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Masuda A, Okamoto T, Kawachi T, Takeda JI, Hamaguchi T, Ohno K. Blending and separating dynamics of RNA-binding proteins develop architectural splicing networks spreading throughout the nucleus. Mol Cell 2024:S1097-2765(24)00544-6. [PMID: 39053456 DOI: 10.1016/j.molcel.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/28/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
The eukaryotic nucleus has a highly organized structure. Although the spatiotemporal arrangement of spliceosomes on nascent RNA drives splicing, the nuclear architecture that directly supports this process remains unclear. Here, we show that RNA-binding proteins (RBPs) assembled on RNA form meshworks in human and mouse cells. Core and accessory RBPs in RNA splicing make two distinct meshworks adjacently but distinctly distributed throughout the nucleus. This is achieved by mutual exclusion dynamics between the charged and uncharged intrinsically disordered regions (IDRs) of RBPs. These two types of meshworks compete for spatial occupancy on pre-mRNA to regulate splicing. Furthermore, the optogenetic enhancement of the RBP meshwork causes aberrant splicing, particularly of genes involved in neurodegeneration. Genetic mutations associated with neurodegenerative diseases are often found in the IDRs of RBPs, and cells harboring these mutations exhibit impaired meshwork formation. Our results uncovered the spatial organization of RBP networks to drive RNA splicing.
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Affiliation(s)
- Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Takaaki Okamoto
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshihiko Kawachi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomonari Hamaguchi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan; Graduate School of Nutritional Sciences, Nagoya University of Arts and Sciences, Nisshin, Japan
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2
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Norris S, Hu JK, Shubin NH. Whole Tissue Imaging of Cellular Boundaries at Sub-Micron Resolutions for Automatic Cell Segmentation: Applications in Epithelial Bending of Ectodermal Appendages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600880. [PMID: 38979339 PMCID: PMC11230380 DOI: 10.1101/2024.06.26.600880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
For decades, biologists have relied on confocal microscopy to understand cellular morphology and the fine details of tissue structure. However, traditional confocal microscopy of tissues have limited penetration depths of light ∼ 100 µm due to tissue opaqueness. Researchers have, thus, developed tissue clearing protocols to be used with confocal microscopy, however, current clearing protocols are not compatible with labels of cell boundaries, especially at high enough resolution to precisely segment individual cells. In this work, we devise a method to retain markers of cell boundaries, and refractive index-match the tissues with water to enable tissue imaging at high magnification using long working distance water dipping objectives. The sub-micron resolution of these images allows us to automatically segment each individual cell using a trained neural network segmentation model. These segmented images can then be utilized to quantify cell properties and morphology of the entire three-dimensional tissue. As an example application, we first test our methodology on mandibles of mutant mice that express fluorescent proteins in their membranes. We then examine a non-model animal, the catshark, and explore the cellular properties of their dental lamina and dermal denticles, which are invaginating and evaginating ectodermal structures, respectively. We, thus, demonstrate that the technique presented here provides a powerful tool to quantify, in high-throughput, the 3D structures of cells and tissues during organ morphogenesis.
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3
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Dong PT, Shi W, He X, Borisy GG. Adhesive interactions within microbial consortia can be differentiated at the single-cell level through expansion microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600639. [PMID: 38979233 PMCID: PMC11230439 DOI: 10.1101/2024.06.25.600639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Investigating microbe-microbe interactions at the single-cell level is critical to unraveling the ecology and dynamics of microbial communities. In many situations, microbes assemble themselves into densely packed multi-species biofilms. The density and complexity pose acute difficulties for visualizing individual cells and analyzing their interactions. Here, we address this problem through an unconventional application of expansion microscopy, which allows for the 'decrowding' of individual bacterial cells within a multispecies community. Expansion microscopy generally has been carried out under isotropic expansion conditions and used as a resolution-enhancing method. In our variation of expansion microscopy, we carry out expansion under heterotropic conditions; that is, we expand the space between bacterial cells but not the space within individual cells. The separation of individual bacterial cells from each other reflects the competition between the expansion force pulling them apart and the adhesion force holding them together. We employed heterotropic expansion microscopy to study the relative strength of adhesion in model biofilm communities. These included mono and dual-species Streptococcus biofilms, and a three-species synthetic community (Fusobacterium nucleatum, Streptococcus mutans, and Streptococcus sanguinis) under conditions that facilitated interspecies coaggregation. Using adhesion mutants, we investigated the interplay between F. nucleatum outer membrane protein RadD and different Streptococcus species. We also examined the Schaalia-TM7 epibiont association. Quantitative proximity analysis was used to evaluate the separation of individual microbial members. Our study demonstrates that heterotropic expansion microscopy can 'decrowd' dense biofilm communities, improve visualization of individual bacterial members, and enable analysis of microbe-microbe adhesive interactions at the single-cell level.
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Affiliation(s)
- Pu-Ting Dong
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA 02142, USA
| | - Wenyuan Shi
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA 02142, USA
| | - Xuesong He
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA 02142, USA
| | - Gary G. Borisy
- Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA 02142, USA
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4
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Liu J, Tan YY, Zheng W, Wang Y, Ju LA, Su QP. Nanoscale insights into hematology: super-resolved imaging on blood cell structure, function, and pathology. J Nanobiotechnology 2024; 22:363. [PMID: 38910248 PMCID: PMC11194919 DOI: 10.1186/s12951-024-02605-2] [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: 03/27/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
Fluorescence nanoscopy, also known as super-resolution microscopy, has transcended the conventional resolution barriers and enabled visualization of biological samples at nanometric resolutions. A series of super-resolution techniques have been developed and applied to investigate the molecular distribution, organization, and interactions in blood cells, as well as the underlying mechanisms of blood-cell-associated diseases. In this review, we provide an overview of various fluorescence nanoscopy technologies, outlining their current development stage and the challenges they are facing in terms of functionality and practicality. We specifically explore how these innovations have propelled forward the analysis of thrombocytes (platelets), erythrocytes (red blood cells) and leukocytes (white blood cells), shedding light on the nanoscale arrangement of subcellular components and molecular interactions. We spotlight novel biomarkers uncovered by fluorescence nanoscopy for disease diagnosis, such as thrombocytopathies, malignancies, and infectious diseases. Furthermore, we discuss the technological hurdles and chart out prospective avenues for future research directions. This review aims to underscore the significant contributions of fluorescence nanoscopy to the field of blood cell analysis and disease diagnosis, poised to revolutionize our approach to exploring, understanding, and managing disease at the molecular level.
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Affiliation(s)
- Jinghan Liu
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yuping Yolanda Tan
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
- Heart Research Institute, Newtown, NSW, 2042, Australia
| | - Wen Zheng
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Yao Wang
- School of Biomedical Engineering, The University of Sydney, Darlington, NSW, 2008, Australia
| | - Lining Arnold Ju
- School of Biomedical Engineering, The University of Sydney, Darlington, NSW, 2008, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
- Heart Research Institute, Newtown, NSW, 2042, Australia
| | - Qian Peter Su
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia.
- Heart Research Institute, Newtown, NSW, 2042, Australia.
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5
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Chan YH, Pathmasiri KC, Pierre-Jacques D, Hibbard MC, Tao N, Fischer JL, Yang E, Cologna SM, Gao R. Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics. Nat Commun 2024; 15:5036. [PMID: 38866734 PMCID: PMC11169460 DOI: 10.1038/s41467-024-49384-w] [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: 09/10/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
A technique capable of label-free detection, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of native biomolecules in intact specimens. However, MSI has often been precluded from single-cell applications due to the spatial resolution limit set forth by the physical and instrumental constraints of the method. By taking advantage of the reversible interaction between the analytes and a superabsorbent hydrogel, we have developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome the spatial resolution limits of modern mass spectrometers. With GAMSI, we show that the spatial resolution of MALDI-MSI can be enhanced ~3-6-fold to the sub-micrometer level without changing the existing mass spectrometry hardware or analysis pipeline. This approach will vastly enhance the accessibility of MSI-based spatial analysis at the cellular scale.
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Affiliation(s)
- Yat Ho Chan
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | - Maddison C Hibbard
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | | | - Stephanie M Cologna
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA
| | - Ruixuan Gao
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA.
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA.
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA.
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6
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Borisova E, Newman AG, Couce Iglesias M, Dannenberg R, Schaub T, Qin B, Rusanova A, Brockmann M, Koch J, Daniels M, Turko P, Jahn O, Kaplan DR, Rosário M, Iwawaki T, Spahn CMT, Rosenmund C, Meierhofer D, Kraushar ML, Tarabykin V, Ambrozkiewicz MC. Protein translation rate determines neocortical neuron fate. Nat Commun 2024; 15:4879. [PMID: 38849354 PMCID: PMC11161512 DOI: 10.1038/s41467-024-49198-w] [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: 05/27/2022] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
The mammalian neocortex comprises an enormous diversity regarding cell types, morphology, and connectivity. In this work, we discover a post-transcriptional mechanism of gene expression regulation, protein translation, as a determinant of cortical neuron identity. We find specific upregulation of protein synthesis in the progenitors of later-born neurons and show that translation rates and concomitantly protein half-lives are inherent features of cortical neuron subtypes. In a small molecule screening, we identify Ire1α as a regulator of Satb2 expression and neuronal polarity. In the developing brain, Ire1α regulates global translation rates, coordinates ribosome traffic, and the expression of eIF4A1. Furthermore, we demonstrate that the Satb2 mRNA translation requires eIF4A1 helicase activity towards its 5'-untranslated region. Altogether, we show that cortical neuron diversity is generated by mechanisms operating beyond gene transcription, with Ire1α-safeguarded proteostasis serving as an essential regulator of brain development.
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Affiliation(s)
- Ekaterina Borisova
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Andrew G Newman
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Marta Couce Iglesias
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Rike Dannenberg
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Theres Schaub
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Bo Qin
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Alexandra Rusanova
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Research Institute of Medical Genetics, Tomsk, Russia
| | - Marisa Brockmann
- Institute of Neurophysiology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Janina Koch
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Marieatou Daniels
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Paul Turko
- Institute of Integrative Neuroanatomy, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Olaf Jahn
- Neuroproteomics Group, Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Hermann-Rein-Str. 3, 37075, Göttingen, Germany
- Translational Neuroproteomics Group, Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-University, Von-Siebold-Str. 5, 37075, Göttingen, Germany
| | - David R Kaplan
- Program in Neurosciences and Mental Health, Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Marta Rosário
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Takao Iwawaki
- Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0293, Japan
| | - Christian M T Spahn
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Christian Rosenmund
- Institute of Neurophysiology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Matthew L Kraushar
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Victor Tarabykin
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
| | - Mateusz C Ambrozkiewicz
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
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7
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Britto LS, Balasubramani D, Desai S, Phillips P, Trehan N, Cesarman E, Koff JL, Singh A. T Cells Spatially Regulate B Cell Receptor Signaling in Lymphomas through H3K9me3 Modifications. Adv Healthc Mater 2024:e2401192. [PMID: 38837879 DOI: 10.1002/adhm.202401192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/27/2024] [Indexed: 06/07/2024]
Abstract
Activated B cell-like diffuse large B-cell lymphoma (ABC-DLBCL) is a subtype associated with poor survival outcomes. Despite identifying therapeutic targets through molecular characterization, targeted therapies have limited success. New strategies using immune-competent tissue models are needed to understand how DLBCL cells evade treatment. Here, synthetic hydrogel-based lymphoma organoids are used to demonstrate how signals in the lymphoid tumor microenvironment (Ly-TME) can alter B cell receptor (BCR) signaling and specific histone modifications, tri-methylation of histone 3 at lysine 9 (H3K9me3), dampening the effects of BCR pathway inhibition. Using imaging modalities, T cells increase DNA methyltransferase 3A expression and cytoskeleton formation in proximal ABC-DLBCL cells, regulated by H3K9me3. Expansion microscopy on lymphoma organoids reveals T cells increase the size and quantity of segregated H3K9me3 clusters in ABC-DLBCL cells. Findings suggest the re-organization of higher-order chromatin structures that may contribute to evasion or resistance to therapy via the emergence of novel transcriptional states. Treating ABC-DLBCL cells with a G9α histone methyltransferase inhibitor reverses T cell-mediated modulation of H3K9me3 and overcomes T cell-mediated attenuation of treatment response to BCR pathway inhibition. This study emphasizes the Ly-TME's role in altering DLBCL fate and suggests targeting aberrant signaling and microenvironmental cross-talk that can benefit high-risk patients.
