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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sachs S, Reinhard S, Eilts J, Sauer M, Werner C. Visualizing the trans-synaptic arrangement of synaptic proteins by expansion microscopy. Front Cell Neurosci 2024; 18:1328726. [PMID: 38486709 PMCID: PMC10937466 DOI: 10.3389/fncel.2024.1328726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024] Open
Abstract
High fidelity synaptic neurotransmission in the millisecond range is provided by a defined structural arrangement of synaptic proteins. At the presynapse multi-epitope scaffolding proteins are organized spatially at release sites to guarantee optimal binding of neurotransmitters at receptor clusters. The organization of pre- and postsynaptic proteins in trans-synaptic nanocolumns would thus intuitively support efficient information transfer at the synapse. Visualization of these protein-dense regions as well as the minute size of protein-packed synaptic clefts remains, however, challenging. To enable efficient labeling of these protein complexes, we developed post-gelation immunolabeling expansion microscopy combined with Airyscan super-resolution microscopy. Using ~8-fold expanded samples, Airyscan enables multicolor fluorescence imaging with 20-40 nm spatial resolution. Post-immunolabeling of decrowded (expanded) samples provides increased labeling efficiency and allows the visualization of trans-synaptic nanocolumns. Our approach is ideally suited to investigate the pathological impact on nanocolumn arrangement e.g., in limbic encephalitis with autoantibodies targeting trans-synaptic leucine-rich glioma inactivated 1 protein (LGI1).
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Affiliation(s)
| | | | | | | | - Christian Werner
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
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Hofbauer B, Zandawala M, Reinhard N, Rieger D, Werner C, Evers JF, Wegener C. The neuropeptide pigment-dispersing factor signals independently of Bruchpilot-labelled active zones in daily remodelled terminals of Drosophila clock neurons. Eur J Neurosci 2024. [PMID: 38414155 DOI: 10.1111/ejn.16294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/29/2024]
Abstract
The small ventrolateral neurons (sLNvs) are key components of the central clock in the Drosophila brain. They signal via the neuropeptide pigment-dispersing factor (PDF) to align the molecular clockwork of different central clock neurons and to modulate downstream circuits. The dorsal terminals of the sLNvs undergo daily morphological changes that affect presynaptic sites organised by the active zone protein Bruchpilot (BRP), a homolog of mammalian ELKS proteins. However, the role of these presynaptic sites for PDF release is ill-defined. Here, we combined expansion microscopy with labelling of active zones by endogenously tagged BRP to examine the spatial correlation between PDF-containing dense-core vesicles and BRP-labelled active zones. We found that the number of BRP-labelled puncta in the sLNv terminals was similar while their density differed between Zeitgeber time (ZT) 2 and 14. The relative distance between BRP- and PDF-labelled puncta was increased in the morning, around the reported time of PDF release. Spontaneous dense-core vesicle release profiles of sLNvs in a publicly available ssTEM dataset (FAFB) consistently lacked spatial correlation to BRP-organised active zones. RNAi-mediated downregulation of brp and other active zone proteins expressed by the sLNvs did not affect PDF-dependent locomotor rhythmicity. In contrast, down-regulation of genes encoding proteins of the canonical vesicle release machinery, the dense-core vesicle-related protein CADPS, as well as PDF impaired locomotor rhythmicity. Taken together, our study suggests that PDF release from the sLNvs is independent of BRP-organised active zones, while BRP may be redistributed to active zones in a time-dependent manner.
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Affiliation(s)
- Benedikt Hofbauer
- Biocenter, Theodor-Boveri-Institute, Neurobiology and Genetics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Meet Zandawala
- Biocenter, Theodor-Boveri-Institute, Neurobiology and Genetics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
- Department of Biochemistry and Molecular Biology, University of Nevada Reno, Reno, NV, USA
| | - Nils Reinhard
- Biocenter, Theodor-Boveri-Institute, Neurobiology and Genetics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Dirk Rieger
- Biocenter, Theodor-Boveri-Institute, Neurobiology and Genetics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Christian Werner
- Biocenter, Theodor-Boveri-Institute, Department of Biotechnology and Biophysics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Jan Felix Evers
- Centre for organismal studies COS, Universität Heidelberg, Heidelberg, Germany
- Cairn GmbH, Heidelberg, Germany
| | - Christian Wegener
- Biocenter, Theodor-Boveri-Institute, Neurobiology and Genetics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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Vojnovic I, Caspari OD, Hoşkan MA, Endesfelder U. Combining single-molecule and expansion microscopy in fission yeast to visualize protein structures at the nanostructural level. Open Biol 2024; 14:230414. [PMID: 38320620 PMCID: PMC10846934 DOI: 10.1098/rsob.230414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024] Open
Abstract
In this work, we have developed an expansion microscopy (ExM) protocol that combines ExM with photoactivated localization microscopy (ExPALM) for yeast cell imaging, and report a robust protocol for single-molecule and expansion microscopy of fission yeast, abbreviated as SExY. Our optimized SExY protocol retains about 50% of the fluorescent protein signal, doubling the amount obtained compared to the original protein retention ExM (proExM) protocol. It allows for a fivefold, highly isotropic expansion of fission yeast cells, which we carefully controlled while optimizing protein yield. We demonstrate the SExY method on several exemplary molecular targets and explicitly introduce low-abundant protein targets (e.g. nuclear proteins such as cbp1 and mis16, and the centromere-specific histone protein cnp1). The SExY protocol optimizations increasing protein yield could be beneficial for many studies, when targeting low abundance proteins, or for studies that rely on genetic labelling for various reasons (e.g. for proteins that cannot be easily targeted by extrinsic staining or in case artefacts introduced by unspecific staining interfere with data quality).
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Affiliation(s)
- Ilijana Vojnovic
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Oliver D. Caspari
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Microbiology, Institute Pasteur, Paris, France
| | - Mehmet Ali Hoşkan
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
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Day JH, Della Santina CM, Maretich P, Auld AL, Schnieder KK, Shin T, Boyden ES, Boyer LA. HiExM: high-throughput expansion microscopy enables scalable super-resolution imaging. bioRxiv 2024:2023.02.07.527509. [PMID: 36798312 PMCID: PMC9934540 DOI: 10.1101/2023.02.07.527509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Expansion microscopy (ExM) enables nanoscale imaging using a standard confocal microscope through the physical, isotropic expansion of fixed immunolabeled specimens. ExM is widely employed to image proteins, nucleic acids, and lipid membranes in single cells at nanoscale resolution; however, current methods cannot be performed in multi-well cell culture plates which limits the number of samples that can be processed simultaneously. We developed High-throughput Expansion Microscopy (HiExM), a robust platform that enables expansion microscopy of cells cultured in a standard 96-well plate. Our method enables consistent ~4.2x expansion within individual wells, across multiple wells, and between plates processed in parallel. We also demonstrate that HiExM can be combined with high-throughput confocal imaging platforms greatly improve the ease and scalability of image acquisition. As an example, we analyzed the effects of doxorubicin, a known cardiotoxic agent, in human cardiomyocytes (CMs) based on Hoechst signal intensity. We show a dose dependent effect on nuclear chromatin that is not observed in unexpanded CMs, suggesting that HiExM improves the detection of cellular phenotypes in response to drug treatment. Our method broadens the application of ExM as a tool for scalable super-resolution imaging in biological research applications.
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Affiliation(s)
- John H. Day
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Catherine Marin Della Santina
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Pema Maretich
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Alexander L. Auld
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Kirsten K. Schnieder
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Tay Shin
- Department of Media Arts and Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Edward S. Boyden
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- Department of Media Arts and Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- McGovern Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- K Lisa Yang Center for Bionics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- Center for Neurobiological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- Koch Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Laurie A. Boyer
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- Koch Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
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Login FH, Dam VS, Nejsum LN. Following the cellular itinerary of renal aquaporin-2 shuttling with 4.5x expansion microscopy. Am J Physiol Cell Physiol 2024; 326:C194-C205. [PMID: 38047301 DOI: 10.1152/ajpcell.00397.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
The shuttling of renal collecting duct aquaporin-2 (AQP2) between intracellular vesicles and the apical plasma membrane is paramount for regulation of renal water reabsorption. The binding of the circulating antidiuretic hormone arginine vasopressin (AVP) to the basolateral AVP receptor increases intracellular cAMP, which ultimately leads to AQP2 plasma membrane accumulation via a dual effect on AQP2 vesicle fusion with the apical plasma membrane and reduced AQP2 endocytosis. This AQP2 plasma membrane accumulation increases water reabsorption and consequently urine concentration. Conventional fluorescent microscopy provides a lateral resolution of ∼250 nm, which is insufficient to resolve the AQP2-containing endosomes/vesicles. Therefore, detailed information regarding the AQP2 vesicular population is still lacking. Newly established 4.5x Expansion Microscopy (ExM) can increase resolution to 60-70 nm. Using 4.5x ExM, we detected AQP2 vesicles/endosomes as small as 79 nm considering an average expansion factor of 4.3 for endosomes. Using different markers of the endosomal system provided detailed information of the cellular AQP2 itinerary upon changes in endogenous cAMP levels. Before cAMP elevation, AQP2 colocalized with early and recycling, but not late endosomes. Forskolin-induced cAMP increase was characterized by AQP2 insertion into the plasma membrane and AQP2 withdrawal from large perinuclear endosomes as well as some localization to lysosomal compartments. Forskolin washout promoted AQP2 endocytosis where AQP2 localized to not only early and recycling endosomes but also late endosomes and lysosomes indicating increased AQP2 degradation. Thus, our results show that 4.5 ExM is an attractive approach to obtain detailed information regarding AQP2 shuttling.NEW & NOTEWORTHY Renal aquaporin-2 (AQP2) imaged by expansion microscopy provides unprecedented 3-D information regarding the AQP2 itinerary in response to changes in cellular cAMP.
