1
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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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2
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Lin J, Mehra D, Marin Z, Wang X, Borges HM, Shen Q, Gałecki S, Haug J, Dean KM. Mechanically Sheared Axially Swept Light-Sheet Microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588892. [PMID: 38645073 PMCID: PMC11030395 DOI: 10.1101/2024.04.10.588892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
We present a mechanically sheared image acquisition format for upright and open-top light-sheet microscopes that automatically places data in its proper spatial context. This approach, which reduces computational post-processing and eliminates unnecessary interpolation or duplication of the data, is demonstrated on an upright variant of Axially Swept Light-Sheet Microscopy (ASLM) that achieves a field of view, measuring 774 x 435 microns, that is 3.2-fold larger than previous models and a raw and isotropic resolution of ∼420 nm. Combined, we demonstrate the power of this approach by imaging sub-diffraction beads, cleared biological tissues, and expanded specimens.
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3
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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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4
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Woodworth MA, Lakadamyali M. Toward a comprehensive view of gene architecture during transcription. Curr Opin Genet Dev 2024; 85:102154. [PMID: 38309073 PMCID: PMC10989512 DOI: 10.1016/j.gde.2024.102154] [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: 08/31/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
The activation of genes within the nucleus of eukaryotic cells is a tightly regulated process, orchestrated by a complex interplay of various physical properties and interacting factors. Studying the multitude of components and features that collectively contribute to gene activation has proven challenging due to the complexities of simultaneously visualizing the dynamic and transiently interacting elements that coalesce within the small space occupied by each individual gene. However, various labeling and imaging advances are now starting to overcome this challenge, enabling visualization of gene activation at different lengths and timescales. In this review, we aim to highlight these microscopy-based advances and suggest how they can be combined to provide a comprehensive view of the mechanisms regulating gene activation.
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Affiliation(s)
- Marcus A Woodworth
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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5
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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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6
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Sakamoto DM, Tamura I, Yi B, Hasegawa S, Saito Y, Yamada N, Takakusagi Y, Kubota SI, Kobayashi M, Harada H, Hanaoka K, Taki M, Nangaku M, Tainaka K, Sando S. Whole-Body and Whole-Organ 3D Imaging of Hypoxia Using an Activatable Covalent Fluorescent Probe Compatible with Tissue Clearing. ACS NANO 2024; 18:5167-5179. [PMID: 38301048 DOI: 10.1021/acsnano.3c12716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Elucidation of biological phenomena requires imaging of microenvironments in vivo. Although the seamless visualization of in vivo hypoxia from the level of whole-body to single-cell has great potential to discover unknown phenomena in biological and medical fields, no methodology for achieving it has been established thus far. Here, we report the whole-body and whole-organ imaging of hypoxia, an important microenvironment, at single-cell resolution using activatable covalent fluorescent probes compatible with tissue clearing. We initially focused on overcoming the incompatibility of fluorescent dyes and refractive index matching solutions (RIMSs), which has greatly hindered the development of fluorescent molecular probes in the field of tissue clearing. The fluorescent dyes compatible with RIMS were then incorporated into the development of activatable covalent fluorescent probes for hypoxia. We combined the probes with tissue clearing, achieving comprehensive single-cell-resolution imaging of hypoxia in a whole mouse body and whole organs.
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Affiliation(s)
- Daichi M Sakamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Iori Tamura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Bo Yi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Sho Hasegawa
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Yutaro Saito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Naoki Yamada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoichi Takakusagi
- Quantum Hyperpolarized MRI Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba-city 263-8555, Japan
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba-city 263-8555, Japan
| | - Shimpei I Kubota
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo, Hokkaido 060-0815, Japan
| | - Minoru Kobayashi
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Genome Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Harada
- Laboratory of Cancer Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Genome Dynamics, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenjiro Hanaoka
- Division of Analytical Chemistry for Drug Discovery, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules, Nagoya University, Furo, Chikusa, Nagoya 464-8601, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata 951-8585, Japan
- Gftd DeSci, Gftd DAO, Nishikawa Building, 20 Kikuicho, Shinjuku-ku, Tokyo 162-0044, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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7
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Hu K, Sun Q, Chen R, Xu T, Li Y, Chen L, Wang A, Qi H, Shao D, Yue H, Wang Y, Tang Z, Wang Y, Liu C, Lv H, Wang F, Xu H. Expanding the toolset of fluorescent covalent staining of biological samples by labeling carboxylate and phosphate groups. JOURNAL OF BIOPHOTONICS 2023; 16:e202300027. [PMID: 37644491 DOI: 10.1002/jbio.202300027] [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: 01/26/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Recently, fluorescent covalent staining methods have been developed for visualization of anatomical structures in cells and tissues. Coupled with expansion microscopy, these stains revealed various ultrastructural details. However, the covalently stainable chemical groups have been limited to amines, carbohydrates, and thiols. Here, we developed procedures for covalently labeling tissues for carboxylate and phosphate groups, utilizing carbodiimide crosslinker chemistry. In porcine kidney tissues, the carboxylate and phosphate stain provides 1.8-4.8-fold higher signal intensity than those from the three existing stains. In cancer cells, such stain allows 2-8-fold more accurate identification of nucleoli than the amine stain. In expansion microscopy samples, such stain reveals a variety of sub-cellular structures in tissues when combined with the amine stain. Such stain also allows imaging of lipid-based structures in cultured cells. With these advantages, this new covalent staining method further expands the toolset for fluorescent visualization of histology.
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Affiliation(s)
- Kexin Hu
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Qimeng Sun
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Ruifen Chen
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tinghao Xu
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Yuncheng Li
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Lili Chen
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Aidong Wang
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hejing Qi
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Danni Shao
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Huanning Yue
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Yaning Wang
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Ziqi Tang
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Yi Wang
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Chunfeng Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haijun Lv
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Fen Wang
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Huizhong Xu
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
- Institute for Advanced Study, Soochow University, Suzhou, Jiangsu, China
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8
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Louvel V, Haase R, Mercey O, Laporte MH, Eloy T, Baudrier É, Fortun D, Soldati-Favre D, Hamel V, Guichard P. iU-ExM: nanoscopy of organelles and tissues with iterative ultrastructure expansion microscopy. Nat Commun 2023; 14:7893. [PMID: 38036510 PMCID: PMC10689735 DOI: 10.1038/s41467-023-43582-8] [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: 11/21/2022] [Accepted: 11/14/2023] [Indexed: 12/02/2023] Open
Abstract
Expansion microscopy (ExM) is a highly effective technique for super-resolution fluorescence microscopy that enables imaging of biological samples beyond the diffraction limit with conventional fluorescence microscopes. Despite the development of several enhanced protocols, ExM has not yet demonstrated the ability to achieve the precision of nanoscopy techniques such as Single Molecule Localization Microscopy (SMLM). Here, to address this limitation, we have developed an iterative ultrastructure expansion microscopy (iU-ExM) approach that achieves SMLM-level resolution. With iU-ExM, it is now possible to visualize the molecular architecture of gold-standard samples, such as the eight-fold symmetry of nuclear pores or the molecular organization of the conoid in Apicomplexa. With its wide-ranging applications, from isolated organelles to cells and tissue, iU-ExM opens new super-resolution avenues for scientists studying biological structures and functions.
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Affiliation(s)
- Vincent Louvel
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Romuald Haase
- Department of Microbiology and Molecular medicine, University of Geneva, Geneva, Switzerland
| | - Olivier Mercey
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Marine H Laporte
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Thibaut Eloy
- ICube - UMR7357, CNRS, University of Strasbourg, Strasbourg, France
| | - Étienne Baudrier
- ICube - UMR7357, CNRS, University of Strasbourg, Strasbourg, France
| | - Denis Fortun
- ICube - UMR7357, CNRS, University of Strasbourg, Strasbourg, France
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular medicine, University of Geneva, Geneva, Switzerland
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
| | - Paul Guichard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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9
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Sheard TMD, Shakespeare TB, Seehra RS, Spencer ME, Suen KM, Jayasinghe I. Differential labelling of human sub-cellular compartments with fluorescent dye esters and expansion microscopy. NANOSCALE 2023; 15:18489-18499. [PMID: 37942554 PMCID: PMC10667587 DOI: 10.1039/d3nr01129a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/07/2023] [Indexed: 11/10/2023]
Abstract
Amine-reactive esters of aromatic fluorescent dyes are emerging as imaging probes for nondescript staining of cellular and tissue architectures. We characterised the staining patterns of 14 fluorescent dye ester species with varying physical and spectral properties in the broadly studied human HeLa cell line. When combined with the super-resolution technique expansion microscopy (ExM) involving swellable acrylamide hydrogels, fluorescent esters reveal nanoscale features including cytoplasmic membrane-bound compartments and nucleolar densities. We observe differential labelling patterns linked to the biochemical properties of the conjugated dye. Alterations in staining density and compartment specificity were seen depending on the timepoint of application in the ExM protocol. Additional complexity in labelling patterns was detected arising from inter-ester interactions. Our findings raise a number of considerations for the use of fluorescent esters. We demonstrate esters as a useful addition to the repertoire of stains of the cellular proteome, whether applied either on their own to visualise overall cellular morphology, or as counterstains providing ultrastructural context alongside specific target markers like antibodies.
