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Yao L, Zhang L, Chen L, Fei Y, Lamon S, Gu M, Mi L, Wang J, Ma J. Visualizing highly bright and uniform cellular ultrastructure by expansion-microscopy with tetrahedral DNA nanostructures. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 260:113034. [PMID: 39288552 DOI: 10.1016/j.jphotobiol.2024.113034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 08/24/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024]
Abstract
Expansion Microscopy (ExM) is a widely used super-resolution technique that enables imaging of structures beyond the diffraction limit of light. However, ExM suffers from weak labeling signals and expansion distortions, limiting its applicability. Here, we present an innovative approach called Tetrahedral DNA nanostructure Expansion Microscopy (TDN-ExM), addressing these limitations by using tetrahedral DNA nanostructures (TDNs) for fluorescence labeling. Our approach demonstrates a 3- to 10-fold signal amplification due to the multivertex nature of TDNs, allowing the modification of multiple dyes. Previous studies have confirmed minimal distortion on a large scale, and our strategy can reduce the distortion at the ultrastructural level in samples because it does not rely on anchoring agents and is not affected by digestion. This results in a brighter fluorescence, better uniformity, and compatibility with different labeling strategies and optical super-resolution technologies. We validated the utility of TDN-ExM by imaging various biological structures with improved resolutions and signal-to-noise ratios.
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Affiliation(s)
- Longfang Yao
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai 200093, China; Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Li Zhang
- Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems (MRICS), School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Liwen Chen
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Simone Lamon
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai 200093, China
| | - Min Gu
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai 200093, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Jing Wang
- Institute of Photonic Chips, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai 200093, China.
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, 220 Handan Road, Shanghai 200433, China; Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems (MRICS), School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China.
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2
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Leng Y, Britten CN, Tarannum F, Foley K, Billings C, Liu Y, Walters KB. Stimuli-Responsive Phosphate Hydrogel: A Study on Swelling Behavior, Mechanical Properties, and Application in Expansion Microscopy. ACS OMEGA 2024; 9:37687-37701. [PMID: 39281925 PMCID: PMC11391540 DOI: 10.1021/acsomega.4c02475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/18/2024]
Abstract
Phosphorus-based stimuli-responsive hydrogels have potential in a wide range of applications due to their ionizable phosphorus groups, biocompatibility, and tunable swelling capacity utilizing hydrogel design parameters and external stimuli. In this study, poly(2-methacryloyloxyethyl phosphate) (PMOEP) hydrogels were synthesized via aqueous activators regenerated by electron transfer atomic transfer radical polymerization using ascorbic acid as the reducing agent. Swelling and deswelling behaviors of PMOEP hydrogels were examined in different salt solutions, pH conditions, and temperatures. The degree of swelling in salt solutions followed CaCl2 < MgCl2 < KCl < NaCl with a decrease in swelling rate at higher concentrations until reaching a saturation point. In water, the degree of swelling increased significantly around neutral pH and remained constant at basic pH values. The effects of polymerization conditions, including pH, temperature (30, 40, 50 °C), and MOEP concentration (40, 50, 60% v/v MOEP/H2O), on the hydrogel swelling behavior in various salt solutions were also investigated. PMOEP hydrogels showed a decrease in the degree of swelling as the pH was increased above the native pH of the monomer solution. Scanning electron microscopy and energy-dispersive spectroscopy were utilized to examine the microstructure and chemical composition of the dried hydrogel after salt solution swelling. Cytotoxicity testing using rat bone marrow stem cells confirmed the biocompatibility of the PMOEP hydrogels. A unique feature of this effort was evaluation of these phosphate hydrogels for use in expansion microscopy where a significant twofold enhancement in cellular expansion capacity was showcased utilizing 4T1 mouse breast cancer cells. This comprehensive study provides valuable insights into the stimuli-responsive behavior and expansion characteristics of phosphate hydrogels, highlighting their potential in diverse biomedical applications.
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Affiliation(s)
- Yokly Leng
- School of Chemical, Materials, and Biological Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Collin N Britten
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Fatema Tarannum
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Kayla Foley
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Christopher Billings
- School of Aerospace and Mechanical Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Yingtao Liu
- School of Aerospace and Mechanical Engineering, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Keisha B Walters
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
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3
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Soukup J, Zelená M, Weisz F, Kostelanská M, Nohýnková E, Tůmová P. Imaging Giardia intestinalis cellular organisation using expansion microscopy reveals atypical centrin localisation. Exp Parasitol 2024; 266:108831. [PMID: 39243847 DOI: 10.1016/j.exppara.2024.108831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/12/2024] [Accepted: 08/27/2024] [Indexed: 09/09/2024]
Abstract
Advanced imaging of microorganisms, including protists, is challenging due to their small size. Specimen expansion prior to imaging is thus beneficial to increase resolution and cellular details. Here, we present a sample preparation workflow for improved observations of the single-celled eukaryotic pathogen Giardia intestinalis (Excavata, Metamonada). The binucleated trophozoites colonize the small intestine of humans and animals and cause a diarrhoeal disease. Their remarkable morphology includes two nuclei and a pronounced microtubular cytoskeleton enabling cell motility, attachment and proliferation. By use of expansion and confocal microscopy, we resolved in a great detail subcellular structures and organelles of the parasite cell. The acquired spatial resolution enabled novel observations of centrin localization at Giardia basal bodies. Interestingly, non-luminal centrin localization between the Giardia basal bodies was observed, which is an atypical eukaryotic arrangement. Our protocol includes antibody staining and can be used for the localization of epitope-tagged proteins, as well as for differential organelle labelling by amino reactive esters. This fast and simple technique is suitable for routine use without a superresolution microscopy equipment.
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Affiliation(s)
- J Soukup
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - M Zelená
- Laboratory of Cell Motility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - F Weisz
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - M Kostelanská
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - E Nohýnková
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - P Tůmová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic.
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4
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Jetishi C, Balmer EA, Berger BM, Faso C, Ochsenreiter T. Expansion of metabolically labelled endocytic organelles and cytoskeletal cell structures in Giardia lamblia using optimised U-ExM protocols. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:198-206. [PMID: 38975021 PMCID: PMC11224680 DOI: 10.15698/mic2024.06.825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 07/09/2024]
Abstract
Understanding cellular ultrastructure is tightly bound to microscopic resolution and the ability to identify individual components at that resolution. Expansion microscopy has revolutionised this topic. Here we present and compare two protocols of ultrastructure expansion microscopy that allow for 4.5-fold mostly isotropic expansion and the use of antibodies, metabolic labelling, and DNA stains to demarcate individual regions such as the endoplasmic reticulum, the nuclei, the peripheral endocytic compartments as well as the ventral disc and the cytoskeleton in Giardia lamblia. We present an optimised, shortened, and modular protocol that can be swiftly adjusted to the investigators needs in this important protozoan model organism.
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Affiliation(s)
- Clirim Jetishi
- Institute of Cell Biology, University of BernBernSwitzerland
- Graduate School for Cellular and Biomedical Sciences, University of BernBernSwitzerland
| | - Erina A Balmer
- Institute of Cell Biology, University of BernBernSwitzerland
- Graduate School for Cellular and Biomedical Sciences, University of BernBernSwitzerland
| | - Bianca M Berger
- Institute of Cell Biology, University of BernBernSwitzerland
- Graduate School for Cellular and Biomedical Sciences, University of BernBernSwitzerland
| | - Carmen Faso
- Institute of Cell Biology, University of BernBernSwitzerland
- Multidisciplinary Center for Infectious Diseases, University of BernBernSwitzerland
- Institute of Infectious Diseases, University of BernBernSwitzerland.
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5
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Hümpfer N, Thielhorn R, Ewers H. Expanding boundaries - a cell biologist's guide to expansion microscopy. J Cell Sci 2024; 137:jcs260765. [PMID: 38629499 PMCID: PMC11058692 DOI: 10.1242/jcs.260765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Expansion microscopy (ExM) is a revolutionary novel approach to increase resolution in light microscopy. In contrast to super-resolution microscopy methods that rely on sophisticated technological advances, including novel instrumentation, ExM instead is entirely based on sample preparation. In ExM, labeled target molecules in fixed cells are anchored in a hydrogel, which is then physically enlarged by osmotic swelling. The isotropic swelling of the hydrogel pulls the labels apart from one another, and their relative organization can thus be resolved using conventional microscopes even if it was below the diffraction limit of light beforehand. As ExM can additionally benefit from the technical resolution enhancements achieved by super-resolution microscopy, it can reach into the nanometer range of resolution with an astoundingly low degree of error induced by distortion during the physical expansion process. Because the underlying chemistry is well understood and the technique is based on a relatively simple procedure, ExM is easily reproducible in non-expert laboratories and has quickly been adopted to address an ever-expanding spectrum of problems across the life sciences. In this Review, we provide an overview of this rapidly expanding new field, summarize the most important insights gained so far and attempt to offer an outlook on future developments.
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Affiliation(s)
- Nadja Hümpfer
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ria Thielhorn
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Helge Ewers
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
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6
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Vojnovic I, Caspari OD, Hoşkan MA, Endesfelder U. Combining single-molecule and expansion microscopy in fission yeast to visualize protein structures at the nanostructural level. Open Biol 2024; 14:230414. [PMID: 38320620 PMCID: PMC10846934 DOI: 10.1098/rsob.230414] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024] Open
Abstract
In this work, we have developed an expansion microscopy (ExM) protocol that combines ExM with photoactivated localization microscopy (ExPALM) for yeast cell imaging, and report a robust protocol for single-molecule and expansion microscopy of fission yeast, abbreviated as SExY. Our optimized SExY protocol retains about 50% of the fluorescent protein signal, doubling the amount obtained compared to the original protein retention ExM (proExM) protocol. It allows for a fivefold, highly isotropic expansion of fission yeast cells, which we carefully controlled while optimizing protein yield. We demonstrate the SExY method on several exemplary molecular targets and explicitly introduce low-abundant protein targets (e.g. nuclear proteins such as cbp1 and mis16, and the centromere-specific histone protein cnp1). The SExY protocol optimizations increasing protein yield could be beneficial for many studies, when targeting low abundance proteins, or for studies that rely on genetic labelling for various reasons (e.g. for proteins that cannot be easily targeted by extrinsic staining or in case artefacts introduced by unspecific staining interfere with data quality).