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Affiliation(s)
- Frédéric H Login
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Vibeke S Dam
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lene N Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Kubala JM, Laursen KB, Schreiner R, Williams RM, van der Mijn JC, Crowley MJ, Mongan NP, Nanus DM, Heller DA, Gudas LJ. NDUFA4L2 reduces mitochondrial respiration resulting in defective lysosomal trafficking in clear cell renal cell carcinoma. Cancer Biol Ther 2023; 24:2170669. [PMID: 36722045 PMCID: PMC9897797 DOI: 10.1080/15384047.2023.2170669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In clear cell renal cell carcinoma (ccRCC), activation of hypoxic signaling induces NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2 (NDUFA4L2) expression. Over 90% of ccRCCs exhibit overexpression of NDUFA4L2, which we previously showed contributes to ccRCC proliferation and survival. The function of NDUFA4L2 in ccRCC has not been fully elucidated. NDUFA4L2 was reported to reduce mitochondrial respiration via mitochondrial complex I inhibition. We found that NDUFA4L2 expression in human ccRCC cells increases the extracellular acidification rate, indicative of elevated glycolysis. Conversely, NDUFA4L2 expression in non-cancerous kidney epithelial cells decreases oxygen consumption rate while increasing extracellular acidification rate, suggesting that a Warburg-like effect is induced by NDUFA4L2 alone. We performed mass-spectrometry (MS)-based proteomics of NDUFA4L2 associated complexes. Comparing RCC4-P (parental) ccRCC cells with RCC4 in which NDUFA4L2 is knocked out by CRISPR-Cas9 (RCC4-KO-643), we identified 3,215 proteins enriched in the NDUFA4L2 immunoprecipitates. Among the top-ranking pathways were "Metabolic Reprogramming in Cancer" and "Glycolysis Activation in Cancer (Warburg Effect)." We also show that NDUFA4L2 enhances mitochondrial fragmentation, interacts with lysosomes, and increases mitochondrial-lysosomal associations, as assessed by high-resolution fluorescence microscopy and live cell imaging. We identified 161 lysosomal proteins, including Niemann-Pick Disease Type C Intracellular Cholesterol Transporters 1 and 2 (NPC1, NPC2), that are associated with NDUFA4L2 in RCC4-P cells. RCC4-P cells have larger and decreased numbers of lysosomes relative to RCC4 NDUFA4L2 knockout cells. These findings suggest that NDUFA4L2 regulates mitochondrial-lysosomal associations and potentially lysosomal size and abundance. Consequently, NDUFA4L2 may regulate not only mitochondrial, but also lysosomal functions in ccRCC.
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Affiliation(s)
- Jaclyn M. Kubala
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA,CONTACT Lorraine J. Gudas Department of Pharmacology, Weill Cornell Medicine, New York, NY10065
| | | | - Ryan Schreiner
- Division of Regenerative Medicine Research, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ryan M. Williams
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Biomedical Engineering, the City College of New York, New York, NY, USA
| | | | - Michael J. Crowley
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Nigel P. Mongan
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA,Faculty of Medicine and Health Sciences, Center for Cancer Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - David M. Nanus
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Urology; New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Daniel A. Heller
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Lorraine J. Gudas
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA,Department of Urology; New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
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Hurley ME, Shah SS, Sheard TMD, Kirton HM, Steele DS, Gamper N, Jayasinghe I. Super-Resolution Analysis of the Origins of the Elementary Events of ER Calcium Release in Dorsal Root Ganglion Neurons. Cells 2023; 13:38. [PMID: 38201242 PMCID: PMC10778190 DOI: 10.3390/cells13010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Coordinated events of calcium (Ca2+) released from the endoplasmic reticulum (ER) are key second messengers in excitable cells. In pain-sensing dorsal root ganglion (DRG) neurons, these events can be observed as Ca2+ sparks, produced by a combination of ryanodine receptors (RyR) and inositol 1,4,5-triphosphate receptors (IP3R1). These microscopic signals offer the neuronal cells with a possible means of modulating the subplasmalemmal Ca2+ handling, initiating vesicular exocytosis. With super-resolution dSTORM and expansion microscopies, we visualised the nanoscale distributions of both RyR and IP3R1 that featured loosely organised clusters in the subplasmalemmal regions of cultured rat DRG somata. We adapted a novel correlative microscopy protocol to examine the nanoscale patterns of RyR and IP3R1 in the locality of each Ca2+ spark. We found that most subplasmalemmal sparks correlated with relatively small groups of RyR whilst larger sparks were often associated with larger groups of IP3R1. These data also showed spontaneous Ca2+ sparks in <30% of the subplasmalemmal cell area but consisted of both these channel species at a 3.8-5 times higher density than in nonactive regions of the cell. Taken together, these observations reveal distinct patterns and length scales of RyR and IP3R1 co-clustering at contact sites between the ER and the surface plasmalemma that encode the positions and the quantity of Ca2+ released at each Ca2+ spark.
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Affiliation(s)
- Miriam E. Hurley
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Shihab S. Shah
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas M. D. Sheard
- School of Biosciences, Faculty of Science, The University of Sheffield, Sheffield S10 2TN, UK
| | - Hannah M. Kirton
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Derek S. Steele
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nikita Gamper
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Izzy Jayasinghe
- School of Biosciences, Faculty of Science, The University of Sheffield, Sheffield S10 2TN, UK
- EMBL Australia Node in Single Molecule Science, School of Biomedical Science, University of New South Wales, Kensington, Sydney 2052, Australia
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10
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Liffner B, Cepeda Diaz AK, Blauwkamp J, Anaguano D, Frolich S, Muralidharan V, Wilson DW, Dvorin JD, Absalon S. Atlas of Plasmodium falciparum intraerythrocytic development using expansion microscopy. eLife 2023; 12:RP88088. [PMID: 38108809 PMCID: PMC10727503 DOI: 10.7554/elife.88088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Apicomplexan parasites exhibit tremendous diversity in much of their fundamental cell biology, but study of these organisms using light microscopy is often hindered by their small size. Ultrastructural expansion microscopy (U-ExM) is a microscopy preparation method that physically expands the sample by ~4.5×. Here, we apply U-ExM to the human malaria parasite Plasmodium falciparum during the asexual blood stage of its lifecycle to understand how this parasite is organized in three dimensions. Using a combination of dye-conjugated reagents and immunostaining, we have cataloged 13 different P. falciparum structures or organelles across the intraerythrocytic development of this parasite and made multiple observations about fundamental parasite cell biology. We describe that the outer centriolar plaque and its associated proteins anchor the nucleus to the parasite plasma membrane during mitosis. Furthermore, the rhoptries, Golgi, basal complex, and inner membrane complex, which form around this anchoring site while nuclei are still dividing, are concurrently segregated and maintain an association to the outer centriolar plaque until the start of segmentation. We also show that the mitochondrion and apicoplast undergo sequential fission events while maintaining an association with the outer centriolar plaque during cytokinesis. Collectively, this study represents the most detailed ultrastructural analysis of P. falciparum during its intraerythrocytic development to date and sheds light on multiple poorly understood aspects of its organelle biogenesis and fundamental cell biology.
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Affiliation(s)
- Benjamin Liffner
- Department of Pharmacology and Toxicology, Indiana University School of MedicineIndianapolisUnited States
| | - Ana Karla Cepeda Diaz
- Biological and Biomedical Sciences, Harvard Medical SchoolBostonUnited States
- Division of Infectious Diseases, Boston Children’s HospitalBostonUnited States
| | - James Blauwkamp
- Department of Pharmacology and Toxicology, Indiana University School of MedicineIndianapolisUnited States
| | - David Anaguano
- Center for Tropical and Emerging Global Diseases, University of GeorgiaAthensUnited States
- Department of Cellular Biology, Franklin College of Arts and Sciences, University of GeorgiaAthensUnited States
| | - Sonja Frolich
- Research Centre for Infectious Diseases, School of Biological Sciences, University of AdelaideAdelaideAustralia
- Institute for Photonics and Advanced Sensing, University of AdelaideAdelaideAustralia
| | - Vasant Muralidharan
- Center for Tropical and Emerging Global Diseases, University of GeorgiaAthensUnited States
- Department of Cellular Biology, Franklin College of Arts and Sciences, University of GeorgiaAthensUnited States
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, University of AdelaideAdelaideAustralia
- Institute for Photonics and Advanced Sensing, University of AdelaideAdelaideAustralia
- Burnet Institute, 85 Commercial RoadMelbourneAustralia
| | - Jeffrey D Dvorin
- Division of Infectious Diseases, Boston Children’s HospitalBostonUnited States
- Department of Pediatrics, Harvard Medical SchoolBostonUnited States
| | - Sabrina Absalon
- Department of Pharmacology and Toxicology, Indiana University School of MedicineIndianapolisUnited States
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11
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Pierron M, Woglar A, Busso C, Jha K, Mikeladze‐Dvali T, Croisier M, Gönczy P. Centriole elimination during Caenorhabditis elegans oogenesis initiates with loss of the central tube protein SAS-1. EMBO J 2023; 42:e115076. [PMID: 37987153 PMCID: PMC10711648 DOI: 10.15252/embj.2023115076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023] Open
Abstract
In most metazoans, centrioles are lost during oogenesis, ensuring that the zygote is endowed with the correct number of two centrioles, which are paternally contributed. How centriole architecture is dismantled during oogenesis is not understood. Here, we analyze with unprecedent detail the ultrastructural and molecular changes during oogenesis centriole elimination in Caenorhabditis elegans. Centriole elimination begins with loss of the so-called central tube and organelle widening, followed by microtubule disassembly. The resulting cluster of centriolar proteins then disappears gradually, usually moving in a microtubule- and dynein-dependent manner to the plasma membrane. Our analysis indicates that neither Polo-like kinases nor the PCM, which modulate oogenesis centriole elimination in Drosophila, do so in C. elegans. Furthermore, we demonstrate that the central tube protein SAS-1 normally departs initially from the organelle, which loses integrity earlier in sas-1 mutants. Overall, our work provides novel mechanistic insights regarding the fundamental process of oogenesis centriole elimination.
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Affiliation(s)
- Marie Pierron
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life SciencesSwiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
| | - Alexander Woglar
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life SciencesSwiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
| | - Coralie Busso
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life SciencesSwiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
| | - Keshav Jha
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life SciencesSwiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
| | | | - Marie Croisier
- BIO‐EM platform, School of Life SciencesSwiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life SciencesSwiss Federal Institute of Technology Lausanne (EPFL)LausanneSwitzerland
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12
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Hu K, Sun Q, Chen R, Xu T, Li Y, Chen L, Wang A, Qi H, Shao D, Yue H, Wang Y, Tang Z, Wang Y, Liu C, Lv H, Wang F, Xu H. Expanding the toolset of fluorescent covalent staining of biological samples by labeling carboxylate and phosphate groups. J Biophotonics 2023; 16:e202300027. [PMID: 37644491 DOI: 10.1002/jbio.202300027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Recently, fluorescent covalent staining methods have been developed for visualization of anatomical structures in cells and tissues. Coupled with expansion microscopy, these stains revealed various ultrastructural details. However, the covalently stainable chemical groups have been limited to amines, carbohydrates, and thiols. Here, we developed procedures for covalently labeling tissues for carboxylate and phosphate groups, utilizing carbodiimide crosslinker chemistry. In porcine kidney tissues, the carboxylate and phosphate stain provides 1.8-4.8-fold higher signal intensity than those from the three existing stains. In cancer cells, such stain allows 2-8-fold more accurate identification of nucleoli than the amine stain. In expansion microscopy samples, such stain reveals a variety of sub-cellular structures in tissues when combined with the amine stain. Such stain also allows imaging of lipid-based structures in cultured cells. With these advantages, this new covalent staining method further expands the toolset for fluorescent visualization of histology.