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Affiliation(s)
- Thomas M D Sheard
- School of Biosciences, Faculty of Science, University of Sheffield, Sheffield S10 2TN, UK.
| | - Tayla B Shakespeare
- School of Biosciences, Faculty of Science, University of Sheffield, Sheffield S10 2TN, UK.
| | - Rajpinder S Seehra
- School of Biosciences, Faculty of Science, University of Sheffield, Sheffield S10 2TN, UK.
| | - Michael E Spencer
- School of Biosciences, Faculty of Science, University of Sheffield, Sheffield S10 2TN, UK.
| | - Kin M Suen
- School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Izzy Jayasinghe
- School of Biosciences, Faculty of Science, University of Sheffield, Sheffield S10 2TN, UK.
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, Australia.
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10
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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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11
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Klena N, Maltinti G, Batman U, Pigino G, Guichard P, Hamel V. An In-depth Guide to the Ultrastructural Expansion Microscopy (U-ExM) of Chlamydomonas reinhardtii. Bio Protoc 2023; 13:e4792. [PMID: 37719077 PMCID: PMC10502176 DOI: 10.21769/bioprotoc.4792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 09/19/2023] Open
Abstract
Expansion microscopy is an innovative method that enables super-resolution imaging of biological materials using a simple confocal microscope. The principle of this method relies on the physical isotropic expansion of a biological specimen cross-linked to a swellable polymer, stained with antibodies, and imaged. Since its first development, several improved versions of expansion microscopy and adaptations for different types of samples have been produced. Here, we show the application of ultrastructure expansion microscopy (U-ExM) to investigate the 3D organization of the green algae Chlamydomonas reinhardtii cellular ultrastructure, with a particular emphasis on the different types of sample fixation that can be used, as well as compatible staining procedures including membranes. Graphical overview.
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Affiliation(s)
| | | | - Umut Batman
- Department of Molecular and Cellular Biology, Section of Biology, University of Geneva, Geneva, Switzerland
| | | | - Paul Guichard
- Department of Molecular and Cellular Biology, Section of Biology, University of Geneva, Geneva, Switzerland
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, Section of Biology, University of Geneva, Geneva, Switzerland
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12
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Michalska JM, Lyudchik J, Velicky P, Štefaničková H, Watson JF, Cenameri A, Sommer C, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas P, Danzl JG. Imaging brain tissue architecture across millimeter to nanometer scales. Nat Biotechnol 2023:10.1038/s41587-023-01911-8. [PMID: 37653226 DOI: 10.1038/s41587-023-01911-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 07/20/2023] [Indexed: 09/02/2023]
Abstract
Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.
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Affiliation(s)
- Julia M Michalska
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Julia Lyudchik
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Philipp Velicky
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Core Facility Imaging, Medical University of Vienna, Vienna, Austria
| | - Hana Štefaničková
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Jake F Watson
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Alban Cenameri
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Christoph Sommer
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Nicole Amberg
- Department of Neurology, Division of Neuropathology and Neurochemistry, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | | | - Karl Roessler
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Thomas Czech
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Romana Höftberger
- Department of Neurology, Division of Neuropathology and Neurochemistry, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Sandra Siegert
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Gaia Novarino
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Peter Jonas
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Johann G Danzl
- Institute of Science and Technology Austria, Klosterneuburg, Austria.
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13
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Borges H, Lin J, Marin Z, Dean KM. Quantitative Cleared Tissue Imaging. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2091-2092. [PMID: 37612944 DOI: 10.1093/micmic/ozad067.1082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Hazel Borges
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jinlong Lin
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zach Marin
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
- Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX, USA
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14
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Glaser A, Chandrashekar J, Vasquez J, Arshadi C, Ouellette N, Jiang X, Baka J, Kovacs G, Woodard M, Seshamani S, Cao K, Clack N, Recknagel A, Grim A, Balaram P, Turschak E, Liddell A, Rohde J, Hellevik A, Takasaki K, Barner LE, Logsdon M, Chronopoulos C, de Vries S, Ting J, Perlmutter S, Kalmbach B, Dembrow N, Reid RC, Feng D, Svoboda K. Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544277. [PMID: 37425699 PMCID: PMC10327101 DOI: 10.1101/2023.06.08.544277] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure of cells and tissues at sub-diffraction resolutions and near single molecule sensitivity, driving discoveries in diverse fields of biology, including neuroscience. Biological tissue is organized over scales of nanometers to centimeters. Harnessing molecular imaging across three-dimensional samples on this scale requires new types of microscopes with larger fields of view and working distance, as well as higher imaging throughput. We present a new expansion-assisted selective plane illumination microscope (ExA-SPIM) with diffraction-limited and aberration-free performance over a large field of view (85 mm 2 ) and working distance (35 mm). Combined with new tissue clearing and expansion methods, the microscope allows nanoscale imaging of centimeter-scale samples, including entire mouse brains, with diffraction-limited resolutions and high contrast without sectioning. We illustrate ExA-SPIM by reconstructing individual neurons across the mouse brain, imaging cortico-spinal neurons in the macaque motor cortex, and tracing axons in human white matter.
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15
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Luaces JP, Toro-Urrego N, Otero-Losada M, Capani F. What do we know about blood-testis barrier? current understanding of its structure and physiology. Front Cell Dev Biol 2023; 11:1114769. [PMID: 37397257 PMCID: PMC10307970 DOI: 10.3389/fcell.2023.1114769] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Blood-testis barrier (BTB) creates a particular compartment in the seminiferous epithelium. Contacting Sertoli cell-Sertoli cell plasma membranes possess specialized junction proteins which present a complex dynamic of formation and dismantling. Thus, these specialized structures facilitate germ cell movement across the BTB. Junctions are constantly rearranged during spermatogenesis while the BTB preserves its barrier function. Imaging methods are essential to studying the dynamic of this sophisticated structure in order to understand its functional morphology. Isolated Sertoli cell cultures cannot represent the multiple interactions of the seminiferous epithelium and in situ studies became a fundamental approach to analyze BTB dynamics. In this review, we discuss the contributions of high-resolution microscopy studies to enlarge the body of morphofunctional data to understand the biology of the BTB as a dynamic structure. The first morphological evidence of the BTB was based on a fine structure of the junctions, which was resolved with Transmission Electron Microscopy. The use of conventional Fluorescent Light Microscopy to examine labelled molecules emerged as a fundamental technique for elucidating the precise protein localization at the BTB. Then laser-scanning confocal microscopy allowed the study of three-dimensional structures and complexes at the seminiferous epithelium. Several junction proteins, like the transmembrane, scaffold and signaling proteins, were identified in the testis using traditional animal models. BTB morphology was analyzed in different physiological conditions as the spermatocyte movement during meiosis, testis development, and seasonal spermatogenesis, but also structural elements, proteins, and BTB permeability were studied. Under pathological, pharmacological, or pollutant/toxic conditions, there are significant studies that provide high-resolution images which help to understand the dynamic of the BTB. Notwithstanding the advances, further research using new technologies is required to gain information on the BTB. Super-resolution light microscopy is needed to provide new research with high-quality images of targeted molecules at a nanometer-scale resolution. Finally, we highlight research areas that warrant future studies, pinpointing new microscopy approaches and helping to improve our ability to understand this barrier complexity.