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Affiliation(s)
- Lucy S Britto
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Deepali Balasubramani
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Sona Desai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Phunterion Phillips
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Neev Trehan
- St Richards Hospital, University Hospitals Sussex NHS Foundation Trust, Chichester, West Sussex, PO19 6SE, UK
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jean L Koff
- Winship Cancer Center, Emory University School of Medicine, Atlanta, GA, 30307, USA
| | - Ankur Singh
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30318, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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8
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Bullard MR, Cervantes JCM, Quaicoe NB, Jin A, Adams DA, Lin JM, Iliadis E, Seidler TM, Cervantes-Sandoval I, He HY. Accelerated protein retention expansion microscopy using microwave radiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593228. [PMID: 38766072 PMCID: PMC11100821 DOI: 10.1101/2024.05.11.593228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Protein retention expansion microscopy (ExM) retains genetically encoded fluorescent proteins or antibody-conjugated fluorescent probes in fixed tissue and isotropically expands the tissue through a swellable polymer network to allow nanoscale (<70 nm) resolution on diffraction-limited confocal microscopes. Despite numerous advantages ExM brings to biological studies, the full protocol is time-consuming and can take multiple days to complete. Here, we adapted the ExM protocol to the vibratome-sectioned brain tissue of Xenopus laevis tadpoles and implemented a microwave-assisted protocol to reduce the workflow from days to hours. In addition to the significantly accelerated processing time, our microwave-assisted ExM (M/WExM) protocol maintains the superior resolution and signal-to-noise ratio of the original ExM protocol. Furthermore, the M/WExM protocol yields higher magnitude of expansion, suggesting that in addition to accelerating the process through increased diffusion rate of reagents, microwave radiation may also facilitate the expansion process. To demonstrate the applicability of this method to other specimens and protocols, we adapted the microwave-accelerated protocol to whole mount adult brain tissue of Drosophila melanogaster fruit flies, and successfully reduced the total processing time of a widely-used Drosophila IHC-ExM protocol from 6 days to 2 days. Our results demonstrate that with appropriate adjustment of the microwave parameters (wattage, pulse duration, interval, and number of cycles), this protocol can be readily adapted to different model organisms and tissue types to greatly increase the efficiency of ExM experiments.
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Affiliation(s)
| | | | | | - Amanda Jin
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Danya A. Adams
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Jessica M. Lin
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Elena Iliadis
- Department of Biology, Georgetown University, Washington, DC 20057
| | - Tess M. Seidler
- Department of Biology, Georgetown University, Washington, DC 20057
| | | | - Hai-yan He
- Department of Biology, Georgetown University, Washington, DC 20057
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9
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Castagnini D, Palma K, Jara-Wilde J, Navarro N, González MJ, Toledo J, Canales-Huerta N, Scavone P, Härtel S. Proteus mirabilis biofilm expansion microscopy yields over 4-fold magnification for super-resolution of biofilm structure and subcellular DNA organization. J Microbiol Methods 2024; 220:106927. [PMID: 38561125 DOI: 10.1016/j.mimet.2024.106927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Bacterial biofilms form when bacteria attach to surfaces and generate an extracellular matrix that embeds and stabilizes a growing community. Detailed visualization and quantitative analysis of biofilm architecture by optical microscopy are limited by the law of diffraction. Expansion Microscopy (ExM) is a novel Super-Resolution technique where specimens are physically enlarged by a factor of ∼4, prior to observation by conventional fluorescence microscopy. ExM requires homogenization of rigid constituents of biological components by enzymatic digestion. We developed an ExM approach capable of expanding 48-h old Proteus mirabilis biofilms 4.3-fold (termed PmbExM), close to the theoretic maximum expansion factor without gross shape distortions. Our protocol, based on lytic and glycoside-hydrolase enzymatic treatments, degrades rigid components in bacteria and extracellular matrix. Our results prove PmbExM to be a versatile and easy-to-use Super-Resolution approach for enabling studies of P. mirabilis biofilm architecture, assembly, and even intracellular features, such as DNA organization.
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Affiliation(s)
- Dante Castagnini
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile
| | - Karina Palma
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Jorge Jara-Wilde
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nicolás Navarro
- Advanced Center for Chronic Diseases ACCDiS, Santiago, Chile.; Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - María José González
- Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Jorge Toledo
- Red de Equipamiento Científico Avanzado REDECA, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nicole Canales-Huerta
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile
| | - Paola Scavone
- Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Steffen Härtel
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile; National Center for Health Information Systems CENS, Santiago, Chile.; Red de Equipamiento Científico Avanzado REDECA, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Centro de Modelamiento Matemático, Universidad de Chile, Beauchef 851, Casilla 170-3, Santiago, Chile.
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10
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White-Mathieu BM, Baskin JM. Super-Resolution Imaging of Clickable Lipids With Lipid Expansion Microscopy (LExM). Curr Protoc 2024; 4:e1051. [PMID: 38779885 PMCID: PMC11125533 DOI: 10.1002/cpz1.1051] [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: 05/25/2024]
Abstract
Fluorescent imaging of cellular membranes is challenged by the size of lipid bilayers, which are smaller than the diffraction limit of light. Recently, expansion microscopy (ExM) has emerged as an approachable super-resolution method that requires only widely accessible confocal microscopes. In this method, biomolecules of interest are anchored to hydrogel-based, polymeric networks that are expanded through osmosis to physically separate and resolve features smaller than the diffraction limit of light. Whereas ExM has been employed for super-resolution imaging of proteins, DNA, RNA, and glycans, the application of this method to the study of lipids is challenged by the requirement of permeabilization procedures that remove lipids and compromise the integrity of the membrane. Here, we describe our recently developed protocols for lipid expansion microscopy (LExM), a method that enables ExM of membranes without permeabilization. These detailed protocols and accompanying commentary sections aim to make LExM accessible to any experimentalist interested in imaging membranes with super-resolution. © 2024 Wiley Periodicals LLC. Basic Protocol 1: LExM of alkyne-choline lipids Basic Protocol 2: LExM of IMPACT-labeled lipids Basic Protocol 3: LExM of clickable cholesterol Basic Protocol 4: Determining the expansion factor.
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Affiliation(s)
- Brittany M. White-Mathieu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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11
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Delling JP, Bauer HF, Gerlach-Arbeiter S, Schön M, Jacob C, Wagner J, Pedro MT, Knöll B, Boeckers TM. Combined expansion and STED microscopy reveals altered fingerprints of postsynaptic nanostructure across brain regions in ASD-related SHANK3-deficiency. Mol Psychiatry 2024:10.1038/s41380-024-02559-9. [PMID: 38649753 DOI: 10.1038/s41380-024-02559-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Synaptic dysfunction is a key feature of SHANK-associated disorders such as autism spectrum disorder, schizophrenia, and Phelan-McDermid syndrome. Since detailed knowledge of their effect on synaptic nanostructure remains limited, we aimed to investigate such alterations in ex11|SH3 SHANK3-KO mice combining expansion and STED microscopy. This enabled high-resolution imaging of mosaic-like arrangements formed by synaptic proteins in both human and murine brain tissue. We found distinct shape-profiles as fingerprints of the murine postsynaptic scaffold across brain regions and genotypes, as well as alterations in the spatial and molecular organization of subsynaptic domains under SHANK3-deficient conditions. These results provide insights into synaptic nanostructure in situ and advance our understanding of molecular mechanisms underlying synaptic dysfunction in neuropsychiatric disorders.
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Affiliation(s)
- Jan Philipp Delling
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany.
- Max Planck Institute of Psychiatry, Munich, 80804, Germany.
| | | | | | - Michael Schön
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany
| | - Christian Jacob
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany
| | - Jan Wagner
- Department of Neurology, Ulm University, Ulm, 89081, Germany
| | | | - Bernd Knöll
- Institute of Neurobiochemistry, Ulm University, Ulm, 89081, Germany
| | - Tobias M Boeckers
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, 89081, Germany.
- Ulm Site, DZNE, Ulm, 89081, Germany.
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12
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Pannoni KE, Fischer QS, Tarannum R, Cawley ML, Alsalman MM, Acosta N, Ezigbo C, Gil DV, Campbell LA, Farris S. MCU-enriched dendritic mitochondria regulate plasticity in distinct hippocampal circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.10.566606. [PMID: 37986798 PMCID: PMC10659405 DOI: 10.1101/2023.11.10.566606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Mitochondria are dynamic organelles that are morphologically and functionally diverse across cell types and subcellular compartments in order to meet unique energy demands. Mitochondrial dysfunction has been implicated in a wide variety of neurological disorders, including psychiatric disorders like schizophrenia and bipolar disorder. Despite it being well known that mitochondria are essential for synaptic transmission and synaptic plasticity, the mechanisms regulating mitochondria in support of normal synapse function are incompletely understood. The mitochondrial calcium uniporter (MCU) regulates calcium entry into the mitochondria, which in turn regulates the bioenergetics and distribution of mitochondria to active synapses. Evidence suggests that calcium influx via MCU couples neuronal activity to mitochondrial metabolism and ATP production, which would allow neurons to rapidly adapt to changing energy demands. Intriguingly, MCU is uniquely enriched in hippocampal CA2 distal dendrites relative to neighboring hippocampal CA1 or CA3 distal dendrites, however, the functional significance of this enrichment is not clear. Synapses from the entorhinal cortex layer II (ECII) onto CA2 distal dendrites readily express long term potentiation (LTP), unlike the LTP-resistant synapses from CA3 onto CA2 proximal dendrites, but the mechanisms underlying these different plasticity profiles are unknown. We hypothesized that enrichment of MCU near ECII-CA2 synapses promotes LTP in an otherwise plasticity-restricted cell type. Using a CA2-specific MCU knockout (cKO) mouse, we found that MCU is required for LTP at distal dendrite synapses but does not affect the lack of LTP at proximal dendrite synapses. Loss of LTP at ECII-CA2 synapses correlated with a trend for decreased spine density in CA2 distal dendrites of cKO mice compared to control (CTL) mice, which was predominantly seen in immature spines. Moreover, mitochondria were significantly smaller and more numerous across all dendritic layers of CA2 in cKO mice compared to CTL mice, suggesting an overall increase in mitochondrial fragmentation. Fragmented mitochondria might have functional changes, such as altered ATP production, that might explain a deficit in synaptic plasticity. Collectively, our data reveal that MCU regulates layer-specific forms of plasticity in CA2 dendrites, potentially by maintaining proper mitochondria morphology and distribution within dendrites. Differences in MCU expression across different cell types and circuits might be a general mechanism to tune the sensitivity of mitochondria to cytoplasmic calcium levels to power synaptic plasticity.
