1
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Zou X, Wen S, Xu L, Gao L, Wang X, Hu X, Han J, Han S. Signal-sustained imaging of mitophagy with an Enzyme-Activatable Metabolic Lipid-Labeling Probe. Autophagy 2024. [PMID: 38873937 DOI: 10.1080/15548627.2024.2367192] [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: 11/30/2023] [Accepted: 06/08/2024] [Indexed: 06/15/2024] Open
Abstract
Imaging of mitophagy is of significance as aberrant mitophagy is engaged in multiple diseases. Mitophagy has been imaged with synthetic or biotic pH sensors by reporting pH acidification en route delivery into lysosomes. To circumvent uncertainty of acidity-dependent signals, we herein report an enzyme-activatable probe covalently attached on mitochondrial inner membrane (ECAM) for signal-persist mitophagy imaging. ECAM is operated via ΔΨm-driven accumulation of Mito-proGreen in mitochondria and covalent linking of the trapped probe with azidophospholipids metabolically incorporated into the mitochondrial inner membrane. Upon mitophagy, ECAM is delivered into lysosomes and hydrolyzed by LNPEP/leucyl aminopeptidase, yielding turn-on green fluorescence that is immune to lysosomal acidity changes and stably retained in fixed cells. With ECAM, phorbol-12-myristate-13-acetate (PMA) was identified as a highly potent inducer of mitophagy. Overcoming signal susceptibility of pH probes and liability of ΔΨm probes to dissipation from stressed mitochondria, ECAM offers an attractive tool to study mitophagy and mitophagy-inducing therapeutic agents.
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Affiliation(s)
- Xiaoxue Zou
- The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Shixiong Wen
- State key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lichun Xu
- The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Lei Gao
- The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xunxiang Wang
- The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xiao Hu
- The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Jiahuai Han
- State key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shoufa Han
- The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory for Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- Academician Workstation of Immune Cell Signal Transduction, School of Basic Medicine, Chongqing Medical University, Chongqing, China
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2
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Mino T, Nonaka H, Hamachi I. Molecular anchoring and fluorescent labeling in animals compatible with tissue clearing for 3D imaging. Curr Opin Chem Biol 2024; 81:102474. [PMID: 38838505 DOI: 10.1016/j.cbpa.2024.102474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Analyzing the quantity and distribution of molecules throughout intact biological tissue is crucial for understanding various biological phenomena. Traditional methods involving destructive extraction result in the loss of spatial information. Conversely, tissue-clearing techniques combined with fluorescence imaging have recently emerged as a powerful tool for deep tissue imaging without sacrificing spatial coverage. Key to this approach is the anchoring and labeling of targets in intact tissue. In this review, methods for anchoring and labeling proteins, lipids, carbohydrates, and small molecules are presented. Future directions include the development of activity-based probes that work in vivo and mark transient events with spatial information to enable a deeper understanding of biological phenomena.
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Affiliation(s)
- Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan.
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3
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Kesharwani A, Gujrati V. Multimodal techniques and strategies for chemical and metabolic imaging at the single-cell level. Curr Opin Biotechnol 2024; 88:103149. [PMID: 38810301 DOI: 10.1016/j.copbio.2024.103149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Single-cell chemical and metabolic imaging technologies provide unprecedented insights into individual cell dynamics, advancing our understanding of cellular processes, molecular interactions, and metabolic activities. Advances in fluorescence, Raman, optoacoustic (photoacoustic), or mass spectrometry methods have paved the way to characterize metabolites, signaling molecules, and other moieties within individual cells. These modalities can also lead to single-cell imaging capabilities by targeting endogenous cell contrast or by employing exogenous contrast generation techniques, including contrast agents that target specific cell structure or function. In this review, we present key developments, summarize recent applications in single-cell interrogation and imaging, and illustrate their advantages, limitations, and outlook.
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Affiliation(s)
- Ajay Kesharwani
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Vipul Gujrati
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine and Health, Technical University of Munich, Munich, Germany.
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4
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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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5
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Shin TW, Wang H, Zhang C, An B, Lu Y, Zhang E, Lu X, Karagiannis ED, Kang JS, Emenari A, Symvoulidis P, Asano S, Lin L, Costa EK, Marblestone AH, Kasthuri N, Tsai LH, Boyden ES. Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583776. [PMID: 38496681 PMCID: PMC10942445 DOI: 10.1101/2024.03.07.583776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Lipid membranes are key to the nanoscale compartmentalization of biological systems, but fluorescent visualization of them in intact tissues, with nanoscale precision, is challenging to do with high labeling density. Here, we report ultrastructural membrane expansion microscopy (umExM), which combines a novel membrane label and optimized expansion microscopy protocol, to support dense labeling of membranes in tissues for nanoscale visualization. We validated the high signal-to-background ratio, and uniformity and continuity, of umExM membrane labeling in brain slices, which supported the imaging of membranes and proteins at a resolution of ~60 nm on a confocal microscope. We demonstrated the utility of umExM for the segmentation and tracing of neuronal processes, such as axons, in mouse brain tissue. Combining umExM with optical fluctuation imaging, or iterating the expansion process, yielded ~35 nm resolution imaging, pointing towards the potential for electron microscopy resolution visualization of brain membranes on ordinary light microscopes.
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Affiliation(s)
- Tay Won Shin
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hao Wang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Picower Inst. for Learning and Memory, Cambridge
| | - Chi Zhang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Bobae An
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Yangning Lu
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Elizabeth Zhang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Xiaotang Lu
- Department of Cellular and Molecular Biology, Harvard University, Cambridge, MA, United States
| | | | - Jeong Seuk Kang
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Amauche Emenari
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Panagiotis Symvoulidis
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Shoh Asano
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Leanne Lin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Emma K. Costa
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Adam H. Marblestone
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- present address: Convergent Research
| | - Narayanan Kasthuri
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, USA
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Picower Inst. for Learning and Memory, Cambridge
| | - Edward S. Boyden
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- K. Lisa Yang Center for Bionics, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
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6
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Li Y, Wang H, Chen Y, Ding L, Ju H. In Situ Glycan Analysis and Editing in Living Systems. JACS AU 2024; 4:384-401. [PMID: 38425935 PMCID: PMC10900212 DOI: 10.1021/jacsau.3c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 03/02/2024]
Abstract
Besides proteins and nucleic acids, carbohydrates are also ubiquitous building blocks of living systems. Approximately 70% of mammalian proteins are glycosylated. Glycans not only provide structural support for living systems but also act as crucial regulators of cellular functions. As a result, they are considered essential pieces of the life science puzzle. However, research on glycans has lagged far behind that on proteins and nucleic acids. The main reason is that glycans are not direct products of gene coding, and their synthesis is nontemplated. In addition, the diversity of monosaccharide species and their linkage patterns contribute to the complexity of the glycan structures, which is the molecular basis for their diverse functions. Research in glycobiology is extremely challenging, especially for the in situ elucidation of glycan structures and functions. There is an urgent need to develop highly specific glycan labeling tools and imaging methods and devise glycan editing strategies. This Perspective focuses on the challenges of in situ analysis of glycans in living systems at three spatial levels (i.e., cell, tissue, and in vivo) and highlights recent advances and directions in glycan labeling, imaging, and editing tools. We believe that examining the current development landscape and the existing bottlenecks can drive the evolution of in situ glycan analysis and intervention strategies and provide glycan-based insights for clinical diagnosis and therapeutics.
