1
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Marshall KE, Mengham K, Spink MC, Vania L, Pollard HJ, Darrow MC, Duke E, Harkiolaki M, Serpell LC. Correlative cryo-soft X-ray tomography and cryo-structured illumination microscopy reveal changes to lysosomes in amyloid-β-treated neurons. Structure 2024; 32:585-593.e3. [PMID: 38471506 DOI: 10.1016/j.str.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/20/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
Protein misfolding is common to neurodegenerative diseases (NDs) including Alzheimer's disease (AD), which is partly characterized by the self-assembly and accumulation of amyloid-beta in the brain. Lysosomes are a critical component of the proteostasis network required to degrade and recycle material from outside and within the cell and impaired proteostatic mechanisms have been implicated in NDs. We have previously established that toxic amyloid-beta oligomers are endocytosed, accumulate in lysosomes, and disrupt the endo-lysosomal system in neurons. Here, we use pioneering correlative cryo-structured illumination microscopy and cryo-soft X-ray tomography imaging techniques to reconstruct 3D cellular architecture in the native state revealing reduced X-ray density in lysosomes and increased carbon dense vesicles in oligomer treated neurons compared with untreated cells. This work provides unprecedented visual information on the changes to neuronal lysosomes inflicted by amyloid beta oligomers using advanced methods in structural cell biology.
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Affiliation(s)
- Karen E Marshall
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, BN1 9QG Brighton, UK.
| | - Kurtis Mengham
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, BN1 9QG Brighton, UK
| | - Matthew C Spink
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, OX11 0DE Didcot, UK
| | - Lyra Vania
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, BN1 9QG Brighton, UK
| | - Hannah Jane Pollard
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, BN1 9QG Brighton, UK
| | - Michele C Darrow
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, OX11 0DE Didcot, UK
| | - Elizabeth Duke
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, OX11 0DE Didcot, UK
| | - Maria Harkiolaki
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, OX11 0DE Didcot, UK
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, BN1 9QG Brighton, UK.
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2
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Leclerc S, Gupta A, Ruokolainen V, Chen JH, Kunnas K, Ekman AA, Niskanen H, Belevich I, Vihinen H, Turkki P, Perez-Berna AJ, Kapishnikov S, Mäntylä E, Harkiolaki M, Dufour E, Hytönen V, Pereiro E, McEnroe T, Fahy K, Kaikkonen MU, Jokitalo E, Larabell CA, Weinhardt V, Mattola S, Aho V, Vihinen-Ranta M. Progression of herpesvirus infection remodels mitochondrial organization and metabolism. PLoS Pathog 2024; 20:e1011829. [PMID: 38620036 PMCID: PMC11045090 DOI: 10.1371/journal.ppat.1011829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/25/2024] [Accepted: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
Viruses target mitochondria to promote their replication, and infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteracting viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Here we show extensive transcriptional remodeling of protein-encoding host genes involved in the respiratory chain, apoptosis, and structural organization of mitochondria as herpes simplex virus type 1 lytic infection proceeds from early to late stages of infection. High-resolution microscopy and interaction analyses unveiled infection-induced emergence of rough, thin, and elongated mitochondria relocalized to the perinuclear area, a significant increase in the number and clustering of endoplasmic reticulum-mitochondria contact sites, and thickening and shortening of mitochondrial cristae. Finally, metabolic analyses demonstrated that reactivation of ATP production is accompanied by increased mitochondrial Ca2+ content and proton leakage as the infection proceeds. Overall, the significant structural and functional changes in the mitochondria triggered by the viral invasion are tightly connected to the progression of the virus infection.
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Affiliation(s)
- Simon Leclerc
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Alka Gupta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Visa Ruokolainen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Kari Kunnas
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Axel A. Ekman
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Henri Niskanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilya Belevich
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Paula Turkki
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ana J. Perez-Berna
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Valles, Barcelona, Spain
| | | | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, United Kingdom
| | - Eric Dufour
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa Hytönen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab laboratories, Tampere, Finland
| | - Eva Pereiro
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Valles, Barcelona, Spain
| | | | | | - Minna U. Kaikkonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Finland
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Venera Weinhardt
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Salla Mattola
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Vesa Aho
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
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3
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Pepe A, Groen J, Zurzolo C, Sartori-Rupp A. Correlative cryo-microscopy pipelines for in situ cellular studies. Methods Cell Biol 2024; 187:175-203. [PMID: 38705624 DOI: 10.1016/bs.mcb.2024.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Correlative cryo-microscopy pipelines combining light and electron microscopy and tomography in cryogenic conditions (cryoCLEM) on the same sample are powerful methods for investigating the structure of specific cellular targets identified by a fluorescent tag within their unperturbed cellular environment. CryoCLEM approaches circumvent one of the inherent limitations of cryo EM, and specifically cryo electron tomography (cryoET), of identifying the imaged structures in the crowded 3D environment of cells. Whereas several cryoCLEM approaches are based on thinning the sample by cryo FIB milling, here we present detailed protocols of two alternative cryoCLEM approaches for in situ studies of adherent cells at the single-cell level without the need for such cryo-thinning. The first approach is a complete cryogenic pipeline in which both fluorescence and electronic imaging are performed on frozen-hydrated samples, the second is a hybrid cryoCLEM approach in which fluorescence imaging is performed at room temperature, followed by rapid freezing and subsequent cryoEM imaging. We provide a detailed description of the two methods we have employed for imaging fluorescently labeled cellular structures with thickness below 350-500nm, such as cell protrusions and organelles located in the peripheral areas of the cells.
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Affiliation(s)
- Anna Pepe
- Membrane Traffic and Pathogenesis, Institut Pasteur, Paris, France
| | - Johannes Groen
- NanoImaging Core Facility, Institut Pasteur, Paris, France; Dynamics of Host-Pathogen Interactions, Institut Pasteur, Paris, France
| | - Chiara Zurzolo
- Membrane Traffic and Pathogenesis, Institut Pasteur, Paris, France
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4
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Fahy K, Kapishnikov S, Donnellan M, McEnroe T, O'Reilly F, Fyans W, Sheridan P. Laboratory based correlative cryo-soft X-ray tomography and cryo-fluorescence microscopy. Methods Cell Biol 2024; 187:293-320. [PMID: 38705628 DOI: 10.1016/bs.mcb.2024.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Cryo-soft X-ray tomography is the unique technology that can image whole intact cells in 3D under normal and pathological conditions without labelling or fixation, at high throughput and spatial resolution. The sample preparation is relatively straightforward; requiring just fast freezing of the specimen before transfer to the microscope for imaging. It is also possible to image chemically fixed samples where necessary. The technique can be correlated with cryo fluorescence microscopy to localize fluorescent proteins to organelles within the whole cell volume. Cryo-correlated light and soft X-ray tomography is particularly useful for the study of gross morphological changes brought about by disease or drugs. For example, viral fluorescent tags can be co-localized to sites of viral replication in the soft X-ray volume. In general this approach is extremely useful in the study of complex 3D organelle structure, nanoparticle uptake or in the detection of rare events in the context of whole cell structure. The main challenge of soft X-ray tomography is that the soft X-ray illumination required for imaging has heretofore only been available at a small number of synchrotron labs worldwide. Recently, a compact device with a footprint small enough to fit in a standard laboratory setting has been deployed ("the SXT-100") and is routinely imaging cryo prepared samples addressing a variety of disease and drug research applications. The SXT-100 facilitates greater access to this powerful technique and greatly increases the scope and throughput of potential research projects. Furthermore, the availability of cryo-soft X-ray tomography in the laboratory will accelerate the development of novel correlative and multimodal workflows by integration with light and electron microscope based approaches. It also allows for co-location of this powerful imaging modality at BSL3 labs or other facilities where safety or intellectual property considerations are paramount. Here we describe the compact SXT-100 microscope along with its novel integrated cryo-fluorescence imaging capability.
