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Miller ADC, Chowdhury SP, Hanson HW, Linderman SK, Ghasemi HI, Miller WD, Morrissey MA, Richardson CD, Gardner BM, Mukherjee A. Engineering water exchange is a safe and effective method for magnetic resonance imaging in diverse cell types. J Biol Eng 2024; 18:30. [PMID: 38649904 PMCID: PMC11035135 DOI: 10.1186/s13036-024-00424-5] [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: 09/26/2023] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Aquaporin-1 (Aqp1), a water channel, has garnered significant interest for cell-based medicine and in vivo synthetic biology due to its ability to be genetically encoded to produce magnetic resonance signals by increasing the rate of water diffusion in cells. However, concerns regarding the effects of Aqp1 overexpression and increased membrane diffusivity on cell physiology have limited its widespread use as a deep-tissue reporter. In this study, we present evidence that Aqp1 generates strong diffusion-based magnetic resonance signals without adversely affecting cell viability or morphology in diverse cell lines derived from mice and humans. Our findings indicate that Aqp1 overexpression does not induce ER stress, which is frequently associated with heterologous expression of membrane proteins. Furthermore, we observed that Aqp1 expression had no detrimental effects on native biological activities, such as phagocytosis, immune response, insulin secretion, and tumor cell migration in the analyzed cell lines. These findings should serve to alleviate any lingering safety concerns regarding the utilization of Aqp1 as a genetic reporter and should foster its broader application as a noninvasive reporter for in vivo studies.
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Affiliation(s)
- Austin D C Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Soham P Chowdhury
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Hadley W Hanson
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Sarah K Linderman
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Hannah I Ghasemi
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Wyatt D Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA, 93106, USA
| | - Meghan A Morrissey
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Chris D Richardson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Brooke M Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Arnab Mukherjee
- 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.
- Department of Bioengineering, University of California, Santa Barbara, CA, 93106, USA.
- Department of Chemistry, University of California, Santa Barbara, CA, 93106, USA.
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.
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Chacko AN, Miller AD, Dhanabalan KM, Mukherjee A. Exploring the potential of water channels for developing MRI reporters and sensors without the need for exogenous contrast agents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576580. [PMID: 38328035 PMCID: PMC10849501 DOI: 10.1101/2024.01.21.576580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Genetically encoded reporters for magnetic resonance imaging (MRI) offer a valuable technology for making molecular-scale measurements of biological processes within living organisms with high anatomical resolution and whole-organ coverage without relying on ionizing radiation. However, most MRI reporters rely on contrast agents, typically paramagnetic metals and metal complexes, which often need to be supplemented exogenously to create optimal contrast. To eliminate the need for contrast agents, we previously introduced aquaporin-1, a mammalian water channel, as a new reporter gene for the fully autonomous detection of genetically labeled cells using diffusion-weighted MRI. In this study, we aimed to expand the toolbox of diffusion-based genetic reporters by modulating aquaporin membrane trafficking and harnessing the evolutionary diversity of water channels across species. We identified a number of new water channels that functioned as diffusion-weighted reporter genes. In addition, we show that loss-of-function variants of yeast and human aquaporins can be leveraged to design first-in-class diffusion-based sensors for detecting the activity of a model protease within living cells.
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Affiliation(s)
| | | | | | - Arnab Mukherjee
- Department of Chemistry
- Biomolecular Science and Engineering Graduate Program
- Department of Chemical Engineering
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Miller ADC, Chowdhury SP, Hanson HW, Linderman SK, Ghasemi HI, Miller WD, Morrissey MA, Richardson CD, Gardner BM, Mukherjee A. Engineering water exchange is a safe and effective method for magnetic resonance imaging in diverse cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566095. [PMID: 37986852 PMCID: PMC10659288 DOI: 10.1101/2023.11.07.566095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Aquaporin-1 (Aqp1), a water channel, has garnered significant interest for cell-based medicine and in vivo synthetic biology due to its ability to be genetically encoded to produce magnetic resonance signals by increasing the rate of water diffusion in cells. However, concerns regarding the effects of Aqp1 overexpression and increased membrane diffusivity on cell physiology have limited its widespread use as a deep-tissue reporter. In this study, we present evidence that Aqp1 generates strong diffusion-based magnetic resonance signals without adversely affecting cell viability or morphology in diverse cell lines derived from mice and humans. Our findings indicate that Aqp1 overexpression does not induce ER stress, which is frequently associated with heterologous expression of membrane proteins. Furthermore, we observed that Aqp1 expression had no detrimental effects on native biological activities, such as phagocytosis, immune response, insulin secretion, and tumor cell migration in the analyzed cell lines. These findings should serve to alleviate any lingering safety concerns regarding the utilization of Aqp1 as a genetic reporter and should foster its broader application as a noninvasive reporter for in vivo studies.