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Affiliation(s)
- Yiran Li
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Haiqi Wang
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Yunlong Chen
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Lin Ding
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
- Chemistry
and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
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7
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Pang Z, Cravatt BF, Ye L. Deciphering Drug Targets and Actions with Single-Cell and Spatial Resolution. Annu Rev Pharmacol Toxicol 2024; 64:507-526. [PMID: 37722721 DOI: 10.1146/annurev-pharmtox-033123-123610] [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: 09/20/2023]
Abstract
Recent advances in chemical, molecular, and genetic approaches have provided us with an unprecedented capacity to identify drug-target interactions across the whole proteome and genome. Meanwhile, rapid developments of single-cell and spatial omics technologies are revolutionizing our understanding of the molecular architecture of biological systems. However, a significant gap remains in how we align our understanding of drug actions, traditionally based on molecular affinities, with the in vivo cellular and spatial tissue heterogeneity revealed by these newer techniques. Here, we review state-of-the-art methods for profiling drug-target interactions and emerging multiomics tools to delineate the tissue heterogeneity at single-cell resolution. Highlighting the recent technical advances enabling high-resolution, multiplexable in situ small-molecule drug imaging (clearing-assisted tissue click chemistry, or CATCH), we foresee the integration of single-cell and spatial omics platforms, data, and concepts into the future framework of defining and understanding in vivo drug-target interactions and mechanisms of actions.
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Affiliation(s)
- Zhengyuan Pang
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California, USA;
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA;
| | - Li Ye
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California, USA;
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
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8
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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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9
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Zhang Q, Kuang G, Wang L, Duan P, Sun W, Ye F. Designing Bioorthogonal Reactions for Biomedical Applications. RESEARCH (WASHINGTON, D.C.) 2023; 6:0251. [PMID: 38107023 PMCID: PMC10723801 DOI: 10.34133/research.0251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 12/19/2023]
Abstract
Bioorthogonal reactions are a class of chemical reactions that can be carried out in living organisms without interfering with other reactions, possessing high yield, high selectivity, and high efficiency. Since the first proposal of the conception by Professor Carolyn Bertozzi in 2003, bioorthogonal chemistry has attracted great attention and has been quickly developed. As an important chemical biology tool, bioorthogonal reactions have been applied broadly in biomedicine, including bio-labeling, nucleic acid functionalization, drug discovery, drug activation, synthesis of antibody-drug conjugates, and proteolysis-targeting chimeras. Given this, we summarized the basic knowledge, development history, research status, and prospects of bioorthogonal reactions and their biomedical applications. The main purpose of this paper is to furnish an overview of the intriguing bioorthogonal reactions in a variety of biomedical applications and to provide guidance for the design of novel reactions to enrich bioorthogonal chemistry toolkits.
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Affiliation(s)
- Qingfei Zhang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
| | - Gaizhen Kuang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Li Wang
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Ping Duan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Weijian Sun
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Fangfu Ye
- Wenzhou Institute,
University of Chinese Academy of Sciences, Wenzhou 325001, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics,
Chinese Academy of Sciences, Beijing 100190, China
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10
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Wang UTT, Tian X, Liou YH, Lee SP, Hu HT, Lu CH, Lin PT, Cheng YJ, Chen P, Chen BC. Protein and lipid expansion microscopy with trypsin and tyramide signal amplification for 3D imaging. Sci Rep 2023; 13:21922. [PMID: 38081848 PMCID: PMC10713663 DOI: 10.1038/s41598-023-48959-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Expansion microscopy, whereby the relative positions of biomolecules are physically increased via hydrogel expansion, can be used to reveal ultrafine structures of cells under a conventional microscope. Despite its utility for achieving super-resolution imaging, expansion microscopy suffers a major drawback, namely reduced fluorescence signals caused by excessive proteolysis and swelling effects. This caveat results in a lower photon budget and disfavors fluorescence imaging over a large field of view that can cover an entire expanded cell, especially in 3D. In addition, the complex procedures and specialized reagents of expansion microscopy hinder its popularization. Here, we modify expansion microscopy by deploying trypsin digestion to reduce protein loss and tyramide signal amplification to enhance fluorescence signal for point-scanning-based imaging. We name our new methodology TT-ExM to indicate dual trypsin and tyramide treatments. TT-ExM may be applied for both antibody and lipid staining. TT-ExM displayed enhanced protein retention for endoplasmic reticulum and mitochondrial markers in COS-7 cell cultures. Importantly, TT-ExM-based lipid staining clearly revealed the complex 3D membrane structures in entire expanded cells. Through combined lipid and DNA staining, our TT-ExM methodology highlighted mitochondria by revealing their DNA and membrane structures in cytoplasm, as well as the lipid-rich structures formed via phase separation in nuclei at interphase. We also observed lipid-rich chromosome matrices in the mitotic cells. These high-quality 3D images demonstrate the practicality of TT-ExM. Thus, readily available reagents can be deployed in TT-ExM to significantly enhance fluorescence signals and generate high-quality and ultrafine-resolution images under confocal microscopy.
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Affiliation(s)
- Ueh-Ting Tim Wang
- Affiliated Senior High School of National Taiwan Normal University, Taipei, 106348, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taipei, 11529, Taiwan
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yae-Huei Liou
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Sue-Ping Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiao-Tang Hu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Institute and Undergraduate Program of Electro-Optical Engineering, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Po-Ting Lin
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Ya-Jen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
- Neuroscience Program, NPAS, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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11
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Valdivieso González D, Jara J, Almendro-Vedia VG, Orgaz B, López-Montero I. Expansion microscopy applied to mono- and dual-species biofilms. NPJ Biofilms Microbiomes 2023; 9:92. [PMID: 38049404 PMCID: PMC10696089 DOI: 10.1038/s41522-023-00460-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
Expansion microscopy (ExM) is a new super-resolution technique based on embedding the biological sample within a hydrogel and its physical expansion after swelling. This allows increasing its size by several times while preserving its structural details. Applied to prokaryotic cells, ExM requires digestion steps for efficient expansion as bacteria are surrounded by a rigid cell wall. Furthermore, bacteria can live in social groups forming biofilms, where cells are protected from environmental stresses by a self-produced matrix. The extracellular matrix represents an additional impenetrable barrier for ExM. Here we optimize the current protocols of ExM and apply them to mono- and dual-species biofilms formed by clinical isolates of Limosilactobacillus reuteri, Enterococcus faecalis, Serratia marcescens and Staphylococcus aureus. Using scanning electron microscopy for comparison, our results demonstrate that embedded bacteria expanded 3-fold. Moreover, ExM allowed visualizing the three-dimensional architecture of the biofilm and identifying the distribution of different microbial species and their interactions. We also detected the presence of the extracellular matrix after expansion with a specific stain of the polysaccharide component. The potential applications of ExM in biofilms will improve our understanding of these complex communities and have far-reaching implications for industrial and clinical research.