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Affiliation(s)
- Kenneth Fahy
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland.
| | | | | | - Tony McEnroe
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland
| | - Fergal O'Reilly
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland; University College Dublin, School of Physics, Dublin, Ireland; University College Dublin, School of Biology and Environmental Sciences, Dublin, Ireland
| | - William Fyans
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland
| | - Paul Sheridan
- SiriusXT Ltd., Stillorgan Industrial Park, Dublin, Ireland
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5
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Castro V, Pérez-Berna AJ, Calvo G, Pereiro E, Gastaminza P. Three-Dimensional Remodeling of SARS-CoV2-Infected Cells Revealed by Cryogenic Soft X-ray Tomography. ACS NANO 2023; 17:22708-22721. [PMID: 37939169 PMCID: PMC10690842 DOI: 10.1021/acsnano.3c07265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Plus-strand RNA viruses are proficient at remodeling host cell membranes for optimal viral genome replication and the production of infectious progeny. These ultrastructural alterations result in the formation of viral membranous organelles and may be observed by different imaging techniques, providing nanometric resolution. Guided by confocal and electron microscopy, this study describes the generation of wide-field volumes using cryogenic soft-X-ray tomography (cryo-SXT) on SARS-CoV-2-infected human lung adenocarcinoma cells. Confocal microscopy showed accumulation of double-stranded RNA (dsRNA) and nucleocapsid (N) protein in compact perinuclear structures, preferentially found around centrosomes at late stages of the infection. Transmission electron microscopy (TEM) showed accumulation of membranous structures in the vicinity of the infected cell nucleus, forming a viral replication organelle containing characteristic double-membrane vesicles and virus-like particles within larger vesicular structures. Cryo-SXT revealed viral replication organelles very similar to those observed by TEM but indicated that the vesicular organelle observed in TEM sections is indeed a vesiculo-tubular network that is enlarged and elongated at late stages of the infection. Overall, our data provide additional insight into the molecular architecture of the SARS-CoV-2 replication organelle.
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Affiliation(s)
- Victoria Castro
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
| | | | - Gema Calvo
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
| | - Eva Pereiro
- ALBA
Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Valles, Spain
| | - Pablo Gastaminza
- Centro
Nacional de Biotecnología. Calle Darwin, 3, 28049 Madrid, Spain
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6
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Golyshev SA, Kazakov EP, Kireev II, Reunov DG, Malyshev IV. Soft X-ray Microscopy in Cell Biology: Current Status, Contributions and Prospects. Acta Naturae 2023; 15:32-43. [PMID: 38234603 PMCID: PMC10790358 DOI: 10.32607/actanaturae.26551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
The recent advances achieved in microscopy technology have led to a significant breakthrough in biological research. Super-resolution fluorescent microscopy now allows us to visualize subcellular structures down to the pin-pointing of the single molecules in them, while modern electron microscopy has opened new possibilities in the study of protein complexes in their native, intracellular environment at near-atomic resolution. Nonetheless, both fluorescent and electron microscopy have remained beset by their principal shortcomings: the reliance on labeling procedures and severe sample volume limitations, respectively. Soft X-ray microscopy is a candidate method that can compensate for the shortcomings of both technologies by making possible observation of the entirety of the cellular interior without chemical fixation and labeling with an isotropic resolution of 40-70 nm. This will thus bridge the resolution gap between light and electron microscopy (although this gap is being narrowed, it still exists) and resolve the issue of compatibility with the former, and possibly in the near future, the latter methods. This review aims to assess the current state of soft X-ray microscopy and its impact on our understanding of the subcellular organization. It also attempts to look into the future of X-ray microscopy, particularly as relates to its seamless integration into the cell biology toolkit.
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Affiliation(s)
- S. A. Golyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - E. P. Kazakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - I. I. Kireev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - D. G. Reunov
- Institute of Physics of Microstructures RAS, Nizhny Novgorod, 603950 Russian Federation
| | - I. V. Malyshev
- Institute of Physics of Microstructures RAS, Nizhny Novgorod, 603950 Russian Federation
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7
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Rojas‐Gómez A, Dosil SG, Chichón FJ, Fernández‐Gallego N, Ferrarini A, Calvo E, Calzada‐Fraile D, Requena S, Otón J, Serrano A, Tarifa R, Arroyo M, Sorrentino A, Pereiro E, Vázquez J, Valpuesta JM, Sánchez‐Madrid F, Martín‐Cófreces NB. Chaperonin CCT controls extracellular vesicle production and cell metabolism through kinesin dynamics. J Extracell Vesicles 2023; 12:e12333. [PMID: 37328936 PMCID: PMC10276179 DOI: 10.1002/jev2.12333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/02/2023] [Indexed: 06/18/2023] Open
Abstract
Cell proteostasis includes gene transcription, protein translation, folding of de novo proteins, post-translational modifications, secretion, degradation and recycling. By profiling the proteome of extracellular vesicles (EVs) from T cells, we have found the chaperonin complex CCT, involved in the correct folding of particular proteins. By limiting CCT cell-content by siRNA, cells undergo altered lipid composition and metabolic rewiring towards a lipid-dependent metabolism, with increased activity of peroxisomes and mitochondria. This is due to dysregulation of the dynamics of interorganelle contacts between lipid droplets, mitochondria, peroxisomes and the endolysosomal system. This process accelerates the biogenesis of multivesicular bodies leading to higher EV production through the dynamic regulation of microtubule-based kinesin motors. These findings connect proteostasis with lipid metabolism through an unexpected role of CCT.