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Affiliation(s)
- Kexin Hu
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Qimeng Sun
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Ruifen Chen
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tinghao Xu
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Yuncheng Li
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Lili Chen
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Aidong Wang
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hejing Qi
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Danni Shao
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Huanning Yue
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Yaning Wang
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Ziqi Tang
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Yi Wang
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Chunfeng Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haijun Lv
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Fen Wang
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Huizhong Xu
- School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
- Institute for Advanced Study, Soochow University, Suzhou, Jiangsu, China
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13
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Wen G, Lycas MD, Jia Y, Leen V, Sauer M, Hofkens J. Trifunctional Linkers Enable Improved Visualization of Actin by Expansion Microscopy. ACS Nano 2023; 17:20589-20600. [PMID: 37787755 DOI: 10.1021/acsnano.3c07510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Expansion microscopy (ExM) revolutionized the field of super-resolution microscopy by allowing for subdiffraction resolution fluorescence imaging on standard fluorescence microscopes. However, it has been found that it is hard to visualize actin filaments efficiently using ExM. To improve actin imaging, multifunctional molecules have been designed with moderate success. Here, we present optimized methods for phalloidin conjugate grafting that have a high efficiency for both cellular and tissue samples. Our optimized strategy improves anchoring and signal retention by ∼10 times. We demonstrate the potential of optimized trifunctional linkers (TRITON) for actin imaging in combination with immunolabeling using different ExM protocols. 10X ExM of actin labeled with optimized TRITON enabled us to visualize the periodicity of actin rings in cultured hippocampal neurons and brain slices by Airyscan confocal microscopy. Thus, TRITON linkers provide an efficient grafting method, especially in cases in which the concentration of target-bound monomers is insufficient for high-quality ExM.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Matthew Domenic Lycas
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Yuqing Jia
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, Netherlands
| | - Volker Leen
- Chrometra Scientific, Kortenaken 3470, Belgium
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven, 3001, Belgium
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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15
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Cheng Z, Stefani C, Skillman T, Klimas A, Lee A, DiBernardo EF, Brown KM, Milman T, Wang Y, Gallagher BR, Lagree K, Jena BP, Pulido JS, Filler SG, Mitchell AP, Hiller NL, Lacy‐Hulbert A, Zhao Y. MicroMagnify: A Multiplexed Expansion Microscopy Method for Pathogens and Infected Tissues. Adv Sci (Weinh) 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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/29/2023] [Indexed: 09/03/2023]
Abstract
Super-resolution optical imaging tools are crucial in microbiology to understand the complex structures and behavior of microorganisms such as bacteria, fungi, and viruses. However, the capabilities of these tools, particularly when it comes to imaging pathogens and infected tissues, remain limited. MicroMagnify (µMagnify) is developed, a nanoscale multiplexed imaging method for pathogens and infected tissues that are derived from an expansion microscopy technique with a universal biomolecular anchor. The combination of heat denaturation and enzyme cocktails essential is found for robust cell wall digestion and expansion of microbial cells and infected tissues without distortion. µMagnify efficiently retains biomolecules suitable for high-plex fluorescence imaging with nanoscale precision. It demonstrates up to eightfold expansion with µMagnify on a broad range of pathogen-containing specimens, including bacterial and fungal biofilms, infected culture cells, fungus-infected mouse tone, and formalin-fixed paraffin-embedded human cornea infected by various pathogens. Additionally, an associated virtual reality tool is developed to facilitate the visualization and navigation of complex 3D images generated by this method in an immersive environment allowing collaborative exploration among researchers worldwide. µMagnify is a valuable imaging platform for studying how microbes interact with their host systems and enables the development of new diagnosis strategies against infectious diseases.
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Affiliation(s)
- Zhangyu Cheng
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Caroline Stefani
- Benaroya Research Institute at Virginia Mason1201 9th AveSeattleWA98101USA
| | | | - Aleksandra Klimas
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Aramchan Lee
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Emma F. DiBernardo
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Karina Mueller Brown
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Tatyana Milman
- Wills Eye Hospital and Jefferson University HospitalPhiladelphiaPA19107USA
| | - Yuhong Wang
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Brendan R. Gallagher
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Katherine Lagree
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Bhanu P. Jena
- Viron Molecular Medicine Institute201 Washington StreetBostonMA02201USA
- Department of PhysiologyWayne State University42 W Warren AveDetroitMI48202USA
- NanoBioScience InstituteWayne State University42 W Warren AveDetroitMI48202USA
- Center for Molecular Medicine & GeneticsSchool of MedicineWayne State University42 W Warren AveDetroitMI48202USA
| | - Jose S. Pulido
- Wills Eye Hospital and Jefferson University HospitalPhiladelphiaPA19107USA
| | - Scott G. Filler
- Lundquist Institute for Biomedical Innovation at Harbor‐UCLA Medical Center1124 W Carson StTorranceCA90502USA
- David Geffen School of Medicine at UCLA10833 Le Conte AveLos AngelesCA90095USA
| | - Aaron P. Mitchell
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
- Department of MicrobiologyUniversity of Georgia210 S Jackson streetAthensGA30602USA
| | - N. Luisa Hiller
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
| | - Adam Lacy‐Hulbert
- Benaroya Research Institute at Virginia Mason1201 9th AveSeattleWA98101USA
| | - Yongxin Zhao
- Department of Biological SciencesCarnegie Mellon University4400 Fifth AvenuePittsburghPA15213USA
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16
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Eilts J, Reinhard S, Michetschläger N, Werner C, Sauer M. Enhanced synaptic protein visualization by multicolor super-resolution expansion microscopy. Neurophotonics 2023; 10:044412. [PMID: 37886043 PMCID: PMC10599331 DOI: 10.1117/1.nph.10.4.044412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 10/28/2023]
Abstract
Significance Understanding the organization of biomolecules into complexes and their dynamics is crucial for comprehending cellular functions and dysfunctions, particularly in neuronal networks connected by synapses. In the last two decades, various powerful super-resolution (SR) microscopy techniques have been developed that produced stunning images of synapses and their molecular organization. However, current SR microscopy methods do not permit multicolor fluorescence imaging with 20 to 30 nm spatial resolution. Aim We developed a method that enables 4-color fluorescence imaging of synaptic proteins in neurons with 20 to 30 nm lateral resolution. Approach We used post-expansion immunolabeling of eightfold expanded hippocampal neurons in combination with Airyscan and structured illumination microscopy (SIM). Results We demonstrate that post-expansion immunolabeling of approximately eightfold expanded hippocampal neurons enables efficient labeling of synaptic proteins in crowded compartments with minimal linkage error and enables in combination with Airyscan and SIM four-color three-dimensional fluorescence imaging with 20 to 30 nm lateral resolution. Using immunolabeling of Synaptobrevin 2 as an efficient marker of the vesicle pool allowed us to identify individual synaptic vesicles colocalized with Rab3-interacting molecule 1 and 2 (RIM1/2), a marker of pre-synaptic fusion sites. Conclusions Our optimized expansion microscopy approach improves the visualization and location of pre- and post-synaptic proteins and can thus provide invaluable insights into the spatial organization of proteins at synapses.
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Affiliation(s)
- Janna Eilts
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Sebastian Reinhard
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Nikolas Michetschläger
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Christian Werner
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
| | - Markus Sauer
- University of Würzburg, Department of Biotechnology and Biophysics, Biocenter, Würzburg, Germany
- University of Würzburg, Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, Würzburg, Germany
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Xie J, Han D, Xu S, Zhang H, Li Y, Zhang M, Deng Z, Tian J, Ye Q. An Image-Based High-Throughput and High-Content Drug Screening Method Based on Microarray and Expansion Microscopy. ACS Nano 2023; 17:15516-15528. [PMID: 37548636 DOI: 10.1021/acsnano.3c01865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
A high-efficiency drug screening method is urgently needed due to the expanding number of potential targets and the extremely long time required to assess them. To date, high throughput and high content have not been successfully combined in image-based drug screening, which is the main obstacle to improve the efficiency. Here, we establish a high-throughput and high-content drug screening method by preparing a superhydrophobic microwell array plate (SMAP) and combining it with protein-retention expansion microscopy (proExM). Primarily, we described a flexible method to prepare the SMAP based on photolithography. Cells were cultured in the SMAP and treated with different drugs using a microcolumn-microwell sandwiching technology. After drug treatment, proExM was applied to realize super-resolution imaging. As a demonstration, a 7 × 7 image array of microtubules was successfully collected within 3 h with 68 nm resolution using this method. Qualitative and quantitative analyses of microtubule and mitochondria morphological changes after drug treatment suggested that more details were revealed after applying proExM, demonstrating the successful combination of high throughput and high content.
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Affiliation(s)
- Junfang Xie
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Daobo Han
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Shuai Xu
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Haitong Zhang
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Yonghe Li
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Mingshan Zhang
- Institute of Modern Optics, Nankai University, Tianjin 300350, China
| | - Zhichao Deng
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Jianguo Tian
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
| | - Qing Ye
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, China
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19
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Rathi P, Gupta P, Debnath A, Baldi H, Wang Y, Gupta R, Raman B, Singamaneni S. Plasmon-Enhanced Expansion Microscopy. Nano Lett 2023. [PMID: 37307329 DOI: 10.1021/acs.nanolett.3c01256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Expansion microscopy (ExM) is a rapidly emerging super-resolution microscopy technique that involves isotropic expansion of biological samples to improve spatial resolution. However, fluorescence signal dilution due to volumetric expansion is a hindrance to the widespread application of ExM. Here, we introduce plasmon-enhanced expansion microscopy (p-ExM) by harnessing an ultrabright fluorescent nanoconstruct, called plasmonic-fluor (PF), as a nanolabel. The unique structure of PFs renders nearly 15000-fold brighter fluorescence signal intensity and higher fluorescence retention following the ExM protocol (nearly 76%) compared to their conventional counterparts (<16% for IR-650). Individual PFs can be easily imaged using conventional fluorescence microscopes, making them excellent "digital" labels for ExM. We demonstrate that p-ExM enables improved tracing and decrypting of neural networks labeled with PFs, as evidenced by improved quantification of morphological markers (nearly a 2.5-fold increase in number of neurite terminal points). Overall, p-ExM complements the existing ExM techniques for probing structure-function relationships of various biological systems.