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Affiliation(s)
- David Valdivieso González
- Dto. Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps. Juan XXIII 1, 28040, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (Imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain
| | - Josué Jara
- Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Víctor G Almendro-Vedia
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps. Juan XXIII 1, 28040, Madrid, Spain
- Sección Departamental de Farmacia Galénica y Tecnología Alimentaria, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (Imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain
| | - Belén Orgaz
- Sección Departamental de Farmacia Galénica y Tecnología Alimentaria, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
| | - Iván López-Montero
- Dto. Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain.
- Instituto Pluridisciplinar, Universidad Complutense de Madrid, Ps. Juan XXIII 1, 28040, Madrid, Spain.
- Instituto de Investigación Biomédica Hospital Doce de Octubre (Imas12), Avda. de Córdoba s/n, 28041, Madrid, Spain.
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12
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Uematsu M, Baskin JM. Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level. Cold Spring Harb Perspect Biol 2023; 15:a041407. [PMID: 37604586 PMCID: PMC10691496 DOI: 10.1101/cshperspect.a041407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.
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Affiliation(s)
- Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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13
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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: 0] [Impact Index Per Article: 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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14
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Park S, Wang X, Li X, Huang X, Fong KC, Yu C, Tran AA, Scipioni L, Dai Z, Huang L, Shi X. Proximity Labeling Expansion Microscopy (PL-ExM) resolves structure of the interactome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566477. [PMID: 38014020 PMCID: PMC10680661 DOI: 10.1101/2023.11.09.566477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Elucidating the spatial relationships within the protein interactome is pivotal to understanding the organization and regulation of protein-protein interactions. However, capturing the 3D architecture of the interactome presents a dual challenge: precise interactome labeling and super-resolution imaging. To bridge this gap, we present the Proximity Labeling Expansion Microscopy (PL-ExM). This innovation combines proximity labeling (PL) to spatially biotinylate interacting proteins with expansion microscopy (ExM) to increase imaging resolution by physically enlarging cells. PL-ExM unveils intricate details of the 3D interactome's spatial layout in cells using standard microscopes, including confocal and Airyscan. Multiplexing PL-ExM imaging was achieved by pairing the PL with immunofluorescence staining. These multicolor images directly visualize how interactome structures position specific proteins in the protein-protein interaction network. Furthermore, PL-ExM stands out as an assessment method to gauge the labeling radius and efficiency of different PL techniques. The accuracy of PL-ExM is validated by our proteomic results from PL mass spectrometry. Thus, PL-ExM is an accessible solution for 3D mapping of the interactome structure and an accurate tool to access PL quality.
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15
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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: 0] [Impact Index Per Article: 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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16
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Cui Y, Yang G, Goodwin DR, O’Flanagan CH, Sinha A, Zhang C, Kitko KE, Shin TW, Park D, Aparicio S, Boyden ES. Expansion microscopy using a single anchor molecule for high-yield multiplexed imaging of proteins and RNAs. PLoS One 2023; 18:e0291506. [PMID: 37729182 PMCID: PMC10511132 DOI: 10.1371/journal.pone.0291506] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
Expansion microscopy (ExM), by physically enlarging specimens in an isotropic fashion, enables nanoimaging on standard light microscopes. Key to existing ExM protocols is the equipping of different kinds of molecules, with different kinds of anchoring moieties, so they can all be pulled apart from each other by polymer swelling. Here we present a multifunctional anchor, an acrylate epoxide, that enables proteins and RNAs to be equipped with anchors in a single experimental step. This reagent simplifies ExM protocols and reduces cost (by 2-10-fold for a typical multiplexed ExM experiment) compared to previous strategies for equipping RNAs with anchors. We show that this united ExM (uniExM) protocol can be used to preserve and visualize RNA transcripts, proteins in biologically relevant ultrastructures, and sets of RNA transcripts in patient-derived xenograft (PDX) cancer tissues and may support the visualization of other kinds of biomolecular species as well. uniExM may find many uses in the simple, multimodal nanoscale analysis of cells and tissues.
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Affiliation(s)
- Yi Cui
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Gaojie Yang
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Daniel R. Goodwin
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Ciara H. O’Flanagan
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Anubhav Sinha
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, Massachusetts, United States of America
| | - Chi Zhang
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Kristina E. Kitko
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Tay Won Shin
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Demian Park
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Edward S. Boyden
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, United States of America
- Koch Institute for Cancer Research, MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, MIT, Cambridge, Massachusetts, United States of America
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17
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Yang C, Shitamukai A, Yang S, Kawaguchi A. Advanced Techniques Using In Vivo Electroporation to Study the Molecular Mechanisms of Cerebral Development Disorders. Int J Mol Sci 2023; 24:14128. [PMID: 37762431 PMCID: PMC10531473 DOI: 10.3390/ijms241814128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
The mammalian cerebral cortex undergoes a strictly regulated developmental process. Detailed in situ visualizations, imaging of these dynamic processes, and in vivo functional gene studies significantly enhance our understanding of brain development and related disorders. This review introduces basic techniques and recent advancements in in vivo electroporation for investigating the molecular mechanisms underlying cerebral diseases. In utero electroporation (IUE) is extensively used to visualize and modify these processes, including the forced expression of pathological mutants in human diseases; thus, this method can be used to establish animal disease models. The advent of advanced techniques, such as genome editing, including de novo knockout, knock-in, epigenetic editing, and spatiotemporal gene regulation, has further expanded our list of investigative tools. These tools include the iON expression switch for the precise control of timing and copy numbers of exogenous genes and TEMPO for investigating the temporal effects of genes. We also introduce the iGONAD method, an improved genome editing via oviductal nucleic acid delivery approach, as a novel genome-editing technique that has accelerated brain development exploration. These advanced in vivo electroporation methods are expected to provide valuable insights into pathological conditions associated with human brain disorders.
