine , Novartis Institutes for BioMedical Research , Basel , Switzerland
| | - Rémi Terranova
- Preclinical Safety , Translational Medicine , Novartis Institutes for BioMedical Research , Basel , Switzerland
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36
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Kogenaru M, Isalan M. Drug-Inducible Control of Lethality Genes: A Low Background Destabilizing Domain Architecture Applied to the Gal4-UAS System in Drosophila. ACS Synth Biol 2018; 7:1496-1506. [PMID: 29733646 PMCID: PMC6008732 DOI: 10.1021/acssynbio.7b00302] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Indexed: 11/28/2022]
Abstract
Destabilizing domains (DDs) are genetic tags that conditionally control the level of abundance of proteins-of-interest (POI) with specific stabilizing small-molecule drugs, rapidly and reversibly, in a wide variety of organisms. The amount of the DD-tagged fusion protein directly impacts its molecular function. Hence, it is important that the background levels be tightly regulated in the absence of any drug. This is especially true for classes of proteins that function at extremely low levels, such as lethality genes involved in tissue development and certain transcriptional activator proteins. Here, we establish the uninduced background and induction levels for two widely used DDs (FKBP and DHFR) by developing an accurate quantification method. We show that both DDs exhibit functional background levels in the absence of a drug, but each to a different degree. To overcome this limitation, we systematically test a double architecture for these DDs (DD-POI-DD) that completely suppresses the protein's function in an uninduced state, while allowing tunable functional levels upon adding a drug. As an example, we generate a drug-stabilizable Gal4 transcriptional activator with extremely low background levels. We show that this functions in vivo in the widely used Gal4-UAS bipartite expression system in Drosophila melanogaster. By regulating a cell death gene, we demonstrate that only the low background double architecture enables tight regulation of the lethal phenotype in vivo. These improved tools will enable applications requiring exceptionally tight control of protein function in living cells and organisms.
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Affiliation(s)
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
- Imperial College Centre
for
Synthetic Biology, Imperial College London, London, SW7 2AZ, United Kingdom
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37
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Kitada T, DiAndreth B, Teague B, Weiss R. Programming gene and engineered-cell therapies with synthetic biology. Science 2018; 359:359/6376/eaad1067. [PMID: 29439214 DOI: 10.1126/science.aad1067] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gene and engineered-cell therapies promise to treat diseases by genetically modifying cells to carry out therapeutic tasks. Although the field has had some success in treating monogenic disorders and hematological malignancies, current approaches are limited to overexpression of one or a few transgenes, constraining the diseases that can be treated with this approach and leading to potential concerns over safety and efficacy. Synthetic gene networks can regulate the dosage, timing, and localization of gene expression and therapeutic activity in response to small molecules and disease biomarkers. Such "programmable" gene and engineered-cell therapies will provide new interventions for incurable or difficult-to-treat diseases.
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Affiliation(s)
- Tasuku Kitada
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Breanna DiAndreth
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian Teague
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ron Weiss
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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38
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The dTAG system for immediate and target-specific protein degradation. Nat Chem Biol 2018; 14:431-441. [PMID: 29581585 DOI: 10.1038/s41589-018-0021-8] [Citation(s) in RCA: 556] [Impact Index Per Article: 92.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 02/02/2018] [Indexed: 01/19/2023]
Abstract
Dissection of complex biological systems requires target-specific control of the function or abundance of proteins. Genetic perturbations are limited by off-target effects, multicomponent complexity, and irreversibility. Most limiting is the requisite delay between modulation to experimental measurement. To enable the immediate and selective control of single protein abundance, we created a chemical biology system that leverages the potency of cell-permeable heterobifunctional degraders. The dTAG system pairs a novel degrader of FKBP12F36V with expression of FKBP12F36V in-frame with a protein of interest. By transgene expression or CRISPR-mediated locus-specific knock-in, we exemplify a generalizable strategy to study the immediate consequence of protein loss. Using dTAG, we observe an unexpected superior antiproliferative effect of pan-BET bromodomain degradation over selective BRD4 degradation, characterize immediate effects of KRASG12V loss on proteomic signaling, and demonstrate rapid degradation in vivo. This technology platform will confer kinetic resolution to biological investigation and provide target validation in the context of drug discovery.