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Affiliation(s)
- Austin D C Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106, USA
| | - Soham P Chowdhury
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Hadley W Hanson
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106, USA
| | - Sarah K Linderman
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Hannah I Ghasemi
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Wyatt D Miller
- Biomolecular Science and Engineering Graduate Program, University of California, Santa Barbara, CA 93106, USA
| | - Meghan A Morrissey
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Chris D Richardson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Brooke M Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Arnab Mukherjee
- 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
- Department of Bioengineering, University of California, Santa Barbara, CA 93106, USA
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
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Chowdhury R, Wan J, Gardier R, Rafael-Patino J, Thiran JP, Gibou F, Mukherjee A. Molecular Imaging with Aquaporin-Based Reporter Genes: Quantitative Considerations from Monte Carlo Diffusion Simulations. ACS Synth Biol 2023; 12:3041-3049. [PMID: 37793076 DOI: 10.1021/acssynbio.3c00372] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Aquaporins provide a unique approach for imaging genetic activity in deep tissues by increasing the rate of cellular water diffusion, which generates a magnetic resonance contrast. However, distinguishing aquaporin signals from the tissue background is challenging because water diffusion is influenced by structural factors, such as cell size and packing density. Here, we developed a Monte Carlo model to analyze how cell radius and intracellular volume fraction quantitatively affect aquaporin signals. We demonstrated that a differential imaging approach based on subtracting signals at two diffusion times can improve specificity by unambiguously isolating aquaporin signals from the tissue background. We further used Monte Carlo simulations to analyze the connection between diffusivity and the percentage of cells engineered to express aquaporin and established a mapping that accurately determined the volume fraction of aquaporin-expressing cells in mixed populations. The quantitative framework developed in this study will enable a broad range of applications in biomedical synthetic biology, requiring the use of aquaporins to noninvasively monitor the location and function of genetically engineered devices in live animals.
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Affiliation(s)
| | | | - Remy Gardier
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Jonathan Rafael-Patino
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), 1005 Lausanne, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), 1005 Lausanne, Switzerland
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Dan Q, Jiang X, Wang R, Dai Z, Sun D. Biogenic Imaging Contrast Agents. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207090. [PMID: 37401173 PMCID: PMC10477908 DOI: 10.1002/advs.202207090] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/08/2023] [Indexed: 07/05/2023]
Abstract
Imaging contrast agents are widely investigated in preclinical and clinical studies, among which biogenic imaging contrast agents (BICAs) are developing rapidly and playing an increasingly important role in biomedical research ranging from subcellular level to individual level. The unique properties of BICAs, including expression by cells as reporters and specific genetic modification, facilitate various in vitro and in vivo studies, such as quantification of gene expression, observation of protein interactions, visualization of cellular proliferation, monitoring of metabolism, and detection of dysfunctions. Furthermore, in human body, BICAs are remarkably helpful for disease diagnosis when the dysregulation of these agents occurs and can be detected through imaging techniques. There are various BICAs matched with a set of imaging techniques, including fluorescent proteins for fluorescence imaging, gas vesicles for ultrasound imaging, and ferritin for magnetic resonance imaging. In addition, bimodal and multimodal imaging can be realized through combining the functions of different BICAs, which helps overcome the limitations of monomodal imaging. In this review, the focus is on the properties, mechanisms, applications, and future directions of BICAs.
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Affiliation(s)
- Qing Dan
- Shenzhen Key Laboratory for Drug Addiction and Medication SafetyDepartment of UltrasoundInstitute of Ultrasonic MedicinePeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhen518036P. R. China
| | - Xinpeng Jiang
- Department of Biomedical EngineeringCollege of Future TechnologyPeking UniversityBeijing100871P. R. China
| | - Run Wang
- Shenzhen Key Laboratory for Drug Addiction and Medication SafetyDepartment of UltrasoundInstitute of Ultrasonic MedicinePeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhen518036P. R. China
| | - Zhifei Dai
- Department of Biomedical EngineeringCollege of Future TechnologyPeking UniversityBeijing100871P. R. China
| | - Desheng Sun
- Shenzhen Key Laboratory for Drug Addiction and Medication SafetyDepartment of UltrasoundInstitute of Ultrasonic MedicinePeking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterShenzhen518036P. R. China
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Thankarajan E, Oz S, Saady A, Kulbitski K, Kompanets MO, Eisen MS, Berlin S. SNAP-Tag-Targeted MRI-Fluorescent Multimodal Probes. Chembiochem 2023; 24:e202300172. [PMID: 37092744 DOI: 10.1002/cbic.202300172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/02/2023] [Accepted: 04/24/2023] [Indexed: 04/25/2023]
Abstract
Magnetic resonance imaging (MRI) is a powerful imaging modality, widely employed in research and clinical settings. However, MRI images suffer from low signals and a lack of target specificity. We aimed to develop a multimodal imaging probe to detect targeted cells by MRI and fluorescence microscopy. We synthesized a trifunctional imaging probe consisting of a SNAP-tag substrate for irreversible and specific labelling of cells, cyanine dyes for bright fluorescence, and a chelated GdIII molecule for enhancing MRI contrast. Our probes exhibit specific and efficient labelling of genetically defined cells (expressing SNAP-tag at their membrane), bright fluorescence and MRI signal. Our synthetic approach provides a versatile platform for the production of multimodal imaging probes, particularly for light microscopy and MRI.