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Affiliation(s)
- Ilijana Vojnovic
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Oliver D. Caspari
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Microbiology, Institute Pasteur, Paris, France
| | - Mehmet Ali Hoşkan
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
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7
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Park S, Shi X. Expansion Microscopy of Ciliary Proteins. Methods Mol Biol 2024; 2725:79-88. [PMID: 37856018 DOI: 10.1007/978-1-0716-3507-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Label-retention expansion microscopy (LR-ExM) is a sample preparation technique, which embeds the cells or tissues in a swellable hydrogel and expands the sample so that one can achieve a high resolution with any conventional fluorescence microscopes. Fluorescence loss during polymerization and protein denaturation have been a major limitation of standard expansion microscopy. To minimize fluorescence loss, LR-ExM uses trifunctional anchors, which can survive from polymerization and denaturation, and then introduce fluorophores after expansion. By using LR-ExM, one can study the structure of primary cilia at molecular-scale resolution with a much higher signal-to-noise ratio, compared with previously introduced expansion microscopy methods. In this chapter, we describe a detailed procedure showing how LR-ExM is used to study ciliary proteins.
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Affiliation(s)
- Sohyeon Park
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA
| | - Xiaoyu Shi
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA.
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA.
- Department of Chemistry, University of California Irvine, Irvine, CA, USA.
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8
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Grafe M, Pitzen V, Meyer I, Gräf R. Superresolution Expansion Microscopy in Dictyostelium Amoebae. Methods Mol Biol 2024; 2814:29-44. [PMID: 38954195 DOI: 10.1007/978-1-0716-3894-1_2] [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] [Indexed: 07/04/2024]
Abstract
Expansion microscopy (ExM) is a superresolution technique for fixed specimens that improves resolution of a given microscopy system approximately fourfold. The gain in resolution in ExM is not achieved by improvement of the resolution of the microscope itself but by isotropic expansion of the sample. To achieve this, the sample is cross-linked to an expandable gel matrix that swells approximately fourfold by incubation in water. We have applied the method to Dictyostelium amoebae and discuss the pros and cons of different labeling techniques in combination with pre- and post-expansion staining protocols.
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Affiliation(s)
- Marianne Grafe
- Department of Cell Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Valentin Pitzen
- Department of Cell Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Irene Meyer
- Department of Cell Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Ralph Gräf
- Department of Cell Biology, University of Potsdam, Potsdam-Golm, Germany.
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9
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Bandeira PT, Ortiz SFDN, Benchimol M, de Souza W. Expansion Microscopy of trichomonads. Exp Parasitol 2023; 255:108629. [PMID: 37802179 DOI: 10.1016/j.exppara.2023.108629] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 10/08/2023]
Abstract
Light microscopy has significantly advanced in recent decades, especially concerning the increased resolution obtained in fluorescence images. Here we present the Expansion Microscopy (ExM) technique in two parasites, Trichomonas vaginalis and Tritrichomonas foetus, which significantly improved the localization of distinct proteins closely associated with cytoskeleton by immunofluorescence microscopy. The ExM techniques have been used in various cell types, tissues and other protist parasites. It requires the embedment of the samples in a swellable gel that is highly hydrophilic. As a result, cells are expanded 4.5 times in an isotropic manner, offering a spatial resolution of ∼70 nm. We used this new methodology not only to observe the structural organization of protozoa in more detail but also to increase the resolution by immunofluorescence microscopy of two major proteins such as tubulin, found in structures formed by microtubules, and costain 1, the only protein identified until now in the T. foetus's costa, a unique rod-shaped like structure. The individualized microtubules of the axostyle were seen for the first time in fluorescence microscopy and several other details are presented after this technique.
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Affiliation(s)
- Paula Terra Bandeira
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Sharmila Fiama das Neves Ortiz
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Marlene Benchimol
- BIOTRANS-CAXIAS, Universidade do Grande Rio. UNIGRANRIO, Rio de Janeiro, 96200-000, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil.
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Centro de Pesquisa em Medicina de Precisão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil; Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
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10
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Wen G, Lycas MD, Jia Y, Leen V, Sauer M, Hofkens J. Trifunctional Linkers Enable Improved Visualization of Actin by Expansion Microscopy. ACS NANO 2023; 17:20589-20600. [PMID: 37787755 DOI: 10.1021/acsnano.3c07510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Expansion microscopy (ExM) revolutionized the field of super-resolution microscopy by allowing for subdiffraction resolution fluorescence imaging on standard fluorescence microscopes. However, it has been found that it is hard to visualize actin filaments efficiently using ExM. To improve actin imaging, multifunctional molecules have been designed with moderate success. Here, we present optimized methods for phalloidin conjugate grafting that have a high efficiency for both cellular and tissue samples. Our optimized strategy improves anchoring and signal retention by ∼10 times. We demonstrate the potential of optimized trifunctional linkers (TRITON) for actin imaging in combination with immunolabeling using different ExM protocols. 10X ExM of actin labeled with optimized TRITON enabled us to visualize the periodicity of actin rings in cultured hippocampal neurons and brain slices by Airyscan confocal microscopy. Thus, TRITON linkers provide an efficient grafting method, especially in cases in which the concentration of target-bound monomers is insufficient for high-quality ExM.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Matthew Domenic Lycas
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Yuqing Jia
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, Netherlands
| | - Volker Leen
- Chrometra Scientific, Kortenaken 3470, Belgium
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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11
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Damstra HGJ, Passmore JB, Serweta AK, Koutlas I, Burute M, Meye FJ, Akhmanova A, Kapitein LC. GelMap: intrinsic calibration and deformation mapping for expansion microscopy. Nat Methods 2023; 20:1573-1580. [PMID: 37723243 PMCID: PMC10555834 DOI: 10.1038/s41592-023-02001-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/04/2023] [Indexed: 09/20/2023]
Abstract
Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy by physically expanding biological specimen in three dimensions. Nonetheless, using ExM for quantitative or diagnostic applications requires robust quality control methods to precisely determine expansion factors and to map deformations due to anisotropic expansion. Here we present GelMap, a flexible workflow to introduce a fluorescent grid into pre-expanded hydrogels that scales with expansion and reports deformations. We demonstrate that GelMap can be used to precisely determine the local expansion factor and to correct for deformations without the use of cellular reference structures or pre-expansion ground-truth images. Moreover, we show that GelMap aids sample navigation for correlative uses of expansion microscopy. Finally, we show that GelMap is compatible with expansion of tissue and can be readily implemented as a quality control step into existing ExM workflows.
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Affiliation(s)
- Hugo G J Damstra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Josiah B Passmore
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Albert K Serweta
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ioannis Koutlas
- Department of Translational Neuroscience, Brain Center, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mithila Burute
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Frank J Meye
- Department of Translational Neuroscience, Brain Center, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands.
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12
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Cheng Z, Stefani C, Skillman T, Klimas A, Lee A, DiBernardo EF, Brown KM, Milman T, Wang Y, Gallagher BR, Lagree K, Jena BP, Pulido JS, Filler SG, Mitchell AP, Hiller NL, Lacy‐Hulbert A, Zhao Y. MicroMagnify: A Multiplexed Expansion Microscopy Method for Pathogens and Infected Tissues. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302249. [PMID: 37658522 PMCID: PMC10602566 DOI: 10.1002/advs.202302249] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/29/2023] [Indexed: 09/03/2023]
Abstract
Super-resolution optical imaging tools are crucial in microbiology to understand the complex structures and behavior of microorganisms such as bacteria, fungi, and viruses. However, the capabilities of these tools, particularly when it comes to imaging pathogens and infected tissues, remain limited. MicroMagnify (µMagnify) is developed, a nanoscale multiplexed imaging method for pathogens and infected tissues that are derived from an expansion microscopy technique with a universal biomolecular anchor. The combination of heat denaturation and enzyme cocktails essential is found for robust cell wall digestion and expansion of microbial cells and infected tissues without distortion. µMagnify efficiently retains biomolecules suitable for high-plex fluorescence imaging with nanoscale precision. It demonstrates up to eightfold expansion with µMagnify on a broad range of pathogen-containing specimens, including bacterial and fungal biofilms, infected culture cells, fungus-infected mouse tone, and formalin-fixed paraffin-embedded human cornea infected by various pathogens. Additionally, an associated virtual reality tool is developed to facilitate the visualization and navigation of complex 3D images generated by this method in an immersive environment allowing collaborative exploration among researchers worldwide. µMagnify is a valuable imaging platform for studying how microbes interact with their host systems and enables the development of new diagnosis strategies against infectious diseases.