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39
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Moser SC, Voerman JSA, Buckley DL, Winter GE, Schliehe C. Acute Pharmacologic Degradation of a Stable Antigen Enhances Its Direct Presentation on MHC Class I Molecules. Front Immunol 2018; 8:1920. [PMID: 29358938 PMCID: PMC5766668 DOI: 10.3389/fimmu.2017.01920] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/14/2017] [Indexed: 12/23/2022] Open
Abstract
Bifunctional degraders, also referred to as proteolysis-targeting chimeras (PROTACs), are a recently developed class of small molecules. They were designed to specifically target endogenous proteins for ubiquitin/proteasome-dependent degradation and to thereby interfere with pathological mechanisms of diseases, including cancer. In this study, we hypothesized that this process of acute pharmacologic protein degradation might increase the direct MHC class I presentation of degraded targets. By studying this question, we contribute to an ongoing discussion about the origin of peptides feeding the MHC class I presentation pathway. Two scenarios have been postulated: peptides can either be derived from homeostatic turnover of mature proteins and/or from short-lived defective ribosomal products (DRiPs), but currently, it is still unclear to what ratio and efficiency both pathways contribute to the overall MHC class I presentation. We therefore generated the intrinsically stable model antigen GFP-S8L-F12 that was susceptible to acute pharmacologic degradation via the previously described degradation tag (dTAG) system. Using different murine cell lines, we show here that the bifunctional molecule dTAG-7 induced rapid proteasome-dependent degradation of GFP-S8L-F12 and simultaneously increased its direct presentation on MHC class I molecules. Using the same model in a doxycycline-inducible setting, we could further show that stable, mature antigen was the major source of peptides presented, thereby excluding a dominant role of DRiPs in our system. This study is, to our knowledge, the first to investigate targeted pharmacologic protein degradation in the context of antigen presentation and our data point toward future applications by strategically combining therapies using bifunctional degraders with their stimulating effect on direct MHC class I presentation.
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Affiliation(s)
- Sarah C Moser
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jane S A Voerman
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Dennis L Buckley
- Department for Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christopher Schliehe
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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40
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Li S, Liu Z, Li J, Liu A, Zhu L, Yu K, Zhang K. Effects of Shield1 on the viral replication of varicella‑zoster virus containing FKBP‑tagged ORF4 and 48. Mol Med Rep 2017; 17:763-770. [PMID: 29115621 PMCID: PMC5780153 DOI: 10.3892/mmr.2017.7986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 08/02/2017] [Indexed: 12/24/2022] Open
Abstract
The present study aimed to explore the effects of a stabilizing ligand, Shield-1, on the replication of recombinant varicella-zoster virus (VZV) containing FK506 binding protein (FKPB) tags in essential open reading frames (ORF) 4 and 48. A specific galactokinase (galK) selection method was conducted, following the addition of galK labels to VZV ORF4 and 48, using a SW102 VZV bacterial artificial chromosome (BAC) system. Subsequently, recombinant VZV containing FKPB tags in ORF4 and 48 was constructed by counterselection and homologous recombination. Recombinant viral plasmids containing FKPB-tagged VZV ORF4 and 48 were extracted and transfected into human acute retinal pigment epithelial ARPE-19 cells. The results demonstrated that the FKPB-tagged viral protein was rapidly degraded by proteases in recombinant virus-infected ARPE-19 cells. In addition, the recombinant VZVORF4-FKBP-ORF48-FKBP virus could not grow if a synthetic ligand of FKBP, Shield1, was not added to the ARPE-19 cell culture medium; however, the degradation of FKPB-tagged viral protein was prevented if Shield1 was added to the ARPE-19 cell culture medium, thereby allowing viral replication in ARPE-19 cells. These results indicated that Shield1 may regulate replication of recombinant VZVORF4-FKBP-ORF48-FKBP following transfection into human epithelial cells.