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Affiliation(s)
- Ebaston Thankarajan
- Department of Neuroscience, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3525422, Israel
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Shimrit Oz
- Department of Neuroscience, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3525422, Israel
| | - Abed Saady
- Department of Neuroscience, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3525422, Israel
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
- Present address: School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Kseniya Kulbitski
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Mykhail O Kompanets
- L.M. Litvinenko Institute of Physico-Organic Chemistry and Coal Chemistry, National Academy of Sciences of Ukraine, Kyiv, 02660, Ukraine
| | - Moris S Eisen
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Shai Berlin
- Department of Neuroscience, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3525422, Israel
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Chowdhury R, Wan J, Gardier R, Rafael-Patino J, Thiran JP, Gibou F, Mukherjee A. Molecular imaging with aquaporin-based reporter genes: quantitative considerations from Monte Carlo diffusion simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544324. [PMID: 37333205 PMCID: PMC10274877 DOI: 10.1101/2023.06.09.544324] [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
Aquaporins provide a new class of genetic tools for imaging molecular activity in deep tissues by increasing the rate of cellular water diffusion, which generates magnetic resonance contrast. However, distinguishing aquaporin contrast from the tissue background is challenging because water diffusion is also influenced by structural factors such as cell size and packing density. Here, we developed and experimentally validated a Monte Carlo model to analyze how cell radius and intracellular volume fraction quantitatively affect aquaporin signals. We demonstrated that a differential imaging approach based on time-dependent changes in diffusivity can improve specificity by unambiguously isolating aquaporin-driven contrast from the tissue background. Finally, we used Monte Carlo simulations to analyze the connection between diffusivity and the percentage of cells engineered to express aquaporin, and established a simple mapping that accurately determined the volume fraction of aquaporin-expressing cells in mixed populations. This study creates a framework for broad applications of aquaporins, particularly in biomedicine and in vivo synthetic biology, where quantitative methods to measure the location and performance of genetic devices in whole vertebrates are necessary.
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Affiliation(s)
- Rochishnu Chowdhury
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Jinyang Wan
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Remy Gardier
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jonathan Rafael-Patino
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Jean-Philippe Thiran
- Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Radiology Department, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Frederic Gibou
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA
- Department of Computer Science, 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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8
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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Recent Advances in the Study of Gas Vesicle Proteins and Application of Gas Vesicles in Biomedical Research. Life (Basel) 2022; 12:life12091455. [PMID: 36143491 PMCID: PMC9501494 DOI: 10.3390/life12091455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 12/01/2022] Open
Abstract
The formation of gas vesicles has been investigated in bacteria and haloarchaea for more than 50 years. These air-filled nanostructures allow cells to stay at a certain height optimal for growth in their watery environment. Several gvp genes are involved and have been studied in Halobacterium salinarum, cyanobacteria, Bacillus megaterium, and Serratia sp. ATCC39006 in more detail. GvpA and GvpC form the gas vesicle shell, and additional Gvp are required as minor structural proteins, chaperones, an ATP-hydrolyzing enzyme, or as gene regulators. We analyzed the Gvp proteins of Hbt. salinarum with respect to their protein–protein interactions, and developed a model for the formation of these nanostructures. Gas vesicles are also used in biomedical research. Since they scatter waves and produce ultrasound contrast, they could serve as novel contrast agent for ultrasound or magnetic resonance imaging. Additionally, gas vesicles were engineered as acoustic biosensors to determine enzyme activities in cells. These applications are based on modifications of the surface protein GvpC that alter the mechanical properties of the gas vesicles. In addition, gas vesicles have been decorated with GvpC proteins fused to peptides of bacterial or viral pathogens and are used as tools for vaccine development.
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Yun J, Baldini M, Chowdhury R, Mukherjee A. Designing Protein-Based Probes for Sensing Biological Analytes with Magnetic Resonance Imaging. ANALYSIS & SENSING 2022; 2:e202200019. [PMID: 37409177 PMCID: PMC10321474 DOI: 10.1002/anse.202200019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Genetically encoded sensors provide unique advantages for monitoring biological analytes with molecular and cellular-level specificity. While sensors derived from fluorescent proteins represent staple tools in biological imaging, these probes are limited to optically accessible preparations owing to physical curbs on light penetration. In contrast to optical methods, magnetic resonance imaging (MRI) may be used to noninvasively look inside intact organisms at any arbitrary depth and over large fields of view. These capabilities have spurred the development of innovative methods to connect MRI readouts with biological targets using protein-based probes that are in principle genetically encodable. Here, we highlight the state-of-the-art in MRI-based biomolecular sensors, focusing on their physical mechanisms, quantitative characteristics, and biological applications. We also describe how innovations in reporter gene technology are creating new opportunities to engineer MRI sensors that are sensitive to dilute biological targets.
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Affiliation(s)
- Jason Yun
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
| | - Michelle Baldini
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Rochishnu Chowdhury
- Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
- Department of Chemistry, University of California, Santa Barbara, CA 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for BioEngineering, University of California, Santa Barbara, CA 93106, USA
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11
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Zheng N, Li M, Wu Y, Kaewborisuth C, Li Z, Gui Z, Wu J, Cai A, Lin K, Su KP, Xiang H, Tian X, Manyande A, Xu F, Wang J. A novel technology for in vivo detection of cell type-specific neural connection with AQP1-encoding rAAV2-retro vector and metal-free MRI. Neuroimage 2022; 258:119402. [PMID: 35732245 DOI: 10.1016/j.neuroimage.2022.119402] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 06/18/2022] [Accepted: 06/18/2022] [Indexed: 01/10/2023] Open
Abstract
A mammalian brain contains numerous neurons with distinct cell types for complex neural circuits. Virus-based circuit tracing tools are powerful in tracking the interaction among the different brain regions. However, detecting brain-wide neural networks in vivo remains challenging since most viral tracing systems rely on postmortem optical imaging. We developed a novel approach that enables in vivo detection of brain-wide neural connections based on metal-free magnetic resonance imaging (MRI). The recombinant adeno-associated virus (rAAV) with retrograde ability, the rAAV2-retro, encoding the human water channel aquaporin 1 (AQP1) MRI reporter gene was generated to label neural connections. The mouse was micro-injected with the virus at the Caudate Putamen (CPU) region and subjected to detection with Diffusion-weighted MRI (DWI). The prominent structure of the CPU-connected network was clearly defined. In combination with a Cre-loxP system, rAAV2-retro expressing Cre-dependent AQP1 provides a CPU-connected network of specific type neurons. Here, we established a sensitive, metal-free MRI-based strategy for in vivo detection of cell type-specific neural connections in the whole brain, which could visualize the dynamic changes of neural networks in rodents and potentially in non-human primates.