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Affiliation(s)
- Zhangyu Cheng
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Caroline Stefani
- Benaroya Research Institute at Virginia Mason1201 9th AveSeattleWA98101USA
| | | | - Aleksandra Klimas
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Aramchan Lee
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Emma F. DiBernardo
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Karina Mueller Brown
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Tatyana Milman
- Wills Eye Hospital and Jefferson University HospitalPhiladelphiaPA19107USA
| | - Yuhong Wang
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Brendan R. Gallagher
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Katherine Lagree
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Bhanu P. Jena
- Viron Molecular Medicine Institute201 Washington StreetBostonMA02201USA
- Department of PhysiologyWayne State University42 W Warren AveDetroitMI48202USA
- NanoBioScience InstituteWayne State University42 W Warren AveDetroitMI48202USA
- Center for Molecular Medicine & GeneticsSchool of MedicineWayne State University42 W Warren AveDetroitMI48202USA
| | - Jose S. Pulido
- Wills Eye Hospital and Jefferson University HospitalPhiladelphiaPA19107USA
| | - Scott G. Filler
- Lundquist Institute for Biomedical Innovation at Harbor‐UCLA Medical Center1124 W Carson StTorranceCA90502USA
- David Geffen School of Medicine at UCLA10833 Le Conte AveLos AngelesCA90095USA
| | - Aaron P. Mitchell
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
- Department of MicrobiologyUniversity of Georgia210 S Jackson streetAthensGA30602USA
| | - N. Luisa Hiller
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Adam Lacy‐Hulbert
- Benaroya Research Institute at Virginia Mason1201 9th AveSeattleWA98101USA
| | - Yongxin Zhao
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
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13
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Zhuang Y, Shi X. Expansion microscopy: A chemical approach for super-resolution microscopy. Curr Opin Struct Biol 2023; 81:102614. [PMID: 37253290 PMCID: PMC11103276 DOI: 10.1016/j.sbi.2023.102614] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/13/2023] [Accepted: 05/01/2023] [Indexed: 06/01/2023]
Abstract
Super-resolution microscopy is a series of imaging techniques that bypass the diffraction limit of resolution. Since the 1990s, optical approaches, such as single-molecular localization microscopy, have allowed us to visualize biological samples from the sub-organelle to the molecular level. Recently, a chemical approach called expansion microscopy emerged as a new trend in super-resolution microscopy. It physically enlarges cells and tissues, which leads to an increase in the effective resolution of any microscope by the length expansion factor. Compared with optical approaches, expansion microscopy has a lower cost and higher imaging depth but requires a more complex procedure. The integration of expansion microscopy and advanced microscopes significantly pushed forward the boundary of super-resolution microscopy. This review covers the current state of the art in expansion microscopy, including the latest methods and their applications, as well as challenges and opportunities for future research.
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Affiliation(s)
- Yinyin Zhuang
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA. https://twitter.com/YinyinZhuang
| | - Xiaoyu Shi
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, CA 92697, USA; Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA.
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14
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Klimas A, Gallagher BR, Wijesekara P, Fekir S, DiBernardo EF, Cheng Z, Stolz DB, Cambi F, Watkins SC, Brody SL, Horani A, Barth AL, Moore CI, Ren X, Zhao Y. Magnify is a universal molecular anchoring strategy for expansion microscopy. Nat Biotechnol 2023; 41:858-869. [PMID: 36593399 PMCID: PMC10264239 DOI: 10.1038/s41587-022-01546-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/05/2022] [Indexed: 01/03/2023]
Abstract
Expansion microscopy enables nanoimaging with conventional microscopes by physically and isotropically magnifying preserved biological specimens embedded in a crosslinked water-swellable hydrogel. Current expansion microscopy protocols require prior treatment with reactive anchoring chemicals to link specific labels and biomolecule classes to the gel. We describe a strategy called Magnify, which uses a mechanically sturdy gel that retains nucleic acids, proteins and lipids without the need for a separate anchoring step. Magnify expands biological specimens up to 11 times and facilitates imaging of cells and tissues with effectively around 25-nm resolution using a diffraction-limited objective lens of about 280 nm on conventional optical microscopes or with around 15 nm effective resolution if combined with super-resolution optical fluctuation imaging. We demonstrate Magnify on a broad range of biological specimens, providing insight into nanoscopic subcellular structures, including synaptic proteins from mouse brain, podocyte foot processes in formalin-fixed paraffin-embedded human kidney and defects in cilia and basal bodies in drug-treated human lung organoids.
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Affiliation(s)
- Aleksandra Klimas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Brendan R Gallagher
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Piyumi Wijesekara
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Sinda Fekir
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Emma F DiBernardo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhangyu Cheng
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Donna B Stolz
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Franca Cambi
- Veterans Administration Pittsburgh, Pittsburgh, PA, USA
- Department of Neurology/PIND, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven L Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alison L Barth
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Christopher I Moore
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yongxin Zhao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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15
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Saal KA, Shaib AH, Mougios N, Crzan D, Opazo F, Rizzoli SO. Heat denaturation enables multicolor X10-STED microscopy. Sci Rep 2023; 13:5366. [PMID: 37005431 PMCID: PMC10067834 DOI: 10.1038/s41598-023-32524-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/29/2023] [Indexed: 04/04/2023] Open
Abstract
Expansion microscopy (ExM) improves imaging quality by physically enlarging the biological specimens. In principle, combining a large expansion factor with optical super-resolution should provide extremely high imaging precision. However, large expansion factors imply that the expanded specimens are dim and are therefore poorly suited for optical super-resolution. To solve this problem, we present a protocol that ensures the expansion of the samples up to 10-fold, in a single expansion step, through high-temperature homogenization (X10ht). The resulting gels exhibit a higher fluorescence intensity than gels homogenized using enzymatic digestion (based on proteinase K). This enables the sample analysis by multicolor stimulated emission depletion (STED) microscopy, for a final resolution of 6-8 nm in neuronal cell cultures or isolated vesicles. X10ht also enables the expansion of 100-200 µm thick brain samples, up to 6-fold. The better epitope preservation also enables the use of nanobodies as labeling probes and the implementation of post-expansion signal amplification. We conclude that X10ht is a promising tool for nanoscale resolution in biological samples.
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Affiliation(s)
- Kim Ann Saal
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Ali H Shaib
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Nikolaos Mougios
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Sieboldt-Str. 3a, 37075, Göttingen, Germany
| | - Dagmar Crzan
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
- NanoTag Biotechnologies GmbH, Rudolf Wissell Str. 28a, 37079, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Sieboldt-Str. 3a, 37075, Göttingen, Germany
| | - Silvio O Rizzoli
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Sieboldt-Str. 3a, 37075, Göttingen, Germany.
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16
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Chang TJB, Hsu JCC, Yang TT. Single-molecule localization microscopy reveals the ultrastructural constitution of distal appendages in expanded mammalian centrioles. Nat Commun 2023; 14:1688. [PMID: 36973278 PMCID: PMC10043031 DOI: 10.1038/s41467-023-37342-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
Distal appendages (DAPs) are vital in cilia formation, mediating vesicular and ciliary docking to the plasma membrane during early ciliogenesis. Although numerous DAP proteins arranging a nine-fold symmetry have been studied using superresolution microscopy analyses, the extensive ultrastructural understanding of the DAP structure developing from the centriole wall remains elusive owing to insufficient resolution. Here, we proposed a pragmatic imaging strategy for two-color single-molecule localization microscopy of expanded mammalian DAP. Importantly, our imaging workflow enables us to push the resolution limit of a light microscope well close to a molecular level, thus achieving an unprecedented mapping resolution inside intact cells. Upon this workflow, we unravel the ultra-resolved higher-order protein complexes of the DAP and its associated proteins. Intriguingly, our images show that C2CD3, microtubule triplet, MNR, CEP90, OFD1, and ODF2 jointly constitute a unique molecular configuration at the DAP base. Moreover, our finding suggests that ODF2 plays an auxiliary role in coordinating and maintaining DAP nine-fold symmetry. Together, we develop an organelle-based drift correction protocol and a two-color solution with minimum crosstalk, allowing a robust localization microscopy imaging of expanded DAP structures deep into the gel-specimen composites.