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Affiliation(s)
- Shuying Li
- School of Basic Medical Sciences, North China University of Science and Technology (Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases), Tangshan, Hebei 063000, P.R. China
| | - Zhanjun Liu
- School of Basic Medical Sciences, North China University of Science and Technology (Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases), Tangshan, Hebei 063000, P.R. China
| | - Ji Li
- School of Basic Medical Sciences, North China University of Science and Technology (Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases), Tangshan, Hebei 063000, P.R. China
| | - Aihua Liu
- School of Basic Medical Sciences, North China University of Science and Technology (Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases), Tangshan, Hebei 063000, P.R. China
| | - Lihua Zhu
- School of Basic Medical Sciences, North China University of Science and Technology (Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases), Tangshan, Hebei 063000, P.R. China
| | - Kui Yu
- School of Basic Medical Sciences, North China University of Science and Technology (Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases), Tangshan, Hebei 063000, P.R. China
| | - Ke Zhang
- School of Basic Medical Sciences, North China University of Science and Technology (Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases), Tangshan, Hebei 063000, P.R. China
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41
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Gaynor AS, Chen W. Induced prodrug activation by conditional protein degradation. J Biotechnol 2017; 260:62-66. [PMID: 28912080 PMCID: PMC6595225 DOI: 10.1016/j.jbiotec.2017.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/24/2017] [Accepted: 09/10/2017] [Indexed: 11/17/2022]
Abstract
Enzyme prodrug therapies hold potential as a targeted treatment option for cancer patients. However, off-target effects can be detrimental to patient health and represent a safety concern. This concern can be alleviated by including a failsafe mechanism that can abort the therapy in healthy cells. This feature can be included in enzyme prodrug therapies by use of conditional degradation tags, which degrade the protein unless stabilized. We call this process Degradation-Directed Enzyme Prodrug Therapy (DDEPT). Herein, we use traceless shielding (TShld), a mechanism that degrades a protein of interest unless it is rescued by the addition of rapamycin, to test this concept. We demonstrated that TShld rapidly yielded only native protein products within 1h after rapamycin addition. The rapid protection phenotype of TShld was further adapted to rescue yeast cytosine deaminase, a prodrug converting enzyme. As expected, cell viability was adversely affected only in the presence of both 5-fluorocytosine (5-FC) and rapamycin. We believe that the DDEPT system can be easily combined with other targeting strategies to further increase the safety of prodrug therapies.
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Affiliation(s)
- Andrew S Gaynor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, USA.
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42
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Affiliation(s)
- George M. Burslem
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
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43
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Delivering safer immunotherapies for cancer. Adv Drug Deliv Rev 2017; 114:79-101. [PMID: 28545888 DOI: 10.1016/j.addr.2017.05.011] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 05/05/2017] [Accepted: 05/17/2017] [Indexed: 12/14/2022]
Abstract
Cancer immunotherapy is now a powerful clinical reality, with a steady progression of new drug approvals and a massive pipeline of additional treatments in clinical and preclinical development. However, modulation of the immune system can be a double-edged sword: Drugs that activate immune effectors are prone to serious non-specific systemic inflammation and autoimmune side effects. Drug delivery technologies have an important role to play in harnessing the power of immune therapeutics while avoiding on-target/off-tumor toxicities. Here we review mechanisms of toxicity for clinically-relevant immunotherapeutics, and discuss approaches based in drug delivery technology to enhance the safety and potency of these treatments. These include strategies to merge drug delivery with adoptive cellular therapies, targeting immunotherapies to tumors or select immune cells, and localizing therapeutics intratumorally. Rational design employing lessons learned from the drug delivery and nanomedicine fields has the potential to facilitate immunotherapy reaching its full potential.