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Affiliation(s)
- Ning Zheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, China
| | - Mei Li
- The Brain Cognition and Brain Disease Institute (BCBDI), NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yang Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Challika Kaewborisuth
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand
| | - Zhen Li
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhu Gui
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinfeng Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, China
| | - Aoling Cai
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, China
| | - Kangguang Lin
- Department of Affective Disorders, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kuan-Pin Su
- Department of Psychiatry, China Medical University Hospital, Taichung City, Taiwan, China
| | - Hongbing Xiang
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuebi Tian
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Anne Manyande
- School of Human and Social Sciences, University of West London, Middlesex, TW8 9GA, UK
| | - Fuqiang Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, China; The Brain Cognition and Brain Disease Institute (BCBDI), NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jie Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Wuhan 430071, China; Institute of Neuroscience and Brain Diseases, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China.
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12
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Targeting visualization of malignant tumor based on the alteration of DWI signal generated by hTERT promoter–driven AQP1 overexpression. Eur J Nucl Med Mol Imaging 2022; 49:2310-2322. [DOI: 10.1007/s00259-022-05684-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/09/2022] [Indexed: 02/07/2023]
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13
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Sugaya K. Characterization of cells expressing MRI reporters for the analysis of epigenetics. Anal Biochem 2021; 633:114395. [PMID: 34600867 DOI: 10.1016/j.ab.2021.114395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/25/2021] [Indexed: 11/17/2022]
Abstract
Epigenetics is thought to be involved in highly advanced life phenomena, and its regulation has created new opportunities in regenerative medicine. Mintbody (modification-specific intracellular antibody) can track a posttranslational protein modification in epigenetics using a genetic system encoded within a single chain of variable fragments tagged with a fluorescent protein. Magnetic resonance imaging (MRI) is a technique that allows observation of specific molecules in living organisms. The ferritin heavy chain (FTH1) is one of the MRI reporters used in mammals. The combination of FTH1 with mintbody may show remarkable ability as a reporter for MRI to investigate epigenetics in the deep part of a living organism. This article discusses the suitability and safety of FTH1 for use in the analysis of epigenetics by MRI. Cells expressing the FTH1 hybrid of mintbody showed insufficiently increased sensitivity by MRI even in the presence of excess iron. After incubation with ferric ammonium citrate, DNA damage was found in cells expressing the FTH1 hybrid of mintbody. The use of FTH1 as a genetically encoded reporter for MRI appears to be limited by the requirement of metal and its relatively low sensitivity. These results suggest future directionality and the possibility of studying epigenetics in vivo.
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Affiliation(s)
- Kimihiko Sugaya
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences (NIRS), National Institute for Quantum and Radiological Science and Technology (QST), Chiba, Japan.
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14
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Genicio N, Bañobre-López M, Gröhn O, Gallo J. Ratiometric magnetic resonance imaging: Contrast agent design towards better specificity and quantification. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Miller ADC, Ozbakir HF, Mukherjee A. Calcium-responsive contrast agents for functional magnetic resonance imaging. ACTA ACUST UNITED AC 2021; 2:021301. [PMID: 34085055 DOI: 10.1063/5.0041394] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023]
Abstract
Calcium ions represent one of the key second messengers accompanying neural activity and synaptic signaling. Accordingly, dynamic imaging of calcium fluctuations in living organisms represents a cornerstone technology for discovering neural mechanisms that underlie memory, determine behavior, and modulate emotional states as well as how these mechanisms are perturbed by neurological disease and brain injury. While optical technologies are well established for high resolution imaging of calcium dynamics, physical limits on light penetration hinder their application for whole-brain imaging in intact vertebrates. Unlike optics, magnetic resonance imaging (MRI) enables noninvasive large-scale imaging across vertebrates of all sizes. This has motivated the development of several sensors that leverage innovative physicochemical mechanisms to sensitize MRI contrast to intracellular and extracellular changes in calcium. Here, we review the current state-of-the-art in MRI-based calcium sensors, focusing on fundamental aspects of sensor performance, in vivo applications, and challenges related to sensitivity. We also highlight how innovations at the intersection of reporter gene technology and gene delivery open potential opportunities for mapping calcium activity in genetically targeted cells, complementing the benefits of small molecule probes and nanoparticle sensors.
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Affiliation(s)
- Austin D C Miller
- Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106, USA
| | - Harun F Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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16
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Farhadi A, Sigmund F, Westmeyer GG, Shapiro MG. Genetically encodable materials for non-invasive biological imaging. NATURE MATERIALS 2021; 20:585-592. [PMID: 33526879 PMCID: PMC8606175 DOI: 10.1038/s41563-020-00883-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Many questions in basic biology and medicine require the ability to visualize the function of specific cells and molecules inside living organisms. In this context, technologies such as ultrasound, optoacoustics and magnetic resonance provide non-invasive imaging access to deep-tissue regions, as used in many laboratories and clinics to visualize anatomy and physiology. In addition, recent work has enabled these technologies to image the location and function of specific cells and molecules inside the body by coupling the physics of sound waves, nuclear spins and light absorption to unique protein-based materials. These materials, which include air-filled gas vesicles, capsid-like nanocompartments, pigment-producing enzymes and transmembrane transporters, enable new forms of biomolecular and cellular contrast. The ability of these protein-based contrast agents to be genetically encoded and produced by cells creates opportunities for unprecedented in vivo studies of cellular function, while their amenability to genetic engineering enables atomic-level design of their physical, chemical and biological properties.