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Affiliation(s)
- Priya Rathi
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Prashant Gupta
- Department of Mechanical Engineering and Materials Science, and Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Avishek Debnath
- Department of Mechanical Engineering and Materials Science, and Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Harsh Baldi
- Department of Mechanical Engineering and Materials Science, and Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Yixuan Wang
- Department of Mechanical Engineering and Materials Science, and Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Rohit Gupta
- Department of Mechanical Engineering and Materials Science, and Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Baranidharan Raman
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Srikanth Singamaneni
- Department of Mechanical Engineering and Materials Science, and Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Thielhorn R, Heing-Becker I, Hümpfer N, Rentsch J, Haag R, Licha K, Ewers H. Controlled grafting expansion microscopy. Angew Chem Int Ed Engl 2023:e202302318. [PMID: 37158034 DOI: 10.1002/anie.202302318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023]
Abstract
Expansion microscopy (ExM) is a recently developed technique that allows for the resolution of structures below the diffraction limit by physically enlarging a hydrogel-embedded facsimile of the biological sample. The target structure is labeled and this label must be retained in a relative position true to the original, smaller state before expansion by linking it into the gel. However, gel formation and digestion lead to a significant loss in target-delivered label, resulting in weak signal. To overcome this problem, we have here developed an agent combining targeting, fluorescent labeling and gel linkage in a single small molecule. Similar approaches in the past have still suffered from significant loss of label. Here we show that this loss is due to insufficient surface grafting of fluorophores into the hydrogel and develop a solution by increasing the amount of target-bound monomers. Overall, we obtain a significant improvement in fluorescence signal retention and our new dye allows the resolution of nuclear pores as ring-like structures, similar to STED microscopy. We furthermore provide mechanistic insight into dye retention in ExM.
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Affiliation(s)
- Ria Thielhorn
- Freie Universitat Berlin, Institut für Chemie und Biochemie, GERMANY
| | | | - Nadja Hümpfer
- Freie Universitat Berlin, Institut für Chemie und Biochemie, GERMANY
| | - Jakob Rentsch
- Freie Universitat Berlin, Institut für Chemie und Biochemie, GERMANY
| | - Rainer Haag
- Freie Universitat Berlin, Institut für Chemie und Biochemie, GERMANY
| | - Kai Licha
- Freie Universitat Berlin, Institut für Chemie und Biochemie, GERMANY
| | - Helge Ewers
- Freie Universitat Berlin, chemistry and biochemistry, Thielallee 63, 14195, Berlin, GERMANY
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Cui Y, Zhang X, Li X, Lin J. Multiscale microscopy to decipher plant cell structure and dynamics. New Phytol 2023; 237:1980-1997. [PMID: 36477856 DOI: 10.1111/nph.18641] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
New imaging methodologies with high contrast and molecular specificity allow researchers to analyze dynamic processes in plant cells at multiple scales, from single protein and RNA molecules to organelles and cells, to whole organs and tissues. These techniques produce informative images and quantitative data on molecular dynamics to address questions that cannot be answered by conventional biochemical assays. Here, we review selected microscopy techniques, focusing on their basic principles and applications in plant science, discussing the pros and cons of each technique, and introducing methods for quantitative analysis. This review thus provides guidance for plant scientists in selecting the most appropriate techniques to decipher structures and dynamic processes at different levels, from protein dynamics to morphogenesis.
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Affiliation(s)
- Yaning Cui
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xi Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
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24
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John A, M Bader S, Madiedo Soler N, Wiradiputri K, Tichkule S, Smyth ST, Ralph SA, Jex AR, Scott NE, Tonkin CJ, Goddard-Borger ED. Conservation, abundance, glycosylation profile, and localization of the TSP protein family in Cryptosporidium parvum. J Biol Chem 2023; 299:103006. [PMID: 36775128 PMCID: PMC10034466 DOI: 10.1016/j.jbc.2023.103006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Cryptosporidium parvum is a zoonotic apicomplexan parasite and a common cause of diarrheal disease worldwide. The development of vaccines to prevent or limit infection remains an important goal for tackling cryptosporidiosis. At present, the only approved vaccine against any apicomplexan parasite targets a conserved adhesin possessing a thrombospondin repeat domain. C. parvum possesses 12 orthologous thrombospondin repeat domain-containing proteins known as CpTSP1-12, though little is known about these potentially important antigens. Here, we explore the architecture and conservation of the CpTSP protein family, as well as their abundance at the protein level within the sporozoite stage of the life cycle. We examine the glycosylation states of these proteins using a combination of glycopeptide enrichment techniques to demonstrate that these proteins are modified with C-, O-, and N-linked glycans. Using expansion microscopy, and an antibody against the C-linked mannose that is unique to the CpTSP protein family within C. parvum, we show that these proteins are found both on the cell surface and in structures that resemble the secretory pathway of C. parvum sporozoites. Finally, we generated a polyclonal antibody against CpTSP1 to show that it is found at the cell surface and within micronemes, in a pattern reminiscent of other apicomplexan motility-associated adhesins, and is present both in sporozoites and meronts. This work sheds new light on an understudied family of C. parvum proteins that are likely to be important to both parasite biology and the development of vaccines against cryptosporidiosis.
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Affiliation(s)
- Alan John
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Stefanie M Bader
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Niccolay Madiedo Soler
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Kharizta Wiradiputri
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Swapnil Tichkule
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Sean T Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Aaron R Jex
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
| | - Christopher J Tonkin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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25
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Hou M, Xing F, Yang J, Hu F, Pan L, Xu J. Molecular Resolution Mapping of Erythrocyte Cytoskeleton by Ultrastructure Expansion Single-Molecule Localization Microscopy. Small Methods 2023; 7:e2201243. [PMID: 36543363 DOI: 10.1002/smtd.202201243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/26/2022] [Indexed: 06/17/2023]
Abstract
The combination of expansion microscopy and single-molecule localization microscopy has the potential to approach the molecular resolution. However, this combination meets challenges due to the hydrogel shrinkage in the presence of imaging buffer. Here, a method of ultrastructure expansion single-molecule localization microscopy (U-ExSMLM) based on skillfully adhering the gel onto poly-l-lysine (pLL)-coated coverslip is developed to prevent lateral shrinkage of the hydrogel. U-ExSMLM is then applied to dissect the membrane cytoskeleton organization of human erythrocytes at molecular resolution. The resolved nanoscale spatial distributions of cytoskeleton proteins, including the N/C-termini of β-spectrin, protein 4.1, and tropomodulin, show good agreement with the acknowledged model of erythrocyte cytoskeleton structure, demonstrating the reliability of U-ExSMLM. Furthermore, the concentration of pLL is adjusted to preserve the physiological biconcave morphology of erythrocytes, and it is found that the spectrin cytoskeleton in the dimple regions has lower density and larger length than that in the rim regions, which provides the direct evidence for cytoskeleton asymmetry in human erythrocytes. Therefore, the integrated method offers future opportunities to study the ultrastructure of membrane cytoskeleton at molecular resolution.
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Affiliation(s)
- Mengdi Hou
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
| | - Fulin Xing
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
| | - Jianyu Yang
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
| | - Fen Hu
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
| | - Leiting Pan
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300071, China
- Shenzhen Research Institute of Nankai University, Shenzhen, Guangdong, 518083, China
| | - Jingjun Xu
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Nankai University, Tianjin, 300071, China
- Shenzhen Research Institute of Nankai University, Shenzhen, Guangdong, 518083, China
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26
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Wen G, Leen V, Jia Y, Rohand T, Hofkens J. Improved Dye Survival in Expansion Microscopy through Stabilizer-Conjugated Linkers. Chemistry 2022; 28:e202202404. [PMID: 36031562 PMCID: PMC9828348 DOI: 10.1002/chem.202202404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 01/12/2023]
Abstract
Expansion microscopy (ExM) has been widely used to detect biomolecules in cultured cells and tissue samples due to its enablement of super resolution imaging with conventional microscopes, via physical expansion of samples. However, reaction conditions inherent to the process bring about strong fluorescent signal loss during polymerization and digestion and thus limit the brightness of the signal obtained post expansion. Here, we explore the impact of stabilizer-containing organic fluorophores in ExM, as a mitigation strategy for this radical-induced dye degradation. Through direct conjugation of 4-nitrophenylalanine (NPA) to our previously developed trifunctional reagents, we validate and demonstrate that these multifunctional linkers enable visualization of different organelles with improved fluorescent intensity, owning to protection of the dyes to radical induced degradation as well as to photoprotection upon imaging. At this point, we cannot disentangle the relative contribution of both mechanisms. Furthermore, we report anchoring linkers that allow straightforward application of NPA or Trolox to commercially available fluorophore-conjugated antibodies. We show that these anchoring linkers enable complete retention of biological targets while increasing fluorophore photostability. Our results provide guidance in exploring these stabilizer-modified agents in ExM and methods for increased signal survival through the polymerization steps of the ExM protocols.
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Affiliation(s)
- Gang Wen
- Department of ChemistryKU LeuvenLeuven3001Belgium
| | | | - Yuqing Jia
- Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
| | - Taoufik Rohand
- Laboratory of Analytical & Molecular Chemistry Faculty Polydisciplinaire of Safi Department of ChemistryUniversity Cadi Ayyad46000SafiMorocco
| | - Johan Hofkens
- Department of ChemistryKU LeuvenLeuven3001Belgium,Max Planck Institute for Polymer Research55128MainzGermany
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27
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Sheard TMD, Hurley ME, Smith AJ, Colyer J, White E, Jayasinghe I. Three-dimensional visualization of the cardiac ryanodine receptor clusters and the molecular-scale fraying of dyads. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210316. [PMID: 36189802 PMCID: PMC9527906 DOI: 10.1098/rstb.2021.0316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Clusters of ryanodine receptor calcium channels (RyRs) form the primary molecular machinery of intracellular calcium signalling in cardiomyocytes. While a range of optical super-resolution microscopy techniques have revealed the nanoscale structure of these clusters, the three-dimensional (3D) nanoscale topologies of the clusters have remained mostly unresolved. In this paper, we demonstrate the exploitation of molecular-scale resolution in enhanced expansion microscopy (EExM) along with various 2D and 3D visualization strategies to observe the topological complexities, geometries and molecular sub-domains within the RyR clusters. Notably, we observed sub-domains containing RyR-binding protein junctophilin-2 (JPH2) occupying the central regions of RyR clusters in the deeper interior of the myocytes (including dyads), while the poles were typically devoid of JPH2, lending to a looser RyR arrangement. By contrast, peripheral RyR clusters exhibited variable co-clustering patterns and ratios between RyR and JPH2. EExM images of dyadic RyR clusters in right ventricular (RV) myocytes isolated from rats with monocrotaline-induced RV failure revealed hallmarks of RyR cluster fragmentation accompanied by breaches in the JPH2 sub-domains. Frayed RyR patterns observed adjacent to these constitute new evidence that the destabilization of the RyR arrays inside the JPH2 sub-domains may seed the primordial foci of dyad remodelling observed in heart failure. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.