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44
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Senturk S, Shirole NH, Nowak DG, Corbo V, Pal D, Vaughan A, Tuveson DA, Trotman LC, Kinney JB, Sordella R. Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. Nat Commun 2017; 8:14370. [PMID: 28224990 DOI: 10.1101/023366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/21/2016] [Indexed: 05/21/2023] Open
Abstract
The CRISPR/Cas9 system is a powerful tool for studying gene function. Here, we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional Cas9 expression and temporal control of gene editing in the presence of an FKBP12 synthetic ligand. This system can be easily adapted to co-express, from the same promoter, DD-Cas9 with any other gene of interest without co-modulation of the latter. In particular, when co-expressed with inducible Cre-ERT2, our system enables parallel, independent manipulation of alleles targeted by Cas9 and traditional recombinase with single-cell specificity. We anticipate this platform will be used for the systematic characterization and identification of essential genes, as well as the investigation of the interactions between functional genes.
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Affiliation(s)
- Serif Senturk
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Nitin H Shirole
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Dawid G Nowak
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Vincenzo Corbo
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Debjani Pal
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Alexander Vaughan
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - David A Tuveson
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Lloyd C Trotman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Justin B Kinney
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Raffaella Sordella
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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45
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Senturk S, Shirole NH, Nowak DG, Corbo V, Pal D, Vaughan A, Tuveson DA, Trotman LC, Kinney JB, Sordella R. Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. Nat Commun 2017; 8:14370. [PMID: 28224990 PMCID: PMC5322564 DOI: 10.1038/ncomms14370] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/21/2016] [Indexed: 12/25/2022] Open
Abstract
The CRISPR/Cas9 system is a powerful tool for studying gene function. Here, we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional Cas9 expression and temporal control of gene editing in the presence of an FKBP12 synthetic ligand. This system can be easily adapted to co-express, from the same promoter, DD-Cas9 with any other gene of interest without co-modulation of the latter. In particular, when co-expressed with inducible Cre-ERT2, our system enables parallel, independent manipulation of alleles targeted by Cas9 and traditional recombinase with single-cell specificity. We anticipate this platform will be used for the systematic characterization and identification of essential genes, as well as the investigation of the interactions between functional genes.
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Affiliation(s)
- Serif Senturk
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Nitin H. Shirole
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Dawid G. Nowak
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Vincenzo Corbo
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Debjani Pal
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Alexander Vaughan
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - David A. Tuveson
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Lloyd C. Trotman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Justin B. Kinney
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Raffaella Sordella
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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46
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Tomoshige S, Naito M, Hashimoto Y, Ishikawa M. Degradation of HaloTag-fused nuclear proteins using bestatin-HaloTag ligand hybrid molecules. Org Biomol Chem 2016; 13:9746-50. [PMID: 26338696 DOI: 10.1039/c5ob01395j] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have developed a protein knockdown technology using hybrid small molecules designed as conjugates of a ligand for the target protein and a ligand for ubiquitin ligase cellular inhibitor of apoptosis protein 1 (cIAP1). However, this technology has several limitations. Here, we report the development of a novel protein knockdown system to address these limitations. In this system, target proteins are fused with HaloTag to provide a common binding site for a degradation inducer. We designed and synthesized small molecules consisting of alkyl chloride as the HaloTag-binding degradation inducer, which binds to HaloTag, linked to BE04 (2), which binds to cIAP1. Using this system, we successfully knocked down HaloTag-fused cAMP responsive element binding protein 1 (HaloTag-CREB1) and HaloTag-fused c-jun (HaloTag-c-jun), which are ligand-unknown nuclear proteins, in living cells. HaloTag-binding degradation inducers can be synthesized easily, and are expected to be useful as biological tools for pan-degradation of HaloTag-fused proteins.