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Affiliation(s)
- Katy E. Pannoni
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Quentin S. Fischer
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Renesa Tarannum
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia
| | - Mikel L. Cawley
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia
| | - Mayd M. Alsalman
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Nicole Acosta
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Chisom Ezigbo
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Daniela V. Gil
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Logan A. Campbell
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Shannon Farris
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia
- Virginia Tech Carilion School of Medicine, Roanoke, Virginia
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13
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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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14
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Orlowski A, Karippaparambil J, Paumier JM, Ghanta S, Pallares E, Tandukar J, Gao R, Gowrishankar S. Axonal organelle buildup from loss of AP-4 complex function causes exacerbation of amyloid plaque pathology and gliosis in Alzheimer's disease mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587499. [PMID: 38617351 PMCID: PMC11014495 DOI: 10.1101/2024.03.31.587499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Lysosomes and related precursor organelles robustly build up in swollen axons that surround amyloid plaques and disrupted axonal lysosome transport has been implicated in worsening Alzheimer's pathology. Our prior studies have revealed that loss of Adaptor protein-4 (AP-4) complex function, linked primarily to Spastic Paraplegia (HSP), leads to a similar build of lysosomes in structures we term "AP-4 dystrophies". Surprisingly, these AP-4 dystrophies were also characterized by enrichment of components of APP processing machinery, β-site cleaving enzyme 1 (BACE1) and Presenilin 2. Our studies examining whether the abnormal axonal lysosome build up resulting from AP-4 loss could lead to amyloidogenesis revealed that the loss of AP-4 complex function in an Alzheimer's disease model resulted in a strong increase in size and abundance of amyloid plaques in the hippocampus and corpus callosum as well as increased microglial association with the plaques. Interestingly, we found a further increase in enrichment of the secretase, BACE1, in the axonal swellings of the plaques of Alzheimer model mice lacking AP-4 complex compared to those having normal AP-4 complex function, suggestive of increased amyloidogenic processing under this condition. Additionally, the exacerbation of plaque pathology was region-specific as it did not increase in the cortex. The burden of the AP-4 linked axonal dystrophies/AP-4 dystrophies was higher in the corpus callosum and hippocampus compared to the cortex, establishing the critical role of AP-4 -dependent axonal lysosome transport and maturation in regulating amyloidogenic amyloid precursor protein processing.
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Affiliation(s)
- Alex Orlowski
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Joseph Karippaparambil
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Jean-Michel Paumier
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Shraddha Ghanta
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Eduardo Pallares
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
| | - Jamuna Tandukar
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Ruixuan Gao
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL 60607 USA
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612 USA
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15
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Sanfilippo P, Kim AJ, Bhukel A, Yoo J, Mirshahidi PS, Pandey V, Bevir H, Yuen A, Mirshahidi PS, Guo P, Li HS, Wohlschlegel JA, Aso Y, Zipursky SL. Mapping of multiple neurotransmitter receptor subtypes and distinct protein complexes to the connectome. Neuron 2024; 112:942-958.e13. [PMID: 38262414 PMCID: PMC10957333 DOI: 10.1016/j.neuron.2023.12.014] [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: 08/28/2023] [Revised: 12/03/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024]
Abstract
Neurons express various combinations of neurotransmitter receptor (NR) subunits and receive inputs from multiple neuron types expressing different neurotransmitters. Localizing NR subunits to specific synaptic inputs has been challenging. Here, we use epitope-tagged endogenous NR subunits, expansion light-sheet microscopy, and electron microscopy (EM) connectomics to molecularly characterize synapses in Drosophila. We show that in directionally selective motion-sensitive neurons, different multiple NRs elaborated a highly stereotyped molecular topography with NR localized to specific domains receiving cell-type-specific inputs. Developmental studies suggested that NRs or complexes of them with other membrane proteins determine patterns of synaptic inputs. In support of this model, we identify a transmembrane protein selectively associated with a subset of spatially restricted synapses and demonstrate its requirement for synapse formation through genetic analysis. We propose that mechanisms that regulate the precise spatial distribution of NRs provide a molecular cartography specifying the patterns of synaptic connections onto dendrites.
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Affiliation(s)
- Piero Sanfilippo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander J Kim
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anuradha Bhukel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Juyoun Yoo
- Neuroscience Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pegah S Mirshahidi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Vijaya Pandey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Harry Bevir
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ashley Yuen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Parmis S Mirshahidi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Peiyi Guo
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hong-Sheng Li
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yoshinori Aso
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - S Lawrence Zipursky
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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16
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Pesce L, Ricci P, Sportelli G, Belcari N, Sancataldo G. Expansion and Light-Sheet Microscopy for Nanoscale 3D Imaging. SMALL METHODS 2024:e2301715. [PMID: 38461540 DOI: 10.1002/smtd.202301715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/10/2024] [Indexed: 03/12/2024]
Abstract
Expansion Microscopy (ExM) and Light-Sheet Fluorescence Microscopy (LSFM) are forefront imaging techniques that enable high-resolution visualization of biological specimens. ExM enhances nanoscale investigation using conventional fluorescence microscopes, while LSFM offers rapid, minimally invasive imaging over large volumes. This review explores the joint advancements of ExM and LSFM, focusing on the excellent performance of the integrated modality obtained from the combination of the two, which is refer to as ExLSFM. In doing so, the chemical processes required for ExM, the tailored optical setup of LSFM for examining expanded samples, and the adjustments in sample preparation for accurate data collection are emphasized. It is delve into various specimen types studied using this integrated method and assess its potential for future applications. The goal of this literature review is to enrich the comprehension of ExM and LSFM, encouraging their wider use and ongoing development, looking forward to the upcoming challenges, and anticipating innovations in these imaging techniques.
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Affiliation(s)
- Luca Pesce
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Pietro Ricci
- Department of Applied Physics, University of Barcelona, C/Martí i Franquès, 1, Barcelona, 08028, Spain
| | - Giancarlo Sportelli
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Nicola Belcari
- Department of Physics - Enrico Fermi, University of Pisa, Largo Pontecorvo, 3, Pisa, 56127, Italy
| | - Giuseppe Sancataldo
- Department of Physics - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, Palermo, 90128, Italy
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17
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Agi E, Reifenstein ET, Wit C, Schneider T, Kauer M, Kehribar M, Kulkarni A, von Kleist M, Hiesinger PR. Axonal self-sorting without target guidance in Drosophila visual map formation. Science 2024; 383:1084-1092. [PMID: 38452066 DOI: 10.1126/science.adk3043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
The idea of guidance toward a target is central to axon pathfinding and brain wiring in general. In this work, we show how several thousand axonal growth cones self-pattern without target-dependent guidance during neural superposition wiring in Drosophila. Ablation of all target lamina neurons or loss of target adhesion prevents the stabilization but not the development of the pattern. Intravital imaging at the spatiotemporal resolution of growth cone dynamics in intact pupae and data-driven dynamics simulations reveal a mechanism by which >30,000 filopodia do not explore potential targets, but instead simultaneously generate and navigate a dynamic filopodial meshwork that steers growth directions. Hence, a guidance mechanism can emerge from the interactions of the axons being guided, suggesting self-organization as a more general feature of brain wiring.
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Affiliation(s)
- Egemen Agi
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Eric T Reifenstein
- Department of Mathematics, Free University of Berlin, 14195 Berlin, Germany
| | - Charlotte Wit
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Teresa Schneider
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Monika Kauer
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Melinda Kehribar
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Abhishek Kulkarni
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
| | - Max von Kleist
- Department of Mathematics, Free University of Berlin, 14195 Berlin, Germany
| | - P Robin Hiesinger
- Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany
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18
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Faust TE, Lee YH, O’Connor CD, Boyle MA, Gunner G, Badimon A, Ayata P, Schaefer A, Schafer DP. Microglia-astrocyte crosstalk regulates synapse remodeling via Wnt signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.579178. [PMID: 38370645 PMCID: PMC10871360 DOI: 10.1101/2024.02.08.579178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Astrocytes and microglia are emerging key regulators of activity-dependent synapse remodeling that engulf and remove synapses in response to changes in neural activity. Yet, the degree to which these cells communicate to coordinate this process remains an open question. Here, we use whisker removal in postnatal mice to induce activity-dependent synapse removal in the barrel cortex. We show that astrocytes do not engulf synapses in this paradigm. Instead, astrocytes reduce their contact with synapses prior to microglia-mediated synapse engulfment. We further show that reduced astrocyte-contact with synapses is dependent on microglial CX3CL1-CX3CR1 signaling and release of Wnts from microglia following whisker removal. These results demonstrate an activity-dependent mechanism by which microglia instruct astrocyte-synapse interactions, which then provides a permissive environment for microglia to remove synapses. We further show that this mechanism is critical to remodel synapses in a changing sensory environment and this signaling is upregulated in several disease contexts.
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Affiliation(s)
- Travis E. Faust
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Yi-Han Lee
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Ciara D. O’Connor
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada K7L 3N6
- These authors contributed equally
| | - Margaret A. Boyle
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- These authors contributed equally
| | - Georgia Gunner
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Ana Badimon
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Patricia and John Rosenwald Laboratory of Neurobiology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Pinar Ayata
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Neuroscience Initiative, Advanced Science Research Center, The City University of New York Graduate Center, New York, NY 10031, USA
| | - Anne Schaefer
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Dorothy P. Schafer
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Lead contact
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19
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Haak A, Lesslich HM, Dietzel ID. Visualization of the membrane surface and cytoskeleton of oligodendrocyte progenitor cell growth cones using a combination of scanning ion conductance and four times expansion microscopy. Biol Chem 2024; 405:31-41. [PMID: 37950644 DOI: 10.1515/hsz-2023-0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/17/2023] [Indexed: 11/13/2023]
Abstract
Growth cones of oligodendrocyte progenitor cells (OPCs) are challenging to investigate with conventional light microscopy due to their small size. Especially substructures such as filopodia, lamellipodia and their underlying cytoskeleton are difficult to resolve with diffraction limited microscopy. Light microscopy techniques, which surpass the diffraction limit such as stimulated emission depletion microscopy, often require expensive setups and specially trained personnel rendering them inaccessible to smaller research groups. Lately, the invention of expansion microscopy (ExM) has enabled super-resolution imaging with any light microscope without the need for additional equipment. Apart from the necessary resolution, investigating OPC growth cones comes with another challenge: Imaging the topography of membranes, especially label- and contact-free, is only possible with very few microscopy techniques one of them being scanning ion conductance microscopy (SICM). We here present a new imaging workflow combining SICM and ExM, which enables the visualization of OPC growth cone nanostructures. We correlated SICM recordings and ExM images of OPC growth cones captured with a conventional widefield microscope. This enabled the visualization of the growth cones' membrane topography as well as their underlying actin and tubulin cytoskeleton.
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Affiliation(s)
- Annika Haak
- Nanoscopy, RUBION, Ruhr-Universität Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
| | - Heiko M Lesslich
- Nanoscopy, RUBION, Ruhr-Universität Bochum, Universitätsstraße 150, D-44801 Bochum, Germany
| | - Irmgard D Dietzel
- Department of Biochemistry II, Electrobiochemistry of Neural Cells, Ruhr-Universität Bochum, D-44801 Bochum, Germany
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20
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Murigneux E, Softic L, Aubé C, Grandi C, Judith D, Bruce J, Le Gall M, Guillonneau F, Schmitt A, Parissi V, Berlioz-Torrent C, Meertens L, Hansen MMK, Gallois-Montbrun S. Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly. Nat Commun 2024; 15:640. [PMID: 38245532 PMCID: PMC10799903 DOI: 10.1038/s41467-024-44958-0] [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: 12/13/2022] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
Considerable progress has been made in understanding the molecular host-virus battlefield during SARS-CoV-2 infection. Nevertheless, the assembly and egress of newly formed virions are less understood. To identify host proteins involved in viral morphogenesis, we characterize the proteome of SARS-CoV-2 virions produced from A549-ACE2 and Calu-3 cells, isolated via ultracentrifugation on sucrose cushion or by ACE-2 affinity capture. Bioinformatic analysis unveils 92 SARS-CoV-2 virion-associated host factors, providing a valuable resource to better understand the molecular environment of virion production. We reveal that G3BP1 and G3BP2 (G3BP1/2), two major stress granule nucleators, are embedded within virions and unexpectedly favor virion production. Furthermore, we show that G3BP1/2 participate in the formation of cytoplasmic membrane vesicles, that are likely virion assembly sites, consistent with a proviral role of G3BP1/2 in SARS-CoV-2 dissemination. Altogether, these findings provide new insights into host factors required for SARS-CoV-2 assembly with potential implications for future therapeutic targeting.