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Affiliation(s)
- J. P. Luaces
- Centro de Altos Estudios en Ciencias Humanas y de la Salud, Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas, CAECIHS.UAI-CONICET, Buenos Aires, Argentina
| | - N. Toro-Urrego
- Centro de Altos Estudios en Ciencias Humanas y de la Salud, Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas, CAECIHS.UAI-CONICET, Buenos Aires, Argentina
| | - M. Otero-Losada
- Centro de Altos Estudios en Ciencias Humanas y de la Salud, Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas, CAECIHS.UAI-CONICET, Buenos Aires, Argentina
| | - F. Capani
- Centro de Altos Estudios en Ciencias Humanas y de la Salud, Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas, CAECIHS.UAI-CONICET, Buenos Aires, Argentina
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
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16
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Liu JTC, Glaser AK, Poudel C, Vaughan JC. Nondestructive 3D Pathology with Light-Sheet Fluorescence Microscopy for Translational Research and Clinical Assays. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:231-252. [PMID: 36854208 DOI: 10.1146/annurev-anchem-091222-092734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In recent years, there has been a revived appreciation for the importance of spatial context and morphological phenotypes for both understanding disease progression and guiding treatment decisions. Compared with conventional 2D histopathology, which is the current gold standard of medical diagnostics, nondestructive 3D pathology offers researchers and clinicians the ability to visualize orders of magnitude more tissue within their natural volumetric context. This has been enabled by rapid advances in tissue-preparation methods, high-throughput 3D microscopy instrumentation, and computational tools for processing these massive feature-rich data sets. Here, we provide a brief overview of many of these technical advances along with remaining challenges to be overcome. We also speculate on the future of 3D pathology as applied in translational investigations, preclinical drug development, and clinical decision-support assays.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
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17
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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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18
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Rashpa R, Klages N, Schvartz D, Pasquarello C, Brochet M. The Skp1-Cullin1-FBXO1 complex is a pleiotropic regulator required for the formation of gametes and motile forms in Plasmodium berghei. Nat Commun 2023; 14:1312. [PMID: 36898988 PMCID: PMC10006092 DOI: 10.1038/s41467-023-36999-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Malaria-causing parasites of the Plasmodium genus undergo multiple developmental phases in the human and the mosquito hosts, regulated by various post-translational modifications. While ubiquitination by multi-component E3 ligases is key to regulate a wide range of cellular processes in eukaryotes, little is known about its role in Plasmodium. Here we show that Plasmodium berghei expresses a conserved SKP1/Cullin1/FBXO1 (SCFFBXO1) complex showing tightly regulated expression and localisation across multiple developmental stages. It is key to cell division for nuclear segregation during schizogony and centrosome partitioning during microgametogenesis. It is additionally required for parasite-specific processes including gamete egress from the host erythrocyte, as well as integrity of the apical and the inner membrane complexes (IMC) in merozoite and ookinete, two structures essential for the dissemination of these motile stages. Ubiquitinomic surveys reveal a large set of proteins ubiquitinated in a FBXO1-dependent manner including proteins important for egress and IMC organisation. We additionally demonstrate an interplay between FBXO1-dependent ubiquitination and phosphorylation via calcium-dependent protein kinase 1. Altogether we show that Plasmodium SCFFBXO1 plays conserved roles in cell division and is also important for parasite-specific processes in the mammalian and mosquito hosts.
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Affiliation(s)
- Ravish Rashpa
- University of Geneva, Faculty of Medicine, Department of Microbiology and Molecular Medicine, Geneva, Switzerland.
| | - Natacha Klages
- University of Geneva, Faculty of Medicine, Department of Microbiology and Molecular Medicine, Geneva, Switzerland
| | - Domitille Schvartz
- University of Geneva, Faculty of Medicine, Proteomics Core Facility, Geneva, Switzerland
| | - Carla Pasquarello
- University of Geneva, Faculty of Medicine, Proteomics Core Facility, Geneva, Switzerland
| | - Mathieu Brochet
- University of Geneva, Faculty of Medicine, Department of Microbiology and Molecular Medicine, Geneva, Switzerland.
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19
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Affiliation(s)
- Sven Truckenbrodt
- Convergent Research, E11 Bio. 1600 Harbor Bay Parkway, Alameda, California94502, United States
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20
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Hinterndorfer K, Laporte MH, Mikus F, Tafur L, Bourgoint C, Prouteau M, Dey G, Loewith R, Guichard P, Hamel V. Ultrastructure expansion microscopy reveals the cellular architecture of budding and fission yeast. J Cell Sci 2022; 135:286062. [PMID: 36524422 PMCID: PMC10112979 DOI: 10.1242/jcs.260240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
ABSTRACT
The budding and fission yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have served as invaluable model organisms to study conserved fundamental cellular processes. Although super-resolution microscopy has in recent years paved the way to a better understanding of the spatial organization of molecules in cells, its wide use in yeasts has remained limited due to the specific know-how and instrumentation required, contrasted with the relative ease of endogenous tagging and live-cell fluorescence microscopy. To facilitate super-resolution microscopy in yeasts, we have extended the ultrastructure expansion microscopy (U-ExM) method to both S. cerevisiae and S. pombe, enabling a 4-fold isotropic expansion. We demonstrate that U-ExM allows imaging of the microtubule cytoskeleton and its associated spindle pole body, notably unveiling the Sfi1p–Cdc31p spatial organization on the appendage bridge structure. In S. pombe, we validate the method by monitoring the homeostatic regulation of nuclear pore complex number through the cell cycle. Combined with NHS-ester pan-labelling, which provides a global cellular context, U-ExM reveals the subcellular organization of these two yeast models and provides a powerful new method to augment the already extensive yeast toolbox.
This article has an associated First Person interview with Kerstin Hinterndorfer and Felix Mikus, two of the joint first authors of the paper.
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Affiliation(s)
- Kerstin Hinterndorfer
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Marine H. Laporte
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Felix Mikus
- European Molecular Biology Laboratory 2 Cell Biology and Biophysics , , Heidelberg , Germany
| | - Lucas Tafur
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Clélia Bourgoint
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Manoel Prouteau
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Gautam Dey
- European Molecular Biology Laboratory 2 Cell Biology and Biophysics , , Heidelberg , Germany
| | - Robbie Loewith
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Paul Guichard
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Virginie Hamel
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
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21
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Pac J, Koo DJ, Cho H, Jung D, Choi MH, Choi Y, Kim B, Park JU, Kim SY, Lee Y. Three-dimensional imaging and analysis of pathological tissue samples with de novo generation of citrate-based fluorophores. SCIENCE ADVANCES 2022; 8:eadd9419. [PMID: 36383671 PMCID: PMC9668299 DOI: 10.1126/sciadv.add9419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Two-dimensional (2D) histopathology based on the observation of thin tissue slides is the current paradigm in diagnosis and prognosis. However, labeling strategies in conventional histopathology are limited in compatibility with 3D imaging combined with tissue clearing techniques. Here, we present a rapid and efficient volumetric imaging technique of pathological tissues called 3D tissue imaging through de novo formation of fluorophores, or 3DNFC, which is the integration of citrate-based fluorogenic reaction DNFC and tissue clearing techniques. 3DNFC markedly increases the fluorescence intensity of tissues by generating fluorophores on nonfluorescent amino-terminal cysteine and visualizes the 3D structure of the tissues to provide their anatomical morphology and volumetric information. Furthermore, the application of 3DNFC to pathological tissue achieves the 3D reconstruction for the unbiased analysis of diverse features of the disorders in their natural context. We suggest that 3DNFC is a promising volumetric imaging method for the prognosis and diagnosis of pathological tissues.