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Affiliation(s)
- Chen Yang
- Human Anatomy and Histology and Embryology, School of Basic Medicine, Harbin Medical University, Harbin 150081, China
- Department of Human Morphology, Okayama University Graduate School of Medicine, Density and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Atsunori Shitamukai
- Department of Human Morphology, Okayama University Graduate School of Medicine, Density and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Shucai Yang
- Human Anatomy and Histology and Embryology, School of Basic Medicine, Harbin Medical University, Harbin 150081, China
| | - Ayano Kawaguchi
- Department of Human Morphology, Okayama University Graduate School of Medicine, Density and Pharmaceutical Sciences, Okayama 700-8558, Japan
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18
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Kraft N, Muenz TS, Reinhard S, Werner C, Sauer M, Groh C, Rössler W. Expansion microscopy in honeybee brains for high-resolution neuroanatomical analyses in social insects. Cell Tissue Res 2023; 393:489-506. [PMID: 37421435 PMCID: PMC10484815 DOI: 10.1007/s00441-023-03803-4] [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] [Received: 01/27/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
The diffraction limit of light microscopy poses a problem that is frequently faced in structural analyses of social insect brains. With the introduction of expansion microscopy (ExM), a tool became available to overcome this limitation by isotropic physical expansion of preserved specimens. Our analyses focus on synaptic microcircuits (microglomeruli, MG) in the mushroom body (MB) of social insects, high-order brain centers for sensory integration, learning, and memory. MG undergo significant structural reorganizations with age, sensory experience, and during long-term memory formation. However, the changes in subcellular architecture involved in this plasticity have only partially been accessed yet. Using the western honeybee Apis mellifera as an experimental model, we established ExM for the first time in a social insect species and applied it to investigate plasticity in synaptic microcircuits within MG of the MB calyces. Using combinations of antibody staining and neuronal tracing, we demonstrate that this technique enables quantitative and qualitative analyses of structural neuronal plasticity at high resolution in a social insect brain.
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Affiliation(s)
- Nadine Kraft
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany.
| | - Thomas S Muenz
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Sebastian Reinhard
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Christian Werner
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Claudia Groh
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Wolfgang Rössler
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
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19
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Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
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Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
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20
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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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21
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Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, Jiang S. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology. Nat Commun 2023; 14:4013. [PMID: 37419873 PMCID: PMC10329015 DOI: 10.1038/s41467-023-39616-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.
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Affiliation(s)
- Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - John-Paul Oliveria
- Department of Translational Medicine, Genentech, Inc., South San Francisco, CA, USA
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bryan J Cannon
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Darci Phillips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Christian M Schürch
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Samuel M Naik
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael B Miller
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Xavier Rovira-Clavé
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA.
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22
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Tang M, Han Y, Jia D, Yang Q, Cheng JX. Far-field super-resolution chemical microscopy. LIGHT, SCIENCE & APPLICATIONS 2023; 12:137. [PMID: 37277396 DOI: 10.1038/s41377-023-01182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Abstract
Far-field chemical microscopy providing molecular electronic or vibrational fingerprint information opens a new window for the study of three-dimensional biological, material, and chemical systems. Chemical microscopy provides a nondestructive way of chemical identification without exterior labels. However, the diffraction limit of optics hindered it from discovering more details under the resolution limit. Recent development of super-resolution techniques gives enlightenment to open this door behind far-field chemical microscopy. Here, we review recent advances that have pushed the boundary of far-field chemical microscopy in terms of spatial resolution. We further highlight applications in biomedical research, material characterization, environmental study, cultural heritage conservation, and integrated chip inspection.
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Affiliation(s)
- Mingwei Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou, 311100, China
| | - Yubing Han
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Danchen Jia
- Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Photonics Center, Boston University, Boston, MA, 02459, USA
| | - Qing Yang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou, 311100, China
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Department of Electrical and Computer Engineering, Photonics Center, Boston University, Boston, MA, 02459, USA.
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23
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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: 25] [Impact Index Per Article: 25.0] [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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24
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Al Mahbuba D, Masuko S, Wang S, Syangtan D, Kang JS, Song Y, Shin TW, Xia K, Zhang F, Linhardt RJ, Boyden ES, Kiessling LL. Dynamic Changes in Heparan Sulfate Nanostructure in Human Pluripotent Stem Cell Differentiation. ACS NANO 2023; 17:7207-7218. [PMID: 37042659 DOI: 10.1021/acsnano.2c10072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Heparan sulfate (HS) is a heterogeneous, cell-surface polysaccharide critical for transducing signals essential for mammalian development. Imaging of signaling proteins has revealed how their localization influences their information transfer. In contrast, the contribution of the spatial distribution and nanostructure of information-rich, signaling polysaccharides like HS is not known. Using expansion microscopy (ExM), we found striking changes in HS nanostructure occur as human pluripotent stem (hPS) cells differentiate, and these changes correlate with growth factor signaling. Our imaging studies show that undifferentiated hPS cells are densely coated with HS displayed as hair-like protrusions. This ultrastructure can recruit fibroblast growth factor for signaling. When the hPS cells differentiate into the ectoderm lineage, HS is localized into dispersed puncta. This striking change in HS distribution coincides with a decrease in fibroblast growth factor binding to neural cells. While developmental variations in HS sequence were thought to be the primary driver of alterations in HS-mediated growth factor signaling, our high-resolution images indicate a role for the HS nanostructure. Our study highlights the utility of high-resolution glycan imaging using ExM. In the case of HS, we found that changes in how the polysaccharide is displayed link to profound differences in growth factor binding.
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Affiliation(s)
- Deena Al Mahbuba
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sayaka Masuko
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shiwei Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- McGovern Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
| | - Deepsing Syangtan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeong Seuk Kang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02139, United States
| | - Yuefan Song
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Tay Won Shin
- Media Arts and Sciences, MIT, Cambridge, Massachusetts 02139, United States
| | - Ke Xia
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Fuming Zhang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Edward S Boyden
- McGovern Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
- Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts 02139, United States
- Media Arts and Sciences, MIT, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
- Koch Institute, MIT, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
- Centers for Neurobiological Engineering and Extreme Bionics, MIT, Cambridge, Massachusetts 02139, United States
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Koch Institute, MIT, Cambridge, Massachusetts 02139, United States
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25
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Zhuo Y, Fu B, Peng R, Ma C, Xie S, Qiu L. Aptamer-based expansion microscopy platform enables signal-amplified imaging of dendritic spines. Talanta 2023; 260:124541. [PMID: 37087946 DOI: 10.1016/j.talanta.2023.124541] [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: 03/07/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/25/2023]
Abstract
Super-resolution imaging of dendritic spines (DS) can provide valuable information for mechanistic studies related to synaptic physiology and neural plasticity, but challenged by their small dimension (50-200 nm) below the spatial resolution of conventional optical microscopes. In this work, by combining the molecular recognition specificity of aptamer with high programmability of DNA nanotechnology, we developed an expansion microscopy (ExM) platform for imaging DS with enhanced spatial resolution and amplified signal output. Our results demonstrated that the aptamer probe could specifically bind to DS of primary hippocampal neurons. With physical expansion, the DS structure could be effectively enlarged by 4-5 folds, leading to the generation of more structural information. Meantime, the aptamer binding signal could be readily amplified by the introduction of DNA signal amplification strategy, overcoming the drawback of fluorescence dilution during the ExM treatment. This platform enabled evaluation of ischemia-induced early stroke based on the morphological change of DS, highlighting a promising avenue for studying nanoscale structures in biological systems.