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Affiliation(s)
- Emilie Murigneux
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Laurent Softic
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Corentin Aubé
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Carmen Grandi
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, the Netherlands
| | - Delphine Judith
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Johanna Bruce
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Morgane Le Gall
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - François Guillonneau
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
- Institut de Cancérologie de l'Ouest (ICO), CRCi2NA-Inserm UMR 1307, CNRS UMR 6075, Nantes Université, Angers, France
| | - Alain Schmitt
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Vincent Parissi
- Microbiologie Fondamentale et Pathogénicité Laboratory (MFP), UMR 5234, « Mobility of pathogenic genomes and chromatin dynamics » team (MobilVIR), CNRS-University of Bordeaux, DyNAVIR network, Bordeaux, France
| | | | - Laurent Meertens
- Université Paris Cité, Inserm U944, CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, the Netherlands
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21
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Dei N, Ishihara K, Matsumoto A, Kojima C. Preparation and Characterization of Acrylic and Methacrylic Phospholipid-Mimetic Polymer Hydrogels and Their Applications in Optical Tissue Clearing. Polymers (Basel) 2024; 16:241. [PMID: 38257040 PMCID: PMC10820725 DOI: 10.3390/polym16020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/28/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The 2-methacryloyloxyethyl phosphorylcholine (MPC) polymers are mimetic to phospholipids, being widely used as biocompatible polymers. In our previous study, MPC polymer hydrogels proved more effective for optical tissue clearing compared to acrylamide (AAm) polymer hydrogels. In the present study, 2-acryloyloxyethyl phosphorylcholine (APC) was synthesized and employed to create hydrogels for a comparative analysis with methacrylic MPC-based hydrogels. APC, an acrylic monomer, was copolymerized with AAm in a similar reactivity. In contrast, MPC, as a methacrylic monomer, demonstrated higher copolymerization reactivity than AAm, leading to a spontaneously delayed two-step polymerization behavior. This suggests that the polymer sequences and network structures became heterogeneous when both methacrylic and acrylic monomers, as well as crosslinkers, were present in the copolymerization system. The molecular weight of the APC polymers was considerably smaller than that of the MPC polymers due to the formation of mid-chain radicals and subsequent β-scission during polymerization. The swelling ratios in water and strain sweep profiles of hydrogels prepared using acrylic and methacrylic compounds differed from those of hydrogels prepared using only acrylic compounds. This implies that copolymerization reactivity influences the polymer network structures and crosslinking density in addition to the copolymer composition. APC-based hydrogels are effective for the optical clearing of tumor tissues and are applicable to both passive and electrophoretic methods.
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Affiliation(s)
- Nanako Dei
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Osaka, Japan (A.M.)
| | - Kazuhiko Ishihara
- Division of Materials & Manufacturing Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan;
| | - Akikazu Matsumoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Osaka, Japan (A.M.)
| | - Chie Kojima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531, Osaka, Japan (A.M.)
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22
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Rumyantseva NA, Golofeeva DM, Vedyaykin AD. SulA does not sequester FtsZ in Escherichia coli cells during the SOS response. Biochem Biophys Res Commun 2024; 691:149313. [PMID: 38035405 DOI: 10.1016/j.bbrc.2023.149313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
In Escherichia coli, the SulA protein is synthesized during the SOS response to arrest cell division. Two possible models of SulA action were proposed: the sequestration and the capping. In current paper, to clarify which model better reflects the SulA effect on cell division upon the SOS response, the FtsZ/SulA ratio was estimated inside cells based on fusion of both FtsZ and SulA to fluorescent protein mNeonGreen. This allowed to quantify this ratio by fluorescence microscopy as well as western blotting; moreover, the effect of SulA on FtsZ distribution patterns in cells was analyzed based on fluorescence microscopy images. The SulA concentration in cells under the SOS response was shown to be several times (about 10) lower than that of FtsZ. The effect of SulA was unequal to corresponding decrease in FtsZ concentration. These results are supported by uneven FtsZ distribution in cells under the SOS response. Together the results of current work indicate that the division arrest by SulA protein in E. coli cells could not be explained by the sequestration model.
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Affiliation(s)
- Natalia A Rumyantseva
- Peter the Great St.Petersburg Polytechnic University (SPbPU), Saint-Petersburg, Russia
| | - Daria M Golofeeva
- Peter the Great St.Petersburg Polytechnic University (SPbPU), Saint-Petersburg, Russia
| | - Alexey D Vedyaykin
- Peter the Great St.Petersburg Polytechnic University (SPbPU), Saint-Petersburg, Russia.
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23
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Veneruso V, Petillo E, Pizzetti F, Orro A, Comolli D, De Paola M, Verrillo A, Baggiolini A, Votano S, Castiglione F, Sponchioni M, Forloni G, Rossi F, Veglianese P. Synergistic Pharmacological Therapy to Modulate Glial Cells in Spinal Cord Injury. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307747. [PMID: 37990971 DOI: 10.1002/adma.202307747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/10/2023] [Indexed: 11/23/2023]
Abstract
Current treatments for modulating the glial-mediated inflammatory response after spinal cord injury (SCI) have limited ability to improve recovery. This is quite likely due to the lack of a selective therapeutic approach acting on microgliosis and astrocytosis, the glia components most involved after trauma, while maximizing efficacy and minimizing side effects. A new nanogel that can selectively release active compounds in microglial cells and astrocytes is developed and characterized. The degree of selectivity and subcellular distribution of the nanogel is evaluated by applying an innovative super-resolution microscopy technique, expansion microscopy. Two different administration schemes are then tested in a SCI mouse model: in an early phase, the nanogel loaded with Rolipram, an anti-inflammatory drug, achieves significant improvement in the animal's motor performance due to the increased recruitment of microglia and macrophages that are able to localize the lesion. Treatment in the late phase, however, gives opposite results, with worse motor recovery because of the widespread degeneration. These findings demonstrate that the nanovector can be selective and functional in the treatment of the glial component in different phases of SCI. They also open a new therapeutic scenario for tackling glia-mediated inflammation after neurodegenerative events in the central nervous system.
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Affiliation(s)
- Valeria Veneruso
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, via Buffi 13, Lugano, 6900, Switzerland
| | - Emilia Petillo
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Fabio Pizzetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Alessandro Orro
- Department of Biomedical Sciences National Research Council, Institute for Biomedical Technologies, Via Fratelli Cervi 93, Segrate, 20054, Italy
| | - Davide Comolli
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Massimiliano De Paola
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Antonietta Verrillo
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, via Buffi 13, Lugano, 6900, Switzerland
- Institute of Oncology Research (IOR), BIOS+, Via Francesco Chiesa 5, Bellinzona, 6500, Switzerland
| | - Arianna Baggiolini
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, via Buffi 13, Lugano, 6900, Switzerland
- Institute of Oncology Research (IOR), BIOS+, Via Francesco Chiesa 5, Bellinzona, 6500, Switzerland
| | - Simona Votano
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Franca Castiglione
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Mattia Sponchioni
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Gianluigi Forloni
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Filippo Rossi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Pietro Veglianese
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, via Buffi 13, Lugano, 6900, Switzerland
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24
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Wang UTT, Tian X, Liou YH, Lee SP, Hu HT, Lu CH, Lin PT, Cheng YJ, Chen P, Chen BC. Protein and lipid expansion microscopy with trypsin and tyramide signal amplification for 3D imaging. Sci Rep 2023; 13:21922. [PMID: 38081848 PMCID: PMC10713663 DOI: 10.1038/s41598-023-48959-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Expansion microscopy, whereby the relative positions of biomolecules are physically increased via hydrogel expansion, can be used to reveal ultrafine structures of cells under a conventional microscope. Despite its utility for achieving super-resolution imaging, expansion microscopy suffers a major drawback, namely reduced fluorescence signals caused by excessive proteolysis and swelling effects. This caveat results in a lower photon budget and disfavors fluorescence imaging over a large field of view that can cover an entire expanded cell, especially in 3D. In addition, the complex procedures and specialized reagents of expansion microscopy hinder its popularization. Here, we modify expansion microscopy by deploying trypsin digestion to reduce protein loss and tyramide signal amplification to enhance fluorescence signal for point-scanning-based imaging. We name our new methodology TT-ExM to indicate dual trypsin and tyramide treatments. TT-ExM may be applied for both antibody and lipid staining. TT-ExM displayed enhanced protein retention for endoplasmic reticulum and mitochondrial markers in COS-7 cell cultures. Importantly, TT-ExM-based lipid staining clearly revealed the complex 3D membrane structures in entire expanded cells. Through combined lipid and DNA staining, our TT-ExM methodology highlighted mitochondria by revealing their DNA and membrane structures in cytoplasm, as well as the lipid-rich structures formed via phase separation in nuclei at interphase. We also observed lipid-rich chromosome matrices in the mitotic cells. These high-quality 3D images demonstrate the practicality of TT-ExM. Thus, readily available reagents can be deployed in TT-ExM to significantly enhance fluorescence signals and generate high-quality and ultrafine-resolution images under confocal microscopy.
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Affiliation(s)
- Ueh-Ting Tim Wang
- Affiliated Senior High School of National Taiwan Normal University, Taipei, 106348, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taipei, 11529, Taiwan
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yae-Huei Liou
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Sue-Ping Lee
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiao-Tang Hu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
- Institute and Undergraduate Program of Electro-Optical Engineering, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Po-Ting Lin
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Ya-Jen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
- Neuroscience Program, NPAS, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.
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25
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Jentoft IMA, Bäuerlein FJB, Welp LM, Cooper BH, Petrovic A, So C, Penir SM, Politi AZ, Horokhovskyi Y, Takala I, Eckel H, Moltrecht R, Lénárt P, Cavazza T, Liepe J, Brose N, Urlaub H, Fernández-Busnadiego R, Schuh M. Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices. Cell 2023; 186:5308-5327.e25. [PMID: 37922900 DOI: 10.1016/j.cell.2023.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/01/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023]
Abstract
Mammalian oocytes are filled with poorly understood structures called cytoplasmic lattices. First discovered in the 1960s and speculated to correspond to mammalian yolk, ribosomal arrays, or intermediate filaments, their function has remained enigmatic to date. Here, we show that cytoplasmic lattices are sites where oocytes store essential proteins for early embryonic development. Using super-resolution light microscopy and cryoelectron tomography, we show that cytoplasmic lattices are composed of filaments with a high surface area, which contain PADI6 and subcortical maternal complex proteins. The lattices associate with many proteins critical for embryonic development, including proteins that control epigenetic reprogramming of the preimplantation embryo. Loss of cytoplasmic lattices by knocking out PADI6 or the subcortical maternal complex prevents the accumulation of these proteins and results in early embryonic arrest. Our work suggests that cytoplasmic lattices enrich maternally provided proteins to prevent their premature degradation and cellular activity, thereby enabling early mammalian development.
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Affiliation(s)
- Ida M A Jentoft
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Felix J B Bäuerlein
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Benjamin H Cooper
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
| | - Arsen Petrovic
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Chun So
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Sarah Mae Penir
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Antonio Z Politi
- Facility for Light Microscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Yehor Horokhovskyi
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Iina Takala
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Heike Eckel
- Kinderwunschzentrum Göttingen, 37081 Göttingen, Germany
| | | | - Peter Lénárt
- Facility for Light Microscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Tommaso Cavazza
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Juliane Liepe
- Quantitative and Systems Biology Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Nils Brose
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
| | - Henning Urlaub
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Rubén Fernández-Busnadiego
- Institute for Neuropathology, University Medical Center Göttingen, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany; Faculty of Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany.