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Affiliation(s)
- Thomas M D Sheard
- School of Biosciences, Faculty of Science, University of Sheffield, Sheffield S10 2TN, UK.,School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Miriam E Hurley
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew J Smith
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - John Colyer
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ed White
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Izzy Jayasinghe
- School of Biosciences, Faculty of Science, University of Sheffield, Sheffield S10 2TN, UK.,School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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28
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Lin C, Lin T, Hsu S, Hsu H. Expansion Microscopy-based imaging for visualization of mitochondria in Drosophila ovarian germline stem cells. FEBS Open Bio 2022; 12:2102-2110. [PMID: 36331359 PMCID: PMC9714352 DOI: 10.1002/2211-5463.13506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/23/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022] Open
Abstract
Recent studies have shown that mitochondrial morphology can modulate organelle function and greatly affect stem cell behavior, thus affecting tissue homeostasis. As such, we previously showed that the accumulation of fragmented mitochondria in aged Drosophila ovarian germline stem cells (GSCs) contributes to age-dependent GSC loss. However, standard immunofluorescence methods to examine mitochondrial morphology yield images with insufficient resolution for rigorous analysis, while 3-dimensional electron microscopy examination of mitochondrial morphology is labor intensive and allows only limited sampling of mitochondria. To overcome these issues, we utilized the expansion microscopy technique to expand GSC samples by 4-fold in combination with mitochondrial immunofluorescence labeling. Here, we present a simple, inexpensive method for nanoscale optical imaging of mitochondria in the germline. This protocol may be beneficial for studies that require visualization of mitochondria or other fine subcellular structures in the Drosophila ovary.
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Affiliation(s)
- Chi‐Hung Lin
- Molecular and Cell Biology, Taiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan,Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan,Institute of Cellular and Organismic BiologyAcademia SinicaTaipeiTaiwan
| | - Tzu‐Yang Lin
- Institute of Cellular and Organismic BiologyAcademia SinicaTaipeiTaiwan
| | - Shao‐Chun Hsu
- Branch Office of Research and DevelopmentNational Taiwan University College of MedicineTaipeiTaiwan
| | - Hwei‐Jan Hsu
- Molecular and Cell Biology, Taiwan International Graduate ProgramAcademia SinicaTaipeiTaiwan,Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan,Institute of Cellular and Organismic BiologyAcademia SinicaTaipeiTaiwan
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29
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Abstract
Fish eyes require high Zn levels to support their early development. Although numerous studies have been conducted on the nutritional and toxic effects of Zn on the eye, the Zn requirement for retinal cell development is still debatable. Moreover, due to the complexity of the retinal structure, it is difficult to clearly visualize each retinal layer and accurately separate cell morphology in vivo by conventional methods. In the present study, we for the first time have achieved nanoscale imaging of retinal anatomy affected by dietary and waterborne Zn exposure by novel expansion microscopy. We demonstrated that the fish retina showed different developmental strategies in response to dietary and aqueous Zn exposures. Excess dietary Zn produced toxicity to retinal photoreceptor cells, resulting in a reduction in cell number and cell area, and this toxicity became severe with biological development. In contrast, waterborne Zn in the natural environment probably failed to meet the Zn requirements of retinal development. Overall, our results indicated that during early development, the Zn requirement of the fish eyes was sensitive, and oversupplementation led to impaired photoreceptor cell development. Our study has provided new perspectives using the powerful and novel expansion microscopy technique in toxicity assessment, enabling ultra-clear visualization of small but complex organ development.
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Affiliation(s)
- Mengyu Wang
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 518057, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong 518057, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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30
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Laporte MH, Bouhlel IB, Bertiaux E, Morrison CG, Giroud A, Borgers S, Azimzadeh J, Bornens M, Guichard P, Paoletti A, Hamel V. Human SFI1 and Centrin form a complex critical for centriole architecture and ciliogenesis. EMBO J 2022; 41:e112107. [PMID: 36125182 DOI: 10.15252/embj.2022112107] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2022] Open
Abstract
Over the course of evolution, the centrosome function has been conserved in most eukaryotes, but its core architecture has evolved differently in some clades, with the presence of centrioles in humans and a spindle pole body (SPB) in yeast. Similarly, the composition of these two core elements has diverged, with the exception of Centrin and SFI1, which form a complex in yeast to initiate SPB duplication. However, it remains unclear whether this complex exists at centrioles and whether its function has been conserved. Here, using expansion microscopy, we demonstrate that human SFI1 is a centriolar protein that associates with a pool of Centrin at the distal end of the centriole. We also find that both proteins are recruited early during procentriole assembly and that depletion of SFI1 results in the loss of the distal pool of Centrin, without altering centriole duplication. Instead, we show that SFI1/Centrin complex is essential for centriolar architecture, CEP164 distribution, and CP110 removal during ciliogenesis. Together, our work reveals a conserved SFI1/Centrin module displaying divergent functions between mammals and yeast.
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Affiliation(s)
- Marine H Laporte
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Imène B Bouhlel
- Institut Curie, UMR 144, CNRS, PSL University, Paris, France
| | - Eloïse Bertiaux
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Ciaran G Morrison
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.,Centre for Chromosome Biology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Alexia Giroud
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Susanne Borgers
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | | | - Michel Bornens
- Institut Curie, UMR 144, CNRS, PSL University, Paris, France
| | - Paul Guichard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Anne Paoletti
- Institut Curie, UMR 144, CNRS, PSL University, Paris, France
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
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31
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Zhang L, Padilla‐Flores T, Hernández VS, Zetter MA, Campos‐Lira E, Escobar LI, Millar RP, Eiden LE. Vasopressin acts as a synapse organizer in limbic regions by boosting PSD95 and GluA1 expression. J Neuroendocrinol 2022; 34:e13164. [PMID: 35666232 PMCID: PMC9787762 DOI: 10.1111/jne.13164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 05/01/2022] [Accepted: 05/10/2022] [Indexed: 12/31/2022]
Abstract
Hypothalamic arginine vasopressin (AVP)-containing magnocellular neurosecretory neurons (AVPMNN) emit collaterals to synaptically innervate limbic regions influencing learning, motivational behaviour, and fear responses. Here, we characterize the dynamics of expression changes of two key determinants for synaptic strength, the postsynaptic density (PSD) proteins AMPAR subunit GluA1 and PSD scaffolding protein 95 (PSD95), in response to in vivo manipulations of AVPMNN neuronal activation state, or exposure to exogenous AVP ex vivo. Both long-term water deprivation in vivo, which powerfully upregulates AVPMNN metabolic activity, and exogenous AVP application ex vivo, in brain slices, significantly increased GluA1 and PSD95 expression as measured by western blotting, in brain regions reportedly receiving direct ascending innervations from AVPMNN (i.e., ventral hippocampus, amygdala and lateral habenula). By contrast, the visual cortex, a region not observed to receive AVPMNN projections, showed no such changes. Ex vivo application of V1a and V1b antagonists to ventral hippocampal slices ablated the AVP stimulated increase in postsynaptic protein expression measured by western blotting. Using a modified expansion microscopy technique, we were able to quantitatively assess the significant augmentation of PSD95 and GLUA1 densities in subcellular compartments in locus coeruleus tyrosine hydroxylase immunopositive fibres, adjacent to AVP axon terminals. Our data strongly suggest that the AVPMNN ascending system plays a role in the regulation of the excitability of targeted neuronal circuits through upregulation of key postsynaptic density proteins corresponding to excitatory synapses.
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Affiliation(s)
- Limei Zhang
- Department of Physiology, School of MedicineNational Autonomous University of MexicoMexico CityMexico
| | - Teresa Padilla‐Flores
- Department of Physiology, School of MedicineNational Autonomous University of MexicoMexico CityMexico
| | - Vito S. Hernández
- Department of Physiology, School of MedicineNational Autonomous University of MexicoMexico CityMexico
| | - Mario A. Zetter
- Department of Physiology, School of MedicineNational Autonomous University of MexicoMexico CityMexico
| | - Elba Campos‐Lira
- Department of Physiology, School of MedicineNational Autonomous University of MexicoMexico CityMexico
| | - Laura I. Escobar
- Department of Physiology, School of MedicineNational Autonomous University of MexicoMexico CityMexico
| | - Robert P. Millar
- Department of Physiology, School of MedicineNational Autonomous University of MexicoMexico CityMexico
- Centre for Neuroendocrinology, Department of ImmunologyUniversity of PretoriaPretoriaSouth Africa
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownCape TownSouth Africa
| | - Lee E. Eiden
- Section on Molecular NeuroscienceNIMH‐IRP, NIHBethesdaMarylandUSA
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32
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Nozawa K, Sogabe T, Hayashi A, Motohashi J, Miura E, Arai I, Yuzaki M. In vivo nanoscopic landscape of neurexin ligands underlying anterograde synapse specification. Neuron 2022; 110:3168-3185.e8. [PMID: 36007521 DOI: 10.1016/j.neuron.2022.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/04/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022]
Abstract
Excitatory synapses are formed and matured by the cooperative actions of synaptic organizers, such as neurexins (Nrxns), neuroligins (Nlgns), LRRTMs, and Cbln1. Recent super-resolution nanoscopy developments have revealed that many synaptic organizers, as well as glutamate receptors and glutamate release machinery, exist as nanoclusters within synapses. However, it is unclear how such nanodomains interact with each other to organize excitatory synapses in vivo. By applying X10 expansion microscopy to epitope tag knockin mice, we found that Cbln1, Nlgn1, and LRRTM1, which share Nrxn as a common presynaptic receptor, form overlapping or separate nanodomains depending on Nrxn with or without a sequence encoded by splice site 4. The size and position of glutamate receptor nanodomains of GluD1, NMDA, and AMPA receptors were regulated by Cbln1, Nlgn1, and LRRTM1 nanodomains, respectively. These findings indicate that Nrxns anterogradely regulate the postsynaptic nanoscopic architecture of glutamate receptors through competition and coordination of Nrxn ligands.