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Affiliation(s)
- Yuting Zhuo
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Bo Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Ruizi Peng
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Changbei Ma
- School of Life Sciences, Central South University, China
| | - Sitao Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China; Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
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26
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Chau TH, Chernykh A, Kawahara R, Thaysen-Andersen M. Critical considerations in N-glycoproteomics. Curr Opin Chem Biol 2023; 73:102272. [PMID: 36758418 DOI: 10.1016/j.cbpa.2023.102272] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023]
Abstract
N-Glycoproteomics, the system-wide study of glycans asparagine-linked to protein carriers, holds a unique and still largely untapped potential to provide deep insights into the complexity and dynamics of the heterogeneous N-glycoproteome. Despite the advent of innovative analytical and informatics tools aiding the analysis, N-glycoproteomics remains challenging and consequently largely restricted to specialised laboratories. Aiming to stimulate discussions of method harmonisation, data standardisation and reporting guidelines to make N-glycoproteomics more reproducible and accessible to the community, we here discuss critical considerations related to the design and execution of N-glycoproteomics experiments and highlight good practices in N-glycopeptide data collection, analysis, interpretation and sharing. Giving the rapid maturation and, expectedly, a wide-spread implementation of N-glycoproteomics capabilities across the community in future years, this piece aims to point out common pitfalls, to encourage good data sharing and documentation practices, and to highlight practical solutions and strategies to enhance the insight into the N-glycoproteome.
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Affiliation(s)
- The Huong Chau
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Anastasia Chernykh
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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27
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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: 0] [Impact Index Per Article: 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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28
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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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29
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Jin GQ, Wang JX, Lu J, Zhang H, Yao Y, Ning Y, Lu H, Gao S, Zhang JL. Two birds one stone: β-fluoropyrrolyl-cysteine S NAr chemistry enabling functional porphyrin bioconjugation. Chem Sci 2023; 14:2070-2081. [PMID: 36845938 PMCID: PMC9944650 DOI: 10.1039/d2sc06209g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Bioconjugation, a synthetic tool that endows small molecules with biocompatibility and target specificity through covalent attachment of a biomolecule, holds promise for next-generation diagnosis or therapy. Besides the establishment of chemical bonding, such chemical modification concurrently allows alteration of the physicochemical properties of small molecules, but this has been paid less attention in designing novel bioconjugates. Here, we report a "two birds one stone" methodology for irreversible porphyrin bioconjugation based on β-fluoropyrrolyl-cysteine SNAr chemistry, in which the β-fluorine of porphyrin is selectively replaced by a cysteine in either peptides or proteins to generate novel β-peptidyl/proteic porphyrins. Notably, due to the distinct electronic nature between fluorine and sulfur, such replacement makes the Q band red-shift to the near-infrared region (NIR, >700 nm). This facilitates intersystem crossing (ISC) to enhance the triplet population and thus singlet oxygen production. This new methodology features water tolerance, a fast reaction time (15 min), good chemo-selectivity, and broad substrate scope, including various peptides and proteins under mild conditions. To demonstrate its potential, we applied porphyrin β-bioconjugates in several scenarios, including (1) cytosolic delivery of functional proteins, (2) metabolic glycan labeling, (3) caspase-3 detection, and (4) tumor-targeting phototheranostics.
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Affiliation(s)
- Guo-Qing Jin
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Jing-Xiang Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Jianhua Lu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Hang Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Yuhang Yao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Yingying Ning
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Song Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China .,Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China.,Spin-X Institute, School of Chemistry and Chemical Engineering, State Key Laboratory of Luminescent Materials and Devices, Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, South China University of Technology Guangzhou 510641 China
| | - Jun-Long Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China .,Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
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30
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Nonaka H, Mino T, Sakamoto S, Oh JH, Watanabe Y, Ishikawa M, Tsushima A, Amaike K, Kiyonaka S, Tamura T, Aricescu AR, Kakegawa W, Miura E, Yuzaki M, Hamachi I. Revisiting PFA-mediated tissue fixation chemistry: FixEL enables trapping of small molecules in the brain to visualize their distribution changes. Chem 2023; 9:523-540. [PMID: 38094901 PMCID: PMC7615374 DOI: 10.1016/j.chempr.2022.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Various small molecules have been used as functional probes for tissue imaging in medical diagnosis and pharmaceutical drugs for disease treatment. The spatial distribution, target selectivity, and diffusion/excretion kinetics of small molecules in structurally complicated specimens are critical for function. However, robust methods for precisely evaluating these parameters in the brain have been limited. Herein, we report a new method termed "fixation-driven chemical cross-linking of exogenous ligands (FixEL)," which traps and images exogenously administered molecules of interest (MOIs) in complex tissues. This method relies on protein-MOI interactions and chemical cross-linking of amine-tethered MOI with paraformaldehyde used for perfusion fixation. FixEL is used to obtain images of the distribution of the small molecules, which addresses selective/nonselective binding to proteins, time-dependent localization changes, and diffusion/retention kinetics of MOIs such as the scaffold of PET tracer derivatives or drug-like small molecules.