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Affiliation(s)
- Ting-Jui Ben Chang
- Department of Physics, National Taiwan University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | | | - T Tony Yang
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
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17
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Wen G, Leen V, Rohand T, Sauer M, Hofkens J. Current Progress in Expansion Microscopy: Chemical Strategies and Applications. Chem Rev 2023; 123:3299-3323. [PMID: 36881995 DOI: 10.1021/acs.chemrev.2c00711] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Expansion microscopy (ExM) is a newly developed super-resolution technique, allowing visualization of biological targets at nanoscale resolution on conventional fluorescence microscopes. Since its introduction in 2015, many efforts have been dedicated to broaden its application range or increase the resolution that can be achieved. As a consequence, recent years have witnessed remarkable advances in ExM. This review summarizes recent progress in ExM, with the focus on the chemical aspects of the method, from chemistries for biomolecule grafting to polymer synthesis and the impact on biological analysis. The combination of ExM with other microscopy techniques, in search of additional resolution improvement, is also discussed. In addition, we compare pre- and postexpansion labeling strategies and discuss the impact of fixation methods on ultrastructure preservation. We conclude this review with a perspective on existing challenges and future directions. We believe that this review will provide a comprehensive understanding of ExM and facilitate its usage and further development.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Volker Leen
- Chrometra Scientific, Kortenaken 3470, Belgium
| | - Taoufik Rohand
- Laboratory of Analytical and Molecular Chemistry, Faculty Polydisciplinaire of Safi, University Cadi Ayyad Marrakech, BP 4162, 46000 Safi, Morocco
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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18
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Zhao Y, Cheng Z, Stefani C, Skillman T, Klimas A, Lee A, DiBernardo E, Mueller Brown K, Milman T, Gallagher B, Lagree K, Jena B, Pulido J, Filler S, Mitchell A, Hiller L, Lacy-Hulbert A. MicroMagnify: a multiplexed expansion microscopy method for pathogens and infected tissues. RESEARCH SQUARE 2023:rs.3.rs-2637060. [PMID: 36945526 PMCID: PMC10029075 DOI: 10.21203/rs.3.rs-2637060/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Super-resolution optical imaging tools are crucial in microbiology to understand the complex structures and behavior of microorganisms such as bacteria, fungi, and viruses. However, the capabilities of these tools, particularly when it comes to imaging pathogens and infected tissues, remain limited. We developed µMagnify, a nanoscale multiplexed imaging method for pathogens and infected tissues that are derived from an expansion microscopy technique with a universal biomolecular anchor. We formulated an enzyme cocktail specifically designed for robust cell wall digestion and expansion of microbial cells without distortion while efficiently retaining biomolecules suitable for high-plex fluorescence imaging with nanoscale precision. Additionally, we developed an associated virtual reality tool to facilitate the visualization and navigation of complex three-dimensional images generated by this method in an immersive environment allowing collaborative exploration among researchers around the world. µMagnify is a valuable imaging platform for studying how microbes interact with their host systems and enables development of new diagnosis strategies against infectious diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Bhanu Jena
- Wayne State University School of Medicine
| | - Jose Pulido
- Wills Eye Hospital and Jefferson University Hospital
| | - Scott Filler
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
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19
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Hawkins TJ, Robson JL, Cole B, Bush SJ. Expansion Microscopy of Plant Cells (PlantExM). Methods Mol Biol 2023; 2604:127-142. [PMID: 36773230 DOI: 10.1007/978-1-0716-2867-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Expansion microscopy (ExM) achieves super-resolution imaging without the need for sophisticated super-resolution microscopy hardware through a combination of physical and optical magnification. Samples are fixed, stained, and embedded in a swellable gel. Following cross-linking of fluorophores to the gel matrix, the components of the sample are digested away and the gel expanded in water. Labeled objects which are too close to be resolved by diffraction-limited microscopy are moved far enough apart that these can now be resolved as individual objects on a standard confocal. Originally developed for animal cells and tissues, ExM for plants requires the additional consideration of cell wall digestion. Super-resolution can be limited in plants due to the size of cells, light scattering of tissues, and variations in refractive index. By removing the components which cause these limitations, ExM opens up the possibility of super-resolution at depth within plant tissues for the first time. Here we describe our method for PlantExM which is optimized for cytoskeleton resolution, which, when also coupled with compatible optical super-resolution technologies, can produce images of the plant cytoskeleton in unprecedented detail.
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Affiliation(s)
| | | | - Bethany Cole
- Department of Biosciences, Durham University, Durham, UK
| | - Simon J Bush
- Department of Biosciences, Durham University, Durham, UK
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20
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Hou M, Xing F, Yang J, Hu F, Pan L, Xu J. Molecular Resolution Mapping of Erythrocyte Cytoskeleton by Ultrastructure Expansion Single-Molecule Localization Microscopy. SMALL METHODS 2023; 7:e2201243. [PMID: 36543363 DOI: 10.1002/smtd.202201243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/26/2022] [Indexed: 06/17/2023]
Abstract
The combination of expansion microscopy and single-molecule localization microscopy has the potential to approach the molecular resolution. However, this combination meets challenges due to the hydrogel shrinkage in the presence of imaging buffer. Here, a method of ultrastructure expansion single-molecule localization microscopy (U-ExSMLM) based on skillfully adhering the gel onto poly-l-lysine (pLL)-coated coverslip is developed to prevent lateral shrinkage of the hydrogel. U-ExSMLM is then applied to dissect the membrane cytoskeleton organization of human erythrocytes at molecular resolution. The resolved nanoscale spatial distributions of cytoskeleton proteins, including the N/C-termini of β-spectrin, protein 4.1, and tropomodulin, show good agreement with the acknowledged model of erythrocyte cytoskeleton structure, demonstrating the reliability of U-ExSMLM. Furthermore, the concentration of pLL is adjusted to preserve the physiological biconcave morphology of erythrocytes, and it is found that the spectrin cytoskeleton in the dimple regions has lower density and larger length than that in the rim regions, which provides the direct evidence for cytoskeleton asymmetry in human erythrocytes. Therefore, the integrated method offers future opportunities to study the ultrastructure of membrane cytoskeleton at molecular resolution.
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Affiliation(s)
- Mengdi Hou
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
| | - Fulin Xing
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
| | - Jianyu Yang
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
| | - Fen Hu
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
| | - Leiting Pan
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300071, China
- Shenzhen Research Institute of Nankai University, Shenzhen, Guangdong, 518083, China
| | - Jingjun Xu
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
- Shenzhen Research Institute of Nankai University, Shenzhen, Guangdong, 518083, China
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21
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Affiliation(s)
- Sven Truckenbrodt
- Convergent Research, E11 Bio. 1600 Harbor Bay Parkway, Alameda, California94502, United States
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22
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Wen G, Leen V, Jia Y, Rohand T, Hofkens J. Improved Dye Survival in Expansion Microscopy through Stabilizer-Conjugated Linkers. Chemistry 2022; 28:e202202404. [PMID: 36031562 PMCID: PMC9828348 DOI: 10.1002/chem.202202404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 01/12/2023]
Abstract
Expansion microscopy (ExM) has been widely used to detect biomolecules in cultured cells and tissue samples due to its enablement of super resolution imaging with conventional microscopes, via physical expansion of samples. However, reaction conditions inherent to the process bring about strong fluorescent signal loss during polymerization and digestion and thus limit the brightness of the signal obtained post expansion. Here, we explore the impact of stabilizer-containing organic fluorophores in ExM, as a mitigation strategy for this radical-induced dye degradation. Through direct conjugation of 4-nitrophenylalanine (NPA) to our previously developed trifunctional reagents, we validate and demonstrate that these multifunctional linkers enable visualization of different organelles with improved fluorescent intensity, owning to protection of the dyes to radical induced degradation as well as to photoprotection upon imaging. At this point, we cannot disentangle the relative contribution of both mechanisms. Furthermore, we report anchoring linkers that allow straightforward application of NPA or Trolox to commercially available fluorophore-conjugated antibodies. We show that these anchoring linkers enable complete retention of biological targets while increasing fluorophore photostability. Our results provide guidance in exploring these stabilizer-modified agents in ExM and methods for increased signal survival through the polymerization steps of the ExM protocols.
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Affiliation(s)
- Gang Wen
- Department of ChemistryKU LeuvenLeuven3001Belgium
| | | | - Yuqing Jia
- Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Taoufik Rohand
- Laboratory of Analytical & Molecular Chemistry Faculty Polydisciplinaire of Safi Department of ChemistryUniversity Cadi Ayyad46000SafiMorocco
| | - Johan Hofkens
- Department of ChemistryKU LeuvenLeuven3001Belgium,Max Planck Institute for Polymer Research55128MainzGermany
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23
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Wang W, Chan YH, Kwon S, Tandukar J, Gao R. Nanoscale fluorescence imaging of biological ultrastructure via molecular anchoring and physical expansion. NANO CONVERGENCE 2022; 9:30. [PMID: 35810234 PMCID: PMC9271151 DOI: 10.1186/s40580-022-00318-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/26/2022] [Indexed: 05/25/2023]
Abstract
Nanoscale imaging of biological samples can provide rich morphological and mechanistic information about biological functions and dysfunctions at the subcellular and molecular level. Expansion microscopy (ExM) is a recently developed nanoscale fluorescence imaging method that takes advantage of physical enlargement of biological samples. In ExM, preserved cells and tissues are embedded in a swellable hydrogel, to which the molecules and fluorescent tags in the samples are anchored. When the hydrogel swells several-fold, the effective resolution of the sample images can be improved accordingly via physical separation of the retained molecules and fluorescent tags. In this review, we focus on the early conception and development of ExM from a biochemical and materials perspective. We first examine the general workflow as well as the numerous variations of ExM developed to retain and visualize a broad range of biomolecules, such as proteins, nucleic acids, and membranous structures. We then describe a number of inherent challenges facing ExM, including those associated with expansion isotropy and labeling density, as well as the ongoing effort to address these limitations. Finally, we discuss the prospect and possibility of pushing the resolution and accuracy of ExM to the single-molecule scale and beyond.
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Affiliation(s)
- Wei Wang
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Yat Ho Chan
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - SoYoung Kwon
- Department of Biomedical and Health Information Sciences, College of Applied Health Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Jamuna Tandukar
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Ruixuan Gao
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA.
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA.
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24
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Faulkner EL, Pike JA, Densham RM, Garlick E, Thomas SG, Neely RK, Morris JR. Imaging nanoscale nuclear structures with expansion microscopy. J Cell Sci 2022; 135:276027. [PMID: 35748225 PMCID: PMC9450888 DOI: 10.1242/jcs.259009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/21/2022] [Indexed: 11/20/2022] Open
Abstract
Commonly applied super-resolution light microscopies have provided insight into subcellular processes at the nanoscale. However, imaging depth, speed, throughput and cost remain significant challenges, limiting the numbers of three-dimensional (3D) nanoscale processes that can be investigated and the number of laboratories able to undertake such analysis. Expansion microscopy (ExM) solves many of these limitations, but its application to imaging nuclear processes has been constrained by concerns of unequal nuclear expansion. Here, we demonstrate the conditions for isotropic expansion of the nucleus at a resolution equal to or better than 120–130 nm (pre-expansion). Using the DNA damage response proteins BRCA1, 53BP1 (also known as TP53BP1) and RAD51 as exemplars, we quantitatively describe the 3D nanoscale organisation of over 50,000 DNA damage response structures. We demonstrate the ability to assess chromatin-regulated events and show the simultaneous assessment of four elements. This study thus demonstrates how ExM can contribute to the investigation of nanoscale nuclear processes. Summary: Expansion microscopy provides quantitative insight into the impact of chromatin modifiers on spatiotemporal organisation of the DNA repair proteins BRCA1, 53BP1 and RAD51 at a resolution of 65–70 nm.