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Affiliation(s)
- Amelia Rojas‐Gómez
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Sara G. Dosil
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Francisco J. Chichón
- Cryoelectron Microscopy UnitCentro Nacional de Biotecnología (CNB‐CSIC)MadridSpain
- Department of Macromolecular StructureCentro Nacional de Biotecnología (CNB‐CSIC)MadridSpain
| | - Nieves Fernández‐Gallego
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Alessia Ferrarini
- Laboratory of Cardiovascular ProteomicsFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Enrique Calvo
- Laboratory of Cardiovascular ProteomicsFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Diego Calzada‐Fraile
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Silvia Requena
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- CIBER de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - Joaquin Otón
- Structural Studies DivisionMRC Laboratory of Molecular BiologyCambridgeUK
- ALBA Synchrotron Light SourceBarcelonaSpain
| | - Alvaro Serrano
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Rocio Tarifa
- Laboratory of Cardiovascular ProteomicsFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
| | - Montserrat Arroyo
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
| | | | | | - Jesus Vázquez
- Laboratory of Cardiovascular ProteomicsFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
- CIBER de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - José M. Valpuesta
- Department of Macromolecular StructureCentro Nacional de Biotecnología (CNB‐CSIC)MadridSpain
| | - Francisco Sánchez‐Madrid
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
- CIBER de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
| | - Noa B. Martín‐Cófreces
- Immunology ServiceHospital Universitario de la Princesa, UAM, IIS‐IPMadridSpain
- Area of Vascular Pathophysiology, Laboratory of Intercellular CommunicationFundación Centro Nacional de Investigaciones Cardiovasculares‐Carlos IIIMadridSpain
- CIBER de Enfermedades Cardiovasculares (CIBERCV)MadridSpain
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8
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Lobato-Márquez D, Conesa JJ, López-Jiménez AT, Divine ME, Pruneda JN, Mostowy S. Septins and K63 ubiquitin chains are present in separate bacterial microdomains during autophagy of entrapped Shigella. J Cell Sci 2023; 136:jcs261139. [PMID: 36939083 PMCID: PMC10264824 DOI: 10.1242/jcs.261139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/21/2023] Open
Abstract
During host cell invasion, Shigella escapes to the cytosol and polymerizes actin for cell-to-cell spread. To restrict cell-to-cell spread, host cells employ cell-autonomous immune responses including antibacterial autophagy and septin cage entrapment. How septins interact with the autophagy process to target Shigella for destruction is poorly understood. Here, we employed a correlative light and cryo-soft X-ray tomography (cryo-SXT) pipeline to study Shigella septin cage entrapment in its near-native state. Quantitative cryo-SXT showed that Shigella fragments mitochondria and enabled visualization of X-ray-dense structures (∼30 nm resolution) surrounding Shigella entrapped in septin cages. Using Airyscan confocal microscopy, we observed lysine 63 (K63)-linked ubiquitin chains decorating septin-cage-entrapped Shigella. Remarkably, septins and K63 chains are present in separate bacterial microdomains, indicating they are recruited separately during antibacterial autophagy. Cryo-SXT and live-cell imaging revealed an interaction between septins and LC3B-positive membranes during autophagy of Shigella. Together, these findings demonstrate how septin-caged Shigella are targeted for autophagy and provide fundamental insights into autophagy-cytoskeleton interactions.
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Affiliation(s)
- Damián Lobato-Márquez
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - José Javier Conesa
- MISTRAL beamline, ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Ana Teresa López-Jiménez
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Michael E. Divine
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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9
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Loconte V, Chen J, Vanslembrouck B, Ekman AA, McDermott G, Le Gros MA, Larabell CA. Soft X-ray tomograms provide a structural basis for whole-cell modeling. FASEB J 2023; 37:e22681. [PMID: 36519968 PMCID: PMC10107707 DOI: 10.1096/fj.202200253r] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Developing in silico models that accurately reflect a whole, functional cell is an ongoing challenge in biology. Current efforts bring together mathematical models, probabilistic models, visual representations, and data to create a multi-scale description of cellular processes. A realistic whole-cell model requires imaging data since it provides spatial constraints and other critical cellular characteristics that are still impossible to obtain by calculation alone. This review introduces Soft X-ray Tomography (SXT) as a powerful imaging technique to visualize and quantify the mesoscopic (~25 nm spatial scale) organelle landscape in whole cells. SXT generates three-dimensional reconstructions of cellular ultrastructure and provides a measured structural framework for whole-cell modeling. Combining SXT with data from disparate technologies at varying spatial resolutions provides further biochemical details and constraints for modeling cellular mechanisms. We conclude, based on the results discussed here, that SXT provides a foundational dataset for a broad spectrum of whole-cell modeling experiments.
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Affiliation(s)
- Valentina Loconte
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Jian‐Hua Chen
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Bieke Vanslembrouck
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Axel A. Ekman
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Gerry McDermott
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Mark A. Le Gros
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
| | - Carolyn A. Larabell
- Department of AnatomyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- National Center for X‐ray TomographyAdvanced Light SourceBerkeleyCaliforniaUSA
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10
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Cossa A, Trépout S, Wien F, Groen J, Le Brun E, Turbant F, Besse L, Pereiro E, Arluison V. Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodeling by Hfq master regulator. J Struct Biol 2022; 214:107912. [PMID: 36283630 DOI: 10.1016/j.jsb.2022.107912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/28/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022]
Abstract
The bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, due to the association of DNA with proteins called Nucleoid Associated Proteins (NAPs). Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq forms amyloid-like structures through its C-terminal region, hence belonging to the bridging family of NAPs. Here, using cryo soft X-ray tomography imaging of native unlabeled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid. More specifically, Hfq influences nucleoid density especially during the stationary growth phase when it is more abundant. Our results indicate that Hfq could regulate nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNAs. Taken together, our findings reveal a new role for this protein in nucleoid remodeling in vivo, that may serve in response to stress conditions and in adapting to changing environments.
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Affiliation(s)
- Antoine Cossa
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Sylvain Trépout
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia.
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
| | - Johannes Groen
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Laetitia Besse
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France
| | - Eva Pereiro
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Université Paris Cité, UFR Sciences du vivant, 75006 Paris cedex, France.