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Affiliation(s)
- Hiroshi Nonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Jae Hoon Oh
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Yu Watanabe
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Mamoru Ishikawa
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - Akihiro Tsushima
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Kazuma Amaike
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Shigeki Kiyonaka
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
| | - A. Radu Aricescu
- Division of Structural Biology, University of Oxford, Oxford OX3 7BN, UK
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Wataru Kakegawa
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
- Department of Neurophysiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Eriko Miura
- Department of Neurophysiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Michisuke Yuzaki
- Department of Neurophysiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Tokyo 102-0075, Japan
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31
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Xia L, Chen M, Dong C, Liu F, Huang H, Feng W, Chen Y. Spatiotemporal Ultrasound-Driven Bioorthogonal Catalytic Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2209179. [PMID: 36529698 DOI: 10.1002/adma.202209179] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/15/2022] [Indexed: 06/17/2023]
Abstract
Bioorthogonal chemistry, referring to the rapid and selective synthesis of imaging and/or therapeutic molecules in live animals via transition metal-mediated non-natural chemical transformation without disrupting endogenous reactions, has greatly expanded the tools and techniques for biomedicine. However, owing to safety concerns associated with metal toxicity, selectivity, sensitivity and stability, efficient bioorthogonal reactions that can be reliably executed in complex biological environments remain challenging. In this study, an intelligent, versatile bioorthogonal catalyst based on ultrasmall poly(acrylic acid)-modified copper nanocomplexes (Cu@PAA NCs) to achieve high spatiotemporal catalytic efficacy is established. The catalytic activity of the Cu@PAA NCs can be reversibly regulated via valence state interconversion between Cu(II) and Cu(I) under exogenous ultrasound irradiation, promoting off-target prodrug activation in lesion sites through the Cu(I)-catalyzed azide-alkyne cycloaddition reaction. Moreover, ultrasound-triggered electron-hole separation endows the Cu@PAA NCs with robust sonosensitizing ability for sonodynamic therapy. Furthermore, the Cu@PAA NCs exhibit enhanced contrast in magnetic resonance and photoacoustic imaging. Notably, the renal-clearable Cu@PAA NCs exhibit intrinsically benign biocompatibility. This spatiotemporally ultrasound-mediated bioorthogonal catalysis not only expands the repertoire of in situ therapeutic agents but also provides a new avenue for disease theranostics.
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Affiliation(s)
- Lili Xia
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Meng Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Caihong Dong
- Department of Ultrasound, Zhongshan Hospital, Fudan University, and Shanghai Institute of Medical Imaging, Shanghai, 200032, China
| | - Feipeng Liu
- Shaanxi Key Laboratory of Flexible Electronics, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Hui Huang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Wei Feng
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Yu Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, China
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32
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Affiliation(s)
- Sven Truckenbrodt
- Convergent Research, E11 Bio. 1600 Harbor Bay Parkway, Alameda, California94502, United States
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33
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He Y, Yao Y, He Y, Huang Z, Luo F, Zhang C, Qi D, Jia T, Wang Z, Sun Z, Yuan X, Zhang S. Surpassing the resolution limitation of structured illumination microscopy by an untrained neural network. BIOMEDICAL OPTICS EXPRESS 2023; 14:106-117. [PMID: 36698670 PMCID: PMC9842007 DOI: 10.1364/boe.479621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Structured illumination microscopy (SIM), as a flexible tool, has been widely applied to observing subcellular dynamics in live cells. It is noted, however, that SIM still encounters a problem with theoretical resolution limitation being only twice over wide-field microscopy, where imaging of finer biological structures and dynamics are significantly constrained. To surpass the resolution limitation of SIM, we developed an image postprocessing method to further improve the lateral resolution of SIM by an untrained neural network, i.e., deep resolution-enhanced SIM (DRE-SIM). DRE-SIM can further extend the spatial frequency components of SIM by employing the implicit priors based on the neural network without training datasets. The further super-resolution capability of DRE-SIM is verified by theoretical simulations as well as experimental measurements. Our experimental results show that DRE-SIM can achieve the resolution enhancement by a factor of about 1.4 compared with conventional SIM. Given the advantages of improving the lateral resolution while keeping the imaging speed, DRE-SIM will have a wide range of applications in biomedical imaging, especially when high-speed imaging mechanisms are integrated into the conventional SIM system.
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Affiliation(s)
- Yu He
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- Contributed equally
| | - Yunhua Yao
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- Contributed equally
| | - Yilin He
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Zhengqi Huang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Fan Luo
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, China
| | - Chonglei Zhang
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, China
| | - Dalong Qi
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Tianqing Jia
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Zhiyong Wang
- School of Mathematical Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Xiaocong Yuan
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, China
| | - Shian Zhang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, China
- Collaborative Innovation Center of Light Manipulations and Applications, Shandong Normal University, Jinan 250358, China
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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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Wang M, Wang WX. Meeting Zn Needs during Medaka Eye Development: Nanoscale Visualization of Retina by Expansion Microscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15780-15790. [PMID: 36266765 DOI: 10.1021/acs.est.2c06479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fish eyes require high Zn levels to support their early development. Although numerous studies have been conducted on the nutritional and toxic effects of Zn on the eye, the Zn requirement for retinal cell development is still debatable. Moreover, due to the complexity of the retinal structure, it is difficult to clearly visualize each retinal layer and accurately separate cell morphology in vivo by conventional methods. In the present study, we for the first time have achieved nanoscale imaging of retinal anatomy affected by dietary and waterborne Zn exposure by novel expansion microscopy. We demonstrated that the fish retina showed different developmental strategies in response to dietary and aqueous Zn exposures. Excess dietary Zn produced toxicity to retinal photoreceptor cells, resulting in a reduction in cell number and cell area, and this toxicity became severe with biological development. In contrast, waterborne Zn in the natural environment probably failed to meet the Zn requirements of retinal development. Overall, our results indicated that during early development, the Zn requirement of the fish eyes was sensitive, and oversupplementation led to impaired photoreceptor cell development. Our study has provided new perspectives using the powerful and novel expansion microscopy technique in toxicity assessment, enabling ultra-clear visualization of small but complex organ development.
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Affiliation(s)
- Mengyu Wang
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 518057, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 518057, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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36
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Shan Z, Ding L, Zhu C, Sun R, Hong W. Medical care of rare and undiagnosed diseases: Prospects and challenges. FUNDAMENTAL RESEARCH 2022; 2:851-858. [PMID: 38933390 PMCID: PMC11197738 DOI: 10.1016/j.fmre.2022.08.018] [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: 06/28/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
Rare and undiagnosed diseases tend to be diverse, misdiagnosed, and difficult to diagnose. In some cases, the disease is progressive and life-threatening. Yet, to date, an estimated 95% of rare diseases have no approved therapy. Therefore, rare and undiagnosed diseases are considered the ultimate challenges for understanding human diseases. Here, we review the research progress, research frontiers, and important scientific issues related to rare and undiagnosed diseases. We mainly focus on five topics: (1) the identification and functional analysis of disease-causing genes; (2) the construction of cells, organoids, and animal models for mechanism validation; (3) subtyping and diagnosis; (4) treatment and drug screening based on causative genes and mutations; and (5) new technologies and methods for studying rare and undiagnosed diseases. In this review, we briefly update and discuss the pathogenic mechanisms and precision medicine for rare and undiagnosed diseases.