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Affiliation(s)
- Kazuya Nozawa
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Taku Sogabe
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ayumi Hayashi
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Junko Motohashi
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Eriko Miura
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Itaru Arai
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Michisuke Yuzaki
- Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan.
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33
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Shi L, Klimas A, Gallagher B, Cheng Z, Fu F, Wijesekara P, Miao Y, Ren X, Zhao Y, Min W. Super-Resolution Vibrational Imaging Using Expansion Stimulated Raman Scattering Microscopy. Adv Sci (Weinh) 2022; 9:e2200315. [PMID: 35521971 PMCID: PMC9284179 DOI: 10.1002/advs.202200315] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/21/2022] [Indexed: 05/16/2023]
Abstract
Stimulated Raman scattering (SRS) microscopy is an emerging technology that provides high chemical specificity for endogenous biomolecules and can circumvent common constraints of fluorescence microscopy including limited capabilities to probe small biomolecules and difficulty resolving many colors simultaneously. However, the resolution of SRS microscopy remains governed by the diffraction limit. To overcome this, a new technique called molecule anchorable gel-enabled nanoscale Imaging of Fluorescence and stimulated Raman scattering microscopy (MAGNIFIERS) that integrates SRS microscopy with expansion microscopy (ExM) is described. MAGNIFIERS offers chemical-specific nanoscale imaging with sub-50 nm resolution and has scalable multiplexity when combined with multiplex Raman probes and fluorescent labels. MAGNIFIERS is used to visualize nanoscale features in a label-free manner with CH vibration of proteins, lipids, and DNA in a broad range of biological specimens, from mouse brain, liver, and kidney to human lung organoid. In addition, MAGNIFIERS is applied to track nanoscale features of protein synthesis in protein aggregates using metabolic labeling of small metabolites. Finally, MAGNIFIERS is used to demonstrate 8-color nanoscale imaging in an expanded mouse brain section. Overall, MAGNIFIERS is a valuable platform for super-resolution label-free chemical imaging, high-resolution metabolic imaging, and highly multiplexed nanoscale imaging, thus bringing SRS to nanoscopy.
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Affiliation(s)
- Lixue Shi
- Department of ChemistryColumbia UniversityNew YorkNY10027USA
| | - Aleksandra Klimas
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Brendan Gallagher
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Zhangyu Cheng
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Feifei Fu
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Piyumi Wijesekara
- Department of Biomedical EngineeringCarnegie Mellon UniversityPittsburghPA15143USA
| | - Yupeng Miao
- Department of ChemistryColumbia UniversityNew YorkNY10027USA
| | - Xi Ren
- Department of Biomedical EngineeringCarnegie Mellon UniversityPittsburghPA15143USA
| | - Yongxin Zhao
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPA15143USA
| | - Wei Min
- Department of ChemistryColumbia UniversityNew YorkNY10027USA
- Kavli Institute for Brain ScienceColumbia UniversityNew YorkNY10027USA
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34
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Abstract
Surface topography on the scale of tens of nanometers to several micrometers substantially affects cell adhesion, migration, and differentiation. Recent studies using electron microscopy and super-resolution microscopy provide insight into how cells interact with surface nanotopography; however, the complex sample preparation and expensive imaging equipment required for these methods makes them not easily accessible. Expansion microscopy (ExM) is an affordable approach to image beyond the diffraction limit, but ExM cannot be readily applied to image the cell-material interface as most materials do not expand. Here, we develop a protocol that allows the use of ExM to resolve the cell-material interface with high resolution. We apply the technique to image the interface between U2OS cells and nanostructured substrates as well as the interface between primary osteoblasts with titanium dental implants. The high spatial resolution enabled by ExM reveals that although AP2 and F-actin both accumulate at curved membranes induced by vertical nanostructures, they are spatially segregated. Using ExM, we also reliably image how osteoblasts interact with roughened titanium implant surfaces below the diffraction limit; this is of great interest to understand osseointegration of the implants but has up to now been a significant technical challenge due to the irregular shape, the large volume, and the opacity of the titanium implants that have rendered them incompatible with other super-resolution techniques. We believe that our protocol will enable the use of ExM as a powerful tool for cell-material interface studies.
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Affiliation(s)
- Melissa L Nakamoto
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Csaba Forró
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Wei Zhang
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Ching-Ting Tsai
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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35
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Abstract
Olfactory sensory neurons (OSNs) in vertebrates detect odorants using multiple cilia, which protrude from the end of the dendrite and require centrioles for their formation. In mouse olfactory epithelium, the centrioles originate in progenitor cells near the basal lamina, often 50-100 μm from the apical surface. It is unknown how centrioles traverse this distance or mature to form cilia. Using high-resolution expansion microscopy, we found that centrioles migrate together, with multiple centrioles per group and multiple groups per OSN, during dendrite outgrowth. Centrioles were found by live imaging to migrate slowly, with a maximum rate of 0.18 µm/minute. Centrioles in migrating groups were associated with microtubule nucleation factors, but acquired rootletin and appendages only in mature OSNs. The parental centriole had preexisting appendages, formed a single cilium before other centrioles, and retained its unique appendage configuration in the mature OSN. We developed an air-liquid interface explant culture system for OSNs and used it to show that centriole migration can be perturbed ex vivo by stabilizing microtubules. We consider these results in the context of a comprehensive model for centriole formation, migration, and maturation in this important sensory cell type.
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Affiliation(s)
- Kaitlin Ching
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Jennifer T Wang
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Tim Stearns
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Genetics, Stanford University School of MedicineStanfordUnited States
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36
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Blatchley MR, Günay KA, Yavitt FM, Hawat EM, Dempsey PJ, Anseth KS. In Situ Super-Resolution Imaging of Organoids and Extracellular Matrix Interactions via Phototransfer by Allyl Sulfide Exchange- Expansion Microscopy (PhASE-ExM). Adv Mater 2022; 34:e2109252. [PMID: 35182403 PMCID: PMC9035124 DOI: 10.1002/adma.202109252] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/08/2022] [Indexed: 05/26/2023]
Abstract
3D organoid models have recently seen a boom in popularity, as they can better recapitulate the complexity of multicellular organs compared to other in vitro culture systems. However, organoids are difficult to image because of the limited penetration depth of high-resolution microscopes and depth-dependent light attenuation, which can limit the understanding of signal transduction pathways and characterization of intimate cell-extracellular matrix (ECM) interactions. To overcome these challenges, phototransfer by allyl sulfide exchange-expansion microscopy (PhASE-ExM) is developed, enabling optical clearance and super-resolution imaging of organoids and their ECM in 3D. PhASE-ExM uses hydrogels prepared via photoinitiated polymerization, which is advantageous as it decouples monomer diffusion into thick organoid cultures from the hydrogel fabrication. Apart from compatibility with organoids cultured in Matrigel, PhASE-ExM enables 3.25× expansion and super-resolution imaging of organoids cultured in synthetic poly(ethylene glycol) (PEG) hydrogels crosslinked via allyl-sulfide groups (PEG-AlS) through simultaneous photopolymerization and radical-mediated chain-transfer reactions that complete in <70 s. Further, PEG-AlS hydrogels can be in situ softened to promote organoid crypt formation, providing a super-resolution imaging platform both for pre- and post-differentiated organoids. Overall, PhASE-ExM is a useful tool to decipher organoid behavior by enabling sub-micrometer scale, 3D visualization of proteins and signal transduction pathways.
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Affiliation(s)
| | | | - F. Max Yavitt
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO, 80303 USA, The BioFrontiers Institute. University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO, 80303 USA
| | - Elijah M. Hawat
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO, 80303 USA
| | - Peter J. Dempsey
- Section of Developmental Biology, Department of Pediatrics, University of Colorado School of Medicine, 1775 Aurora Ct, Aurora, CO, 80045, USA
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37
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Damstra HGJ, Mohar B, Eddison M, Akhmanova A, Kapitein LC, Tillberg PW. Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx). eLife 2022; 11:73775. [PMID: 35179128 PMCID: PMC8887890 DOI: 10.7554/elife.73775] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/30/2022] [Indexed: 12/18/2022] Open
Abstract
Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y, and z. The maximum resolution increase is limited by the expansion factor of the gel, which is four-fold for the original ExM protocol. Variations on the original ExM method have been reported that allow for greater expansion factors but at the cost of ease of adoption or versatility. Here, we systematically explore the ExM recipe space and present a novel method termed Ten-fold Robust Expansion Microscopy (TREx) that, like the original ExM method, requires no specialized equipment or procedures. We demonstrate that TREx gels expand 10-fold, can be handled easily, and can be applied to both thick mouse brain tissue sections and cultured human cells enabling high-resolution subcellular imaging with a single expansion step. Furthermore, we show that TREx can provide ultrastructural context to subcellular protein localization by combining antibody-stained samples with off-the-shelf small-molecule stains for both total protein and membranes.
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Affiliation(s)
- Hugo G J Damstra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Boaz Mohar
- Janelia Research Campus, HHMI, Ashburn, United States
| | - Mark Eddison
- Janelia Research Campus, HHMI, Ashburn, United States
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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38
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Sneve MA, Piatkevich KD. Towards a Comprehensive Optical Connectome at Single Synapse Resolution via Expansion Microscopy. Front Synaptic Neurosci 2022; 13:754814. [PMID: 35115916 PMCID: PMC8803729 DOI: 10.3389/fnsyn.2021.754814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/17/2021] [Indexed: 12/04/2022] Open
Abstract
Mapping and determining the molecular identity of individual synapses is a crucial step towards the comprehensive reconstruction of neuronal circuits. Throughout the history of neuroscience, microscopy has been a key technology for mapping brain circuits. However, subdiffraction size and high density of synapses in brain tissue make this process extremely challenging. Electron microscopy (EM), with its nanoscale resolution, offers one approach to this challenge yet comes with many practical limitations, and to date has only been used in very small samples such as C. elegans, tadpole larvae, fruit fly brain, or very small pieces of mammalian brain tissue. Moreover, EM datasets require tedious data tracing. Light microscopy in combination with tissue expansion via physical magnification-known as expansion microscopy (ExM)-offers an alternative approach to this problem. ExM enables nanoscale imaging of large biological samples, which in combination with multicolor neuronal and synaptic labeling offers the unprecedented capability to trace and map entire neuronal circuits in fully automated mode. Recent advances in new methods for synaptic staining as well as new types of optical molecular probes with superior stability, specificity, and brightness provide new modalities for studying brain circuits. Here we review advanced methods and molecular probes for fluorescence staining of the synapses in the brain that are compatible with currently available expansion microscopy techniques. In particular, we will describe genetically encoded probes for synaptic labeling in mice, zebrafish, Drosophila fruit flies, and C. elegans, which enable the visualization of post-synaptic scaffolds and receptors, presynaptic terminals and vesicles, and even a snapshot of the synaptic activity itself. We will address current methods for applying these probes in ExM experiments, as well as appropriate vectors for the delivery of these molecular constructs. In addition, we offer experimental considerations and limitations for using each of these tools as well as our perspective on emerging tools.