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11
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Bonany M, Pérez-Berná AJ, Dučić T, Pereiro E, Martin-Gómez H, Mas-Moruno C, van Rijt S, Zhao Z, Espanol M, Ginebra MP. Hydroxyapatite nanoparticles-cell interaction: New approaches to disclose the fate of membrane-bound and internalised nanoparticles. BIOMATERIALS ADVANCES 2022; 142:213148. [PMID: 36274359 DOI: 10.1016/j.bioadv.2022.213148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/03/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Hydroxyapatite nanoparticles are popular tools in bone regeneration, but they have also been used for gene delivery and as anticancer drugs. Understanding their mechanism of action, particularly for the latter application, is crucial to predict their toxicity. To this end, we aimed to elucidate the importance of nanoparticle membrane interactions in the cytotoxicity of MG-63 cells using two different types of nanoparticles. In addition, conventional techniques for studying nanoparticle internalisation were evaluated and compared with newer and less exploited approaches. Hydroxyapatite and magnesium-doped hydroxyapatite nanoparticles were used as suspensions or compacted as specular discs. Comparison between cells seeded on the discs and those supplemented with the nanoparticles allowed direct interaction of the cell membrane with the material to be ruled out as the main mechanism of toxicity. In addition, standard techniques such as flow cytometry were inconclusive when used to assess nanoparticles toxicity. Interestingly, the use of intracellular calcium fluorescent probes revealed the presence of a high number of calcium-rich vesicles after nanoparticle supplementation in cell culture. These structures could not be detected by transmission electron microscopy due to their liquid content. However, by using cryo-soft X-ray imaging, which was used to visualise the cellular ultrastructure without further treatment other than vitrification and to quantify the linear absorption coefficient of each organelle, it was possible to identify them as multivesicular bodies, potentially acting as calcium stores. In the study, an advanced state of degradation of the hydroxyapatite and magnesium-doped hydroxyapatite nanoparticles within MG-63 cells was observed. Overall, we demonstrate that the combination of fluorescent calcium probes together with cryo-SXT is an excellent approach to investigate intracellular calcium, especially when found in its soluble form.
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Affiliation(s)
- Mar Bonany
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain
| | | | - Tanja Dučić
- MISTRAL Beamline Experiments Division, ALBA Synchrotron Light Source, 08290 Barcelona, Spain
| | - Eva Pereiro
- MISTRAL Beamline Experiments Division, ALBA Synchrotron Light Source, 08290 Barcelona, Spain
| | - Helena Martin-Gómez
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain
| | - Carlos Mas-Moruno
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain
| | - Sabine van Rijt
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6200, MD, Maastricht, the Netherlands
| | - Zhitong Zhao
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Montserrat Espanol
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain.
| | - Maria-Pau Ginebra
- Biomaterials, Biomechanics and Tissue Engineering Group, Department of Materials Science and Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain; Barcelona Research Centre in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain; Biomedical Engineering Research Center (CREB), UPC, 08028 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
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12
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Integrative modeling of the cell. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1213-1221. [PMID: 36017893 PMCID: PMC9909318 DOI: 10.3724/abbs.2022115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summarize an emerging workflow of whole-cell modeling into five steps: (i) gather information; (ii) represent the modeled system into modules; (iii) translate input information into scoring function; (iv) sample the whole-cell model; (v) validate and interpret the model. In particular, we propose the integrative modeling of the cell by combining available (whole-cell) models to maximize the accuracy, precision, and completeness. In addition, we list quantitative predictions of various aspects of cell biology from existing whole-cell models. Moreover, we discuss the remaining challenges and future directions, and highlight the opportunity to establish an integrative spatiotemporal multi-scale whole-cell model based on a community approach.
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13
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Seifer S, Elbaum M. ClusterAlign: A fiducial tracking and tilt series alignment tool for thick sample tomography. BIOLOGICAL IMAGING 2022; 2:e7. [PMID: 38486831 PMCID: PMC10936405 DOI: 10.1017/s2633903x22000071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/04/2022] [Accepted: 07/18/2022] [Indexed: 03/17/2024]
Abstract
Thick specimens, as encountered in cryo-scanning transmission electron tomography, offer special challenges to conventional reconstruction workflows. The visibility of features, including gold nanoparticles introduced as fiducial markers, varies strongly through the tilt series. As a result, tedious manual refinement may be required in order to produce a successful alignment. Information from highly tilted views must often be excluded to the detriment of axial resolution in the reconstruction. We introduce here an approach to tilt series alignment based on identification of fiducial particle clusters that transform coherently in rotation, essentially those that lie at similar depth. Clusters are identified by comparison of tilted views with a single untilted reference, rather than with adjacent tilts. The software, called ClusterAlign, proves robust to poor signal to noise ratio and varying visibility of the individual fiducials and is successful in carrying the alignment to the ends of the tilt series where other methods tend to fail. ClusterAlign may be used to generate a list of tracked fiducials, to align a tilt series, or to perform a complete 3D reconstruction. Tools to evaluate alignment error by projection matching are included. Execution involves no manual intervention, and adherence to standard file formats facilitates an interface with other software, particularly IMOD/etomo, tomo3d, and tomoalign.
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Affiliation(s)
- Shahar Seifer
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Elbaum
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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14
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Castroflorio E, Pérez Berná AJ, López-Márquez A, Badosa C, Loza-Alvarez P, Roldán M, Jiménez-Mallebrera C. The Capillary Morphogenesis Gene 2 Triggers the Intracellular Hallmarks of Collagen VI-Related Muscular Dystrophy. Int J Mol Sci 2022; 23:ijms23147651. [PMID: 35886995 PMCID: PMC9322809 DOI: 10.3390/ijms23147651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
Collagen VI-related disorders (COL6-RD) represent a severe form of congenital disease for which there is no treatment. Dominant-negative pathogenic variants in the genes encoding α chains of collagen VI are the main cause of COL6-RD. Here we report that patient-derived fibroblasts carrying a common single nucleotide variant mutation are unable to build the extracellular collagen VI network. This correlates with the intracellular accumulation of endosomes and lysosomes triggered by the increased phosphorylation of the collagen VI receptor CMG2. Notably, using a CRISPR-Cas9 gene-editing tool to silence the dominant-negative mutation in patients’ cells, we rescued the normal extracellular collagen VI network, CMG2 phosphorylation levels, and the accumulation of endosomes and lysosomes. Our findings reveal an unanticipated role of CMG2 in regulating endosomal and lysosomal homeostasis and suggest that mutated collagen VI dysregulates the intracellular environment in fibroblasts in collagen VI-related muscular dystrophy.
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Affiliation(s)
- Enrico Castroflorio
- ICFO-The Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Spain;
- Correspondence: (E.C.); (C.J.-M.)
| | | | - Arístides López-Márquez
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain; (A.L.-M.); (C.B.)
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain;
- Centro de Investigaciones Biomédicas en Red de Enfermedades Rara (CIBERER), 28029 Madrid, Spain
| | - Carmen Badosa
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain; (A.L.-M.); (C.B.)