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Affiliation(s)
- Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Felix Sigmund
- Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Synthetic Biomedicine, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Gil Gregor Westmeyer
- Department of Chemistry and TUM School of Medicine, Technical University of Munich, Munich, Germany.
- Institute for Synthetic Biomedicine, Helmholtz Zentrum Muenchen, Neuherberg, Germany.
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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17
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Falcone E, Okafor M, Vitale N, Raibaut L, Sour A, Faller P. Extracellular Cu2+ pools and their detection: From current knowledge to next-generation probes. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213727] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Efremova MV, Bodea SV, Sigmund F, Semkina A, Westmeyer GG, Abakumov MA. Genetically Encoded Self-Assembling Iron Oxide Nanoparticles as a Possible Platform for Cancer-Cell Tracking. Pharmaceutics 2021; 13:pharmaceutics13030397. [PMID: 33809789 PMCID: PMC8002387 DOI: 10.3390/pharmaceutics13030397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 01/15/2023] Open
Abstract
The study of growth and possible metastasis in animal models of tumors would benefit from reliable cell labels for noninvasive whole-organism imaging techniques such as magnetic resonance imaging. Genetically encoded cell-tracking reporters have the advantage that they are contrast-selective for viable cells with intact protein expression machinery. Besides, these reporters do not suffer from dilution during cell division. Encapsulins, which are bacterial protein nanocompartments, can serve as genetically controlled labels for multimodal detection of cells. Such nanocompartments can host various guest molecules inside their lumen. These include, for example, fluorescent proteins or enzymes with ferroxidase activity leading to biomineralization of iron oxide inside the encapsulin nanoshell. The aim of this work was to implement heterologous expression of encapsulin systems from Quasibacillus thermotolerans using the fluorescent reporter protein mScarlet-I and ferroxidase IMEF in the human hepatocellular carcinoma cell line HepG2. The successful expression of self-assembled encapsulin nanocompartments with functional cargo proteins was confirmed by fluorescence microscopy and transmission electron microscopy. Also, coexpression of encapsulin nanoshells, ferroxidase cargo, and iron transporter led to an increase in T2-weighted contrast in magnetic resonance imaging of HepG2 cells. The results demonstrate that the encapsulin cargo system from Q. thermotolerans may be suitable for multimodal imaging of cancer cells and could contribute to further in vitro and in vivo studies.
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Affiliation(s)
- Maria V. Efremova
- Department of Chemistry & TUM School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; (S.-V.B.); (F.S.); (G.G.W.)
- Institute for Synthetic Biomedicine, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Correspondence: (M.V.E.); (M.A.A.); Tel.: +74-95-638-4465 (M.A.A.)
| | - Silviu-Vasile Bodea
- Department of Chemistry & TUM School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; (S.-V.B.); (F.S.); (G.G.W.)
- Institute for Synthetic Biomedicine, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Felix Sigmund
- Department of Chemistry & TUM School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; (S.-V.B.); (F.S.); (G.G.W.)
- Institute for Synthetic Biomedicine, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Alevtina Semkina
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
- V.P. Serbskiy National Medical Research Center of Psychiatry and Narcology, 119034 Moscow, Russia
| | - Gil G. Westmeyer
- Department of Chemistry & TUM School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany; (S.-V.B.); (F.S.); (G.G.W.)
- Institute for Synthetic Biomedicine, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Maxim A. Abakumov
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
- Laboratory “Biomedical Nanomaterials”, National University of Science and Technology “MISiS”, 119049 Moscow, Russia
- Correspondence: (M.V.E.); (M.A.A.); Tel.: +74-95-638-4465 (M.A.A.)
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19
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Derr JB, Tamayo J, Clark JA, Morales M, Mayther MF, Espinoza EM, Rybicka-Jasińska K, Vullev VI. Multifaceted aspects of charge transfer. Phys Chem Chem Phys 2020; 22:21583-21629. [PMID: 32785306 PMCID: PMC7544685 DOI: 10.1039/d0cp01556c] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.
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Affiliation(s)
- James B Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
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20
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Lu GJ, Chou LD, Malounda D, Patel AK, Welsbie DS, Chao DL, Ramalingam T, Shapiro MG. Genetically Encodable Contrast Agents for Optical Coherence Tomography. ACS NANO 2020; 14:7823-7831. [PMID: 32023037 PMCID: PMC7685218 DOI: 10.1021/acsnano.9b08432] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Optical coherence tomography (OCT) has gained wide adoption in biological research and medical imaging due to its exceptional tissue penetration, 3D imaging speed, and rich contrast. However, OCT plays a relatively small role in molecular and cellular imaging due to the lack of suitable biomolecular contrast agents. In particular, while the green fluorescent protein has provided revolutionary capabilities to fluorescence microscopy by connecting it to cellular functions such as gene expression, no equivalent reporter gene is currently available for OCT. Here, we introduce gas vesicles, a class of naturally evolved gas-filled protein nanostructures, as genetically encodable OCT contrast agents. The differential refractive index of their gas compartments relative to surrounding aqueous tissue and their nanoscale motion enables gas vesicles to be detected by static and dynamic OCT. Furthermore, the OCT contrast of gas vesicles can be selectively erased in situ with ultrasound, allowing unambiguous assignment of their location. In addition, gas vesicle clustering modulates their temporal signal, enabling the design of dynamic biosensors. We demonstrate the use of gas vesicles as reporter genes in bacterial colonies and as purified contrast agents in vivo in the mouse retina. Our results expand the utility of OCT to image a wider variety of cellular and molecular processes.