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Affiliation(s)
- Jinyoung Pac
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Dong-Jun Koo
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Hyeongjun Cho
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Dongwook Jung
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Min-ha Choi
- Department of Plastic and Reconstructive Surgery, Seoul National University Boramae Hospital, Seoul National University College of Medicine, 5 Gil 20, Boramae Road, Dongjak-Gu, Seoul 07061, South Korea
| | - Yunjung Choi
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Bohyun Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, South Korea
| | - Ji-Ung Park
- Department of Plastic and Reconstructive Surgery, Seoul National University Boramae Hospital, Seoul National University College of Medicine, 5 Gil 20, Boramae Road, Dongjak-Gu, Seoul 07061, South Korea
| | - Sung-Yon Kim
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Yan Lee
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
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22
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Steib E, Tetley R, Laine RF, Norris DP, Mao Y, Vermot J. TissUExM enables quantitative ultrastructural analysis in whole vertebrate embryos by expansion microscopy. CELL REPORTS METHODS 2022; 2:100311. [PMID: 36313808 PMCID: PMC9606133 DOI: 10.1016/j.crmeth.2022.100311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/11/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022]
Abstract
Super-resolution microscopy reveals the molecular organization of biological structures down to the nanoscale. While it allows the study of protein complexes in single cells, small organisms, or thin tissue sections, there is currently no versatile approach for ultrastructural analysis compatible with whole vertebrate embryos. Here, we present tissue ultrastructure expansion microscopy (TissUExM), a method to expand millimeter-scale and mechanically heterogeneous whole embryonic tissues, including Drosophila wing discs, whole zebrafish, and mouse embryos. TissUExM is designed for the observation of endogenous proteins. It permits quantitative characterization of protein complexes in various organelles at super-resolution in a range of ∼3 mm-sized tissues using conventional microscopes. We demonstrate its strength by investigating tissue-specific ciliary architecture heterogeneity and ultrastructural defects observed upon ciliary protein overexpression. Overall, TissUExM is ideal for performing ultrastructural studies and molecular mapping in situ in whole embryos.
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Affiliation(s)
- Emmanuelle Steib
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Rob Tetley
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Romain F. Laine
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Dominic P. Norris
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Didcot OX11 0RD, UK
| | - Yanlan Mao
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Julien Vermot
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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23
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Pippin JW, Kaverina N, Wang Y, Eng DG, Zeng Y, Tran U, Loretz CJ, Chang A, Akilesh S, Poudel C, Perry HS, O’Connor C, Vaughan JC, Bitzer M, Wessely O, Shankland SJ. Upregulated PD-1 signaling antagonizes glomerular health in aged kidneys and disease. J Clin Invest 2022; 132:e156250. [PMID: 35968783 PMCID: PMC9374384 DOI: 10.1172/jci156250] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/24/2022] [Indexed: 01/21/2023] Open
Abstract
With an aging population, kidney health becomes an important medical and socioeconomic factor. Kidney aging mechanisms are not well understood. We previously showed that podocytes isolated from aged mice exhibit increased expression of programmed cell death protein 1 (PD-1) surface receptor and its 2 ligands (PD-L1 and PD-L2). PDCD1 transcript increased with age in microdissected human glomeruli, which correlated with lower estimated glomerular filtration rate and higher segmental glomerulosclerosis and vascular arterial intima-to-lumen ratio. In vitro studies in podocytes demonstrated a critical role for PD-1 signaling in cell survival and in the induction of a senescence-associated secretory phenotype. To prove PD-1 signaling was critical to podocyte aging, aged mice were injected with anti-PD-1 antibody. Treatment significantly improved the aging phenotype in both kidney and liver. In the glomerulus, it increased the life span of podocytes, but not that of parietal epithelial, mesangial, or endothelial cells. Transcriptomic and immunohistochemistry studies demonstrated that anti-PD-1 antibody treatment improved the health span of podocytes. Administering the same anti-PD-1 antibody to young mice with experimental focal segmental glomerulosclerosis (FSGS) lowered proteinuria and improved podocyte number. These results suggest a critical contribution of increased PD-1 signaling toward both kidney and liver aging and in FSGS.
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Affiliation(s)
| | | | - Yuliang Wang
- Paul G. Allen School of Computer Science and Engineering, and
| | | | - Yuting Zeng
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Uyen Tran
- Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | | | - Anthony Chang
- Department of Pathology, University of Chicago, Chicago, Illinois, USA
| | - Shreeram Akilesh
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Hannah S. Perry
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | | | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Department of Physiology and Biophysics and
| | - Markus Bitzer
- Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Oliver Wessely
- Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Stuart J. Shankland
- Division of Nephrology
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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24
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Shi L, Klimas A, Gallagher B, Cheng Z, Fu F, Wijesekara P, Miao Y, Ren X, Zhao Y, Min W. Super-Resolution Vibrational Imaging Using Expansion Stimulated Raman Scattering Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200315. [PMID: 35521971 PMCID: PMC9284179 DOI: 10.1002/advs.202200315] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/21/2022] [Indexed: 05/16/2023]
Abstract
Stimulated Raman scattering (SRS) microscopy is an emerging technology that provides high chemical specificity for endogenous biomolecules and can circumvent common constraints of fluorescence microscopy including limited capabilities to probe small biomolecules and difficulty resolving many colors simultaneously. However, the resolution of SRS microscopy remains governed by the diffraction limit. To overcome this, a new technique called molecule anchorable gel-enabled nanoscale Imaging of Fluorescence and stimulated Raman scattering microscopy (MAGNIFIERS) that integrates SRS microscopy with expansion microscopy (ExM) is described. MAGNIFIERS offers chemical-specific nanoscale imaging with sub-50 nm resolution and has scalable multiplexity when combined with multiplex Raman probes and fluorescent labels. MAGNIFIERS is used to visualize nanoscale features in a label-free manner with CH vibration of proteins, lipids, and DNA in a broad range of biological specimens, from mouse brain, liver, and kidney to human lung organoid. In addition, MAGNIFIERS is applied to track nanoscale features of protein synthesis in protein aggregates using metabolic labeling of small metabolites. Finally, MAGNIFIERS is used to demonstrate 8-color nanoscale imaging in an expanded mouse brain section. Overall, MAGNIFIERS is a valuable platform for super-resolution label-free chemical imaging, high-resolution metabolic imaging, and highly multiplexed nanoscale imaging, thus bringing SRS to nanoscopy.
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Affiliation(s)
- Lixue Shi
- Department of ChemistryColumbia UniversityNew YorkNY10027USA
| | - Aleksandra Klimas
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Brendan Gallagher
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Zhangyu Cheng
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Feifei Fu
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Piyumi Wijesekara
- Department of Biomedical EngineeringCarnegie Mellon UniversityPittsburghPA15143USA
| | - Yupeng Miao
- Department of ChemistryColumbia UniversityNew YorkNY10027USA
| | - Xi Ren
- Department of Biomedical EngineeringCarnegie Mellon UniversityPittsburghPA15143USA
| | - Yongxin Zhao
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Wei Min
- Department of ChemistryColumbia UniversityNew YorkNY10027USA
- Kavli Institute for Brain ScienceColumbia UniversityNew YorkNY10027USA
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25
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Li H, Warden AR, He J, Shen G, Ding X. Expansion microscopy with ninefold swelling (NIFS) hydrogel permits cellular ultrastructure imaging on conventional microscope. SCIENCE ADVANCES 2022; 8:eabm4006. [PMID: 35507653 PMCID: PMC9067917 DOI: 10.1126/sciadv.abm4006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Superresolution microscopy enables probing of cellular ultrastructures. However, its widespread applications are limited by the need for expensive machinery, specific hardware, and sophisticated data processing. Expansion microscopy (ExM) improves the resolution of conventional microscopy by physically expanding biological specimens before imaging and currently provides ~70-nm resolution, which still lags behind that of modern superresolution microscopy (~30 nm). Here, we demonstrate a ninefold swelling (NIFS) hydrogel, that can reduce ExM resolution to 31 nm when using regular traditional microscopy. We also design a detachable chip that integrates all the experimental operations to facilitate the maximal reproducibility of this high-resolution imaging technology. We demonstrate this technique on the superimaging of nuclear pore complex and clathrin-coated pits, whose structures can hardly be resolved by conventional microscopy. The method presented here offers a universal platform with superresolution imaging to unveil cellular ultrastructural details using standard conventional laboratory microscopes.
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26
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Barner LA, Glaser AK, Mao C, Susaki EA, Vaughan JC, Dintzis SM, Liu JTC. Multiresolution nondestructive 3D pathology of whole lymph nodes for breast cancer staging. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:036501. [PMID: 35315258 PMCID: PMC8936940 DOI: 10.1117/1.jbo.27.3.036501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
SIGNIFICANCE For breast cancer patients, the extent of regional lymph node (LN) metastasis influences the decision to remove all axillary LNs. Metastases are currently identified and classified with visual analysis of a few thin tissue sections with conventional histology that may underrepresent the extent of metastases. AIM We sought to enable nondestructive three-dimensional (3D) pathology of human axillary LNs and to develop a practical workflow for LN staging with our method. We also sought to evaluate whether 3D pathology improves staging accuracy in comparison to two-dimensional (2D) histology. APPROACH We developed a method to fluorescently stain and optically clear LN specimens for comprehensive imaging with multiresolution open-top light-sheet microscopy. We present an efficient imaging and data-processing workflow for rapid evaluation of H&E-like datasets in 3D, with low-resolution screening to identify potential metastases followed by high-resolution localized imaging to confirm malignancy. RESULTS We simulate LN staging with 3D and 2D pathology datasets from 10 metastatic nodes, showing that 2D pathology consistently underestimates metastasis size, including instances in which 3D pathology would lead to upstaging of the metastasis with important implications on clinical treatment. CONCLUSIONS Our 3D pathology method may improve clinical management for breast cancer patients by improving staging accuracy of LN metastases.