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain;
| | - Pablo Loza-Alvarez
- ICFO-The Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Spain;
| | - Mónica Roldán
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain;
- Unitat de Microscòpia Confocal i Imatge Cellular, Servei de Medicina Genètica i Molecular, Institut Pediàtric de Malaties Rares (IPER), Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Cecilia Jiménez-Mallebrera
- Laboratorio de Investigación Aplicada en Enfermedades Neuromusculares, Unidad de Patología Neuromuscular, Servicio de Neuropediatría, Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain; (A.L.-M.); (C.B.)
- Institut de Recerca Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain;
- Centro de Investigaciones Biomédicas en Red de Enfermedades Rara (CIBERER), 28029 Madrid, Spain
- Department of Genetics, University of Barcelona, 08028 Barcelona, Spain
- Correspondence: (E.C.); (C.J.-M.)
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15
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Peddie CJ, Genoud C, Kreshuk A, Meechan K, Micheva KD, Narayan K, Pape C, Parton RG, Schieber NL, Schwab Y, Titze B, Verkade P, Aubrey A, Collinson LM. Volume electron microscopy. NATURE REVIEWS. METHODS PRIMERS 2022; 2:51. [PMID: 37409324 PMCID: PMC7614724 DOI: 10.1038/s43586-022-00131-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 07/07/2023]
Abstract
Life exists in three dimensions, but until the turn of the century most electron microscopy methods provided only 2D image data. Recently, electron microscopy techniques capable of delving deep into the structure of cells and tissues have emerged, collectively called volume electron microscopy (vEM). Developments in vEM have been dubbed a quiet revolution as the field evolved from established transmission and scanning electron microscopy techniques, so early publications largely focused on the bioscience applications rather than the underlying technological breakthroughs. However, with an explosion in the uptake of vEM across the biosciences and fast-paced advances in volume, resolution, throughput and ease of use, it is timely to introduce the field to new audiences. In this Primer, we introduce the different vEM imaging modalities, the specialized sample processing and image analysis pipelines that accompany each modality and the types of information revealed in the data. We showcase key applications in the biosciences where vEM has helped make breakthrough discoveries and consider limitations and future directions. We aim to show new users how vEM can support discovery science in their own research fields and inspire broader uptake of the technology, finally allowing its full adoption into mainstream biological imaging.
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Affiliation(s)
- Christopher J. Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Christel Genoud
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kimberly Meechan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Present address: Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Kristina D. Micheva
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Constantin Pape
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert G. Parton
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole L. Schieber
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Yannick Schwab
- Cell Biology and Biophysics Unit/ Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Aubrey Aubrey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Lucy M. Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
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16
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Loconte V, Singla J, Li A, Chen JH, Ekman A, McDermott G, Sali A, Le Gros M, White KL, Larabell CA. Soft X-ray tomography to map and quantify organelle interactions at the mesoscale. Structure 2022; 30:510-521.e3. [PMID: 35148829 PMCID: PMC9013509 DOI: 10.1016/j.str.2022.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/04/2021] [Accepted: 01/17/2022] [Indexed: 12/11/2022]
Abstract
Inter-organelle interactions are a vital part of normal cellular function; however, these have proven difficult to quantify due to the range of scales encountered in cell biology and the throughput limitations of traditional imaging approaches. Here, we demonstrate that soft X-ray tomography (SXT) can be used to rapidly map ultrastructural reorganization and inter-organelle interactions in intact cells. SXT takes advantage of the naturally occurring, differential X-ray absorption of the carbon-rich compounds in each organelle. Specifically, we use SXT to map the spatiotemporal evolution of insulin vesicles and their co-localization and interaction with mitochondria in pancreatic β cells during insulin secretion and in response to different stimuli. We quantify changes in the morphology, biochemical composition, and relative position of mitochondria and insulin vesicles. These findings highlight the importance of a comprehensive and unbiased mapping at the mesoscale to characterize cell reorganization that would be difficult to detect with other existing methodologies.
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Affiliation(s)
- Valentina Loconte
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jitin Singla
- Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Angdi Li
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian-Hua Chen
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel Ekman
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gerry McDermott
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Science, Department of Pharmaceutical Chemistry, California Institute of Quantitative Bioscience, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mark Le Gros
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kate L White
- Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA.
| | - Carolyn A Larabell
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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17
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Bolitho E, Sanchez-Cano C, Shi H, Quinn PD, Harkiolaki M, Imberti C, Sadler PJ. Single-Cell Chemistry of Photoactivatable Platinum Anticancer Complexes. J Am Chem Soc 2021; 143:20224-20240. [PMID: 34808054 PMCID: PMC8662725 DOI: 10.1021/jacs.1c08630] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 02/08/2023]
Abstract
The Pt(IV) prodrug trans, trans, trans-[Pt(pyridine)2(N3)2(OH)2] (Pt1) and its coumarin derivative trans, trans, trans-[Pt(pyridine)2(N3)2(OH)(coumarin-3-carboxylate)] (Pt2) are promising agents for photoactivated chemotherapy. These complexes are inert in the dark but release Pt(II) species and radicals upon visible light irradiation, resulting in photocytotoxicity toward cancer cells. Here, we have used synchrotron techniques to investigate the in-cell behavior of these prodrugs and visualize, for the first time, changes in cellular morphology and Pt localization upon treatment with and without light irradiation. We show that photoactivation of Pt2 induces remarkable cellular damage with extreme alterations to multiple cellular components, including formation of vacuoles, while also significantly increasing the cellular accumulation of Pt species compared to dark conditions. X-ray absorption near-edge structure (XANES) measurements in cells treated with Pt2 indicate only partial reduction of the prodrug upon irradiation, highlighting that phototoxicity in cancer cells may involve not only Pt(II) photoproducts but also photoexcited Pt(IV) species.