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Affiliation(s)
- Emma L Faulkner
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jeremy A Pike
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,COMPARE, University of Birmingham and University of Nottingham, Midlands, UK
| | - Ruth M Densham
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, B15 2TT, UK
| | - Evelyn Garlick
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,COMPARE, University of Birmingham and University of Nottingham, Midlands, UK
| | - Steven G Thomas
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,COMPARE, University of Birmingham and University of Nottingham, Midlands, UK
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, University of Birmingham, B15 2TT, UK
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25
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Li H, Warden AR, He J, Shen G, Ding X. Expansion microscopy with ninefold swelling (NIFS) hydrogel permits cellular ultrastructure imaging on conventional microscope. SCIENCE ADVANCES 2022; 8:eabm4006. [PMID: 35507653 PMCID: PMC9067917 DOI: 10.1126/sciadv.abm4006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Superresolution microscopy enables probing of cellular ultrastructures. However, its widespread applications are limited by the need for expensive machinery, specific hardware, and sophisticated data processing. Expansion microscopy (ExM) improves the resolution of conventional microscopy by physically expanding biological specimens before imaging and currently provides ~70-nm resolution, which still lags behind that of modern superresolution microscopy (~30 nm). Here, we demonstrate a ninefold swelling (NIFS) hydrogel, that can reduce ExM resolution to 31 nm when using regular traditional microscopy. We also design a detachable chip that integrates all the experimental operations to facilitate the maximal reproducibility of this high-resolution imaging technology. We demonstrate this technique on the superimaging of nuclear pore complex and clathrin-coated pits, whose structures can hardly be resolved by conventional microscopy. The method presented here offers a universal platform with superresolution imaging to unveil cellular ultrastructural details using standard conventional laboratory microscopes.
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26
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Sun Y, Zhang Z, Bing T, Liu J, Li W, Liu X, Zhang N, Shu Y, Wang J, Shangguan D. Aptamer-Based Cell Nucleus Imaging via Expansion Microscopy. Anal Chem 2022; 94:6044-6049. [PMID: 35380789 DOI: 10.1021/acs.analchem.2c00773] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Expansion microscopy (ExM) is a newly developed technology in recent years that enables nanoscale imaging under conventional microscopes. Herein, we report an aptamer-based ExM imaging strategy. A nucleus-targeting aptamer Ch4-1 was chemically labeled with a dye and an acrydite at each end to perform the functions of molecular recognition, fluorescence reporting, and gel anchoring. After binding cell nucleus, the dual labeled aptamer Ac-Ch4-1-FAM directly participated in gelation and anchored in polyacrylamide gel. After expanding the gel, high-resolution imaging was achieved by confocal microscopy. Multicolor ExM imaging was also realized by combining Ac-Ch4-1-FAM, antibodies and fluorescent dyes. This aptamer-based ExM could clearly image the chromatin morphology at different mitotic stages. The expansion process is simple and the aptamer labeling is easy. The aptamer-based ExM holds great promise in super-resolution imaging of cells and tissues.
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Affiliation(s)
- Yue Sun
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhicheng Zhang
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Tao Bing
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiwei Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Shu
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Jianhua Wang
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310013, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Hardin WR, Alas GCM, Taparia N, Thomas EB, Steele-Ogus MC, Hvorecny KL, Halpern AR, Tůmová P, Kollman JM, Vaughan JC, Sniadecki NJ, Paredez AR. The Giardia ventrolateral flange is a lamellar membrane protrusion that supports attachment. PLoS Pathog 2022; 18:e1010496. [PMID: 35482847 PMCID: PMC9089883 DOI: 10.1371/journal.ppat.1010496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/10/2022] [Accepted: 04/04/2022] [Indexed: 12/01/2022] Open
Abstract
Attachment to the intestinal epithelium is critical to the lifestyle of the ubiquitous parasite Giardia lamblia. The ventrolateral flange is a sheet-like membrane protrusion at the interface between parasites and attached surfaces. This structure has been implicated in attachment, but its role has been poorly defined. Here, we identified a novel actin associated protein with putative WH2-like actin binding domains we named Flangin. Flangin complexes with Giardia actin (GlActin) and is enriched in the ventrolateral flange making it a valuable marker for studying the flanges' role in Giardia biology. Live imaging revealed that the flange grows to around 1 μm in width after cytokinesis, then remains uniform in size during interphase, grows in mitosis, and is resorbed during cytokinesis. A flangin truncation mutant stabilizes the flange and blocks cytokinesis, indicating that flange disassembly is necessary for rapid myosin-independent cytokinesis in Giardia. Rho family GTPases are important regulators of membrane protrusions and GlRac, the sole Rho family GTPase in Giardia, was localized to the flange. Knockdown of Flangin, GlActin, and GlRac result in flange formation defects. This indicates a conserved role for GlRac and GlActin in forming membrane protrusions, despite the absence of canonical actin binding proteins that link Rho GTPase signaling to lamellipodia formation. Flangin-depleted parasites had reduced surface contact and when challenged with fluid shear force in flow chambers they had a reduced ability to remain attached, confirming a role for the flange in attachment. This secondary attachment mechanism complements the microtubule based adhesive ventral disc, a feature that may be particularly important during mitosis when the parental ventral disc disassembles in preparation for cytokinesis. This work supports the emerging view that Giardia's unconventional actin cytoskeleton has an important role in supporting parasite attachment.
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Affiliation(s)
- William R. Hardin
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Germain C. M. Alas
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Nikita Taparia
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Elizabeth B. Thomas
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Melissa C. Steele-Ogus
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Kelli L. Hvorecny
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Aaron R. Halpern
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Pavla Tůmová
- Institute of Immunology and Microbiology, 1 Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, United States of America
| | - Nathan J. Sniadecki
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
- Bioengineering, University of Washington, Seattle, Washington, United States of America
- Lab Medicine & Pathology, University of Washington, Seattle, Washington, United States of America
- Center for Cardiovascular Biology, University of Washington, Seattle, Washington, United States of America
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Alexander R. Paredez
- Department of Biology, University of Washington, Seattle, Washington, United States of America
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28
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Steele-Ogus MC, Obenaus AM, Sniadecki NJ, Paredez AR. Disc and Actin Associated Protein 1 influences attachment in the intestinal parasite Giardia lamblia. PLoS Pathog 2022; 18:e1010433. [PMID: 35333908 PMCID: PMC8986099 DOI: 10.1371/journal.ppat.1010433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/06/2022] [Accepted: 03/10/2022] [Indexed: 02/01/2023] Open
Abstract
The deep-branching eukaryote Giardia lamblia is an extracellular parasite that attaches to the host intestine via a microtubule-based structure called the ventral disc. Control of attachment is mediated in part by the movement of two regions of the ventral disc that either permit or exclude the passage of fluid under the disc. Several known disc-associated proteins (DAPs) contribute to disc structure and function, but no force-generating protein has been identified among them. We recently identified several Giardia actin (GlActin) interacting proteins at the ventral disc, which could potentially employ actin polymerization for force generation and disc conformational changes. One of these proteins, Disc and Actin Associated Protein 1 (DAAP1), is highly enriched at the two regions of the disc previously shown to be important for fluid flow during attachment. In this study, we investigate the role of both GlActin and DAAP1 in ventral disc morphology and function. We confirmed interaction between GlActin and DAAP1 through coimmunoprecipitation, and used immunofluorescence to localize both proteins throughout the cell cycle and during trophozoite attachment. Similar to other DAPs, the association of DAAP1 with the disc is stable, except during cell division when the disc disassembles. Depletion of GlActin by translation-blocking antisense morpholinos resulted in both impaired attachment and defects in the ventral disc, indicating that GlActin contributes to disc-mediated attachment. Depletion of DAAP1 through CRISPR interference resulted in intact discs but impaired attachment, gating, and flow under the disc. As attachment is essential for infection, elucidation of these and other molecular mediators is a promising area for development of new therapeutics against a ubiquitous parasite.
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Affiliation(s)
- Melissa C. Steele-Ogus
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Ava M. Obenaus
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Nathan J. Sniadecki
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Alexander R. Paredez
- Department of Biology, University of Washington, Seattle, Washington, United States of America
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29
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Damstra HGJ, Mohar B, Eddison M, Akhmanova A, Kapitein LC, Tillberg PW. Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). eLife 2022; 11:73775. [PMID: 35179128 PMCID: PMC8887890 DOI: 10.7554/elife.73775] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/30/2022] [Indexed: 12/18/2022] Open
Abstract
Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y, and z. The maximum resolution increase is limited by the expansion factor of the gel, which is four-fold for the original ExM protocol. Variations on the original ExM method have been reported that allow for greater expansion factors but at the cost of ease of adoption or versatility. Here, we systematically explore the ExM recipe space and present a novel method termed Ten-fold Robust Expansion Microscopy (TREx) that, like the original ExM method, requires no specialized equipment or procedures. We demonstrate that TREx gels expand 10-fold, can be handled easily, and can be applied to both thick mouse brain tissue sections and cultured human cells enabling high-resolution subcellular imaging with a single expansion step. Furthermore, we show that TREx can provide ultrastructural context to subcellular protein localization by combining antibody-stained samples with off-the-shelf small-molecule stains for both total protein and membranes.