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Affiliation(s)
- Lindsey A. Barner
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Adam K. Glaser
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
| | - Chenyi Mao
- University of Washington, Department of Chemistry, Seattle, Washington, United States
| | - Etsuo A. Susaki
- Juntendo University Graduate School of Medicine, Department of Biochemistry and Systems Biomedicine, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Laboratory for Synthetic Biology, Osaka, Japan
| | - Joshua C. Vaughan
- University of Washington, Department of Chemistry, Seattle, Washington, United States
- University of Washington, Department of Physiology and Biophysics, Seattle, Washington, United States
| | - Suzanne M. Dintzis
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, Washington, United States
| | - Jonathan T. C. Liu
- University of Washington, Department of Mechanical Engineering, Seattle, Washington, United States
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, Washington, United States
- University of Washington, Department of Bioengineering, Seattle, Washington, United States
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27
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Lee MY, Mao C, Glaser AK, Woodworth MA, Halpern AR, Ali A, Liu JTC, Vaughan JC. Fluorescent labeling of abundant reactive entities (FLARE) for cleared-tissue and super-resolution microscopy. Nat Protoc 2022; 17:819-846. [PMID: 35110740 DOI: 10.1038/s41596-021-00667-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 09/21/2021] [Indexed: 11/08/2022]
Abstract
Fluorescence microscopy is a vital tool in biomedical research but faces considerable challenges in achieving uniform or bright labeling. For instance, fluorescent proteins are limited to model organisms, and antibody conjugates can be inconsistent and difficult to use with thick specimens. To partly address these challenges, we developed a labeling protocol that can rapidly visualize many well-contrasted key features and landmarks on biological specimens in both thin and thick tissues or cultured cells. This approach uses established reactive fluorophores to label a variety of biological specimens for cleared-tissue microscopy or expansion super-resolution microscopy and is termed FLARE (fluorescent labeling of abundant reactive entities). These fluorophores target chemical groups and reveal their distribution on the specimens; amine-reactive fluorophores such as hydroxysuccinimidyl esters target accessible amines on proteins, while hydrazide fluorophores target oxidized carbohydrates. The resulting stains provide signals analogous to traditional general histology stains such as H&E or periodic acid-Schiff but use fluorescent probes that are compatible with volumetric imaging. In general, the stains for FLARE are performed in the order of carbohydrates, amine and DNA, and the incubation time for the stains varies from 1 h to 1 d depending on the combination of stains and the type and thickness of the biological specimens. FLARE is powerful, robust and easy to implement in laboratories that already routinely do fluorescence microscopy.
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Affiliation(s)
- Min Yen Lee
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Chenyi Mao
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | | | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Adilijiang Ali
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
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28
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Damstra HGJ, Mohar B, Eddison M, Akhmanova A, Kapitein LC, Tillberg PW. Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). eLife 2022; 11:73775. [PMID: 35179128 PMCID: PMC8887890 DOI: 10.7554/elife.73775] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/30/2022] [Indexed: 12/18/2022] Open
Abstract
Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y, and z. The maximum resolution increase is limited by the expansion factor of the gel, which is four-fold for the original ExM protocol. Variations on the original ExM method have been reported that allow for greater expansion factors but at the cost of ease of adoption or versatility. Here, we systematically explore the ExM recipe space and present a novel method termed Ten-fold Robust Expansion Microscopy (TREx) that, like the original ExM method, requires no specialized equipment or procedures. We demonstrate that TREx gels expand 10-fold, can be handled easily, and can be applied to both thick mouse brain tissue sections and cultured human cells enabling high-resolution subcellular imaging with a single expansion step. Furthermore, we show that TREx can provide ultrastructural context to subcellular protein localization by combining antibody-stained samples with off-the-shelf small-molecule stains for both total protein and membranes.
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Affiliation(s)
- Hugo G J Damstra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Boaz Mohar
- Janelia Research Campus, HHMI, Ashburn, United States
| | - Mark Eddison
- Janelia Research Campus, HHMI, Ashburn, United States
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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29
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Halpern AR, Lee MY, Howard MD, Woodworth MA, Nicovich PR, Vaughan JC. Versatile, do-it-yourself, low-cost spinning disk confocal microscope. BIOMEDICAL OPTICS EXPRESS 2022; 13:1102-1120. [PMID: 35284165 PMCID: PMC8884209 DOI: 10.1364/boe.442087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/20/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Confocal microscopy is an invaluable tool for 3D imaging of biological specimens, however, accessibility is often limited to core facilities due to the high cost of the hardware. We describe an inexpensive do-it-yourself (DIY) spinning disk confocal microscope (SDCM) module based on a commercially fabricated chromium photomask that can be added on to a laser-illuminated epifluorescence microscope. The SDCM achieves strong performance across a wide wavelength range (∼400-800 nm) as demonstrated through a series of biological imaging applications that include conventional microscopy (immunofluorescence, small-molecule stains, and fluorescence in situ hybridization) and super-resolution microscopy (single-molecule localization microscopy and expansion microscopy). This low-cost and simple DIY SDCM is well-documented and should help increase accessibility to confocal microscopy for researchers.
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Affiliation(s)
- Aaron R Halpern
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Min Yen Lee
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Marco D Howard
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | - Marcus A Woodworth
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| | | | - Joshua C Vaughan
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
- University of Washington, Department of Physiology and Biophysics, Seattle, WA 98195, USA
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30
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Xie W, Reder NP, Koyuncu C, Leo P, Hawley S, Huang H, Mao C, Postupna N, Kang S, Serafin R, Gao G, Han Q, Bishop KW, Barner LA, Fu P, Wright JL, Keene CD, Vaughan JC, Janowczyk A, Glaser AK, Madabhushi A, True LD, Liu JTC. Prostate Cancer Risk Stratification via Nondestructive 3D Pathology with Deep Learning-Assisted Gland Analysis. Cancer Res 2022; 82:334-345. [PMID: 34853071 PMCID: PMC8803395 DOI: 10.1158/0008-5472.can-21-2843] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 11/24/2021] [Indexed: 01/07/2023]
Abstract
Prostate cancer treatment planning is largely dependent upon examination of core-needle biopsies. The microscopic architecture of the prostate glands forms the basis for prognostic grading by pathologists. Interpretation of these convoluted three-dimensional (3D) glandular structures via visual inspection of a limited number of two-dimensional (2D) histology sections is often unreliable, which contributes to the under- and overtreatment of patients. To improve risk assessment and treatment decisions, we have developed a workflow for nondestructive 3D pathology and computational analysis of whole prostate biopsies labeled with a rapid and inexpensive fluorescent analogue of standard hematoxylin and eosin (H&E) staining. This analysis is based on interpretable glandular features and is facilitated by the development of image translation-assisted segmentation in 3D (ITAS3D). ITAS3D is a generalizable deep learning-based strategy that enables tissue microstructures to be volumetrically segmented in an annotation-free and objective (biomarker-based) manner without requiring immunolabeling. As a preliminary demonstration of the translational value of a computational 3D versus a computational 2D pathology approach, we imaged 300 ex vivo biopsies extracted from 50 archived radical prostatectomy specimens, of which, 118 biopsies contained cancer. The 3D glandular features in cancer biopsies were superior to corresponding 2D features for risk stratification of patients with low- to intermediate-risk prostate cancer based on their clinical biochemical recurrence outcomes. The results of this study support the use of computational 3D pathology for guiding the clinical management of prostate cancer. SIGNIFICANCE: An end-to-end pipeline for deep learning-assisted computational 3D histology analysis of whole prostate biopsies shows that nondestructive 3D pathology has the potential to enable superior prognostic stratification of patients with prostate cancer.