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26
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Balaram P, Takasaki K, Hellevik A, Tandukar J, Turschak E, MacLennan B, Ouellette N, Torres R, Laughland C, Gliko O, Seshamani S, Perlman E, Taormina M, Peterson E, Juneau Z, Potekhina L, Glaser A, Chandrashekar J, Logsdon M, Cao K, Dylla C, Hatanaka G, Chatterjee S, Ting J, Vumbaco D, Waters J, Bair W, Tsao D, Gao R, Reid C. Microscale visualization of cellular features in adult macaque visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565381. [PMID: 37961179 PMCID: PMC10635096 DOI: 10.1101/2023.11.02.565381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Expansion microscopy and light sheet imaging enable fine-scale resolution of intracellular features that comprise neural circuits. Most current techniques visualize sparsely distributed features across whole brains or densely distributed features within individual brain regions. Here, we visualize dense distributions of immunolabeled proteins across early visual cortical areas in adult macaque monkeys. This process may be combined with multiphoton or magnetic resonance imaging to produce multimodal atlases in large, gyrencephalic brains.
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27
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Kim HY, Lee J, Kim HJ, Lee BE, Jeong J, Cho EJ, Jang HJ, Shin KJ, Kim MJ, Chae YC, Lee SE, Myung K, Baik JH, Suh PG, Kim JI. PLCγ1 in dopamine neurons critically regulates striatal dopamine release via VMAT2 and synapsin III. Exp Mol Med 2023; 55:2357-2375. [PMID: 37907739 PMCID: PMC10689754 DOI: 10.1038/s12276-023-01104-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 11/02/2023] Open
Abstract
Dopamine neurons are essential for voluntary movement, reward learning, and motivation, and their dysfunction is closely linked to various psychological and neurodegenerative diseases. Hence, understanding the detailed signaling mechanisms that functionally modulate dopamine neurons is crucial for the development of better therapeutic strategies against dopamine-related disorders. Phospholipase Cγ1 (PLCγ1) is a key enzyme in intracellular signaling that regulates diverse neuronal functions in the brain. It was proposed that PLCγ1 is implicated in the development of dopaminergic neurons, while the physiological function of PLCγ1 remains to be determined. In this study, we investigated the physiological role of PLCγ1, one of the key effector enzymes in intracellular signaling, in regulating dopaminergic function in vivo. We found that cell type-specific deletion of PLCγ1 does not adversely affect the development and cellular morphology of midbrain dopamine neurons but does facilitate dopamine release from dopaminergic axon terminals in the striatum. The enhancement of dopamine release was accompanied by increased colocalization of vesicular monoamine transporter 2 (VMAT2) at dopaminergic axon terminals. Notably, dopamine neuron-specific knockout of PLCγ1 also led to heightened expression and colocalization of synapsin III, which controls the trafficking of synaptic vesicles. Furthermore, the knockdown of VMAT2 and synapsin III in dopamine neurons resulted in a significant attenuation of dopamine release, while this attenuation was less severe in PLCγ1 cKO mice. Our findings suggest that PLCγ1 in dopamine neurons could critically modulate dopamine release at axon terminals by directly or indirectly interacting with synaptic machinery, including VMAT2 and synapsin III.
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Affiliation(s)
- Hye Yun Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jieun Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hyun-Jin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Byeong Eun Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jaewook Jeong
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Eun Jeong Cho
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hyun-Jun Jang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, 58245, Republic of Korea
| | - Kyeong Jin Shin
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Min Ji Kim
- Department of Life Sciences, Korea University, Seoul, 02841, Korea
| | - Young Chan Chae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Seung Eun Lee
- Research Animal Resource Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Ja-Hyun Baik
- Department of Life Sciences, Korea University, Seoul, 02841, Korea
| | - Pann-Ghill Suh
- Korea Brain Research Institute (KBRI), Daegu, 41062, Republic of Korea
| | - Jae-Ick Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
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28
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Kim HJ, Hwang B, Reva M, Lee J, Lee BE, Lee Y, Cho EJ, Jeong M, Lee SE, Myung K, Baik JH, Park JH, Kim JI. GABAergic-like dopamine synapses in the brain. Cell Rep 2023; 42:113239. [PMID: 37819757 DOI: 10.1016/j.celrep.2023.113239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 08/18/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023] Open
Abstract
Dopamine synapses play a crucial role in volitional movement and reward-related behaviors, while dysfunction of dopamine synapses causes various psychiatric and neurological disorders. Despite this significance, the true biological nature of dopamine synapses remains poorly understood. Here, we show that dopamine transmission is strongly correlated with GABA co-transmission across the brain and dopamine synapses are structured and function like GABAergic synapses with marked regional heterogeneity. In addition, GABAergic-like dopamine synapses are clustered on the dendrites, and GABA transmission at dopamine synapses has distinct physiological properties. Interestingly, the knockdown of neuroligin-2, a key postsynaptic protein at GABAergic synapses, unexpectedly does not weaken GABA co-transmission but instead facilitates it at dopamine synapses in the striatal neurons. More importantly, the attenuation of GABA co-transmission precedes deficits in dopaminergic transmission in animal models of Parkinson's disease. Our findings reveal the spatial and functional nature of GABAergic-like dopamine synapses in health and disease.
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Affiliation(s)
- Hyun-Jin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Byungjae Hwang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Maria Reva
- Institut Pasteur, Unit of Synapse and Circuit Dynamics, CNRS UMR, 3571 Paris, France; Sorbonne University, ED3C, Paris, France
| | - Jieun Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Byeong Eun Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Youngeun Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Eun Jeong Cho
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Minseok Jeong
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seung Eun Lee
- Research Animal Resource Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Kyungjae Myung
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Ja-Hyun Baik
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jung-Hoon Park
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jae-Ick Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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29
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Sanfilippo P, Kim AJ, Bhukel A, Yoo J, Mirshahidi PS, Pandey V, Bevir H, Yuen A, Mirshahidi PS, Guo P, Li HS, Wohlschlegel JA, Aso Y, Zipursky SL. Mapping of multiple neurotransmitter receptor subtypes and distinct protein complexes to the connectome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560011. [PMID: 37873314 PMCID: PMC10592863 DOI: 10.1101/2023.10.02.560011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Neurons express different combinations of neurotransmitter receptor (NR) subunits and receive inputs from multiple neuron types expressing different neurotransmitters. Localizing NR subunits to specific synaptic inputs has been challenging. Here we use epitope tagged endogenous NR subunits, expansion light-sheet microscopy, and EM connectomics to molecularly characterize synapses in Drosophila. We show that in directionally selective motion sensitive neurons, different multiple NRs elaborated a highly stereotyped molecular topography with NR localized to specific domains receiving cell-type specific inputs. Developmental studies suggested that NRs or complexes of them with other membrane proteins determines patterns of synaptic inputs. In support of this model, we identify a transmembrane protein associated selectively with a subset of spatially restricted synapses and demonstrate through genetic analysis its requirement for synapse formation. We propose that mechanisms which regulate the precise spatial distribution of NRs provide a molecular cartography specifying the patterns of synaptic connections onto dendrites.
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Affiliation(s)
- Piero Sanfilippo
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Alexander J Kim
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Anuradha Bhukel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Juyoun Yoo
- Neuroscience Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Pegah S Mirshahidi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Vijaya Pandey
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Harry Bevir
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Ashley Yuen
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Parmis S Mirshahidi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Peiyi Guo
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hong-Sheng Li
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Yoshinori Aso
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - S Lawrence Zipursky
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Lead Contact
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30
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Cheng Z, Stefani C, Skillman T, Klimas A, Lee A, DiBernardo EF, Brown KM, Milman T, Wang Y, Gallagher BR, Lagree K, Jena BP, Pulido JS, Filler SG, Mitchell AP, Hiller NL, Lacy‐Hulbert A, Zhao Y. MicroMagnify: A Multiplexed Expansion Microscopy Method for Pathogens and Infected Tissues. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302249. [PMID: 37658522 PMCID: PMC10602566 DOI: 10.1002/advs.202302249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/29/2023] [Indexed: 09/03/2023]
Abstract
Super-resolution optical imaging tools are crucial in microbiology to understand the complex structures and behavior of microorganisms such as bacteria, fungi, and viruses. However, the capabilities of these tools, particularly when it comes to imaging pathogens and infected tissues, remain limited. MicroMagnify (µMagnify) is developed, a nanoscale multiplexed imaging method for pathogens and infected tissues that are derived from an expansion microscopy technique with a universal biomolecular anchor. The combination of heat denaturation and enzyme cocktails essential is found for robust cell wall digestion and expansion of microbial cells and infected tissues without distortion. µMagnify efficiently retains biomolecules suitable for high-plex fluorescence imaging with nanoscale precision. It demonstrates up to eightfold expansion with µMagnify on a broad range of pathogen-containing specimens, including bacterial and fungal biofilms, infected culture cells, fungus-infected mouse tone, and formalin-fixed paraffin-embedded human cornea infected by various pathogens. Additionally, an associated virtual reality tool is developed to facilitate the visualization and navigation of complex 3D images generated by this method in an immersive environment allowing collaborative exploration among researchers worldwide. µMagnify is a valuable imaging platform for studying how microbes interact with their host systems and enables the development of new diagnosis strategies against infectious diseases.
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Affiliation(s)
- Zhangyu Cheng
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Caroline Stefani
- Benaroya Research Institute at Virginia Mason1201 9th AveSeattleWA98101USA
| | | | - Aleksandra Klimas
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Aramchan Lee
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Emma F. DiBernardo
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Karina Mueller Brown
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Tatyana Milman
- Wills Eye Hospital and Jefferson University HospitalPhiladelphiaPA19107USA
| | - Yuhong Wang
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Brendan R. Gallagher
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Katherine Lagree
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Bhanu P. Jena
- Viron Molecular Medicine Institute201 Washington StreetBostonMA02201USA
- Department of PhysiologyWayne State University42 W Warren AveDetroitMI48202USA
- NanoBioScience InstituteWayne State University42 W Warren AveDetroitMI48202USA
- Center for Molecular Medicine & GeneticsSchool of MedicineWayne State University42 W Warren AveDetroitMI48202USA
| | - Jose S. Pulido
- Wills Eye Hospital and Jefferson University HospitalPhiladelphiaPA19107USA
| | - Scott G. Filler
- Lundquist Institute for Biomedical Innovation at Harbor‐UCLA Medical Center1124 W Carson StTorranceCA90502USA
- David Geffen School of Medicine at UCLA10833 Le Conte AveLos AngelesCA90095USA
| | - Aaron P. Mitchell
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
- Department of MicrobiologyUniversity of Georgia210 S Jackson streetAthensGA30602USA
| | - N. Luisa Hiller
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Adam Lacy‐Hulbert
- Benaroya Research Institute at Virginia Mason1201 9th AveSeattleWA98101USA
| | - Yongxin Zhao
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
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31
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Cui Y, Yang G, Goodwin DR, O’Flanagan CH, Sinha A, Zhang C, Kitko KE, Shin TW, Park D, Aparicio S, Boyden ES. Expansion microscopy using a single anchor molecule for high-yield multiplexed imaging of proteins and RNAs. PLoS One 2023; 18:e0291506. [PMID: 37729182 PMCID: PMC10511132 DOI: 10.1371/journal.pone.0291506] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
Expansion microscopy (ExM), by physically enlarging specimens in an isotropic fashion, enables nanoimaging on standard light microscopes. Key to existing ExM protocols is the equipping of different kinds of molecules, with different kinds of anchoring moieties, so they can all be pulled apart from each other by polymer swelling. Here we present a multifunctional anchor, an acrylate epoxide, that enables proteins and RNAs to be equipped with anchors in a single experimental step. This reagent simplifies ExM protocols and reduces cost (by 2-10-fold for a typical multiplexed ExM experiment) compared to previous strategies for equipping RNAs with anchors. We show that this united ExM (uniExM) protocol can be used to preserve and visualize RNA transcripts, proteins in biologically relevant ultrastructures, and sets of RNA transcripts in patient-derived xenograft (PDX) cancer tissues and may support the visualization of other kinds of biomolecular species as well. uniExM may find many uses in the simple, multimodal nanoscale analysis of cells and tissues.