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Affiliation(s)
- Hugo G J Damstra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Boaz Mohar
- Janelia Research Campus, HHMI, Ashburn, United States
| | - Mark Eddison
- Janelia Research Campus, HHMI, Ashburn, United States
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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30
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Heil HS, Aigner M, Maier S, Gupta P, Evers LMC, Göb V, Kusch C, Meub M, Nieswandt B, Stegner D, Heinze KG. Mapping densely packed αIIbβ3 receptors in murine blood platelets with expansion microscopy. Platelets 2022; 33:849-858. [PMID: 35109754 DOI: 10.1080/09537104.2021.2023735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Interrogating platelets and their densely packed, highly abundant receptor landscape is key to understand platelet clotting, a process that can save lives when stopping blood loss after an injury, but also kill when causing heart attack, stroke, or pulmonary embolism. The underlying key receptor distributions and interactions, in particular the relevance of integrin clustering, are not fully understood is because of highly abundant and densely distributed αIIbβ3 receptors. This makes receptor distributions difficult to assess even by super-resolution fluorescence microscopy. Here, we combine dual-color expansion and confocal microscopy with colocalization analysis to assess platelet receptor organization without the need of a super-resolution microscope. We show that 4x expansion is highly straight-forward for super-resolution microscopy of platelets, while 10x expansion provides higher precision at the price of increased efforts in sample preparation and imaging. Quantifying various receptor colocalization scenarios we demonstrate that expansion microscopy can pinpoint receptor distributions and interactions in resting and activated platelets being superior to conventional methods that fail in such dense 3D scenarios with highly abundant receptors. We reveal the presence of αIIbβ3 clusters in resting platelets, as well as in activated platelets, indicating that they contribute to the rapid platelet response during platelet clotting.
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Affiliation(s)
- Hannah S Heil
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Max Aigner
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Sophia Maier
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Prateek Gupta
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Luise M C Evers
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Vanessa Göb
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.,Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
| | - Charly Kusch
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.,Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Bernhard Nieswandt
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.,Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
| | - David Stegner
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.,Institute of Experimental Biomedicine I, University Hospital Würzburg, Würzburg, Germany
| | - Katrin G Heinze
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
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31
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Laporte MH, Klena N, Hamel V, Guichard P. Visualizing the native cellular organization by coupling cryofixation with expansion microscopy (Cryo-ExM). Nat Methods 2022; 19:216-222. [PMID: 35027766 PMCID: PMC8828483 DOI: 10.1038/s41592-021-01356-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/17/2021] [Indexed: 12/11/2022]
Abstract
Cryofixation has proven to be the gold standard for efficient preservation of native cell ultrastructure compared to chemical fixation, but this approach is not widely used in fluorescence microscopy owing to implementation challenges. Here, we develop Cryo-ExM, a method that preserves native cellular organization by coupling cryofixation with expansion microscopy. This method bypasses artifacts associated with chemical fixation and its simplicity will contribute to its widespread use in super-resolution microscopy.
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Affiliation(s)
- Marine H Laporte
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Nikolai Klena
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Virginie Hamel
- Department of Cell Biology, University of Geneva, Geneva, Switzerland.
| | - Paul Guichard
- Department of Cell Biology, University of Geneva, Geneva, Switzerland.
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32
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Luo Y, Li J, Li B, Xia Y, Wang H, Fu C. Physical Cues of Matrices Reeducate Nerve Cells. Front Cell Dev Biol 2021; 9:731170. [PMID: 34646825 PMCID: PMC8502847 DOI: 10.3389/fcell.2021.731170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/20/2021] [Indexed: 11/15/2022] Open
Abstract
The behavior of nerve cells plays a crucial role in nerve regeneration. The mechanical, topographical, and electrical microenvironment surrounding nerve cells can activate cellular signaling pathways of mechanical transduction to affect the behavior of nerve cells. Recently, biological scaffolds with various physical properties have been developed as extracellular matrix to regulate the behavior conversion of nerve cell, such as neuronal neurite growth and directional differentiation of neural stem cells, providing a robust driving force for nerve regeneration. This review mainly focused on the biological basis of nerve cells in mechanical transduction. In addition, we also highlighted the effect of the physical cues, including stiffness, mechanical tension, two-dimensional terrain, and electrical conductivity, on neurite outgrowth and differentiation of neural stem cells and predicted their potential application in clinical nerve tissue engineering.
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Affiliation(s)
- Yiqian Luo
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Jie Li
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Baoqin Li
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Yuanliang Xia
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Hengyi Wang
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Changfeng Fu
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
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33
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Shi X, Li Q, Dai Z, Tran AA, Feng S, Ramirez AD, Lin Z, Wang X, Chow TT, Chen J, Kumar D, McColloch AR, Reiter JF, Huang EJ, Seiple IB, Huang B. Label-retention expansion microscopy. J Cell Biol 2021; 220:e202105067. [PMID: 34228783 PMCID: PMC8266563 DOI: 10.1083/jcb.202105067] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 11/28/2022] Open
Abstract
Expansion microscopy (ExM) increases the effective resolving power of any microscope by expanding the sample with swellable hydrogel. Since its invention, ExM has been successfully applied to a wide range of cell, tissue, and animal samples. Still, fluorescence signal loss during polymerization and digestion limits molecular-scale imaging using ExM. Here, we report the development of label-retention ExM (LR-ExM) with a set of trifunctional anchors that not only prevent signal loss but also enable high-efficiency labeling using SNAP and CLIP tags. We have demonstrated multicolor LR-ExM for a variety of subcellular structures. Combining LR-ExM with superresolution stochastic optical reconstruction microscopy (STORM), we have achieved molecular resolution in the visualization of polyhedral lattice of clathrin-coated pits in situ.
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Affiliation(s)
- Xiaoyu Shi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA
| | - Qi Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | - Zhipeng Dai
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
| | - Arthur A. Tran
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA
| | - Siyu Feng
- University of California, Berkeley–University of California, San Francisco Joint Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA
| | - Alejandro D. Ramirez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Zixi Lin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Xiaomeng Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Tracy T. Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Jiapei Chen
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Dhivya Kumar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Andrew R. McColloch
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA
| | - Jeremy F. Reiter
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Eric J. Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Ian B. Seiple
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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34
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Gorilak P, Pružincová M, Vachova H, Olšinová M, Schmidt Cernohorska M, Varga V. Expansion microscopy facilitates quantitative super-resolution studies of cytoskeletal structures in kinetoplastid parasites. Open Biol 2021; 11:210131. [PMID: 34465213 PMCID: PMC8437234 DOI: 10.1098/rsob.210131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Expansion microscopy (ExM) has become a powerful super-resolution method in cell biology. It is a simple, yet robust approach, which does not require any instrumentation or reagents beyond those present in a standard microscopy facility. In this study, we used kinetoplastid parasites Trypanosoma brucei and Leishmania major, which possess a complex, yet well-defined microtubule-based cytoskeleton, to demonstrate that this method recapitulates faithfully morphology of structures as previously revealed by a combination of sophisticated electron microscopy (EM) approaches. Importantly, we also show that due to the rapidness of image acquisition and three-dimensional reconstruction of cellular volumes ExM is capable of complementing EM approaches by providing more quantitative data. This is demonstrated on examples of less well-appreciated microtubule structures, such as the neck microtubule of T. brucei or the pocket, cytosolic and multivesicular tubule-associated microtubules of L. major. We further demonstrate that ExM enables identifying cell types rare in a population, such as cells in mitosis and cytokinesis. Three-dimensional reconstruction of an entire volume of these cells provided details on the morphology of the mitotic spindle and the cleavage furrow. Finally, we show that established antibody markers of major cytoskeletal structures function well in ExM, which together with the ability to visualize proteins tagged with small epitope tags will facilitate studies of the kinetoplastid cytoskeleton.
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Affiliation(s)
- Peter Gorilak
- Laboratory of Cell Motility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic,Charles University, Faculty of Science, Albertov 6, Prague, 128 00, Czech Republic
| | - Martina Pružincová
- Laboratory of Cell Motility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
| | - Hana Vachova
- Laboratory of Cell Motility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
| | - Marie Olšinová
- IMCF at BIOCEV, Faculty of Science, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Marketa Schmidt Cernohorska
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
| | - Vladimir Varga
- Laboratory of Cell Motility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
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35
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Wen G, Vanheusden M, Leen V, Rohand T, Vandereyken K, Voet T, Hofkens J. A Universal Labeling Strategy for Nucleic Acids in Expansion Microscopy. J Am Chem Soc 2021; 143:13782-13789. [PMID: 34424689 DOI: 10.1021/jacs.1c05931] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Expansion microscopy (ExM) enables the nanoscale imaging of ribonucleic acids (RNAs) on a conventional fluorescence microscope, providing information on the intricate patterns of gene expression at (sub)cellular resolution and within spatial context. To extend the use of such strategies, we examined a series of multivalent reagents that allow the labeling and grafting of deoxyribonucleic acid (DNA) oligonucleotide probes in a unified approach. We show that the reagents are directly compatible with third-generation in situ hybridization chain reaction RNA FISH (fluorescence in situ hybridization) techniques while displaying complete retention of the targeted transcripts. Furthermore, we validate and demonstrate that our labeling method is compatible with multicolor staining. Through oligonucleotide-conjugated antibodies, we demonstrate excellent performance in ×4 ExM and ×10 ExM, achieving a resolution of ∼50 nm in ×10 ExM for both pre- and postexpansion labeling strategies. Our results indicate that our multivalent molecules enable the rapid functionalization of DNA oligonucleotides for ExM.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | | | | | - Taoufik Rohand
- Faculty Polydisciplinaire of Safi, Department of Chemistry, Laboratory of Analytical & Molecular Chemistry, University Cadi Ayyad, 46000 Safi, Morocco
| | - Katy Vandereyken
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium.,LISCO, KU Leuven Institute for Single-Cell Omics, Leuven 3000, Belgium
| | - Thierry Voet
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium.,LISCO, KU Leuven Institute for Single-Cell Omics, Leuven 3000, Belgium
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium.,LISCO, KU Leuven Institute for Single-Cell Omics, Leuven 3000, Belgium
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36
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Tetra-gel enables superior accuracy in combined super-resolution imaging and expansion microscopy. Sci Rep 2021; 11:16944. [PMID: 34417516 PMCID: PMC8379153 DOI: 10.1038/s41598-021-96258-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/23/2021] [Indexed: 12/02/2022] Open
Abstract
The accuracy of expansion microscopy (ExM) depends on the structural preservation of samples embedded in a hydrogel. However, it has been unknown to what extent gel embedding alters the molecular positions of individual labeled sites. Here, we quantified the accuracy of gel embedding by using stochastic optical reconstruction microscopy (STORM) to image DNA origami with well-defined structures. We found that embedding in hydrogels based on polyacrylamide, the most widely used chemistry in ExM, resulted in random displacements of labeled sites with a standard deviation of ~ 16 nm. In contrast, we found that embedding in tetra-gel, a hydrogel that does not depend on free-radical chain-growth polymerization, preserved labeled sites with a standard deviation of less than 5 nm. By combining tetra-gel ExM with STORM, we were able to resolve 11-nm structural features without the loss in accuracy seen with polyacrylamide gels. Our study thus provides direct measurements of the single-molecule distortions resulting from hydrogel embedding, and presents a way to improve super-resolution microscopy through combination with tetra-gel ExM.