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Affiliation(s)
- Shusuke Tomoshige
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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47
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Development of Inducible Molecular Switches Based on All-in-One Lentiviral Vectors Equipped with Drug Controlled FLP Recombinase. Methods Mol Biol 2016. [PMID: 27317170 DOI: 10.1007/978-1-4939-3753-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Drug-inducible recombination based on flippase (FLP) is frequently used in animal models and in transgenic cell lines to initiate or to abrogate gene expression. Although the system is highly efficient, functional gene analyses depend on the availability of suitable animal models. In contrast, lentiviral vectors are readily available and versatile tools for the transfer of genetic information into a wide variety of target cells, and can be produced at high titer in a timely manner. To combine the advantages of both approaches, we generated a tight, drug-controlled FLP recombinase consisting of a 5' FKBP12 derived conditional destruction domain and a 3' estrogen receptor ligand binding (ERT2) domain. We successfully constructed lentiviral vectors expressing drug-controlled FLP in combination with a fluorescent reporter for recombination of FLP recognition target (FRT) sites located in trans as well as with target alleles located in cis (all-in-one configuration). In this chapter, we describe the design of the drug controlled FLP recombinase, the construction of molecular switches consisting of FLP expressing lentiviral vectors for inducible recombination of target sites located in cis and in trans, as well as the details for the characterization of lentiviral FLP vectors in cell lines.
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48
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Geisinger JM, Turan S, Hernandez S, Spector LP, Calos MP. In vivo blunt-end cloning through CRISPR/Cas9-facilitated non-homologous end-joining. Nucleic Acids Res 2016; 44:e76. [PMID: 26762978 PMCID: PMC4856974 DOI: 10.1093/nar/gkv1542] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 12/23/2015] [Accepted: 12/28/2015] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas9 system facilitates precise DNA modifications by generating RNA-guided blunt-ended double-strand breaks. We demonstrate that guide RNA pairs generate deletions that are repaired with a high level of precision by non-homologous end-joining in mammalian cells. We present a method called knock-in blunt ligation for exploiting these breaks to insert exogenous PCR-generated sequences in a homology-independent manner without loss of additional nucleotides. This method is useful for making precise additions to the genome such as insertions of marker gene cassettes or functional elements, without the need for homology arms. We successfully utilized this method in human and mouse cells to insert fluorescent protein cassettes into various loci, with efficiencies up to 36% in HEK293 cells without selection. We also created versions of Cas9 fused to the FKBP12-L106P destabilization domain in an effort to improve Cas9 performance. Our in vivo blunt-end cloning method and destabilization-domain-fused Cas9 variant increase the repertoire of precision genome engineering approaches.
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Affiliation(s)
- Jonathan M Geisinger
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sören Turan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sophia Hernandez
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura P Spector
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele P Calos
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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49
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Pol J, Buqué A, Aranda F, Bloy N, Cremer I, Eggermont A, Erbs P, Fucikova J, Galon J, Limacher JM, Preville X, Sautès-Fridman C, Spisek R, Zitvogel L, Kroemer G, Galluzzi L. Trial Watch-Oncolytic viruses and cancer therapy. Oncoimmunology 2016; 5:e1117740. [PMID: 27057469 PMCID: PMC4801444 DOI: 10.1080/2162402x.2015.1117740] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/03/2015] [Indexed: 02/06/2023] Open
Abstract
Oncolytic virotherapy relies on the administration of non-pathogenic viral strains that selectively infect and kill malignant cells while favoring the elicitation of a therapeutically relevant tumor-targeting immune response. During the past few years, great efforts have been dedicated to the development of oncolytic viruses with improved specificity and potency. Such an intense wave of investigation has culminated this year in the regulatory approval by the US Food and Drug Administration (FDA) of a genetically engineered oncolytic viral strain for use in melanoma patients. Here, we summarize recent preclinical and clinical advances in oncolytic virotherapy.