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Affiliation(s)
- Weisi Xie
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Nicholas P Reder
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
| | - Can Koyuncu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | - Patrick Leo
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | | | - Hongyi Huang
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Chenyi Mao
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Nadia Postupna
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
| | - Soyoung Kang
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Robert Serafin
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Gan Gao
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Qinghua Han
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Kevin W Bishop
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Lindsey A Barner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Pingfu Fu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Jonathan L Wright
- Department of Urology, University of Washington, Seattle, Washington
| | - C Dirk Keene
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington
- Department of Physiology & Biophysics, Seattle, Washington
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
- Department of Oncology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, Ohio
| | - Lawrence D True
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
| | - Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington.
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington
- Department of Bioengineering, University of Washington, Seattle, Washington
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31
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Laporte MH, Klena N, Hamel V, Guichard P. Visualizing the native cellular organization by coupling cryofixation with expansion microscopy (Cryo-ExM). Nat Methods 2022; 19:216-222. [PMID: 35027766 PMCID: PMC8828483 DOI: 10.1038/s41592-021-01356-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/17/2021] [Indexed: 12/11/2022]
Abstract
Cryofixation has proven to be the gold standard for efficient preservation of native cell ultrastructure compared to chemical fixation, but this approach is not widely used in fluorescence microscopy owing to implementation challenges. Here, we develop Cryo-ExM, a method that preserves native cellular organization by coupling cryofixation with expansion microscopy. This method bypasses artifacts associated with chemical fixation and its simplicity will contribute to its widespread use in super-resolution microscopy.
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Affiliation(s)
- Marine H Laporte
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Nikolai Klena
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Virginie Hamel
- Department of Cell Biology, University of Geneva, Geneva, Switzerland.
| | - Paul Guichard
- Department of Cell Biology, University of Geneva, Geneva, Switzerland.
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32
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Nerdinger S, Schottenberger H, Neuner S, A. Schwartz H, Kreutz C, Müller T, Mayer P, Bonn G, Gelbrich T, J. Griesser U, Wurst K, Kahlenberg V. 2-Arylazoimidazoles Revamped by Quarternization or Dimerization; Another Gain in Functionality of an Industrial Dyestuff Family by Task-Specific Side-Chain Substituents. HETEROCYCLES 2022. [DOI: 10.3987/com-22-s(r)17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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33
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Rashpa R, Brochet M. Expansion microscopy of Plasmodium gametocytes reveals the molecular architecture of a bipartite microtubule organisation centre coordinating mitosis with axoneme assembly. PLoS Pathog 2022; 18:e1010223. [PMID: 35077503 PMCID: PMC8789139 DOI: 10.1371/journal.ppat.1010223] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Transmission of malaria-causing parasites to mosquitoes relies on the production of gametocyte stages and their development into gametes. These stages display various microtubule cytoskeletons and the architecture of the corresponding microtubule organisation centres (MTOC) remains elusive. Combining ultrastructure expansion microscopy (U-ExM) with bulk proteome labelling, we first reconstructed in 3D the subpellicular microtubule network which confers cell rigidity to Plasmodium falciparum gametocytes. Upon activation, as the microgametocyte undergoes three rounds of endomitosis, it also assembles axonemes to form eight flagellated microgametes. U-ExM combined with Pan-ExM further revealed the molecular architecture of the bipartite MTOC coordinating mitosis with axoneme formation. This MTOC spans the nuclear membrane linking cytoplasmic basal bodies to intranuclear bodies by proteinaceous filaments. In P. berghei, the eight basal bodies are concomitantly de novo assembled in a SAS6- and SAS4-dependent manner from a deuterosome-like structure, where centrin, γ-tubulin, SAS4 and SAS6 form distinct subdomains. Basal bodies display a fusion of the proximal and central cores where centrin and SAS6 are surrounded by a SAS4-toroid in the lumen of the microtubule wall. Sequential nucleation of axonemes and mitotic spindles is associated with a dynamic movement of γ-tubulin from the basal bodies to the intranuclear bodies. This dynamic architecture relies on two non-canonical regulators, the calcium-dependent protein kinase 4 and the serine/arginine-protein kinase 1. Altogether, these results provide insights into the molecular organisation of a bipartite MTOC that may reflect a functional transition of a basal body to coordinate axoneme assembly with mitosis.
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Affiliation(s)
- Ravish Rashpa
- University of Geneva, Department of Microbiology and Molecular Medicine, Faculty of Medicine, Geneva, Switzerland
| | - Mathieu Brochet
- University of Geneva, Department of Microbiology and Molecular Medicine, Faculty of Medicine, Geneva, Switzerland
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34
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Shi X, Li Q, Dai Z, Tran AA, Feng S, Ramirez AD, Lin Z, Wang X, Chow TT, Chen J, Kumar D, McColloch AR, Reiter JF, Huang EJ, Seiple IB, Huang B. Label-retention expansion microscopy. J Cell Biol 2021; 220:e202105067. [PMID: 34228783 PMCID: PMC8266563 DOI: 10.1083/jcb.202105067] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 11/28/2022] Open
Abstract
Expansion microscopy (ExM) increases the effective resolving power of any microscope by expanding the sample with swellable hydrogel. Since its invention, ExM has been successfully applied to a wide range of cell, tissue, and animal samples. Still, fluorescence signal loss during polymerization and digestion limits molecular-scale imaging using ExM. Here, we report the development of label-retention ExM (LR-ExM) with a set of trifunctional anchors that not only prevent signal loss but also enable high-efficiency labeling using SNAP and CLIP tags. We have demonstrated multicolor LR-ExM for a variety of subcellular structures. Combining LR-ExM with superresolution stochastic optical reconstruction microscopy (STORM), we have achieved molecular resolution in the visualization of polyhedral lattice of clathrin-coated pits in situ.
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Affiliation(s)
- Xiaoyu Shi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA
| | - Qi Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | - Zhipeng Dai
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
| | - Arthur A. Tran
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA
| | - Siyu Feng
- University of California, Berkeley–University of California, San Francisco Joint Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA
| | - Alejandro D. Ramirez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Zixi Lin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Xiaomeng Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Tracy T. Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Jiapei Chen
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Dhivya Kumar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Andrew R. McColloch
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA
| | - Jeremy F. Reiter
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Eric J. Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Ian B. Seiple
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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Butt L, Unnersjö-Jess D, Höhne M, Schermer B, Edwards A, Benzing T. A mathematical estimation of the physical forces driving podocyte detachment. Kidney Int 2021; 100:1054-1062. [PMID: 34332959 DOI: 10.1016/j.kint.2021.06.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 05/27/2021] [Accepted: 06/18/2021] [Indexed: 01/21/2023]
Abstract
Loss of podocytes, possibly through the detachment of viable cells, is a hallmark of progressive glomerular disease. Podocytes are exposed to considerable physical forces due to pressure and flow resulting in circumferential wall stress and tangential shear stress exerted on the podocyte cell body, which have been proposed to contribute to podocyte depletion. However, estimations of in vivo alterations of physical forces in glomerular disease have been hampered by a lack of quantitative functional and morphological data. Here, we used ultra-resolution data and computational analyses in a mouse model of human disease, hereditary late-onset focal segmental glomerular sclerosis, to calculate increased mechanical stress upon podocyte injury. Transversal shear stress on the lateral walls of the foot processes was prominently increased during the initial stages of podocyte detachment. Thus, our study highlights the importance of targeting glomerular hemodynamics to treat glomerular disease.
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Affiliation(s)
- Linus Butt
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - David Unnersjö-Jess
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; CECAD, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Aurelie Edwards
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; CECAD, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
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36
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Cheng B, Tang Q, Zhang C, Chen X. Glycan Labeling and Analysis in Cells and In Vivo. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:363-387. [PMID: 34314224 DOI: 10.1146/annurev-anchem-091620-091314] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As one of the major types of biomacromolecules in the cell, glycans play essential functional roles in various biological processes. Compared with proteins and nucleic acids, the analysis of glycans in situ has been more challenging. Herein we review recent advances in the development of methods and strategies for labeling, imaging, and profiling of glycans in cells and in vivo. Cellular glycans can be labeled by affinity-based probes, including lectin and antibody conjugates, direct chemical modification, metabolic glycan labeling, and chemoenzymatic labeling. These methods have been applied to label glycans with fluorophores, which enables the visualization and tracking of glycans in cells, tissues, and living organisms. Alternatively, labeling glycans with affinity tags has enabled the enrichment of glycoproteins for glycoproteomic profiling. Built on the glycan labeling methods, strategies enabling cell-selective and tissue-specific glycan labeling and protein-specific glycan imaging have been developed. With these methods and strategies, researchers are now better poised than ever to dissect the biological function of glycans in physiological or pathological contexts.