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37
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Gallagher BR, Zhao Y. Expansion microscopy: A powerful nanoscale imaging tool for neuroscientists. Neurobiol Dis 2021; 154:105362. [PMID: 33813047 PMCID: PMC8600979 DOI: 10.1016/j.nbd.2021.105362] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 01/13/2023] Open
Abstract
One of the biggest unsolved questions in neuroscience is how molecules and neuronal circuitry create behaviors, and how their misregulation or dysfunction results in neurological disease. Light microscopy is a vital tool for the study of neural molecules and circuits. However, the fundamental optical diffraction limit precludes the use of conventional light microscopy for sufficient characterization of critical signaling compartments and nanoscopic organizations of synapse-associated molecules. We have witnessed rapid development of super-resolution microscopy methods that circumvent the resolution limit by controlling the number of emitting molecules in specific imaging volumes and allow highly resolved imaging in the 10-100 nm range. Most recently, Expansion Microscopy (ExM) emerged as an alternative solution to overcome the diffraction limit by physically magnifying biological specimens, including nervous systems. Here, we discuss how ExM works in general and currently available ExM methods. We then review ExM imaging in a wide range of nervous systems, including Caenorhabditis elegans, Drosophila, zebrafish, mouse, and human, and their applications to synaptic imaging, neuronal tracing, and the study of neurological disease. Finally, we provide our prospects for expansion microscopy as a powerful nanoscale imaging tool in the neurosciences.
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Affiliation(s)
- Brendan R Gallagher
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yongxin Zhao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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38
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Matryba P, Łukasiewicz K, Pawłowska M, Tomczuk J, Gołąb J. Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging? Int J Mol Sci 2021; 22:ijms22136730. [PMID: 34201632 PMCID: PMC8268743 DOI: 10.3390/ijms22136730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.
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Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
- The Doctoral School of the Medical University of Warsaw, Medical University of Warsaw, 02-097 Warsaw, Poland
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Correspondence:
| | - Kacper Łukasiewicz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
| | - Monika Pawłowska
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Tomczuk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
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39
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Woodworth MA, Ng KKH, Halpern AR, Pease NA, Nguyen PHB, Kueh HY, Vaughan JC. Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy. Nucleic Acids Res 2021; 49:e82. [PMID: 34048564 PMCID: PMC8373070 DOI: 10.1093/nar/gkab423] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Proper regulation of genome architecture and activity is essential for the development and function of multicellular organisms. Histone modifications, acting in combination, specify these activity states at individual genomic loci. However, the methods used to study these modifications often require either a large number of cells or are limited to targeting one histone mark at a time. Here, we developed a new method called Single Cell Evaluation of Post-TRanslational Epigenetic Encoding (SCEPTRE) that uses Expansion Microscopy (ExM) to visualize and quantify multiple histone modifications at non-repetitive genomic regions in single cells at a spatial resolution of ∼75 nm. Using SCEPTRE, we distinguished multiple histone modifications at a single housekeeping gene, quantified histone modification levels at multiple developmentally-regulated genes in individual cells, and evaluated the relationship between histone modifications and RNA polymerase II loading at individual loci. We find extensive variability in epigenetic states between individual gene loci hidden from current population-averaged measurements. These findings establish SCEPTRE as a new technique for multiplexed detection of combinatorial chromatin states at single genomic loci in single cells.
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Affiliation(s)
- Marcus A Woodworth
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kenneth K H Ng
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas A Pease
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Phuc H B Nguyen
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.,Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
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40
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Yao L, Zhang L, Fei Y, Chen L, Mi L, Ma J. Application of SNAP-Tag in Expansion Super-Resolution Microscopy Using DNA Oligostrands. Front Chem 2021; 9:640519. [PMID: 33996746 PMCID: PMC8119759 DOI: 10.3389/fchem.2021.640519] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Expansion super-resolution technology is a new technology developed in recent years. It anchors the dye on the hydrogel and the dye expands with the expansion of the hydrogel so that a super-resolution map can be obtained under an ordinary microscope. However, by labeling the target protein with a first antibody and secondary antibody, the distance between the fluorescent group and the actual target protein is greatly increased. Although fluorescent proteins can also be used for expansion super-resolution to reduce this effect, the fluorescent protein is often destroyed during sample preparation. To solve this problem, we developed a novel label system for expansion microscopy, based on a DNA oligostrand linked with a fluorescent dye, acrylamide group (linker), and benzoylguanine (BG, a small substrate molecule for SNAP-tag). This protocol greatly reduced the error between the position of fluorescent group and the actual target protein, and also reduced loss of the fluorescent group during sample preparation.
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Affiliation(s)
- Longfang Yao
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Li Zhang
- Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Liwen Chen
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, The Multiscale Research Institute of Complex Systems, School of Life Sciences, Fudan University, Shanghai, China.,Insititute of Biomedical Engineering and Technology, Academy for Engineering and Technology, Fudan University, Shanghai, China
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41
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Derevtsova KZ, Pchitskaya EI, Rakovskaya AV, Bezprozvanny IB. Applying the Expansion Microscopy
Method in Neurobiology. J EVOL BIOCHEM PHYS+ 2021. [DOI: 10.1134/s0022093021030157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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Kolesová H, Olejníčková V, Kvasilová A, Gregorovičová M, Sedmera D. Tissue clearing and imaging methods for cardiovascular development. iScience 2021; 24:102387. [PMID: 33981974 PMCID: PMC8086021 DOI: 10.1016/j.isci.2021.102387] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tissue imaging in 3D using visible light is limited and various clearing techniques were developed to increase imaging depth, but none provides universal solution for all tissues at all developmental stages. In this review, we focus on different tissue clearing methods for 3D imaging of heart and vasculature, based on chemical composition (solvent-based, simple immersion, hyperhydration, and hydrogel embedding techniques). We discuss in detail compatibility of various tissue clearing techniques with visualization methods: fluorescence preservation, immunohistochemistry, nuclear staining, and fluorescent dyes vascular perfusion. We also discuss myocardium visualization using autofluorescence, tissue shrinking, and expansion. Then we overview imaging methods used to study cardiovascular system and live imaging. We discuss heart and vessels segmentation methods and image analysis. The review covers the whole process of cardiovascular system 3D imaging, starting from tissue clearing and its compatibility with various visualization methods to the types of imaging methods and resulting image analysis.
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Affiliation(s)
- Hana Kolesová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - Veronika Olejníčková
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - Alena Kvasilová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martina Gregorovičová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - David Sedmera
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
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43
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Kang M, Lee J, Ko S, Shim SH. Prelabeling Expansion Single-Molecule Localization Microscopy with Minimal Linkage Error. Chembiochem 2021; 22:1396-1399. [PMID: 33325115 DOI: 10.1002/cbic.202000772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Indexed: 11/09/2022]
Abstract
Expansion microscopy combined with single-molecule localization microscopy (ExSMLM) has a potential for approaching molecular resolution. However, ExSMLM faces multiple challenges such as loss of fluorophores and proteins during polymerization, digestion or denaturation, and an increase in linkage error arising from the distance between the fluorophore and the target molecule. Here, we introduce a trifunctional streptavidin to link the target, fluorophore and gel matrix via a biotinylizable peptide tag. The resultant ExSMLM images of vimentin filaments demonstrated high labeling efficiency and a minimal linkage error of ∼5 nm. Our ExSMLM provides a simple and practical means for fluorescence imaging with molecular resolution.