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Affiliation(s)
- Elizabeth
M. Bolitho
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
- Diamond
Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, United
Kingdom
| | - Carlos Sanchez-Cano
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research
and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 San Sebastián, Spain
| | - Huayun Shi
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Paul D. Quinn
- Diamond
Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, United
Kingdom
| | - Maria Harkiolaki
- Diamond
Light Source, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0DE, United
Kingdom
| | - Cinzia Imberti
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Peter J. Sadler
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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18
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Groen J, Palanca A, Aires A, Conesa JJ, Maestro D, Rehbein S, Harkiolaki M, Villar AV, Cortajarena AL, Pereiro E. Correlative 3D cryo X-ray imaging reveals intracellular location and effect of designed antifibrotic protein-nanomaterial hybrids. Chem Sci 2021; 12:15090-15103. [PMID: 34909150 PMCID: PMC8612387 DOI: 10.1039/d1sc04183e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/17/2021] [Indexed: 12/20/2022] Open
Abstract
Revealing the intracellular location of novel therapeutic agents is paramount for the understanding of their effect at the cell ultrastructure level. Here, we apply a novel correlative cryo 3D imaging approach to determine the intracellular fate of a designed protein–nanomaterial hybrid with antifibrotic properties that shows great promise in mitigating myocardial fibrosis. Cryo 3D structured illumination microscopy (cryo-3D-SIM) pinpoints the location and cryo soft X-ray tomography (cryo-SXT) reveals the ultrastructural environment and subcellular localization of this nanomaterial with spatial correlation accuracy down to 70 nm in whole cells. This novel high resolution 3D cryo correlative approach unambiguously locates the nanomaterial after overnight treatment within multivesicular bodies which have been associated with endosomal trafficking events by confocal microscopy. Moreover, this approach allows assessing the cellular response towards the treatment by evaluating the morphological changes induced. This is especially relevant for the future usage of nanoformulations in clinical practices. This correlative super-resolution and X-ray imaging strategy joins high specificity, by the use of fluorescence, with high spatial resolution at 30 nm (half pitch) provided by cryo-SXT in whole cells, without the need of staining or fixation, and can be of particular benefit to locate specific molecules in the native cellular environment in bio-nanomedicine. A novel 3D cryo correlative approach locates designed therapeutic protein–nanomaterial hybrids in whole cells with high specificity and resolution. Detection of treatment-induced morphological changes, crucial for pre-clinical studies, are revealed.![]()
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Affiliation(s)
- J Groen
- MISTRAL Beamline, Experiments Division, ALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain
| | - A Palanca
- Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), University of Cantabria, CSIC 39011 Santander Spain.,Department of Anatomy and Cell Biology, University of Cantabria 39011 Santander Spain
| | - A Aires
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 194 20014 Donostia San Sebastian Spain
| | - J J Conesa
- MISTRAL Beamline, Experiments Division, ALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain .,National Center for Biotechnology CSIC (CNB-CSIC), Department of Macromolecular Structures Cantoblanco 28049 Madrid Spain
| | - D Maestro
- Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), University of Cantabria, CSIC 39011 Santander Spain
| | - S Rehbein
- Helmholtz-Zentrum Berlin für Materialien und Energie, Bessy II D-12489 Berlin Germany
| | - M Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - A V Villar
- Instituto de Biomedicina y Biotecnologia de Cantabria (IBBTEC), University of Cantabria, CSIC 39011 Santander Spain.,Department of Physiology and Pharmacology, University of Cantabria Avd. Herrera Oria s/n Santander Spain
| | - A L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA) Paseo de Miramón 194 20014 Donostia San Sebastian Spain .,Ikerbasque, Basque Foundation for Science 48009 Bilbao Spain
| | - E Pereiro
- MISTRAL Beamline, Experiments Division, ALBA Synchrotron Light Source Cerdanyola del Valles 08290 Barcelona Spain
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19
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Loconte V, Chen JH, Cortese M, Ekman A, Le Gros MA, Larabell C, Bartenschlager R, Weinhardt V. Using soft X-ray tomography for rapid whole-cell quantitative imaging of SARS-CoV-2-infected cells. CELL REPORTS METHODS 2021; 1:100117. [PMID: 34729550 PMCID: PMC8552653 DOI: 10.1016/j.crmeth.2021.100117] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/10/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
High-resolution and rapid imaging of host cell ultrastructure can generate insights toward viral disease mechanism, for example for a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Here, we employ full-rotation soft X-ray tomography (SXT) to examine organelle remodeling induced by SARS-CoV-2 at the whole-cell level with high spatial resolution and throughput. Most of the current SXT systems suffer from a restricted field of view due to use of flat sample supports and artifacts due to missing data. In this approach using cylindrical sample holders, a full-rotation tomogram of human lung epithelial cells is performed in less than 10 min. We demonstrate the potential of SXT imaging by visualizing aggregates of SARS-CoV-2 virions and virus-induced intracellular alterations. This rapid whole-cell imaging approach allows us to visualize the spatiotemporal changes of cellular organelles upon viral infection in a quantitative manner.
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Affiliation(s)
- Valentina Loconte
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg, Germany
| | - Axel Ekman
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Mark A. Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg, Germany
- German Center for Infection Research, Heidelberg Partner Site, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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20
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Garriga D, Chichón FJ, Calisto BM, Ferrero DS, Gastaminza P, Pereiro E, Pérez-Berna AJ. Imaging of Virus-Infected Cells with Soft X-ray Tomography. Viruses 2021; 13:v13112109. [PMID: 34834916 PMCID: PMC8618346 DOI: 10.3390/v13112109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Viruses are obligate parasites that depend on a host cell for replication and survival. Consequently, to fully understand the viral processes involved in infection and replication, it is fundamental to study them in the cellular context. Often, viral infections induce significant changes in the subcellular organization of the host cell due to the formation of viral factories, alteration of cell cytoskeleton and/or budding of newly formed particles. Accurate 3D mapping of organelle reorganization in infected cells can thus provide valuable information for both basic virus research and antiviral drug development. Among the available techniques for 3D cell imaging, cryo-soft X-ray tomography stands out for its large depth of view (allowing for 10 µm thick biological samples to be imaged without further thinning), its resolution (about 50 nm for tomographies, sufficient to detect viral particles), the minimal requirements for sample manipulation (can be used on frozen, unfixed and unstained whole cells) and the potential to be combined with other techniques (i.e., correlative fluorescence microscopy). In this review we describe the fundamentals of cryo-soft X-ray tomography, its sample requirements, its advantages and its limitations. To highlight the potential of this technique, examples of virus research performed at BL09-MISTRAL beamline in ALBA synchrotron are also presented.
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Affiliation(s)
- Damià Garriga
- ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain; (D.G.); (B.M.C.); (E.P.)
| | - Francisco Javier Chichón
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (F.J.C.); (P.G.)
| | - Bárbara M. Calisto
- ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain; (D.G.); (B.M.C.); (E.P.)
| | - Diego S. Ferrero
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Científic de Barcelona, 08028 Barcelona, Spain;
| | - Pablo Gastaminza
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain; (F.J.C.); (P.G.)
| | - Eva Pereiro
- ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain; (D.G.); (B.M.C.); (E.P.)
| | - Ana Joaquina Pérez-Berna
- ALBA Synchrotron Light Source, 08290 Cerdanyola del Vallès, Spain; (D.G.); (B.M.C.); (E.P.)