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Affiliation(s)
- Yi Cui
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Gaojie Yang
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Daniel R. Goodwin
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Ciara H. O’Flanagan
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Anubhav Sinha
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
- Harvard-MIT Program in Health Sciences and Technology, MIT, Cambridge, Massachusetts, United States of America
| | - Chi Zhang
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Kristina E. Kitko
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Tay Won Shin
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Demian Park
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Edward S. Boyden
- McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- Media Arts & Sciences, MIT, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, United States of America
- Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, United States of America
- Koch Institute for Cancer Research, MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, MIT, Cambridge, Massachusetts, United States of America
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32
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Kraft N, Muenz TS, Reinhard S, Werner C, Sauer M, Groh C, Rössler W. Expansion microscopy in honeybee brains for high-resolution neuroanatomical analyses in social insects. Cell Tissue Res 2023; 393:489-506. [PMID: 37421435 PMCID: PMC10484815 DOI: 10.1007/s00441-023-03803-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
The diffraction limit of light microscopy poses a problem that is frequently faced in structural analyses of social insect brains. With the introduction of expansion microscopy (ExM), a tool became available to overcome this limitation by isotropic physical expansion of preserved specimens. Our analyses focus on synaptic microcircuits (microglomeruli, MG) in the mushroom body (MB) of social insects, high-order brain centers for sensory integration, learning, and memory. MG undergo significant structural reorganizations with age, sensory experience, and during long-term memory formation. However, the changes in subcellular architecture involved in this plasticity have only partially been accessed yet. Using the western honeybee Apis mellifera as an experimental model, we established ExM for the first time in a social insect species and applied it to investigate plasticity in synaptic microcircuits within MG of the MB calyces. Using combinations of antibody staining and neuronal tracing, we demonstrate that this technique enables quantitative and qualitative analyses of structural neuronal plasticity at high resolution in a social insect brain.
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Affiliation(s)
- Nadine Kraft
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany.
| | - Thomas S Muenz
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Sebastian Reinhard
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Christian Werner
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Claudia Groh
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
| | - Wolfgang Rössler
- Department of Behavioral Physiology and Sociobiology (Zoology II), Theodor-Boveri-Institute, Biocenter, Julius Maximilian University, Würzburg, 97074, Germany
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33
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Patt L, Tascio D, Domingos C, Timmermann A, Jabs R, Henneberger C, Steinhäuser C, Seifert G. Impact of Developmental Changes of GABA A Receptors on Interneuron-NG2 Glia Transmission in the Hippocampus. Int J Mol Sci 2023; 24:13490. [PMID: 37686294 PMCID: PMC10488269 DOI: 10.3390/ijms241713490] [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: 06/22/2023] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
NG2 glia receive synaptic input from neurons, but the functional impact of this glial innervation is not well understood. In the developing cerebellum and somatosensory cortex the GABAergic input might regulate NG2 glia differentiation and myelination, and a switch from synaptic to extrasynaptic neuron-glia signaling was reported in the latter region. Myelination in the hippocampus is sparse, and most NG2 glia retain their phenotype throughout adulthood, raising the question of the properties and function of neuron-NG2 glia synapses in that brain region. Here, we compared spontaneous and evoked GABAA receptor-mediated currents of NG2 glia in juvenile and adult hippocampi of mice of either sex and assessed the mode of interneuron-glial signaling changes during development. With patch-clamp and pharmacological analyses, we found a decrease in innervation of hippocampal NG2 glia between postnatal days 10 and 60. At the adult stage, enhanced activation of extrasynaptic receptors occurred, indicating a spillover of GABA. This switch from synaptic to extrasynaptic receptor activation was accompanied by downregulation of γ2 and upregulation of the α5 subunit. Molecular analyses and high-resolution expansion microscopy revealed mechanisms of glial GABAA receptor trafficking and clustering. We found that gephyrin and radixin are organized in separate clusters along glial processes. Surprisingly, the developmental loss of γ2 and postsynaptic receptors were not accompanied by altered glial expression of scaffolding proteins, auxiliary receptor subunits or postsynaptic interaction proteins. The GABAergic input to NG2 glia might contribute to the release of neurotrophic factors from these cells and influence neuronal synaptic plasticity.
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Affiliation(s)
- Linda Patt
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (L.P.); (D.T.); (C.D.); (A.T.); (R.J.); (C.H.)
| | - Dario Tascio
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (L.P.); (D.T.); (C.D.); (A.T.); (R.J.); (C.H.)
| | - Catia Domingos
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (L.P.); (D.T.); (C.D.); (A.T.); (R.J.); (C.H.)
| | - Aline Timmermann
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (L.P.); (D.T.); (C.D.); (A.T.); (R.J.); (C.H.)
| | - Ronald Jabs
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (L.P.); (D.T.); (C.D.); (A.T.); (R.J.); (C.H.)
| | - Christian Henneberger
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (L.P.); (D.T.); (C.D.); (A.T.); (R.J.); (C.H.)
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Christian Steinhäuser
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (L.P.); (D.T.); (C.D.); (A.T.); (R.J.); (C.H.)
| | - Gerald Seifert
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (L.P.); (D.T.); (C.D.); (A.T.); (R.J.); (C.H.)
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34
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Petsakou A, Liu Y, Liu Y, Comjean A, Hu Y, Perrimon N. Epithelial Ca 2+ waves triggered by enteric neurons heal the gut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553227. [PMID: 37645990 PMCID: PMC10461974 DOI: 10.1101/2023.08.14.553227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
A fundamental and unresolved question in regenerative biology is how tissues return to homeostasis after injury. Answering this question is essential for understanding the etiology of chronic disorders such as inflammatory bowel diseases and cancer. We used the Drosophila midgut to investigate this question and discovered that during regeneration a subpopulation of cholinergic enteric neurons triggers Ca2+ currents among enterocytes to promote return of the epithelium to homeostasis. Specifically, we found that down-regulation of the cholinergic enzyme Acetylcholinesterase in the epithelium enables acetylcholine from defined enteric neurons, referred as ARCENs, to activate nicotinic receptors in enterocytes found near ARCEN-innervations. This activation triggers high Ca2+ influx that spreads in the epithelium through Inx2/Inx7 gap junctions promoting enterocyte maturation followed by reduction of proliferation and inflammation. Disrupting this process causes chronic injury consisting of ion imbalance, Yki activation and increase of inflammatory cytokines together with hyperplasia, reminiscent of inflammatory bowel diseases. Altogether, we found that during gut regeneration the conserved cholinergic pathway facilitates epithelial Ca2+ waves that heal the intestinal epithelium. Our findings demonstrate nerve- and bioelectric-dependent intestinal regeneration which advance the current understanding of how a tissue returns to its homeostatic state after injury and could ultimately help existing therapeutics.
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Affiliation(s)
| | - Yifang Liu
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Ying Liu
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Aram Comjean
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, USA
- Howard Hughes Medical Institute, Boston, USA
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35
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Pownall ME, Miao L, Vejnar CE, M’Saad O, Sherrard A, Frederick MA, Benitez MD, Boswell CW, Zaret KS, Bewersdorf J, Giraldez AJ. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023; 381:92-100. [PMID: 37410825 PMCID: PMC10372697 DOI: 10.1126/science.ade5308] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
Abstract
Nanoscale chromatin organization regulates gene expression. Although chromatin is notably reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. In this work, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed "kiss and kick", in which enhancer-promoter contacts are transient and released by transcriptional elongation. Our results demonstrate that ChromExM is broadly applicable to study nanoscale nuclear organization.
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Affiliation(s)
- Mark E. Pownall
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Charles E. Vejnar
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Ons M’Saad
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
| | - Alice Sherrard
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Megan A. Frederick
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria D.J. Benitez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Curtis W. Boswell
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
- Department of Physics, Yale University; New Haven, CT 06510, USA
- Nanobiology Institute, Yale University; West Haven, CT 06477, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Cancer Center, Yale University School of Medicine; New Haven, CT 06510, USA
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36
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Kilic Z, Schweiger M, Moyer C, Pressé S. Monte Carlo samplers for efficient network inference. PLoS Comput Biol 2023; 19:e1011256. [PMID: 37463156 DOI: 10.1371/journal.pcbi.1011256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/09/2023] [Indexed: 07/20/2023] Open
Abstract
Accessing information on an underlying network driving a biological process often involves interrupting the process and collecting snapshot data. When snapshot data are stochastic, the data's structure necessitates a probabilistic description to infer underlying reaction networks. As an example, we may imagine wanting to learn gene state networks from the type of data collected in single molecule RNA fluorescence in situ hybridization (RNA-FISH). In the networks we consider, nodes represent network states, and edges represent biochemical reaction rates linking states. Simultaneously estimating the number of nodes and constituent parameters from snapshot data remains a challenging task in part on account of data uncertainty and timescale separations between kinetic parameters mediating the network. While parametric Bayesian methods learn parameters given a network structure (with known node numbers) with rigorously propagated measurement uncertainty, learning the number of nodes and parameters with potentially large timescale separations remain open questions. Here, we propose a Bayesian nonparametric framework and describe a hybrid Bayesian Markov Chain Monte Carlo (MCMC) sampler directly addressing these challenges. In particular, in our hybrid method, Hamiltonian Monte Carlo (HMC) leverages local posterior geometries in inference to explore the parameter space; Adaptive Metropolis Hastings (AMH) learns correlations between plausible parameter sets to efficiently propose probable models; and Parallel Tempering takes into account multiple models simultaneously with tempered information content to augment sampling efficiency. We apply our method to synthetic data mimicking single molecule RNA-FISH, a popular snapshot method in probing transcriptional networks to illustrate the identified challenges inherent to learning dynamical models from these snapshots and how our method addresses them.
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Affiliation(s)
- Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Max Schweiger
- Center for Biological Physics, ASU, Tempe, Arizona, United States of America
- Department of Physics ASU, Tempe, Arizona, United States of America
| | - Camille Moyer
- Center for Biological Physics, ASU, Tempe, Arizona, United States of America
- School of Mathematics and Statistical Sciences, ASU, Tempe, Arizona, United States of America
| | - Steve Pressé
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- Center for Biological Physics, ASU, Tempe, Arizona, United States of America
- School of Molecular Sciences, ASU, Tempe, Arizona, United States of America
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37
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Chan YH, Pathmasiri KC, Pierre-Jacques D, Cologna SM, Gao R. Gel-assisted mass spectrometry imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543480. [PMID: 37398444 PMCID: PMC10312618 DOI: 10.1101/2023.06.02.543480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Compatible with label-free detection and quantification, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of biomolecules in intact specimens. Yet, the spatial resolution of MSI is limited by the method's physical and instrumental constraints, which often preclude it from single-cell and subcellular applications. By taking advantage of the reversible interaction of analytes with superabsorbent hydrogels, we developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome these limits. With GAMSI, the spatial resolution of lipid and protein MALDI-MSI can be enhanced severalfold without changing the existing mass spectrometry hardware and analysis pipeline. This approach will further enhance the accessibility to (sub)cellular-scale MALDI-MSI-based spatial omics.
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Affiliation(s)
- Yat Ho Chan
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
| | | | | | - Stephanie M. Cologna
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago; Chicago, IL 60607, USA
| | - Ruixuan Gao
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago; Chicago, IL 60607, USA
- Department of Biological Sciences, University of Illinois Chicago; Chicago, IL 60607, USA
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38
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Sun C, Desch K, Nassim-Assir B, Giandomenico SL, Nemcova P, Langer JD, Schuman EM. An abundance of free regulatory (19 S) proteasome particles regulates neuronal synapses. Science 2023; 380:eadf2018. [PMID: 37228199 DOI: 10.1126/science.adf2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/04/2023] [Indexed: 05/27/2023]
Abstract
The proteasome, the major protein-degradation machine in cells, regulates neuronal synapses and long-term information storage. Here, using super-resolution microscopy, we found that the two essential subcomplexes of the proteasome, the regulatory (19S) and catalytic (20S) particles, are differentially distributed within individual rat cortical neurons. We discovered an unexpected abundance of free 19S particles near synapses. The free neuronal 19S particles bind and deubiquitylate lysine 63-ubiquitin (Lys63-ub), a non-proteasome-targeting ubiquitin linkage. Pull-down assays revealed a significant overrepresentation of synaptic molecules as Lys63-ub interactors. Inhibition of the 19S deubiquitylase activity significantly altered excitatory synaptic transmission and reduced the synaptic availability of AMPA receptors at multiple trafficking points in a proteasome-independent manner. Together, these results reveal a moonlighting function of the regulatory proteasomal subcomplex near synapses.