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Affiliation(s)
- George J. Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Li-dek Chou
- OCT Medical Imaging Inc., 9272 Jeronimo Road, Irvine, CA 92618, USA
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Amit K. Patel
- Shiley Eye Institute, Andrew Viterbi Department of Ophthalmology, University of California San Diego, La Jolla, CA 92093, USA
| | - Derek S. Welsbie
- Shiley Eye Institute, Andrew Viterbi Department of Ophthalmology, University of California San Diego, La Jolla, CA 92093, USA
| | - Daniel L. Chao
- Shiley Eye Institute, Andrew Viterbi Department of Ophthalmology, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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21
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Schuerle S, Furubayashi M, Soleimany AP, Gwisai T, Huang W, Voigt C, Bhatia SN. Genetic Encoding of Targeted Magnetic Resonance Imaging Contrast Agents for Tumor Imaging. ACS Synth Biol 2020; 9:392-401. [PMID: 31922737 DOI: 10.1021/acssynbio.9b00416] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Tumor-selective contrast agents have the potential to aid in the diagnosis and treatment of cancer using noninvasive imaging modalities such as magnetic resonance imaging (MRI). Such contrast agents can consist of magnetic nanoparticles incorporating functionalities that respond to cues specific to tumor environments. Genetically engineering magnetotactic bacteria to display peptides has been investigated as a means to produce contrast agents that combine the robust image contrast effects of magnetosomes with the transgenic-targeting peptides displayed on their surface. This work reports the first use of magnetic nanoparticles that display genetically encoded pH low insertion peptide (pHLIP), a long peptide intended to enhance MRI contrast by targeting the extracellular acidity associated with the tumors. To demonstrate the modularity of this versatile platform to incorporate diverse targeting ligands by genetic engineering, we also incorporated the cyclic αv integrin-binding peptide iRGD into separate magnetosomes. Specifically, we investigate their potential for enhanced binding and tumor imaging both in vitro and in vivo. Our experiments indicate that these tailored magnetosomes retain their magnetic properties, making them well suited as T2 contrast agents, while exhibiting an increased binding compared to the binding in wild-type magnetosomes.
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Affiliation(s)
- Simone Schuerle
- Institute for Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Maiko Furubayashi
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Ava P. Soleimany
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard Graduate Program in Biophysics, Harvard University, Boston, Massachusetts 02115, United States
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Tinotenda Gwisai
- Institute for Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Wei Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Marble Center for Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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22
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Ozbakir HF, Anderson NT, Fan KC, Mukherjee A. Beyond the Green Fluorescent Protein: Biomolecular Reporters for Anaerobic and Deep-Tissue Imaging. Bioconjug Chem 2020; 31:293-302. [PMID: 31794658 PMCID: PMC7033020 DOI: 10.1021/acs.bioconjchem.9b00688] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging represents cornerstone technology for studying biological function at the cellular and molecular levels. The technology's centerpiece is a prolific collection of genetic reporters based on the green fluorescent protein (GFP) and related analogs. More than two decades of protein engineering have endowed the GFP repertoire with an incredible assortment of fluorescent proteins, allowing scientists immense latitude in choosing reporters tailored to various cellular and environmental contexts. Nevertheless, GFP and derivative reporters have specific limitations that hinder their unrestricted use for molecular imaging. These challenges have inspired the development of new reporter proteins and imaging mechanisms. Here, we review how these developments are expanding the frontiers of reporter gene techniques to enable nondestructive studies of cell function in anaerobic environments and deep inside intact animals-two important biological contexts that are fundamentally incompatible with the use of GFP-based reporters.
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Affiliation(s)
- Harun F. Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Nolan T. Anderson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kang-Ching Fan
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry, University of California, Santa Barbara, California 93106, United States
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California, Santa Barbara, California 93106, United States
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23
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Dailey PJ, Elbeik T, Holodniy M. Companion and complementary diagnostics for infectious diseases. Expert Rev Mol Diagn 2020; 20:619-636. [PMID: 32031431 DOI: 10.1080/14737159.2020.1724784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Companion diagnostics (CDx) are important in oncology therapeutic decision-making, but specific regulatory-approved CDx for infectious disease treatment are officially lacking. While not approved as CDx, several ID diagnostics are used as CDx. The diagnostics community, manufacturers, and regulatory agencies have made major efforts to ensure that diagnostics for new antimicrobials are available at or near release of new agents. AREAS COVERED This review highlights the status of Complementary and companion diagnostic (c/CDx) in the infectious disease literature, with a focus on genotypic antimicrobial resistance testing against pathogens as a class of diagnostic tests. EXPERT OPINION CRISPR, sepsis markers, and narrow spectrum antimicrobials, in addition to current and emerging technologies, present opportunities for infectious disease c/CDx. Challenges include slow guideline revision, high costs for regulatory approval, lengthy buy in by agencies, discordant pharmaceutical/diagnostic partnerships, and higher treatment costs. The number of patients and available medications used to treat different infectious diseases is well suited to support competing diagnostic tests. However, newer approaches to treatment (for example, narrow spectrum antibiotics), may be well suited for a small number of patients, i.e. a niche market in support of a CDx. The current emphasis is rapid and point-of-care (POC) diagnostic platforms as well as changes in treatment.