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Affiliation(s)
- Jonathan Pol
- INSERM, U1138, Paris, France
- Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Center de Recherche des Cordeliers, Paris, France
- Gustave Roussy Cancer Campus, Villejuif, France
| | - Aitziber Buqué
- INSERM, U1138, Paris, France
- Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Center de Recherche des Cordeliers, Paris, France
- Gustave Roussy Cancer Campus, Villejuif, France
| | - Fernando Aranda
- Group of Immune receptors of the Innate and Adaptive System, Institut d’Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Norma Bloy
- INSERM, U1138, Paris, France
- Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Center de Recherche des Cordeliers, Paris, France
- Gustave Roussy Cancer Campus, Villejuif, France
| | - Isabelle Cremer
- INSERM, U1138, Paris, France
- Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 13, Center de Recherche des Cordeliers, Paris, France
| | | | | | - Jitka Fucikova
- Sotio, Prague, Czech Republic
- Dept. of Immunology, 2nd Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Jérôme Galon
- INSERM, U1138, Paris, France
- Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Laboratory of Integrative Cancer Immunology, Centre de Recherche des Cordeliers, Paris, France
| | | | | | - Catherine Sautès-Fridman
- INSERM, U1138, Paris, France
- Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 13, Center de Recherche des Cordeliers, Paris, France
| | - Radek Spisek
- Sotio, Prague, Czech Republic
- Dept. of Immunology, 2nd Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, Villejuif, France
- INSERM, U1015, CICBT507, Villejuif, France
| | - Guido Kroemer
- INSERM, U1138, Paris, France
- Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Center de Recherche des Cordeliers, Paris, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
- Department of Women’s and Children’s Health, Karolinska University Hospital, Stockholm, Sweden
| | - Lorenzo Galluzzi
- INSERM, U1138, Paris, France
- Université Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée par la Ligue Nationale contre le Cancer, Center de Recherche des Cordeliers, Paris, France
- Gustave Roussy Cancer Campus, Villejuif, France
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Auffenberg E, Jurik A, Mattusch C, Stoffel R, Genewsky A, Namendorf C, Schmid RM, Rammes G, Biel M, Uhr M, Moosmang S, Michalakis S, Wotjak CT, Thoeringer CK. Remote and reversible inhibition of neurons and circuits by small molecule induced potassium channel stabilization. Sci Rep 2016; 6:19293. [PMID: 26757616 PMCID: PMC4725838 DOI: 10.1038/srep19293] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 12/09/2015] [Indexed: 01/12/2023] Open
Abstract
Manipulating the function of neurons and circuits that translate electrical and chemical signals into behavior represents a major challenges in neuroscience. In addition to optogenetic methods using light-activatable channels, pharmacogenetic methods with ligand induced modulation of cell signaling and excitability have been developed. However, they are largely based on ectopic expression of exogenous or chimera proteins. Now, we describe the remote and reversible expression of a Kir2.1 type potassium channel using the chemogenetic technique of small molecule induced protein stabilization. Based on shield1-mediated shedding of a destabilizing domain fused to a protein of interest and inhibition of protein degradation, this principle has been adopted for biomedicine, but not in neuroscience so far. Here, we apply this chemogenetic approach in brain research for the first time in order to control a potassium channel in a remote and reversible manner. We could show that shield1-mediated ectopic Kir2.1 stabilization induces neuronal silencing in vitro and in vivo in the mouse brain. We also validated this novel pharmacogenetic method in different neurobehavioral paradigms.The DD-Kir2.1 may complement the existing portfolio of pharmaco- and optogenetic techniques for specific neuron manipulation, but it may also provide an example for future applications of this principle in neuroscience research.
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Affiliation(s)
- Eva Auffenberg
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Germany
| | - Angela Jurik
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Germany
| | - Corinna Mattusch
- Institute of Anesthesiology, Technical University of Munich, Germany
| | - Rainer Stoffel
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Andreas Genewsky
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Christian Namendorf
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Germany
| | - Gerhard Rammes
- Institute of Anesthesiology, Technical University of Munich, Germany
| | - Martin Biel
- Center for Integrated Protein Science Munich (CIPSM) and Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-University of Munich, Germany
| | - Manfred Uhr
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Sven Moosmang
- Institute of Pharmacology, Technical University of Munich, Germany
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich (CIPSM) and Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-University of Munich, Germany
| | - Carsten T Wotjak
- Max Planck Institute of Psychiatry, Department of Stress Physiology and Neurogenetics, Munich, Germany
| | - Christoph K Thoeringer
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Germany
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