- Correspondence: ; Tel.: +34-93-592-4371
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21
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Panneels V, Diaz A, Imsand C, Guizar-Sicairos M, Müller E, Bittermann AG, Ishikawa T, Menzel A, Kaech A, Holler M, Grimm C, Schertler G. Imaging of retina cellular and subcellular structures using ptychographic hard X-ray tomography. J Cell Sci 2021; 134:272479. [PMID: 34494099 DOI: 10.1242/jcs.258561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022] Open
Abstract
Ptychographic hard X-ray computed tomography (PXCT) is a recent method allowing imaging with quantitative electron-density contrast. Here, we imaged, at cryogenic temperature and without sectioning, cellular and subcellular structures of a chemically fixed and stained wild-type mouse retina, including axons and synapses, with complete isotropic 3D information over tens of microns. Comparison with tomograms of degenerative retina from a mouse model of retinitis pigmentosa illustrates the potential of this method for analyzing disease processes like neurodegeneration at sub-200 nm resolution. As a non-destructive imaging method, PXCT is very suitable for correlative imaging. Within the outer plexiform layer containing the photoreceptor synapses, we identified somatic synapses. We used a small region inside the X-ray-imaged sample for further high-resolution focused ion beam/scanning electron microscope tomography. The subcellular structures of synapses obtained with the X-ray technique matched the electron microscopy data, demonstrating that PXCT is a powerful scanning method for tissue volumes of more than 60 cells and sensitive enough for identification of regions as small as 200 nm, which remain available for further structural and biochemical investigations.
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Affiliation(s)
- Valerie Panneels
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Ana Diaz
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Cornelia Imsand
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8952 Schlieren, Switzerland
| | - Manuel Guizar-Sicairos
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Elisabeth Müller
- Division of Biology and Chemistry, Laboratory for Nanoscale Biology, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Anne Greet Bittermann
- ScopeM, Scientific Center for Optical and Electron Microscopy, ETH Zurich, 8093 Zurich, Switzerland
| | - Takashi Ishikawa
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland.,Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Menzel
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich, 8006 Zurich, Switzerland
| | - Mirko Holler
- Division of Photon Science, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Christian Grimm
- Laboratory for Retinal Cell Biology, Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8952 Schlieren, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, 5232 Villigen, Switzerland.,Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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22
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Okolo CA, Kounatidis I, Groen J, Nahas KL, Balint S, Fish TM, Koronfel MA, Cortajarena AL, Dobbie IM, Pereiro E, Harkiolaki M. Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures. Nat Protoc 2021; 16:2851-2885. [PMID: 33990802 DOI: 10.1038/s41596-021-00522-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
3D correlative microscopy methods have revolutionized biomedical research, allowing the acquisition of multidimensional information to gain an in-depth understanding of biological systems. With the advent of relevant cryo-preservation methods, correlative imaging of cryogenically preserved samples has led to nanometer resolution imaging (2-50 nm) under harsh imaging regimes such as electron and soft X-ray tomography. These methods have now been combined with conventional and super-resolution fluorescence imaging at cryogenic temperatures to augment information content from a given sample, resulting in the immediate requirement for protocols that facilitate hassle-free, unambiguous cross-correlation between microscopes. We present here sample preparation strategies and a direct comparison of different working fiducialization regimes that facilitate 3D correlation of cryo-structured illumination microscopy and cryo-soft X-ray tomography. Our protocol has been tested at two synchrotron beamlines (B24 at Diamond Light Source in the UK and BL09 Mistral at ALBA in Spain) and has led to the development of a decision aid that facilitates experimental design with the strategic use of markers based on project requirements. This protocol takes between 1.5 h and 3.5 d to complete, depending on the cell populations used (adherent cells may require several days to grow on sample carriers).
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Affiliation(s)
- Chidinma A Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | | | - Kamal L Nahas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stefan Balint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas M Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Mohamed A Koronfel
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Eva Pereiro
- Beamline 09-MISTRAL, ALBA Synchrotron, Barcelona, Spain
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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23
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Anthony EJ, Bolitho EM, Bridgewater HE, Carter OWL, Donnelly JM, Imberti C, Lant EC, Lermyte F, Needham RJ, Palau M, Sadler PJ, Shi H, Wang FX, Zhang WY, Zhang Z. Metallodrugs are unique: opportunities and challenges of discovery and development. Chem Sci 2020; 11:12888-12917. [PMID: 34123239 PMCID: PMC8163330 DOI: 10.1039/d0sc04082g] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Metals play vital roles in nutrients and medicines and provide chemical functionalities that are not accessible to purely organic compounds. At least 10 metals are essential for human life and about 46 other non-essential metals (including radionuclides) are also used in drug therapies and diagnostic agents. These include platinum drugs (in 50% of cancer chemotherapies), lithium (bipolar disorders), silver (antimicrobials), and bismuth (broad-spectrum antibiotics). While the quest for novel and better drugs is now as urgent as ever, drug discovery and development pipelines established for organic drugs and based on target identification and high-throughput screening of compound libraries are less effective when applied to metallodrugs. Metallodrugs are often prodrugs which undergo activation by ligand substitution or redox reactions, and are multi-targeting, all of which need to be considered when establishing structure-activity relationships. We focus on early-stage in vitro drug discovery, highlighting the challenges of evaluating anticancer, antimicrobial and antiviral metallo-pharmacophores in cultured cells, and identifying their targets. We highlight advances in the application of metal-specific techniques that can assist the preclinical development, including synchrotron X-ray spectro(micro)scopy, luminescence, and mass spectrometry-based methods, combined with proteomic and genomic (metallomic) approaches. A deeper understanding of the behavior of metals and metallodrugs in biological systems is not only key to the design of novel agents with unique mechanisms of action, but also to new understanding of clinically-established drugs.
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Affiliation(s)
- Elizabeth J Anthony
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Elizabeth M Bolitho
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Hannah E Bridgewater
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Oliver W L Carter
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Jane M Donnelly
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Cinzia Imberti
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Edward C Lant
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Frederik Lermyte
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Russell J Needham
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Marta Palau
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Huayun Shi
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Fang-Xin Wang
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Wen-Ying Zhang
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Zijin Zhang
- Department of Chemistry, University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
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24
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Jamme F, Cinquin B, Gohon Y, Pereiro E, Réfrégiers M, Froissard M. Synchrotron multimodal imaging in a whole cell reveals lipid droplet core organization. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:772-778. [PMID: 32381780 PMCID: PMC7206545 DOI: 10.1107/s1600577520003847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
A lipid droplet (LD) core of a cell consists mainly of neutral lipids, triacylglycerols and/or steryl esters (SEs). The structuration of these lipids inside the core is still under debate. Lipid segregation inside LDs has been observed but is sometimes suggested to be an artefact of LD isolation and chemical fixation. LD imaging in their native state and in unaltered cellular environments appears essential to overcome these possible technical pitfalls. Here, imaging techniques for ultrastructural study of native LDs in cellulo are provided and it is shown that LDs are organized structures. Cryo soft X-ray tomography and deep-ultraviolet (DUV) transmittance imaging are showing a partitioning of SEs at the periphery of the LD core. Furthermore, DUV transmittance and tryptophan/tyrosine auto-fluorescence imaging on living cells are combined to obtain complementary information on cell chemical contents. This multimodal approach paves the way for a new label-free organelle imaging technique in living cells.