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Affiliation(s)
- Madison A Sneve
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, United States
| | - Kiryl D Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
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39
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Wang Y, Eddison M, Fleishman G, Weigert M, Xu S, Wang T, Rokicki K, Goina C, Henry FE, Lemire AL, Schmidt U, Yang H, Svoboda K, Myers EW, Saalfeld S, Korff W, Sternson SM, Tillberg PW. EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization. Cell 2021; 184:6361-6377.e24. [PMID: 34875226 DOI: 10.1016/j.cell.2021.11.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/22/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022]
Abstract
Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.
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Affiliation(s)
- Yuhan Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Mark Eddison
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Greg Fleishman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Institute of Bioengineering, School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Shengjin Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Tim Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Konrad Rokicki
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Cristian Goina
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Fredrick E Henry
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Uwe Schmidt
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Hui Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Scott M Sternson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Paul W Tillberg
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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Scardigli M, Pesce L, Brady N, Mazzamuto G, Gavryusev V, Silvestri L, Hof PR, Destrieux C, Costantini I, Pavone FS. Comparison of Different Tissue Clearing Methods for Three-Dimensional Reconstruction of Human Brain Cellular Anatomy Using Advanced Imaging Techniques. Front Neuroanat 2021; 15:752234. [PMID: 34867215 PMCID: PMC8632656 DOI: 10.3389/fnana.2021.752234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/13/2021] [Indexed: 01/29/2023] Open
Abstract
The combination of tissue clearing techniques with advanced optical microscopy facilitates the achievement of three-dimensional (3D) reconstruction of macroscopic specimens at high resolution. Whole mouse organs or even bodies have been analyzed, while the reconstruction of the human nervous system remains a challenge. Although several tissue protocols have been proposed, the high autofluorescence and variable post-mortem conditions of human specimens negatively affect the quality of the images in terms of achievable transparency and staining contrast. Moreover, homogeneous staining of high-density epitopes, such as neuronal nuclear antigen (NeuN), creates an additional challenge. Here, we evaluated different tissue transformation approaches to find the best solution to uniformly clear and label all neurons in the human cerebral cortex using anti-NeuN antibodies in combination with confocal and light-sheet fluorescence microscopy (LSFM). Finally, we performed mesoscopic high-resolution 3D reconstruction of the successfully clarified and stained samples with LSFM.
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Affiliation(s)
- Marina Scardigli
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy.,Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Luca Pesce
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy.,Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Niamh Brady
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy.,National Institute of Optics, National Research Council, Rome, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy.,Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy.,Department of Physics and Astronomy, University of Florence, Florence, Italy.,National Institute of Optics, National Research Council, Rome, Italy
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy.,National Institute of Optics, National Research Council, Rome, Italy.,Department of Biology, University of Florence, Florence, Italy
| | - Francesco S Pavone
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy.,Department of Physics and Astronomy, University of Florence, Florence, Italy.,National Institute of Optics, National Research Council, Rome, Italy
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41
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Lee CM, Tian X, Tsao C, Chen P, Huang TN, Hsueh YP, Chen BC. Macro Photography with Lightsheet Illumination Enables Whole Expanded Brain Imaging with Single-cell Resolution. Discoveries (Craiova) 2021; 9:e133. [PMID: 34849398 PMCID: PMC8626140 DOI: 10.15190/d.2021.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/26/2021] [Accepted: 07/13/2021] [Indexed: 01/19/2023] Open
Abstract
Macro photography allows direct visualization of the enlarged whole mouse brain by a combination of lightsheet illumination and expansion microscopy with single-cell resolution. Taking advantage of the long working distance of a camera lens, we imaged a 3.7 cm thick, transparent, fluorescently-labeled expanded brain. In order to improve 3D sectioning capability, we used lightsheet excitation confined as the depth of field of the camera lens. Using 4x sample expansion and 5x optical magnification, macro photography enables imaging of expanded whole mouse brain with an effective resolution of 300 nm, which provides the subcellular structural information at the organ level.
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Affiliation(s)
- Chia-Ming Lee
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan.,Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chieh Tsao
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Tzyy-Nan Huang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan.,Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
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42
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Endo M, Maruoka H, Okabe S. Advanced Technologies for Local Neural Circuits in the Cerebral Cortex. Front Neuroanat 2021; 15:757499. [PMID: 34803616 PMCID: PMC8595196 DOI: 10.3389/fnana.2021.757499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The neural network in the brain can be viewed as an integrated system assembled from a large number of local neural circuits specialized for particular brain functions. Activities of neurons in local neural circuits are thought to be organized both spatially and temporally under the rules optimized for their roles in information processing. It is well perceived that different areas of the mammalian neocortex have specific cognitive functions and distinct computational properties. However, the organizational principles of the local neural circuits in different cortical regions have not yet been clarified. Therefore, new research principles and related neuro-technologies that enable efficient and precise recording of large-scale neuronal activities and synaptic connections are necessary. Innovative technologies for structural analysis, including tissue clearing and expansion microscopy, have enabled super resolution imaging of the neural circuits containing thousands of neurons at a single synapse resolution. The imaging resolution and volume achieved by new technologies are beyond the limits of conventional light or electron microscopic methods. Progress in genome editing and related technologies has made it possible to label and manipulate specific cell types and discriminate activities of multiple cell types. These technologies will provide a breakthrough for multiscale analysis of the structure and function of local neural circuits. This review summarizes the basic concepts and practical applications of the emerging technologies and new insight into local neural circuits obtained by these technologies.
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Affiliation(s)
- Masaaki Endo
- Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hisato Maruoka
- Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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43
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Liffner B, Absalon S. Expansion Microscopy Reveals Plasmodium falciparum Blood-Stage Parasites Undergo Anaphase with A Chromatin Bridge in the Absence of Mini-Chromosome Maintenance Complex Binding Protein. Microorganisms 2021; 9:microorganisms9112306. [PMID: 34835432 PMCID: PMC8620465 DOI: 10.3390/microorganisms9112306] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
The malaria parasite Plasmodium falciparum undergoes closed mitosis, which occurs within an intact nuclear envelope, and differs significantly from its human host. Mitosis is underpinned by the dynamics of microtubules and the nuclear envelope. To date, our ability to study P. falciparum mitosis by microscopy has been hindered by the small size of the P. falciparum nuclei. Ultrastructure expansion microscopy (U-ExM) has recently been developed for P. falciparum, allowing the visualization of mitosis at the individual nucleus level. Using U-ExM, three intranuclear microtubule structures are observed: hemispindles, mitotic spindles, and interpolar spindles. A previous study demonstrated that the mini-chromosome maintenance complex binding-protein (MCMBP) depletion caused abnormal nuclear morphology and microtubule defects. To investigate the role of microtubules following MCMBP depletion and study the nuclear envelope in these parasites, we developed the first nuclear stain enabled by U-ExM in P. falciparum. MCMBP-deficient parasites show aberrant hemispindles and mitotic spindles. Moreover, anaphase chromatin bridges and individual nuclei containing multiple microtubule structures were observed following MCMBP knockdown. Collectively, this study refines our understanding of MCMBP-deficient parasites and highlights the utility of U-ExM coupled with a nuclear envelope stain for studying mitosis in P. falciparum.
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Affiliation(s)
- Benjamin Liffner
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sabrina Absalon
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Abstract
The recently developed ultrastructure expansion microscopy (U-ExM) technique allows us to increase the spatial resolution within a cell or tissue for microscopic imaging through the physical expansion of the sample. In this study, we validate the use of U-ExM in Trypanosoma brucei measuring the expansion factors of several different compartments/organelles and thus verify the isotropic expansion of the cell. We furthermore demonstrate the use of this sample preparation protocol for future studies by visualizing the nucleus and kDNA, as well as proteins of the cytoskeleton, the basal body, the mitochondrion and the endoplasmic reticulum. Lastly, we discuss the challenges and opportunities of U-ExM.
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Affiliation(s)
- Ana Kalichava
- Institute of Cell Biology, University of Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
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45
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Gorilak P, Pružincová M, Vachova H, Olšinová M, Schmidt Cernohorska M, Varga V. Expansion microscopy facilitates quantitative super-resolution studies of cytoskeletal structures in kinetoplastid parasites. Open Biol 2021; 11:210131. [PMID: 34465213 PMCID: PMC8437234 DOI: 10.1098/rsob.210131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Expansion microscopy (ExM) has become a powerful super-resolution method in cell biology. It is a simple, yet robust approach, which does not require any instrumentation or reagents beyond those present in a standard microscopy facility. In this study, we used kinetoplastid parasites Trypanosoma brucei and Leishmania major, which possess a complex, yet well-defined microtubule-based cytoskeleton, to demonstrate that this method recapitulates faithfully morphology of structures as previously revealed by a combination of sophisticated electron microscopy (EM) approaches. Importantly, we also show that due to the rapidness of image acquisition and three-dimensional reconstruction of cellular volumes ExM is capable of complementing EM approaches by providing more quantitative data. This is demonstrated on examples of less well-appreciated microtubule structures, such as the neck microtubule of T. brucei or the pocket, cytosolic and multivesicular tubule-associated microtubules of L. major. We further demonstrate that ExM enables identifying cell types rare in a population, such as cells in mitosis and cytokinesis. Three-dimensional reconstruction of an entire volume of these cells provided details on the morphology of the mitotic spindle and the cleavage furrow. Finally, we show that established antibody markers of major cytoskeletal structures function well in ExM, which together with the ability to visualize proteins tagged with small epitope tags will facilitate studies of the kinetoplastid cytoskeleton.