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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
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Che Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
- Beijing National Laboratory for Molecular 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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Zhu C, Wang A, Chen L, Guo L, Ye J, Chen Q, Wang Q, Yao G, Xia Q, Cai T, Guo J, Yang Z, Sun Z, Xu Y, Lu G, Zhang Z, Cao J, Liu Y, Xu H. Measurement of expansion factor and distortion for expansion microscopy using isolated renal glomeruli as landmarks. JOURNAL OF BIOPHOTONICS 2021; 14:e202100001. [PMID: 33856738 DOI: 10.1002/jbio.202100001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/14/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Expansion microscopy has enabled super resolution imaging of biological samples. The accurate measurement of expansion factor and distortion typically requires locating and imaging the same region of interest in the sample before and after expansion, which is often time-consuming to achieve. Here we introduce a convenient method for relocation by utilizing isolated porcine glomeruli as landmarks during expansion. Following heat denaturation and proteinase K digestion protocols, the glomeruli exhibit expansion factor of 3.5 to 4 (only 7%-16% less expanded than the hydrogel), and 1% to 2% of relative distortion. Due to its appropriate size of 100 to 300 μm, the location of the glomerulus in the sample are visible to eyes, while its detailed shape only requires bright field microscopy. For expansion factors ranging from 3 to 10, the region in the vicinity of the glomerulus can be easily re-identified, and sometimes allows quantification of expansion factor and distortion under bright field without fluorescent labels.
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Affiliation(s)
- Chen Zhu
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Optoelectronic Science and Engineering, Soochow University, Suzhou, China
| | - Aidong Wang
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lili Chen
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Liangsheng Guo
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jiajia Ye
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Qilin Chen
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Qi Wang
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Optoelectronic Science and Engineering, Soochow University, Suzhou, China
| | - Guojia Yao
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Qin Xia
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Tianyu Cai
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Jiayun Guo
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zhenyu Yang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zhenglong Sun
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Yuwei Xu
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Guoyuan Lu
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zexin Zhang
- Institute for Advanced Study, Soochow University, Suzhou, China
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, China
| | - Jingyuan Cao
- Department of Nephrology, Taizhou People's Hospital, the Fifth Affiliated Hospital of Nantong University, Taizhou, China
| | - Ying Liu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Huizhong Xu
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
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Sands GB, Ashton JL, Trew ML, Baddeley D, Walton RD, Benoist D, Efimov IR, Smith NP, Bernus O, Smaill BH. It's clearly the heart! Optical transparency, cardiac tissue imaging, and computer modelling. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 168:18-32. [PMID: 34126113 DOI: 10.1016/j.pbiomolbio.2021.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/10/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022]
Abstract
Recent developments in clearing and microscopy enable 3D imaging with cellular resolution up to the whole organ level. These methods have been used extensively in neurobiology, but their uptake in other fields has been much more limited. Application of this approach to the human heart and effective use of the data acquired present challenges of scale and complexity. Four interlinked issues need to be addressed: 1) efficient clearing and labelling of heart tissue, 2) fast microscopic imaging of human-scale samples, 3) handling and processing of multi-terabyte 3D images, and 4) extraction of structural information in computationally tractable structure-based models of cardiac function. Preliminary studies show that each of these requirements can be achieved with the appropriate application and development of existing technologies.
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Affiliation(s)
- Gregory B Sands
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand.
| | - Jesse L Ashton
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - Mark L Trew
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - David Baddeley
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand; Department of Cell Biology, Yale University, New Haven CT, 06520, USA
| | - Richard D Walton
- IHU Liryc, Fondation Bordeaux Université, Bordeaux, France; Univ. Bordeaux, Inserm, Centre de Recherche Cardio-Thoracique, U1045, 33000, Bordeaux, France
| | - David Benoist
- IHU Liryc, Fondation Bordeaux Université, Bordeaux, France; Univ. Bordeaux, Inserm, Centre de Recherche Cardio-Thoracique, U1045, 33000, Bordeaux, France
| | - Igor R Efimov
- IHU Liryc, Fondation Bordeaux Université, Bordeaux, France; Department of Biomedical Engineering, The George Washington University, Washington DC, 20052, USA
| | - Nicolas P Smith
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand; Queensland University of Technology, Brisbane 4000, Australia
| | - Olivier Bernus
- IHU Liryc, Fondation Bordeaux Université, Bordeaux, France; Univ. Bordeaux, Inserm, Centre de Recherche Cardio-Thoracique, U1045, 33000, Bordeaux, France
| | - Bruce H Smaill
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
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Matsumoto A, Matsui I, Katsuma Y, Yasuda S, Shimada K, Namba-Hamano T, Sakaguchi Y, Kaimori JY, Takabatake Y, Inoue K, Isaka Y. Quantitative Analyses of Foot Processes, Mitochondria, and Basement Membranes by Structured Illumination Microscopy Using Elastica-Masson- and Periodic-Acid-Schiff-Stained Kidney Sections. Kidney Int Rep 2021; 6:1923-1938. [PMID: 34307987 PMCID: PMC8258503 DOI: 10.1016/j.ekir.2021.04.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Introduction Foot process effacement and mitochondrial fission associate with kidney disease pathogenesis. Electron microscopy is the gold-standard method for their visualization, but the observable area of electron microscopy is smaller than light microscopy. It is important to develop alternative ways to quantitatively evaluate these microstructural changes because the lesion site of renal diseases can be focal. Methods We analyzed elastica-Masson trichrome (EMT) and periodic acid-Schiff (PAS) stained kidney sections using structured illumination microscopy (SIM). Results EMT staining revealed three-dimensional (3D) structures of foot process, whereas ponceau xylidine acid fuchsin azophloxine solution induced fluorescence. Conversion of foot process images into their constituent frequencies by Fourier transform showed that the concentric square of (1/4)2-(1/16)2 in the power spectra (PS) included information for normal periodic structures of foot processes. Foot process integrity, assessed by PS, negatively correlated with proteinuria. EMT-stained sections revealed fragmented mitochondria in mice with mitochondrial injuries and patients with tubulointerstitial nephritis; Fourier transform quantified associated mitochondrial injury. Quantified mitochondrial damage in patients with immunoglobulin A (IgA) nephropathy predicted a decline in estimated glomerular filtration rate (eGFR) after kidney biopsy but did not correlate with eGFR at biopsy. PAS-stained sections, excited by a 640 nm laser, combined with the coefficient of variation values, quantified subtle changes in the basement membranes of patients with membranous nephropathy stage I. Conclusions Kidney microstructures are quantified from sections prepared in clinical practice using SIM.
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Affiliation(s)
- Ayumi Matsumoto
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Isao Matsui
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yusuke Katsuma
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Seiichi Yasuda
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Karin Shimada
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tomoko Namba-Hamano
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yusuke Sakaguchi
- Department of Inter-Organ Communication Research in Kidney Disease, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jun-Ya Kaimori
- Department of Inter-Organ Communication Research in Kidney Disease, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitsugu Takabatake
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazunori Inoue
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Osaka, Japan
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40
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Liu JTC, Glaser AK, Bera K, True LD, Reder NP, Eliceiri KW, Madabhushi A. Harnessing non-destructive 3D pathology. Nat Biomed Eng 2021; 5:203-218. [PMID: 33589781 PMCID: PMC8118147 DOI: 10.1038/s41551-020-00681-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/17/2020] [Indexed: 02/08/2023]
Abstract
High-throughput methods for slide-free three-dimensional (3D) pathological analyses of whole biopsies and surgical specimens offer the promise of modernizing traditional histology workflows and delivering improvements in diagnostic performance. Advanced optical methods now enable the interrogation of orders of magnitude more tissue than previously possible, where volumetric imaging allows for enhanced quantitative analyses of cell distributions and tissue structures that are prognostic and predictive. Non-destructive imaging processes can simplify laboratory workflows, potentially reducing costs, and can ensure that samples are available for subsequent molecular assays. However, the large size of the feature-rich datasets that they generate poses challenges for data management and computer-aided analysis. In this Perspective, we provide an overview of the imaging technologies that enable 3D pathology, and the computational tools-machine learning, in particular-for image processing and interpretation. We also discuss the integration of various other diagnostic modalities with 3D pathology, along with the challenges and opportunities for clinical adoption and regulatory approval.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Kaustav Bera
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nicholas P Reder
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kevin W Eliceiri
- Department of Medical Physics, University of Wisconsin, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, OH, USA.