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Affiliation(s)
- Chao Sun
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | - Kristina Desch
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | | | | | - Paulina Nemcova
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
- Max Planck Institute for Biophysics, 60438 Frankfurt am Main, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
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39
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Sheth V, Chen X, Mettenbrink EM, Yang W, Jones MA, M’Saad O, Thomas AG, Newport RS, Francek E, Wang L, Frickenstein AN, Donahue ND, Holden A, Mjema NF, Green DE, DeAngelis PL, Bewersdorf J, Wilhelm S. Quantifying Intracellular Nanoparticle Distributions with Three-Dimensional Super-Resolution Microscopy. ACS NANO 2023; 17:8376-8392. [PMID: 37071747 PMCID: PMC10643044 DOI: 10.1021/acsnano.2c12808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Super-resolution microscopy can transform our understanding of nanoparticle-cell interactions. Here, we established a super-resolution imaging technology to visualize nanoparticle distributions inside mammalian cells. The cells were exposed to metallic nanoparticles and then embedded within different swellable hydrogels to enable quantitative three-dimensional (3D) imaging approaching electron-microscopy-like resolution using a standard light microscope. By exploiting the nanoparticles' light scattering properties, we demonstrated quantitative label-free imaging of intracellular nanoparticles with ultrastructural context. We confirmed the compatibility of two expansion microscopy protocols, protein retention and pan-expansion microscopy, with nanoparticle uptake studies. We validated relative differences between nanoparticle cellular accumulation for various surface modifications using mass spectrometry and determined the intracellular nanoparticle spatial distribution in 3D for entire single cells. This super-resolution imaging platform technology may be broadly used to understand the nanoparticle intracellular fate in fundamental and applied studies to potentially inform the engineering of safer and more effective nanomedicines.
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Affiliation(s)
- Vinit Sheth
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Xuxin Chen
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Evan M. Mettenbrink
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Wen Yang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Meredith A. Jones
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Ons M’Saad
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, 06510, USA
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, 06520, USA
- Panluminate, Inc. New Haven, Connecticut, 06516, USA
| | - Abigail G. Thomas
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Rylee S. Newport
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Emmy Francek
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Lin Wang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Alex N. Frickenstein
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Nathan D. Donahue
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Alyssa Holden
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Nathan F. Mjema
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Dixy E. Green
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73126, USA
| | - Paul L. DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73126, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, 06510, USA
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, 06520, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut, 06510 USA
- Department of Physics, Yale University, New Haven, Connecticut, 06511, USA
| | - Stefan Wilhelm
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
- Institute for Biomedical Engineering, Science, and Technology (IBEST), Norman, Oklahoma, 73019, USA
- Stephenson Cancer Center, Oklahoma City, Oklahoma, 73104, USA
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40
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Kim S, Phan S, Shaw TR, Ellisman MH, Veatch SL, Barmada SJ, Pappas SS, Dauer WT. TorsinA is essential for the timing and localization of neuronal nuclear pore complex biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538491. [PMID: 37162852 PMCID: PMC10168336 DOI: 10.1101/2023.04.26.538491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nuclear pore complexes (NPCs) regulate information transfer between the nucleus and cytoplasm. NPC defects are linked to several neurological diseases, but the processes governing NPC biogenesis and spatial organization are poorly understood. Here, we identify a temporal window of strongly upregulated NPC biogenesis during neuronal maturation. We demonstrate that the AAA+ protein torsinA, whose loss of function causes the neurodevelopmental movement disorder DYT-TOR1A (DYT1) dystonia, coordinates NPC spatial organization during this period without impacting total NPC density. Using a new mouse line in which endogenous Nup107 is Halo-Tagged, we find that torsinA is essential for correct localization of NPC formation. In the absence of torsinA, the inner nuclear membrane buds excessively at sites of mislocalized, nascent NPCs, and NPC assembly completion is delayed. Our work implies that NPC spatial organization and number are independently regulated and suggests that torsinA is critical for the normal localization and assembly kinetics of NPCs.
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Affiliation(s)
- Sumin Kim
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA
| | - Thomas R. Shaw
- Department of Biophysics, University of Michigan, Ann Arbor, MI
| | - Mark H. Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA
| | - Sarah L. Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, MI
| | - Sami J. Barmada
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Samuel S. Pappas
- Peter O’Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX
- Department of Neurology, UT Southwestern, Dallas, TX
| | - William T. Dauer
- Peter O’Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX
- Department of Neurology, UT Southwestern, Dallas, TX
- Department of Neuroscience, UT Southwestern, Dallas, TX
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41
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Al Mahbuba D, Masuko S, Wang S, Syangtan D, Kang JS, Song Y, Shin TW, Xia K, Zhang F, Linhardt RJ, Boyden ES, Kiessling LL. Dynamic Changes in Heparan Sulfate Nanostructure in Human Pluripotent Stem Cell Differentiation. ACS NANO 2023; 17:7207-7218. [PMID: 37042659 DOI: 10.1021/acsnano.2c10072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Heparan sulfate (HS) is a heterogeneous, cell-surface polysaccharide critical for transducing signals essential for mammalian development. Imaging of signaling proteins has revealed how their localization influences their information transfer. In contrast, the contribution of the spatial distribution and nanostructure of information-rich, signaling polysaccharides like HS is not known. Using expansion microscopy (ExM), we found striking changes in HS nanostructure occur as human pluripotent stem (hPS) cells differentiate, and these changes correlate with growth factor signaling. Our imaging studies show that undifferentiated hPS cells are densely coated with HS displayed as hair-like protrusions. This ultrastructure can recruit fibroblast growth factor for signaling. When the hPS cells differentiate into the ectoderm lineage, HS is localized into dispersed puncta. This striking change in HS distribution coincides with a decrease in fibroblast growth factor binding to neural cells. While developmental variations in HS sequence were thought to be the primary driver of alterations in HS-mediated growth factor signaling, our high-resolution images indicate a role for the HS nanostructure. Our study highlights the utility of high-resolution glycan imaging using ExM. In the case of HS, we found that changes in how the polysaccharide is displayed link to profound differences in growth factor binding.
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Affiliation(s)
- Deena Al Mahbuba
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sayaka Masuko
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shiwei Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- McGovern Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
| | - Deepsing Syangtan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeong Seuk Kang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02139, United States
| | - Yuefan Song
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Tay Won Shin
- Media Arts and Sciences, MIT, Cambridge, Massachusetts 02139, United States
| | - Ke Xia
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Fuming Zhang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Edward S Boyden
- McGovern Institute for Brain Research, MIT, Cambridge, Massachusetts 02139, United States
- Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts 02139, United States
- Media Arts and Sciences, MIT, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
- Koch Institute, MIT, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02139, United States
- Centers for Neurobiological Engineering and Extreme Bionics, MIT, Cambridge, Massachusetts 02139, United States
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Koch Institute, MIT, Cambridge, Massachusetts 02139, United States
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42
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Baden P, Perez MJ, Raji H, Bertoli F, Kalb S, Illescas M, Spanos F, Giuliano C, Calogero AM, Oldrati M, Hebestreit H, Cappelletti G, Brockmann K, Gasser T, Schapira AHV, Ugalde C, Deleidi M. Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism. Nat Commun 2023; 14:1930. [PMID: 37024507 PMCID: PMC10079970 DOI: 10.1038/s41467-023-37454-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 03/17/2023] [Indexed: 04/08/2023] Open
Abstract
Mutations in GBA1, the gene encoding the lysosomal enzyme β-glucocerebrosidase (GCase), which cause Gaucher's disease, are the most frequent genetic risk factor for Parkinson's disease (PD). Here, we employ global proteomic and single-cell genomic approaches in stable cell lines as well as induced pluripotent stem cell (iPSC)-derived neurons and midbrain organoids to dissect the mechanisms underlying GCase-related neurodegeneration. We demonstrate that GCase can be imported from the cytosol into the mitochondria via recognition of internal mitochondrial targeting sequence-like signals. In mitochondria, GCase promotes the maintenance of mitochondrial complex I (CI) integrity and function. Furthermore, GCase interacts with the mitochondrial quality control proteins HSP60 and LONP1. Disease-associated mutations impair CI stability and function and enhance the interaction with the mitochondrial quality control machinery. These findings reveal a mitochondrial role of GCase and suggest that defective CI activity and energy metabolism may drive the pathogenesis of GCase-linked neurodegeneration.
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Affiliation(s)
- Pascale Baden
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Maria Jose Perez
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Hariam Raji
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Federico Bertoli
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Stefanie Kalb
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - María Illescas
- Instituto de Investigación Hospital 12 de Octubre (i + 12), Madrid, 28041, Spain
| | - Fokion Spanos
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Claudio Giuliano
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Unit of Cellular and Molecular Neurobiology, IRCCS Mondino Foundation, 27100, Pavia, Italy
| | - Alessandra Maria Calogero
- Department of Biosciences, Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Milan, Italy
| | - Marvin Oldrati
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Hannah Hebestreit
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Graziella Cappelletti
- Department of Biosciences, Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Milan, Italy
| | - Kathrin Brockmann
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Thomas Gasser
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Anthony H V Schapira
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, Royal Free Campus, London, NW3 2PF, UK
| | - Cristina Ugalde
- Instituto de Investigación Hospital 12 de Octubre (i + 12), Madrid, 28041, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U723, Madrid, Spain
| | - Michela Deleidi
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
- Department of Neurodegenerative Diseases, Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
- Institut Imagine, INSERM UMR1163 Paris Cite' University, 24 boulevard du Montparnasse, 75015, Paris, France.
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43
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Park HH, Choi AA, Xu K. Size-Dependent Suppression of Molecular Diffusivity in Expandable Hydrogels: A Single-Molecule Study. J Phys Chem B 2023; 127:3333-3339. [PMID: 37011131 DOI: 10.1021/acs.jpcb.3c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
By repurposing the recently popularized expansion microscopy to control the meshwork size of hydrogels, we examine the size-dependent suppression of molecular diffusivity in the resultant tuned hydrogel nanomatrices over a wide range of polymer fractions of ∼0.14-7 wt %. With our recently developed single-molecule displacement/diffusivity mapping (SMdM) microscopy methods, we thus show that with a fixed meshwork size, larger molecules exhibit more impeded diffusion and that, for the same molecule, diffusion is progressively more suppressed as the meshwork size is reduced; this effect is more prominent for the larger molecules. Moreover, we show that the meshwork-induced obstruction of diffusion is uncoupled from the suppression of diffusion due to increased solution viscosities. Thus, the two mechanisms, respectively, being diffuser-size-dependent and independent, may separately scale down molecular diffusivity to produce the final diffusion slowdown in complex systems like the cell.