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Affiliation(s)
- Frédéric Jamme
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Bertrand Cinquin
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Yann Gohon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - Eva Pereiro
- MISTRAL Beamline, ALBA Synchrotron, Cerdanyola del Vallès, Barcelona 08290, Spain
| | | | - Marine Froissard
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
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25
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Bolitho EM, Sanchez-Cano C, Huang H, Hands-Portman I, Spink M, Quinn PD, Harkiolaki M, Sadler PJ. X-ray tomography of cryopreserved human prostate cancer cells: mitochondrial targeting by an organoiridium photosensitiser. J Biol Inorg Chem 2020; 25:295-303. [PMID: 32124100 PMCID: PMC7082392 DOI: 10.1007/s00775-020-01761-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/04/2020] [Indexed: 12/14/2022]
Abstract
Abstract The organoiridium complex Ir[(C,N)2(O,O)] (1) where C, N = 1-phenylisoquinoline and O,O = 2,2,6,6-tetramethyl-3,5-heptanedionate is a promising photosensitiser for Photo-Dynamic Therapy (PDT). 1 is not toxic to cells in the dark. However, irradiation of the compound with one-photon blue or two-photon red light generates high levels of singlet oxygen (1O2) (in Zhang et al. Angew Chem Int Ed Engl 56 (47):14898-14902 10.1002/anie.201709082,2017), both within cell monolayers and in tumour models. Moreover, photo-excited 1 oxidises key proteins, causing metabolic alterations in cancer cells with potent antiproliferative activity. Here, the tomograms obtained by cryo-Soft X-ray Tomography (cryo-SXT) of human PC3 prostate cancer cells treated with 1, irradiated with blue light, and cryopreserved to maintain them in their native state, reveal that irradiation causes extensive and specific alterations to mitochondria, but not other cellular components. Such new insights into the effect of 1O2 generation during PDT using iridium photosensitisers on cells contribute to a detailed understanding of their cellular mode of action. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01761-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth M Bolitho
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.,Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0DE, UK
| | - Carlos Sanchez-Cano
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK. .,Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 182, 20014, Donostia-San Sebastián, Spain.
| | - Huaiyi Huang
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Ian Hands-Portman
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Matthew Spink
- Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0DE, UK
| | - Paul D Quinn
- Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0DE, UK
| | - Maria Harkiolaki
- Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0DE, UK.
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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26
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Witte K, Späth A, Finizio S, Donnelly C, Watts B, Sarafimov B, Odstrcil M, Guizar-Sicairos M, Holler M, Fink RH, Raabe J. From 2D STXM to 3D Imaging: Soft X-ray Laminography of Thin Specimens. NANO LETTERS 2020; 20:1305-1314. [PMID: 31951418 DOI: 10.1021/acs.nanolett.9b04782] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
X-ray tomography has become an indispensable tool for studying complex 3D interior structures with high spatial resolution. Three-dimensional imaging using soft X-rays offers powerful contrast mechanisms but has seen limited success with tomography due to the restrictions imposed by the much lower energy of the probe beam. The generalized geometry of laminography, characterized by a tilted axis of rotation, provides nm-scale 3D resolution for the investigation of extended (mm range) but thin (μm to nm) samples that are well suited to soft X-ray studies. This work reports on the implementation of soft X-ray laminography (SoXL) at the scanning transmission X-ray spectromicroscope of the PolLux beamline at the Swiss Light Source, Paul Scherrer Institut, which enables 3D imaging of extended specimens from 270 to 1500 eV. Soft X-ray imaging provides contrast mechanisms for both chemical sensitivity to molecular bonds and oxidation states and magnetic dichroism due to the much stronger attenuation of X-rays in this energy range. The presented examples of applications range from functionalized nanomaterials to biological photonic crystals and sophisticated nanoscaled magnetic domain patterns, thus illustrating the wide fields of research that can benefit from SoXL.
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Affiliation(s)
- Katharina Witte
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Andreas Späth
- Department Chemie und Pharmazie, Physikalische Chemie , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstrasse 3 , 91058 Erlangen , Germany
| | - Simone Finizio
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Claire Donnelly
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge , CB3 0HE , United Kingdom
| | - Benjamin Watts
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Blagoj Sarafimov
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Michal Odstrcil
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Manuel Guizar-Sicairos
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Mirko Holler
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Rainer H Fink
- Department Chemie und Pharmazie, Physikalische Chemie , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstrasse 3 , 91058 Erlangen , Germany
| | - Jörg Raabe
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
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27
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Weinhardt V, Chen JH, Ekman AA, Guo J, Remesh SG, Hammel M, McDermott G, Chao W, Oh S, Le Gros MA, Larabell CA. Switchable resolution in soft x-ray tomography of single cells. PLoS One 2020; 15:e0227601. [PMID: 31978064 PMCID: PMC6980406 DOI: 10.1371/journal.pone.0227601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/24/2019] [Indexed: 11/18/2022] Open
Abstract
The diversity of living cells, in both size and internal complexity, calls for imaging methods with adaptable spatial resolution. Soft x-ray tomography (SXT) is a three-dimensional imaging technique ideally suited to visualizing and quantifying the internal organization of single cells of varying sizes in a near-native state. The achievable resolution of the soft x-ray microscope is largely determined by the objective lens, but switching between objectives is extremely time-consuming and typically undertaken only during microscope maintenance procedures. Since the resolution of the optic is inversely proportional to the depth of focus, an optic capable of imaging the thickest cells is routinely selected. This unnecessarily limits the achievable resolution in smaller cells and eliminates the ability to obtain high-resolution images of regions of interest in larger cells. Here, we describe developments to overcome this shortfall and allow selection of microscope optics best suited to the specimen characteristics and data requirements. We demonstrate that switchable objective capability advances the flexibility of SXT to enable imaging cells ranging in size from bacteria to yeast and mammalian cells without physically modifying the microscope, and we demonstrate the use of this technology to image the same specimen with both optics.
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Affiliation(s)
- Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Axel A. Ekman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Jessica Guo
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Soumya G. Remesh
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Gerry McDermott
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Weilun Chao
- Center for X-ray Optics, Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sharon Oh
- Center for X-ray Optics, Material Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Mark A. Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America
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28
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2019-A year in Biophysical Reviews. Biophys Rev 2019; 11:833-839. [PMID: 31741173 DOI: 10.1007/s12551-019-00607-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
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Biophysical Reviews: promoting the African synchrotron facility, partnering with national biophysical societies, highlighting advances in structural biology. Biophys Rev 2019; 11:495-497. [PMID: 31338694 DOI: 10.1007/s12551-019-00577-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
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