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Affiliation(s)
- Minsu Kang
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Jooyong Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology(UNIST), Ulsan, 44919, Republic of Korea
| | - Sangyoon Ko
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Sang-Hee Shim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul, 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
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44
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Zhao J, Lai HM, Qi Y, He D, Sun H. Current Status of Tissue Clearing and the Path Forward in Neuroscience. ACS Chem Neurosci 2021; 12:5-29. [PMID: 33326739 DOI: 10.1021/acschemneuro.0c00563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Due to the complexity and limited availability of human brain tissues, for decades, pathologists have sought to maximize information gained from individual samples, based on which (patho)physiological processes could be inferred. Recently, new understandings of chemical and physical properties of biological tissues and multiple chemical profiling have given rise to the development of scalable tissue clearing methods allowing superior optical clearing of across-the-scale samples. In the past decade, tissue clearing techniques, molecular labeling methods, advanced laser scanning microscopes, and data visualization and analysis have become commonplace. Combined, they have made 3D visualization of brain tissues with unprecedented resolution and depth widely accessible. To facilitate further advancements and applications, here we provide a critical appraisal of these techniques. We propose a classification system of current tissue clearing and expansion methods that allows users to judge the applicability of individual ones to their questions, followed by a review of the current progress in molecular labeling, optical imaging, and data processing to demonstrate the whole 3D imaging pipeline based on tissue clearing and downstream techniques for visualizing the brain. We also raise the path forward of tissue-clearing-based imaging technology, that is, integrating with state-of-the-art techniques, such as multiplexing protein imaging, in situ signal amplification, RNA detection and sequencing, super-resolution imaging techniques, multiomics studies, and deep learning, for drawing the complete atlas of the human brain and building a 3D pathology platform for central nervous system disorders.
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Affiliation(s)
- Jiajia Zhao
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Hei Ming Lai
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yuwei Qi
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Dian He
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Haitao Sun
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Clinical Biobank Center, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
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45
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Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
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Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
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46
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Kubalová I, Schmidt Černohorská M, Huranová M, Weisshart K, Houben A, Schubert V. Prospects and limitations of expansion microscopy in chromatin ultrastructure determination. Chromosome Res 2020; 28:355-368. [PMID: 32939606 PMCID: PMC7691311 DOI: 10.1007/s10577-020-09637-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 02/04/2023]
Abstract
Expansion microscopy (ExM) is a method to magnify physically a specimen with preserved ultrastructure. It has the potential to explore structural features beyond the diffraction limit of light. The procedure has been successfully used for different animal species, from isolated macromolecular complexes through cells to tissue slices. Expansion of plant-derived samples is still at the beginning, and little is known, whether the chromatin ultrastructure becomes altered by physical expansion. In this study, we expanded isolated barley nuclei and compared whether ExM can provide a structural view of chromatin comparable with super-resolution microscopy. Different fixation and denaturation/digestion conditions were tested to maintain the chromatin ultrastructure. We achieved up to ~4.2-times physically expanded nuclei corresponding to a maximal resolution of ~50-60 nm when imaged by wild-field (WF) microscopy. By applying structured illumination microscopy (SIM, super-resolution) doubling the WF resolution, the chromatin structures were observed at a resolution of ~25-35 nm. WF microscopy showed a preserved nucleus shape and nucleoli. Moreover, we were able to detect chromatin domains, invisible in unexpanded nuclei. However, by applying SIM, we observed that the preservation of the chromatin ultrastructure after the expansion was not complete and that the majority of the tested conditions failed to keep the ultrastructure. Nevertheless, using expanded nuclei, we localized successfully centromere repeats by fluorescence in situ hybridization (FISH) and the centromere-specific histone H3 variant CENH3 by indirect immunolabelling. However, although these repeats and proteins were localized at the correct position within the nuclei (indicating a Rabl orientation), their ultrastructural arrangement was impaired.
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Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Markéta Schmidt Černohorská
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics,, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martina Huranová
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics,, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
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47
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Park CE, Cho Y, Cho I, Jung H, Kim B, Shin JH, Choi S, Kwon SK, Hahn YK, Chang JB. Super-Resolution Three-Dimensional Imaging of Actin Filaments in Cultured Cells and the Brain via Expansion Microscopy. ACS NANO 2020; 14:14999-15010. [PMID: 33095573 DOI: 10.1021/acsnano.0c04915] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Actin is an essential protein in almost all life forms. It mediates diverse biological functions, ranging from controlling the shape of cells and cell movements to cargo transport and the formation of synaptic connections. Multiple diseases are closely related to the dysfunction of actin or actin-related proteins. Despite the biological importance of actin, super-resolution imaging of it in tissue is still challenging, as it forms very dense networks in almost all cells inside the tissue. In this work, we demonstrate multiplexed super-resolution volumetric imaging of actin in both cultured cells and mouse brain slices via expansion microscopy (ExM). By introducing a simple labeling process, which enables the anchoring of an actin probe, phalloidin, to a swellable hydrogel, the multiplexed ExM imaging of actin filaments was achieved. We first showed that this technique could visualize the nanoscale details of actin filament organizations in cultured cells. Then, we applied this technique to mouse brain slices and visualized diverse actin organizations, such as the parallel actin filaments along the long axis of dendrites and dense actin structures in postsynaptic spines. We examined the postsynaptic spines in the mouse brain and showed that the organizations of actin filaments are highly diverse. This technique, which enables the high-throughput 60 nm resolution imaging of actin filaments and other proteins in cultured cells and thick tissue slices, would be a useful tool to study the organization of actin filaments in diverse biological circumstances and how they change under pathological conditions.
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Affiliation(s)
- Chan E Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Youngbin Cho
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - In Cho
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Hyunsu Jung
- Division of Life Sciences, Korea University, Seoul 02841, Korea
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Byeongyeon Kim
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Korea
| | - Jennifer H Shin
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Sungyoung Choi
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Korea
| | - Seok-Kyu Kwon
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Korea
| | - Young Ki Hahn
- Biomedical Convergence Science & Technology, Industrial Technology Advances, Kyungpook National University, Daegu 41566, Korea
| | - Jae-Byum Chang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- KI for Health Science and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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48
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Hamel V, Guichard P. Improving the resolution of fluorescence nanoscopy using post-expansion labeling microscopy. Methods Cell Biol 2020; 161:297-315. [PMID: 33478694 DOI: 10.1016/bs.mcb.2020.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The visualization of the cell ultrastructure and molecular complexes has long been reserved for electron microscopy owing to its nanometric resolution. In recent years, this monopoly has been challenged by super-resolution (SR) fluorescence microscopy, which allows the visualization of cell structures with high spatial resolution, approaching virtually molecular dimensions. However, the resolution of current SR microscopy does not systematically reach the level of the ultrastructural information provided by electron microscopy. In this review, we are discussing the potential of revealing cell ultrastructure using the recent method of expansion microscopy (ExM). In particular, we are discussing the limitations that exist in SR and ExM methods that prevent the visualization of nanometric molecular assemblies and how post-labeling expansion could help alleviate them to reveal the molecular cartography of cells with unprecedented details.
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Affiliation(s)
- Virginie Hamel
- Department of Cell Biology, University of Geneva, Sciences III, Geneva, Switzerland.
| | - Paul Guichard
- Department of Cell Biology, University of Geneva, Sciences III, Geneva, Switzerland.
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49
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Kubalová I, Schmidt Černohorská M, Huranová M, Weisshart K, Houben A, Schubert V. A protocol to expand plant nuclei. Methods Cell Biol 2020; 161:197-216. [PMID: 33478690 DOI: 10.1016/bs.mcb.2020.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The resolution achieved by conventional light microscopy is limited by light diffraction. This obstacle can be overcome either by optical super-resolution techniques or by the recently developed method to physically expand specimens, called expansion microscopy (ExM). The method utilizes polymer chemistry and the ability of a swellable polyelectrolyte hydrogel to absorb water, and thus to expand its size. The procedure was successfully applied to different species and tissue samples, mostly from the animal kingdom. Physically expanded nuclei and chromosomes in combination with specific protein labeling and super-resolution microscopy may provide new insight into the ultrastructure, dynamics, and function of plant chromatin. Here we provide a detailed protocol to expand isolated plant nuclei and visualize proteins by indirect immunolabeling. With the focus on chromatin structure, we expanded isolated barley nuclei from root tips and visualized the centromere-specific histone H3 variant CENH3. The achieved physical expansion of ~4.2 times allowed the detection of DAPI-labeled chromatin structures already by conventional wild-field (WF) microscopy with a maximal resolution of ~50-60nm. By applying structured illumination microscopy (SIM), doubling the WF resolution, chromatin structures at a resolution of ~25-35nm were observed. However, a certain distortion of the centromeric chromatin ultrastructure became obvious.
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Affiliation(s)
- Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Markéta Schmidt Černohorská
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martina Huranová
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
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Wen G, Vanheusden M, Acke A, Valli D, Neely RK, Leen V, Hofkens J. Evaluation of Direct Grafting Strategies via Trivalent Anchoring for Enabling Lipid Membrane and Cytoskeleton Staining in Expansion Microscopy. ACS NANO 2020; 14:7860-7867. [PMID: 32176475 DOI: 10.1101/696039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Super-resolution fluorescence microscopy is a key tool in the elucidation of biological fine structures, providing insights into the distribution and interactions of biomolecular complexes down to the nanometer scale. Expansion microscopy is a recently developed approach for achieving nanoscale resolution on a conventional microscope. Here, biological samples are embedded in an isotropically swollen hydrogel. This physical expansion of the sample allows imaging with resolutions down to the tens-of-nanometers. However, because of the requirement that fluorescent labels are covalently bound to the hydrogel, standard, small-molecule targeting of fluorophores has proven incompatible with expansion microscopy. Here, we show a chemical linking approach that enables direct, covalent grafting of a targeting molecule and fluorophore to the hydrogel in expansion microscopy. We show application of this series of molecules in the antibody-free targeting of the cell cytoskeleton and in an example of lipid membrane staining for expansion microscopy. Furthermore, using this trivalent linker strategy, we demonstrate the benefit of introducing fluorescent labels post-expansion by visualizing an immunostaining through fluorescent oligonucleotide hybridization after expanding the polymer. Our probes allow different labeling approaches that are compatible with expansion microscopy.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
| | | | - Aline Acke
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
| | - Donato Valli
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Volker Leen
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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