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Affiliation(s)
- Peter Gorilak
- Laboratory of Cell Motility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic,Charles University, Faculty of Science, Albertov 6, Prague, 128 00, Czech Republic
| | - Martina Pružincová
- Laboratory of Cell Motility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
| | - Hana Vachova
- Laboratory of Cell Motility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
| | - Marie Olšinová
- IMCF at BIOCEV, Faculty of Science, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Marketa Schmidt Cernohorska
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
| | - Vladimir Varga
- Laboratory of Cell Motility, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
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46
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Yeo SH, Herde MK, Herbison AE. Morphological assessment of GABA and glutamate inputs to GnRH neurons in intact female mice using expansion microscopy. J Neuroendocrinol 2021; 33:e13021. [PMID: 34427015 DOI: 10.1111/jne.13021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/09/2023]
Abstract
The roles GABAergic and glutamatergic inputs in regulating the activity of the gonadotrophin-releasing hormone (GnRH) neurons at the time of the preovulatory surge remain unclear. We used expansion microscopy to compare the density of GABAergic and glutamatergic synapses on the GnRH neuron cell body and proximal dendrite in dioestrous and pro-oestrous female mice. An evaluation of all synapses immunoreactive for synaptophysin revealed that the highest density of inputs to rostral preoptic area GnRH neurons occurred within the first 45 µm of the primary dendrite (approximately 0.19 synapses µm-1 ) with relatively few synapses on the GnRH neuron soma or beyond 45 µm of the dendrite (0.05-0.08 synapses µm-1 ). Triple immunofluorescence labelling demonstrated a predominance of glutamatergic signalling with twice as many vesicular glutamate transporter 2 synapses detected compared to vesicular GABA transporter. Co-labelling with the GABAA receptor scaffold protein gephyrin and the glutamate receptor postsynaptic density marker Homer1 confirmed these observations, as well as the different spatial distribution of GABA and glutamate inputs along the dendrite. Quantitative assessments revealed no differences in synaptophysin, GABA or glutamate synapses at the proximal dendrite and soma of GnRH neurons between dioestrous and pro-oestrous mice. Taken together, these studies demonstrate that the GnRH neuron receives twice as many glutamatergic synapses compared to GABAergic synapses and that these inputs preferentially target the first 45 µm of the GnRH neuron proximal dendrite. These inputs appear to be structurally stable before the onset of pro-oestrous GnRH surge.
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Affiliation(s)
- Shel-Hwa Yeo
- Centre for Neuroendocrinology and Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Michel K Herde
- Centre for Neuroendocrinology and Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Allan E Herbison
- Centre for Neuroendocrinology and Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
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47
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Katrukha EA, Jurriens D, Salas Pastene DM, Kapitein LC. Quantitative mapping of dense microtubule arrays in mammalian neurons. eLife 2021; 10:67925. [PMID: 34313224 PMCID: PMC8416025 DOI: 10.7554/elife.67925] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/24/2021] [Indexed: 11/13/2022] Open
Abstract
The neuronal microtubule cytoskeleton underlies the polarization and proper functioning of neurons, amongst others by providing tracks for motor proteins that drive intracellular transport. Different subsets of neuronal microtubules, varying in composition, stability, and motor preference, are known to exist, but the high density of microtubules has so far precluded mapping their relative abundance and three-dimensional organization. Here, we use different super-resolution techniques (STED, Expansion Microscopy) to explore the nanoscale organization of the neuronal microtubule network in rat hippocampal neurons. This revealed that in dendrites acetylated microtubules are enriched in the core of the dendritic shaft, while tyrosinated microtubules are enriched near the plasma membrane, thus forming a shell around the acetylated microtubules. Moreover, using a novel analysis pipeline we quantified the absolute number of acetylated and tyrosinated microtubules within dendrites and found that they account for 65–75% and ~20–30% of all microtubules, respectively, leaving only few microtubules that do not fall in either category. Because these different microtubule subtypes facilitate different motor proteins, these novel insights help to understand the spatial regulation of intracellular transport. Cells in the body need to control the position of the molecules and other components inside them. To do this, they use a system of proteins that work a bit like a road network. The ‘roads’ are tubular structures known as microtubules, while ‘vehicles’ are transporters, called motor proteins, that ‘walk’ along the microtubules. Microtubule networks are important in all cells, but especially in neurons, which can grow very large. These cells have tree-like branches called dendrites that receive messages from other neurons. Dendrites contain different types of microtubules with many chemical modifications. These modifications consist of specific molecules or ‘groups’ becoming attached to or removed from the microtubules to change their properties – for example, microtubules can be ‘acetylated’ or ‘detyrosinated’. Motor proteins prefer different kinds of microtubules, and so understanding transport inside cells involves creating a precise roadmap showing how many of each type of microtubule exist and where they go. Using different super-resolution microscopy techniques, Katrukha et al. created maps of the microtubules in rat neurons. These show that acetylated microtubules form a core in the centre of the dendrites, while tyrosinated microtubules (which did not undergo detyrosination) line the cell membrane of the dendrites. Katrukha et al. then used the maps to determine that acetylated microtubules account for 65 to 70% of all microtubules, while tyrosinated microtubules make up 20 to 30%. This means that most microtubules fall into these two categories. The work by Katrukha et al. provides one of the first quantitative estimates of the relative amount of acetylated and tyrosinated microtubules, starting to shed light on how cells control their transport network. This could ultimately allow researchers to explore how transport changes in health and disease.
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Affiliation(s)
- Eugene A Katrukha
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Desiree M Salas Pastene
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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48
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Zhu C, Wang A, Chen L, Guo L, Ye J, Chen Q, Wang Q, Yao G, Xia Q, Cai T, Guo J, Yang Z, Sun Z, Xu Y, Lu G, Zhang Z, Cao J, Liu Y, Xu H. Measurement of expansion factor and distortion for expansion microscopy using isolated renal glomeruli as landmarks. J Biophotonics 2021; 14:e202100001. [PMID: 33856738 DOI: 10.1002/jbio.202100001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/14/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Expansion microscopy has enabled super resolution imaging of biological samples. The accurate measurement of expansion factor and distortion typically requires locating and imaging the same region of interest in the sample before and after expansion, which is often time-consuming to achieve. Here we introduce a convenient method for relocation by utilizing isolated porcine glomeruli as landmarks during expansion. Following heat denaturation and proteinase K digestion protocols, the glomeruli exhibit expansion factor of 3.5 to 4 (only 7%-16% less expanded than the hydrogel), and 1% to 2% of relative distortion. Due to its appropriate size of 100 to 300 μm, the location of the glomerulus in the sample are visible to eyes, while its detailed shape only requires bright field microscopy. For expansion factors ranging from 3 to 10, the region in the vicinity of the glomerulus can be easily re-identified, and sometimes allows quantification of expansion factor and distortion under bright field without fluorescent labels.
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Affiliation(s)
- Chen Zhu
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Optoelectronic Science and Engineering, Soochow University, Suzhou, China
| | - Aidong Wang
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lili Chen
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Liangsheng Guo
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jiajia Ye
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Qilin Chen
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Qi Wang
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Optoelectronic Science and Engineering, Soochow University, Suzhou, China
| | - Guojia Yao
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Qin Xia
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Tianyu Cai
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
| | - Jiayun Guo
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zhenyu Yang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zhenglong Sun
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Yuwei Xu
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Guoyuan Lu
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zexin Zhang
- Institute for Advanced Study, Soochow University, Suzhou, China
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, China
| | - Jingyuan Cao
- Department of Nephrology, Taizhou People's Hospital, the Fifth Affiliated Hospital of Nantong University, Taizhou, China
| | - Ying Liu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, China
| | - Huizhong Xu
- Institute for Advanced Study, Soochow University, Suzhou, China
- School of Physical Science and Technology, Soochow University, Suzhou, China
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49
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Kang S, Park S, Song H, Choi D, Park HE, Ahn BH, Kim SY, Lee Y. Expansion Microscopy with a Thermally Adjustable Expansion Factor Using Thermoresponsive Biospecimen-Hydrogel Hybrids. ACS Appl Mater Interfaces 2021; 13:28962-28974. [PMID: 34107679 DOI: 10.1021/acsami.1c07592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Expansion microscopy (ExM) is a technique in which swellable hydrogel-embedded biological samples are physically expanded to effectively increase imaging resolution. Here, we develop thermoresponsive reversible ExM (T-RevExM), in which the expansion factor can be thermally adjusted in a reversible manner. In this method, samples are embedded in thermoresponsive hydrogels and partially digested to allow for reversible swelling of the sample-gel hybrid in a temperature-dependent manner. We first synthesized hydrogels exhibiting lower critical solution temperature (LCST)- and upper critical solution temperature (UCST)-phase transition properties with N-alkyl acrylamide or sulfobetaine monomers, respectively. We then formed covalent hybrids between the LCST or UCST hydrogel and biomolecules across the cultured cells and tissues. The resulting hybrid could be reversibly swelled or deswelled in a temperature-dependent manner, with LCST- and UCST-based hybrids negatively and positively responding to the increase in temperature (termed thermonegative RevExM and thermopositive RevExM, respectively). We further showed reliable imaging of both unexpanded and expanded cells and tissues and demonstrated minimal distortions from the original sample using conventional confocal microscopy. Thus, T-RevExM enables easy adjustment of the size of biological samples and therefore the effective magnification and resolution of the sample, simply by changing the sample temperature.
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Affiliation(s)
- Sunah Kang
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sohyun Park
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hojoon Song
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Dongkil Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Han-Eol Park
- Institute of Molecular Biology and Genetics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Benjamin H Ahn
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sung-Yon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yan Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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50
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Abstract
Expansion microscopy (ExM) is a technique that physically expands preserved cells and tissues before microscope imaging, so that conventional diffraction-limited microscopes can perform nanoscale-resolution imaging. In ExM, biomolecules or their markers are linked to a dense, swellable gel network synthesized throughout a specimen. Mechanical homogenization of the sample (e.g., by protease digestion) and the addition of water enable isotropic swelling of the gel, so that the relative positions of biomolecules are preserved. We previously presented ExM protocols for analyzing proteins and RNAs in cells and tissues. Here we describe a cookbook-style ExM protocol for expanding cultured HeLa cells with immunostained microtubules, aimed to help newcomers familiarize themselves with the experimental setups and skills required to successfully perform ExM. Our aim is to help beginners, or students in a wet-lab classroom setting, learn all the key steps of ExM. © 2020 The Authors.
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Affiliation(s)
- Chi Zhang
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts
| | - Jeong Seuk Kang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts
| | - Shoh M Asano
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Current address, Internal Medicine Research Unit, Pfizer Inc., Cambridge, Massachusetts
| | - Ruixuan Gao
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts.,McGovern Institute, MIT, Cambridge, Massachusetts.,Department of Biological Engineering, MIT, Cambridge, Massachusetts.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts.,Koch Institute for Cancer Research, MIT, Cambridge, Massachusetts
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