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Affiliation(s)
- Peter J Dailey
- School of Public Health, University of California, Berkeley , Berkeley, CA, USA.,The Foundation for Innovative New Diagnostics (FIND) , Geneva, Switzerland
| | - Tarek Elbeik
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA
| | - Mark Holodniy
- VA Palo Alto Health Care System, Department of Veterans Affairs , Palo Alto, CA, USA.,Division of Infectious Diseases and Geographic Medicine, Stanford University , Stanford, CA, USA
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24
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Amirav L, Berlin S, Olszakier S, Pahari SK, Kahn I. Multi-Modal Nano Particle Labeling of Neurons. Front Neurosci 2019; 13:12. [PMID: 30778281 PMCID: PMC6369355 DOI: 10.3389/fnins.2019.00012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 01/08/2019] [Indexed: 01/06/2023] Open
Abstract
The development of imaging methodologies for single cell measurements over extended timescales of up to weeks, in the intact animal, will depend on signal strength, stability, validity and specificity of labeling. Whereas light-microscopy can achieve these with genetically-encoded probes or dyes, this modality does not allow mesoscale imaging of entire intact tissues. Non-invasive imaging techniques, such as magnetic resonance imaging (MRI), outperform light microscopy in field of view and depth of imaging, but do not offer cellular resolution and specificity, suffer from low signal-to-noise ratio and, in some instances, low temporal resolution. In addition, the origins of the signals measured by MRI are either indirect to the process of interest or hard to validate. It is therefore highly warranted to find means to enhance MRI signals to allow increases in resolution and cellular-specificity. To this end, cell-selective bi-functional magneto-fluorescent contrast agents can provide an elegant solution. Fluorescence provides means for identification of labeled cells and particles location after MRI acquisition, and it can be used to facilitate the design of cell-selective labeling of defined targets. Here we briefly review recent available designs of magneto-fluorescent markers and elaborate on key differences between them with respect to durability and relevant cellular highlighting approaches. We further focus on the potential of intracellular labeling and basic functional sensing MRI, with assays that enable imaging cells at microscopic and mesoscopic scales. Finally, we illustrate the qualities and limitations of the available imaging markers and discuss prospects for in vivo neural imaging and large-scale brain mapping.
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Affiliation(s)
- Lilac Amirav
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, Israel
| | - Shai Berlin
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Shunit Olszakier
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, Israel.,Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Sandip K Pahari
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, Israel
| | - Itamar Kahn
- Department of Neuroscience, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
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25
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Farhadi A, Ho G, Kunth M, Ling B, Lakshmanan A, Lu GJ, Bourdeau RW, Schröder L, Shapiro MG. Recombinantly Expressed Gas Vesicles as Nanoscale Contrast Agents for Ultrasound and Hyperpolarized MRI. AIChE J 2018; 64:2927-2933. [PMID: 30555168 DOI: 10.1002/aic.16138] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ultrasound and hyperpolarized magnetic resonance imaging enable the visualization of biological processes in deep tissues. However, few molecular contrast agents are available to connect these modalities to specific aspects of biological function. We recently discovered that a unique class of gas-filled protein nanostructures known as gas vesicles could serve as nanoscale molecular reporters for these modalities. However, the need to produce these nanostructures via expression in specialized cultures of cyanobacteria or haloarchaea limits their broader adoption by other laboratories and hinders genetic engineering of their properties. Here, we describe recombinant expression and purification of Bacillus megaterium gas vesicles using a common laboratory strain of Escherichia coli, and characterize the physical, acoustic and magnetic resonance properties of these nanostructures. Recombinantly expressed gas vesicles produce ultrasound and hyperpolarized 129Xe MRI contrast at sub-nanomolar concentrations, thus validating a simple platform for their production and engineering.
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Affiliation(s)
- Arash Farhadi
- Division of Biology and Biological Engineering; California Institute of Technology; Pasadena CA 91125
| | - Gabrielle Ho
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Martin Kunth
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
- Dept. of Structural Biology, Molecular Imaging; Leibniz-Forschungsinstitute für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Bill Ling
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Anupama Lakshmanan
- Division of Biology and Biological Engineering; California Institute of Technology; Pasadena CA 91125
| | - George J Lu
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Raymond W. Bourdeau
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Leif Schröder
- Dept. of Structural Biology, Molecular Imaging; Leibniz-Forschungsinstitute für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
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Lu GJ, Farhadi A, Mukherjee A, Shapiro MG. Proteins, air and water: reporter genes for ultrasound and magnetic resonance imaging. Curr Opin Chem Biol 2018; 45:57-63. [PMID: 29549770 PMCID: PMC6076850 DOI: 10.1016/j.cbpa.2018.02.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 12/31/2022]
Abstract
A long-standing goal of molecular imaging is to visualize cellular function within the context of living animals, necessitating the development of reporter genes compatible with deeply penetrant imaging modalities such as ultrasound and magnetic resonance imaging (MRI). Until recently, no reporter genes for ultrasound were available, and most genetically encoded reporters for MRI were limited by metal availability or relatively low sensitivity. Here we review how these limitations are being addressed by recently introduced reporter genes based on air-filled and water-transporting biomolecules. We focus on gas-filled protein nanostructures adapted from buoyant microbes, which scatter sound waves, perturb magnetic fields and interact with hyperpolarized nuclei, as well as transmembrane water channels that alter the effective diffusivity of water in tissue.