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Affiliation(s)
- Zhiyan Shan
- Department of Health Sciences, National Natural Science Foundation of China, Beijing 100085, China
- Department of Histology and Embryology, Harbin Medical University, Harbin 150081, China
| | - Lijun Ding
- Department of Health Sciences, National Natural Science Foundation of China, Beijing 100085, China
- Center for Reproductive Medicine and Obstetrics and Gynecology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Caiyun Zhu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Ruijuan Sun
- Department of Health Sciences, National Natural Science Foundation of China, Beijing 100085, China
| | - Wei Hong
- Department of Health Sciences, National Natural Science Foundation of China, Beijing 100085, China
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37
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Abstract
Membranes are multifunctional supramolecular assemblies that encapsulate our cells and the organelles within them. Glycerophospholipids are the most abundant component of membranes. They make up the majority of the lipid bilayer and play both structural and functional roles. Each organelle has a different phospholipid composition critical for its function that results from dynamic interplay and regulation of numerous lipid-metabolizing enzymes and lipid transporters. Because lipid structures and localizations are not directly genetically encoded, chemistry has much to offer to the world of lipid biology in the form of precision tools for visualizing lipid localization and abundance, manipulating lipid composition, and in general decoding the functions of lipids in cells.In this Account, we provide an overview of our recent efforts in this space focused on two overarching and complementary goals: imaging and editing the phospholipidome. On the imaging front, we have harnessed the power of bioorthogonal chemistry to develop fluorescent reporters of specific lipid pathways. Substantial efforts have centered on phospholipase D (PLD) signaling, which generates the humble lipid phosphatidic acid (PA) that acts variably as a biosynthetic intermediate and signaling agent. Though PLD is a hydrolase that generates PA from abundant phosphatidylcholine (PC) lipids, we have exploited its transphosphatidylation activity with exogenous clickable alcohols followed by bioorthogonal tagging to generate fluorescent lipid reporters of PLD signaling in a set of methods termed IMPACT.IMPACT and its variants have facilitated many biological discoveries. Using the rapid and fluorogenic tetrazine ligation, it has revealed the spatiotemporal dynamics of disease-relevant G protein-coupled receptor signaling and interorganelle lipid transport. IMPACT using diazirine photo-cross-linkers has enabled identification of lipid-protein interactions relevant to alcohol-related diseases. Varying the alcohol reporter can allow for organelle-selective labeling, and varying the bioorthogonal detection reagent can afford super-resolution lipid imaging via expansion microscopy. Combination of IMPACT with genome-wide CRISPR screening has revealed genes that regulate physiological PLD signaling.PLD enzymes themselves can also act as tools for precision editing of the phospholipid content of membranes. An optogenetic PLD for conditional blue-light-stimulated synthesis of PA on defined organelle compartments led to the discovery of the role of organelle-specific pools of PA in regulating oncogenic Hippo signaling. Directed enzyme evolution of PLD, enabled by IMPACT, has yielded highly active superPLDs with broad substrate tolerance and an ability to edit membrane phospholipid content and synthesize designer phospholipids in vitro. Finally, azobenzene-containing PA analogues represent an alternative, all-chemical strategy for light-mediated control of PA signaling.Collectively, the strategies described here summarize our progress to date in tackling the challenge of assigning precise functions to defined pools of phospholipids in cells. They also point to new challenges and directions for future study, including extension of imaging and membrane editing tools to other classes of lipids. We envision that continued application of bioorthogonal chemistry, optogenetics, and directed evolution will yield new tools and discoveries to interrogate the phospholipidome and reveal new mechanisms regulating phospholipid homeostasis and roles for phospholipids in cell signaling.
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Affiliation(s)
- Din-Chi Chiu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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38
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Abstract
Strategies to visualize cellular membranes with light microscopy are restricted by the diffraction limit of light, which far exceeds the dimensions of lipid bilayers. Here, we describe a method for super-resolution imaging of metabolically labeled phospholipids within cellular membranes. Guided by the principles of expansion microscopy, we develop an all-small molecule approach that enables direct chemical anchoring of bioorthogonally labeled phospholipids into a hydrogel network and is capable of super-resolution imaging of cellular membranes. We apply this method, termed lipid expansion microscopy (LExM), to visualize organelle membranes with precision, including a unique class of membrane-bound structures known as nuclear invaginations. Compatible with standard confocal microscopes, LExM will be widely applicable for super-resolution imaging of phospholipids and cellular membranes in numerous physiological contexts.
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Affiliation(s)
- Brittany M White
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Pratik Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, United States
| | - Amanda N Conwell
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kane Wu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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Jin G, Sun D, Xia X, Jiang Z, Cheng B, Ning Y, Wang F, Zhao Y, Chen X, Zhang J. Bioorthogonal Lanthanide Molecular Probes for Near‐Infrared Fluorescence and Mass Spectrometry Imaging. Angew Chem Int Ed Engl 2022; 61:e202208707. [DOI: 10.1002/anie.202208707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Guo‐Qing Jin
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
| | - De‐en Sun
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 P. R. China
| | - Xiaoqian Xia
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 P. R. China
| | - Zhi‐Fan Jiang
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 P. R. China
| | - Yingying Ning
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences CAS Research/Education Center for Excellence in Molecular Sciences National Centre for Mass Spectrometry in Beijing CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences CAS Research/Education Center for Excellence in Molecular Sciences National Centre for Mass Spectrometry in Beijing CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Xing Chen
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Synthetic and Functional Biomolecules Center Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 P. R. China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 P. R. China
| | - Jun‐Long Zhang
- College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 P. R. China
- Chemistry and Chemical Engineering Guangdong Laboratory Shantou 515031 P. R. China
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40
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Jin GQ, Sun DE, Xia X, Jiang ZF, Cheng B, Ning Y, Wang F, Zhao Y, Chen X, Zhang JL. Bioorthogonal Lanthanide Molecular Probes for Near‐Infrared Fluorescence and Mass Spectrometry Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Guo-Qing Jin
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - De-en Sun
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Xiaoqian Xia
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Zhi-Fan Jiang
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Bo Cheng
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Yingying Ning
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Fuyi Wang
- Institute of Chemistry Chinese Academy of Sciences Beijing National Laboratory for Molecular Sciences CHINA
| | - Yao Zhao
- Institute of Chemistry Chinese Academy of Sciences Beijing National Laboratory for Molecular Sciences CHINA
| | - Xing Chen
- Peking University College of Chemistry and Molecular Engineering CHINA
| | - Jun-Long Zhang
- Peking University College of Chemistry and Molecular Engineering Chengfu Road 202 100871 Beijing CHINA
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41
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Sherry DM, Stiles MA. Improved Fluorescent Signal in Expansion Microscopy Using Fluorescent Fab Fragment Secondary Antibodies. MethodsX 2022; 9:101796. [PMID: 36042811 PMCID: PMC9420380 DOI: 10.1016/j.mex.2022.101796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Expansion microscopy (ExM) is a microscopic imaging approach that can achieve super-resolution visualization of fluorescently labeled biological samples using conventional fluorescence microscopy. The method is based on embedding of a fluorescently labeled biological sample in a hydrogel matrix followed by the physical expansion of the specimen, which is then viewed using a conventional fluorescent microscope. Variations of the method can be used to visualize endogenously expressed fluorescent proteins, such as GFP, fluorescently tagged antibodies, nucleic acids, or other fluorescently tagged molecules. A significant challenge of the method is that the physical expansion of the specimen produces a concommitant reduction in fluorescence intensity, which can make imaging difficult. We describe an approach for amplifying fluorescence signal following expansion of immunolabeled tissue sections by applying fluorescently labeled Fab fragment secondary antibodies to intensify fluorescent signal and enhance detection of labeling using conventional fluorescent microscopy. A method to increase immunofluorescence signal intensity of Expansion Microscopy specimens is described. Method utilizes commercially available reagents. Enhances ability to acquire useful images in expanded tissue samples.
