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Liu Z, Lu X, Villette V, Gou Y, Colbert KL, Lai S, Guan S, Land MA, Lee J, Assefa T, Zollinger DR, Korympidou MM, Vlasits AL, Pang MM, Su S, Cai C, Froudarakis E, Zhou N, Patel SS, Smith CL, Ayon A, Bizouard P, Bradley J, Franke K, Clandinin TR, Giovannucci A, Tolias AS, Reimer J, Dieudonné S, St-Pierre F. Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy. Cell 2022; 185:3408-3425.e29. [PMID: 35985322 PMCID: PMC9563101 DOI: 10.1016/j.cell.2022.07.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 04/13/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022]
Abstract
Genetically encoded voltage indicators are emerging tools for monitoring voltage dynamics with cell-type specificity. However, current indicators enable a narrow range of applications due to poor performance under two-photon microscopy, a method of choice for deep-tissue recording. To improve indicators, we developed a multiparameter high-throughput platform to optimize voltage indicators for two-photon microscopy. Using this system, we identified JEDI-2P, an indicator that is faster, brighter, and more sensitive and photostable than its predecessors. We demonstrate that JEDI-2P can report light-evoked responses in axonal termini of Drosophila interneurons and the dendrites and somata of amacrine cells of isolated mouse retina. JEDI-2P can also optically record the voltage dynamics of individual cortical neurons in awake behaving mice for more than 30 min using both resonant-scanning and ULoVE random-access microscopy. Finally, ULoVE recording of JEDI-2P can robustly detect spikes at depths exceeding 400 μm and report voltage correlations in pairs of neurons.
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Affiliation(s)
- Zhuohe Liu
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA
| | - Vincent Villette
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Yueyang Gou
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin L Colbert
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shujuan Lai
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sihui Guan
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michelle A Land
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jihwan Lee
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tensae Assefa
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Daniel R Zollinger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maria M Korympidou
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Center for Integrative Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg, 72076, Germany
| | - Anna L Vlasits
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Center for Integrative Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany
| | - Michelle M Pang
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Sharon Su
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Changjia Cai
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA
| | - Emmanouil Froudarakis
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion 70013, Greece
| | - Na Zhou
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Saumil S Patel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cameron L Smith
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX 77030, USA
| | - Annick Ayon
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Pierre Bizouard
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Jonathan Bradley
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - Katrin Franke
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Center for Integrative Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany; Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Baden-Württemberg, 72076, Germany
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Andrea Giovannucci
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, Chapel Hill, NC 27599, USA
| | - Andreas S Tolias
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jacob Reimer
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stéphane Dieudonné
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris 75005, France
| | - François St-Pierre
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA; Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX 77005, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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8
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Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken SE, Ljubetič A, Edman N, Ueda G, Chow CM, Johnson M, Addetia A, Navarro MJ, Panpradist N, Gale M, Freedman BS, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D. Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Sci Transl Med 2022; 14:eabn1252. [PMID: 35412328 PMCID: PMC9258422 DOI: 10.1126/scitranslmed.abn1252] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy was achieved with a homotrimeric version of the 75-residue angiotensin-converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. Consistent with the design model, in the cryo-electron microscopy structure TRI2-2 forms a tripod at the apex of the spike protein that engaged all three receptor binding domains simultaneously. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than the monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies in greater resistance to viral escape and antigenic drift, and advantages over native receptor traps in lower chances of autoimmune responses.
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Affiliation(s)
- Andrew C. Hunt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Shally Saini
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Louisa Helms
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, 98195, USA
| | - Tien-Ying Hsiang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lisa Kozodoy
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lydia B. Green
- Amgen Research, Biologic Discovery, Burnaby, V5A 1V7, BC, Canada
| | | | | | - Bastian Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Invizyne Technologies Inc., Monrovia, CA, 91016, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Adam L. Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Laboratory Medicine, University of Wisconsin – Madison, Madison, WI, 53705, USA
| | - Natasha M. Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott E. Boyken
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ajasja Ljubetič
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department for Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, SI-1000, Slovenia
| | - Natasha Edman
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, 98195, USA
- USA Medical Scientist Training Program, University of Washington, Seattle, WA, 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cameron M. Chow
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Neolukin Therapeutics Inc., Seattle, WA, 98102, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- The Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin S. Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Kidney Research Institute, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Jesse D. Bloom
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
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