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Affiliation(s)
- George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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27
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Lu GJ, Farhadi A, Szablowski JO, Lee-Gosselin A, Barnes SR, Lakshmanan A, Bourdeau RW, Shapiro MG. Acoustically modulated magnetic resonance imaging of gas-filled protein nanostructures. NATURE MATERIALS 2018; 17:456-463. [PMID: 29483636 PMCID: PMC6015773 DOI: 10.1038/s41563-018-0023-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 01/17/2018] [Indexed: 05/11/2023]
Abstract
Non-invasive biological imaging requires materials capable of interacting with deeply penetrant forms of energy such as magnetic fields and sound waves. Here, we show that gas vesicles (GVs), a unique class of gas-filled protein nanostructures with differential magnetic susceptibility relative to water, can produce robust contrast in magnetic resonance imaging (MRI) at sub-nanomolar concentrations, and that this contrast can be inactivated with ultrasound in situ to enable background-free imaging. We demonstrate this capability in vitro, in cells expressing these nanostructures as genetically encoded reporters, and in three model in vivo scenarios. Genetic variants of GVs, differing in their magnetic or mechanical phenotypes, allow multiplexed imaging using parametric MRI and differential acoustic sensitivity. Additionally, clustering-induced changes in MRI contrast enable the design of dynamic molecular sensors. By coupling the complementary physics of MRI and ultrasound, this nanomaterial gives rise to a distinct modality for molecular imaging with unique advantages and capabilities.
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Affiliation(s)
- George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jerzy O Szablowski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Audrey Lee-Gosselin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Samuel R Barnes
- Department of Radiology, Loma Linda University, Loma Linda, CA, USA
| | - Anupama Lakshmanan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Raymond W Bourdeau
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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28
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Ghosh S, Harvey P, Simon JC, Jasanoff A. Probing the brain with molecular fMRI. Curr Opin Neurobiol 2018; 50:201-210. [PMID: 29649765 DOI: 10.1016/j.conb.2018.03.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 02/12/2018] [Accepted: 03/21/2018] [Indexed: 01/07/2023]
Abstract
One of the greatest challenges of modern neuroscience is to incorporate our growing knowledge of molecular and cellular-scale physiology into integrated, organismic-scale models of brain function in behavior and cognition. Molecular-level functional magnetic resonance imaging (molecular fMRI) is a new technology that can help bridge these scales by mapping defined microscopic phenomena over large, optically inaccessible regions of the living brain. In this review, we explain how MRI-detectable imaging probes can be used to sensitize noninvasive imaging to mechanistically significant components of neural processing. We discuss how a combination of innovative probe design, advanced imaging methods, and strategies for brain delivery can make molecular fMRI an increasingly successful approach for spatiotemporally resolved studies of diverse neural phenomena, perhaps eventually in people.
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Affiliation(s)
- Souparno Ghosh
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Rm. 16-561, Cambridge, MA 02139, United States
| | - Peter Harvey
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Rm. 16-561, Cambridge, MA 02139, United States
| | - Jacob C Simon
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Rm. 16-561, Cambridge, MA 02139, United States
| | - Alan Jasanoff
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Rm. 16-561, Cambridge, MA 02139, United States; Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave., Rm. 16-561, Cambridge, MA 02139, United States; Department of Nuclear Science & Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Rm. 16-561, Cambridge, MA 02139, United States.
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29
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Piraner DI, Farhadi A, Davis HC, Wu D, Maresca D, Szablowski JO, Shapiro MG. Going Deeper: Biomolecular Tools for Acoustic and Magnetic Imaging and Control of Cellular Function. Biochemistry 2017; 56:5202-5209. [PMID: 28782927 PMCID: PMC6058970 DOI: 10.1021/acs.biochem.7b00443] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Most cellular phenomena of interest to mammalian biology occur within the context of living tissues and organisms. However, today's most advanced tools for observing and manipulating cellular function, based on fluorescent or light-controlled proteins, work best in cultured cells, transparent model species, or small, surgically accessed anatomical regions. Their reach into deep tissues and larger animals is limited by photon scattering. To overcome this limitation, we must design biochemical tools that interface with more penetrant forms of energy. For example, sound waves and magnetic fields easily permeate most biological tissues, allowing the formation of images and delivery of energy for actuation. These capabilities are widely used in clinical techniques such as diagnostic ultrasound, magnetic resonance imaging, focused ultrasound ablation, and magnetic particle hyperthermia. Each of these modalities offers spatial and temporal precision that could be used to study a multitude of cellular processes in vivo. However, connecting these techniques to cellular functions such as gene expression, proliferation, migration, and signaling requires the development of new biochemical tools that can interact with sound waves and magnetic fields as optogenetic tools interact with photons. Here, we discuss the exciting challenges this poses for biomolecular engineering and provide examples of recent advances pointing the way to greater depth in in vivo cell biology.
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Affiliation(s)
- Dan I. Piraner
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hunter C. Davis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Di Wu
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - David Maresca
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jerzy O. Szablowski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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