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41
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Han Y, Zhang Z, Liu W, Yao Y, Xu Y, Liu X, Kuang C, Hao X. A Labeling Strategy for Living Specimens in Long-Term/Super-Resolution Fluorescence Imaging. Front Chem 2021; 8:601436. [PMID: 33520932 PMCID: PMC7843436 DOI: 10.3389/fchem.2020.601436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
Despite the urgent need to image living specimens for cutting-edge biological research, most existing fluorescent labeling methods suffer from either poor optical properties or complicated operations required to realize cell-permeability and specificity. In this study, we introduce a method to overcome these limits-taking advantage of the intrinsic affinity of bright and photostable fluorophores, no matter if they are supposed to be live-cell incompatible or not. Incubated with living cells and tissues in particular conditions (concentration and temperature), some Atto and BODIPY dyes show live-cell labeling capability for specific organelles without physical cell-penetration or chemical modifications. Notably, by using Atto 647N as a live-cell mitochondrial marker, we obtain 2.5-time enhancement of brightness and photostability compared with the most commonly used SiR dye in long-term imaging. Our strategy has expanded the scientist's toolbox for understanding the dynamics and interactions of subcellular structures in living specimens.
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Affiliation(s)
- Yubing Han
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Zhimin Zhang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Wenjie Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Yuanfa Yao
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Yingke Xu
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Xu Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Ningbo Research Institute, Zhejiang University, Ningbo, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| | - Cuifang Kuang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Ningbo Research Institute, Zhejiang University, Ningbo, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| | - Xiang Hao
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
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42
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Zhu H, Li J, Li Y, Zheng Z, Guan H, Wang H, Tao K, Liu J, Wang Y, Zhang W, Li C, Li J, Jia L, Bai W, Hu D. Glucocorticoid counteracts cellular mechanoresponses by LINC01569-dependent glucocorticoid receptor-mediated mRNA decay. SCIENCE ADVANCES 2021; 7:7/9/eabd9923. [PMID: 33627425 PMCID: PMC7904261 DOI: 10.1126/sciadv.abd9923] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/08/2021] [Indexed: 05/05/2023]
Abstract
Mechanical stimuli on cells and mechanotransduction are essential in many biological and pathological processes. Glucocorticoid is an important hormone, roles, and mechanisms of which in cellular mechanotransduction remain unknown. Here, we report that glucocorticoid counteracted cellular mechanoresponses dependently on a novel long noncoding RNA (lncRNA), LINC01569 Further, LINC01569 mediated glucocorticoid effects on mechanotransduction by destabilizing messenger RNA (mRNA) of mechanosensors including early growth response protein 1 (EGR1), Cbp/P300-interacting transactivator 2 (CITED2), and bone morphogenic protein 7 (BMP7) in glucocorticoid receptor-mediated mRNA decay (GMD) manner. Mechanistically, LINC01569 directly bound to the GMD factor Y-box-binding protein 1 (YBX1). Then, the LINC01569-YBX1 complex was guided to the mRNAs of EGR1, CITED2, and BMP7 through specific LINC01569-mRNA interaction, thereby contributing to the successful assembly of GMD complex and triggering GMD. Our results uncovered roles of glucocorticoid in cellular mechanotransduction and novel lncRNA-dependent GMD machinery and provided potential strategy for early intervention in mechanical disorder-associated diseases.
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Affiliation(s)
- Huayu Zhu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jun Li
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Yize Li
- Department of Clinical Oncology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Zhao Zheng
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Hao Guan
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Hongtao Wang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Ke Tao
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jiaqi Liu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Yunchuan Wang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wanfu Zhang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Chao Li
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Jie Li
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Wendong Bai
- Department of Endocrinology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
- Department of Clinical Laboratory Center, Xinjiang Command General Hospital of Chinese People's Liberation Army, Urumqi, Xinjiang 830000, China
| | - Dahai Hu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
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Imaging of spine synapses using super-resolution microscopy. Anat Sci Int 2021; 96:343-358. [PMID: 33459976 DOI: 10.1007/s12565-021-00603-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
Neuronal circuits in the neocortex and hippocampus are essential for higher brain functions such as motor learning and spatial memory. In the mammalian forebrain, most excitatory synapses of pyramidal neurons are formed on spines, which are tiny protrusions extending from the dendritic shaft. The spine contains specialized molecular machinery that regulates synaptic transmission and plasticity. Spine size correlates with the efficacy of synaptic transmission, and spine morphology affects signal transduction at the post-synaptic compartment. Plasticity-related changes in the structural and molecular organization of spine synapses are thought to underlie the cellular basis of learning and memory. Recent advances in super-resolution microscopy have revealed the molecular mechanisms of the nanoscale synaptic structures regulating synaptic transmission and plasticity in living neurons, which are difficult to investigate using electron microscopy alone. In this review, we summarize recent advances in super-resolution imaging of spine synapses and discuss the implications of nanoscale structures in the regulation of synaptic function, learning, and memory.
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44
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Pellicciari C. Twenty years of histochemistry in the third millennium, browsing the scientific literature. Eur J Histochem 2020; 64. [PMID: 33478199 PMCID: PMC7789425 DOI: 10.4081/ejh.2020.3213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/23/2022] Open
Abstract
Over the last twenty years, about 240,000 articles where histochemical techniques were used have been published in indexed journals, and their yearly number has progressively increased. The histochemical approach was selected by researchers with very different scientific interests, as the journals in which these articles were published fall within 140 subject categories. The relative proportion of articles in some of these journal categories did change over the years, and browsing the table of contents of the European Journal of Histochemistry, as an example of a strictly histochemical journal, it appeared that in recent years histochemical techniques were preferentially used to mechanistically investigate natural or experimentally induced dynamic processes, with reduced attention to purely descriptive works. It may be foreseen that, in the future, histochemistry will be increasingly focused on studying the molecular pathways responsible for cell differentiation, the maintenance or loss of the differentiated state, and tissue regeneration.
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Hamel V, Guichard P. Improving the resolution of fluorescence nanoscopy using post-expansion labeling microscopy. Methods Cell Biol 2020; 161:297-315. [PMID: 33478694 DOI: 10.1016/bs.mcb.2020.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The visualization of the cell ultrastructure and molecular complexes has long been reserved for electron microscopy owing to its nanometric resolution. In recent years, this monopoly has been challenged by super-resolution (SR) fluorescence microscopy, which allows the visualization of cell structures with high spatial resolution, approaching virtually molecular dimensions. However, the resolution of current SR microscopy does not systematically reach the level of the ultrastructural information provided by electron microscopy. In this review, we are discussing the potential of revealing cell ultrastructure using the recent method of expansion microscopy (ExM). In particular, we are discussing the limitations that exist in SR and ExM methods that prevent the visualization of nanometric molecular assemblies and how post-labeling expansion could help alleviate them to reveal the molecular cartography of cells with unprecedented details.
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Affiliation(s)
- Virginie Hamel
- Department of Cell Biology, University of Geneva, Sciences III, Geneva, Switzerland.
| | - Paul Guichard
- Department of Cell Biology, University of Geneva, Sciences III, Geneva, Switzerland.
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46
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M'Saad O, Bewersdorf J. Light microscopy of proteins in their ultrastructural context. Nat Commun 2020; 11:3850. [PMID: 32737322 PMCID: PMC7395138 DOI: 10.1038/s41467-020-17523-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/03/2020] [Indexed: 11/09/2022] Open
Abstract
Resolving the distribution of specific proteins at the nanoscale in the ultrastructural context of the cell is a major challenge in fluorescence microscopy. We report the discovery of a new principle for an optical contrast equivalent to electron microscopy (EM) which reveals the ultrastructural context of the cells with a conventional confocal microscope. By decrowding the intracellular space through 13 to 21-fold physical expansion while simultaneously retaining the proteins, bulk (pan) labeling of the proteome resolves local protein densities and reveals the cellular nanoarchitecture by standard light microscopy.
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Affiliation(s)
- Ons M'Saad
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- Nanobiology Institute, Yale University, West Haven, CT, USA.
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