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42
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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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43
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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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44
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Wu L, Liu L, Xu B, Huang D, Chen XW. In vitro and in vivo assay of the ER lipid scramblase TMEM41B. STAR Protoc 2022; 3:101333. [PMID: 35496801 PMCID: PMC9043772 DOI: 10.1016/j.xpro.2022.101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lingzhi Wu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Lu Liu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Bolin Xu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Dong Huang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Xiao-Wei Chen
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Corresponding author
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45
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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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46
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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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47
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Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy. Nat Biotechnol 2022; 40:606-617. [PMID: 34782739 DOI: 10.1038/s41587-021-01092-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/10/2021] [Indexed: 02/07/2023]
Abstract
A main determinant of the spatial resolution of live-cell super-resolution (SR) microscopes is the maximum photon flux that can be collected. To further increase the effective resolution for a given photon flux, we take advantage of a priori knowledge about the sparsity and continuity of biological structures to develop a deconvolution algorithm that increases the resolution of SR microscopes nearly twofold. Our method, sparse structured illumination microscopy (Sparse-SIM), achieves ~60-nm resolution at a frame rate of up to 564 Hz, allowing it to resolve intricate structures, including small vesicular fusion pores, ring-shaped nuclear pores formed by nucleoporins and relative movements of inner and outer mitochondrial membranes in live cells. Sparse deconvolution can also be used to increase the three-dimensional resolution of spinning-disc confocal-based SIM, even at low signal-to-noise ratios, which allows four-color, three-dimensional live-cell SR imaging at ~90-nm resolution. Overall, sparse deconvolution will be useful to increase the spatiotemporal resolution of live-cell fluorescence microscopy.
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48
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Wang Z, Wei L, Zeng L, Feng N, Chen J, Chen Y. Click Chemistry-Mediated Particle Counting Sensing via Cu(II)-Polyglutamic Acid Coordination Chemistry and Enzymatic Reaction. Anal Chem 2022; 94:5293-5300. [PMID: 35319873 DOI: 10.1021/acs.analchem.1c05127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An electrical resistance-based particle counter (ERPC) with simple operation and high resolution has proved to be a promising biosensing toolkit, whereas amplification-free ERPC biosensors are incapable of analyzing trace small molecules due to their relatively low sensitivity. In this work, click chemistry-mediated particle counting sensing of small-molecule hazards in food samples with high sensitivity was developed. In this strategy, unbound alkyne-functionalized polystyrene microspheres were collected by magnetic separation from the copper-ion-mediated click reaction between alkyne-functionalized polystyrene microspheres and azido-functionalized magnetic beads, which could be used as signal probes for the readout. This click chemistry-mediated ERPC biosensor converts the detection of targets to the quantification of copper ions or ascorbic acid by performing competitive immunoassay-based coordination chemistry and enzymatic reaction, respectively. The sensitivity of the ERPC biosensor has been improved by an order of magnitude due to the signal amplification effects of click chemistry, coordination adsorption, and enzyme catalysis. Furthermore, because of the efficient separation and enrichment of immunomagnetic beads and the robustness of click chemistry, the interference from food matrixes and immunoassay is effectively reduced, and thus, our strategy is exceedingly suitable for detecting trace targets in complex samples.
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Affiliation(s)
- Zhilong Wang
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Shizishan Street, Hongshan District, Wuhan 430070, China
| | - Luyu Wei
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Shizishan Street, Hongshan District, Wuhan 430070, China
| | - Lingwen Zeng
- Wuhan Zhongke Zhikang Biological Technology Co., Ltd., Gaoxin Avenue, East Lake High-tech Zone, Wuhan 430074, China
| | - Niu Feng
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Shizishan Street, Hongshan District, Wuhan 430070, China
| | - Jianjun Chen
- Wuhan Shangcheng Biotechnology Co., Ltd., Gaoxin Avenue, East Lake New Technology Development Zone, Wuhan 430063, China
| | - Yiping Chen
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Ministry of Education, Shizishan Street, Hongshan District, Wuhan 430070, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Pengfei Road, Dapeng District, Shenzhen 518120, China
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49
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Wang W, Wang S. Cell-based biocomposite engineering directed by polymers. LAB ON A CHIP 2022; 22:1042-1067. [PMID: 35244136 DOI: 10.1039/d2lc00067a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biological cells such as bacterial, fungal, and mammalian cells always exploit sophisticated chemistries and exquisite micro- and nano-structures to execute life activities, providing numerous templates for engineering bioactive and biomorphic materials, devices, and systems. To transform biological cells into functional biocomposites, polymer-directed cell surface engineering and intracellular functionalization have been developed over the past two decades. Polymeric materials can be easily adopted by various cells through polymer grafting or in situ hydrogelation and can successfully bridge cells with other functional materials as interfacial layers, thus achieving the manufacture of advanced biocomposites through bioaugmentation of living cells and transformation of cells into templated materials. This review article summarizes the recent progress in the design and construction of cell-based biocomposites by polymer-directed strategies. Furthermore, the applications of cell-based biocomposites in broad fields such as cell research, biomedicine, and bioenergy are discussed. Last, we provide personal perspectives on challenges and future trends in this interdisciplinary area.
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Affiliation(s)
- Wenshuo Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
| | - Shutao Wang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, CAS Center for Excellence in Nanoscience, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
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50
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Cheng B, Wan Y, Tang Q, Du Y, Xu F, Huang Z, Qin W, Chen X. A Photocaged Azidosugar for
Light‐Controlled
Metabolic Labeling of
Cell‐Surface
Sialoglycans. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bo Cheng
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Yi Wan
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Qi Tang
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Yifei Du
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Feiyang Xu
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
| | - Zhimin Huang
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Wei Qin
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
| | - Xing Chen
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing 100871 China
- Synthetic and Functional Biomolecules Center Peking University Beijing 100871 China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
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