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Affiliation(s)
- Ha H Park
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Alexander A Choi
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
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44
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Wen G, Leen V, Rohand T, Sauer M, Hofkens J. Current Progress in Expansion Microscopy: Chemical Strategies and Applications. Chem Rev 2023; 123:3299-3323. [PMID: 36881995 DOI: 10.1021/acs.chemrev.2c00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Expansion microscopy (ExM) is a newly developed super-resolution technique, allowing visualization of biological targets at nanoscale resolution on conventional fluorescence microscopes. Since its introduction in 2015, many efforts have been dedicated to broaden its application range or increase the resolution that can be achieved. As a consequence, recent years have witnessed remarkable advances in ExM. This review summarizes recent progress in ExM, with the focus on the chemical aspects of the method, from chemistries for biomolecule grafting to polymer synthesis and the impact on biological analysis. The combination of ExM with other microscopy techniques, in search of additional resolution improvement, is also discussed. In addition, we compare pre- and postexpansion labeling strategies and discuss the impact of fixation methods on ultrastructure preservation. We conclude this review with a perspective on existing challenges and future directions. We believe that this review will provide a comprehensive understanding of ExM and facilitate its usage and further development.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Volker Leen
- Chrometra Scientific, Kortenaken 3470, Belgium
| | - Taoufik Rohand
- Laboratory of Analytical and Molecular Chemistry, Faculty Polydisciplinaire of Safi, University Cadi Ayyad Marrakech, BP 4162, 46000 Safi, Morocco
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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45
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Wilmerding A, Espana-Bonilla P, Giakoumakis NN, Saade M. Expansion microscopy of the chick embryo neural tube to overcome molecular crowding at the centrosomes-cilia. STAR Protoc 2023; 4:101997. [PMID: 36609151 PMCID: PMC9850183 DOI: 10.1016/j.xpro.2022.101997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/14/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
We describe an optimized protocol for application of expansion microscopy (ExM) on chick neural tube (NT) which enables different oriented nanoscale resolution imaging of the centrosomes/cilia. We explain embryo NT transversal sections and open-book preparations, immunohistochemistry for labeling, and sample preparation for 5-fold tissue expansion. Further, we detail sample orientation and Fast Airyscan confocal acquisition and show that NT-ExM retains fluorescence signals and overcomes biomolecules crowding in structural features that to date were only imaged with electron microscopy on tissues.
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Affiliation(s)
- Axelle Wilmerding
- Department of Cells and Tissues, Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Parc Científic de Barcelona, C/Baldiri i Reixac 20, 08028 Barcelona, Spain
| | - Paula Espana-Bonilla
- Department of Cells and Tissues, Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Parc Científic de Barcelona, C/Baldiri i Reixac 20, 08028 Barcelona, Spain
| | - Nikolaos-Nikiforos Giakoumakis
- Advanced Digital Microscopy Facility Institute for Research in Biomedicine - IRB, Parc Científic de Barcelona, C/Baldiri Reixac 10, 08028 Barcelona, Spain.
| | - Murielle Saade
- Department of Cells and Tissues, Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Parc Científic de Barcelona, C/Baldiri i Reixac 20, 08028 Barcelona, Spain.
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46
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Zhao Y, Cheng Z, Stefani C, Skillman T, Klimas A, Lee A, DiBernardo E, Mueller Brown K, Milman T, Gallagher B, Lagree K, Jena B, Pulido J, Filler S, Mitchell A, Hiller L, Lacy-Hulbert A. MicroMagnify: a multiplexed expansion microscopy method for pathogens and infected tissues. RESEARCH SQUARE 2023:rs.3.rs-2637060. [PMID: 36945526 PMCID: PMC10029075 DOI: 10.21203/rs.3.rs-2637060/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Super-resolution optical imaging tools are crucial in microbiology to understand the complex structures and behavior of microorganisms such as bacteria, fungi, and viruses. However, the capabilities of these tools, particularly when it comes to imaging pathogens and infected tissues, remain limited. We developed µMagnify, a nanoscale multiplexed imaging method for pathogens and infected tissues that are derived from an expansion microscopy technique with a universal biomolecular anchor. We formulated an enzyme cocktail specifically designed for robust cell wall digestion and expansion of microbial cells without distortion while efficiently retaining biomolecules suitable for high-plex fluorescence imaging with nanoscale precision. Additionally, we developed an associated virtual reality tool to facilitate the visualization and navigation of complex three-dimensional images generated by this method in an immersive environment allowing collaborative exploration among researchers around the world. µMagnify is a valuable imaging platform for studying how microbes interact with their host systems and enables development of new diagnosis strategies against infectious diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Bhanu Jena
- Wayne State University School of Medicine
| | - Jose Pulido
- Wills Eye Hospital and Jefferson University Hospital
| | - Scott Filler
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
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47
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Pannoni K, Gil D, Cawley M, Alsalman M, Campbell L, Farris S. Layer-specific mitochondrial diversity across hippocampal CA2 dendrites. Hippocampus 2023; 33:182-196. [PMID: 36762797 PMCID: PMC9974919 DOI: 10.1002/hipo.23512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 02/11/2023]
Abstract
CA2 is an understudied subregion of the hippocampus that is critical for social memory. Previous studies identified multiple components of the mitochondrial calcium uniporter (MCU) complex as selectively enriched in CA2. The MCU complex regulates calcium entry into mitochondria, which in turn regulates mitochondrial transport and localization to active synapses. We found that MCU is strikingly enriched in CA2 distal apical dendrites, precisely where CA2 neurons receive entorhinal cortical input carrying social information. Furthermore, MCU-enriched mitochondria in CA2 distal dendrites are larger compared to mitochondria in CA2 proximal apical dendrites and neighboring CA1 apical dendrites, which was confirmed in CA2 with genetically labeled mitochondria and electron microscopy. MCU overexpression in neighboring CA1 led to a preferential localization of MCU in the proximal dendrites of CA1 compared to the distal dendrites, an effect not seen in CA2. Our findings demonstrate that mitochondria are molecularly and structurally diverse across hippocampal cell types and circuits, and suggest that MCU can be differentially localized within dendrites, possibly to meet local energy demands.
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Affiliation(s)
- Katy Pannoni
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Daniela Gil
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Mikel Cawley
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia
| | - Mayd Alsalman
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Logan Campbell
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Shannon Farris
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia
- Virginia Tech Carilion School of Medicine, Roanoke, Virginia
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48
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Trebels B, Dippel S, Anders J, Ernst C, Goetz B, Keyser T, Rexer KH, Wimmer EA, Schachtner J. Anatomic and neurochemical analysis of the palpal olfactory system in the red flour beetle Tribolium castaneum, HERBST. Front Cell Neurosci 2023; 17:1097462. [PMID: 36998268 PMCID: PMC10043995 DOI: 10.3389/fncel.2023.1097462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
The paired antennal lobes were long considered the sole primary processing centers of the olfactory pathway in holometabolous insects receiving input from the olfactory sensory neurons of the antennae and mouthparts. In hemimetabolous insects, however, olfactory cues of the antennae and palps are processed separately. For the holometabolous red flour beetle Tribolium castaneum, we could show that primary processing of the palpal and antennal olfactory input also occurs separately and at distinct neuronal centers. While the antennal olfactory sensory neurons project into the antennal lobes, those of the palps project into the paired glomerular lobes and the unpaired gnathal olfactory center. Here we provide an extended analysis of the palpal olfactory pathway by combining scanning electron micrographs with confocal imaging of immunohistochemical staining and reporter expression identifying chemosensory and odorant receptor-expressing neurons in the palpal sensilla. In addition, we extended the anatomical characterization of the gnathal olfactory center by 3D reconstructions and investigated the distribution of several neuromediators. The similarities in the neuromediator repertoire between antennal lobes, glomerular lobes, and gnathal olfactory center underline the role of the latter two as additional primary olfactory processing centers.
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Affiliation(s)
- Björn Trebels
- Animal Physiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- *Correspondence: Joachim Schachtner Björn Trebels Ernst A. Wimmer
| | - Stefan Dippel
- Animal Physiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Janet Anders
- Animal Physiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Clara Ernst
- Animal Physiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Brigitte Goetz
- Animal Physiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Tim Keyser
- Animal Physiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Karl Heinz Rexer
- Biodiversity of Plants, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ernst A. Wimmer
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, Georg-August-University Göttingen, Göttingen, Germany
- *Correspondence: Joachim Schachtner Björn Trebels Ernst A. Wimmer
| | - Joachim Schachtner
- Animal Physiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Clausthal University of Technology, Clausthal-Zellerfeld, Germany
- *Correspondence: Joachim Schachtner Björn Trebels Ernst A. Wimmer
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49
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Timmermann A, Tascio D, Jabs R, Boehlen A, Domingos C, Skubal M, Huang W, Kirchhoff F, Henneberger C, Bilkei-Gorzo A, Seifert G, Steinhäuser C. Dysfunction of NG2 glial cells affects neuronal plasticity and behavior. Glia 2023; 71:1481-1501. [PMID: 36802096 DOI: 10.1002/glia.24352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/20/2023]
Abstract
NG2 glia represents a distinct type of macroglial cells in the CNS and is unique among glia because they receive synaptic input from neurons. They are abundantly present in white and gray matter. While the majority of white matter NG2 glia differentiates into oligodendrocytes, the physiological impact of gray matter NG2 glia and their synaptic input are still ill defined. Here, we asked whether dysfunctional NG2 glia affect neuronal signaling and behavior. We generated mice with inducible deletion of the K+ channel Kir4.1 in NG2 glia and performed comparative electrophysiological, immunohistochemical, molecular and behavioral analyses. Kir4.1 was deleted at postnatal day 23-26 (recombination efficiency about 75%) and mice were investigated 3-8 weeks later. Notably, these mice with dysfunctional NG2 glia demonstrated improved spatial memory as revealed by testing new object location recognition while working and social memory remained unaffected. Focussing on the hippocampus, we found that loss of Kir4.1 potentiated synaptic depolarizations of NG2 glia and stimulated the expression of myelin basic protein while proliferation and differentiation of hippocampal NG2 glia remained largely unaffected. Mice with targeted deletion of the K+ channel in NG2 glia showed impaired long-term potentiation at CA3-CA1 synapses, which could be fully rescued by extracellular application of a TrkB receptor agonist. Our data demonstrate that proper NG2 glia function is important for normal brain function and behavior.
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Affiliation(s)
- Aline Timmermann
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Dario Tascio
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Ronald Jabs
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Anne Boehlen
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Catia Domingos
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Magdalena Skubal
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Wenhui Huang
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), University of Saarland, Homburg, Germany
| | - Frank Kirchhoff
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), University of Saarland, Homburg, Germany
| | - Christian Henneberger
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Institute of Neurology, University College London, London, UK
| | - Andras Bilkei-Gorzo
- Institute of Molecular Psychiatry, Medical Faculty, University of Bonn, Bonn, Germany
| | - Gerald Seifert
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Christian Steinhäuser
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
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50
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Sun J, Song S, Singaram I, Sharma A, Wang W, Hu Y, Lo WT, Koch PA, Zhao JJ, Haucke V, Gao R, Cho W. PI(3,5)P 2 Controls the Signaling Activity of Class I PI3K. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525550. [PMID: 36747849 PMCID: PMC9900776 DOI: 10.1101/2023.01.25.525550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
3'-Phosphoinositides are ubiquitous cellular lipids that play pivotal regulatory roles in health and disease. Generation of 3'-phosphoinositides are driven by three families of phosphoinositide 3-kinases (PI3K) but the mechanisms underlying their regulation and cross-talk are not fully understood. Among 3'-phosphoinositides, phosphatidylinositol-3,5-bisphosphate (PI(3,5)P 2 ) remains the least understood species in terms of its spatiotemporal dynamics and physiological function due to the lack of specific probes. By means of spatiotemporally resolved in situ quantitative imaging of PI(3,5)P 2 using a newly developed ratiometric PI(3,5)P 2 sensor we demonstrate that a special pool of PI(3,5)P 2 is generated on lysosomes and late endosomes in response to growth factor stimulation. This PI(3,5)P 2 pool, the formation of which is mediated by Class II PI3KC2β and PIKFyve, plays a crucial role in terminating the activity of growth factor-stimulated Class I PI3K, one of the most frequently mutated proteins in cancer, via specific interaction with its regulatory p85 subunit. Cancer-causing mutations of Class I PI3K inhibit the p85-PI(3,5)P 2 interaction and thereby induce sustained activation of Class I PI3K. Our results unravel a hitherto unknown tight regulatory interplay between Class I and II PI3Ks mediated by PI(3,5)P 2 , which may be important for controlling the strength of PI3K-mediated growth factor signaling. These results also suggest a new therapeutic possibility of treating cancer patients with p85 mutations.
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