1
|
Beatty KE, López CS. Characteristics of genetic tags for correlative light and electron microscopy. Curr Opin Chem Biol 2023; 76:102369. [PMID: 37453163 DOI: 10.1016/j.cbpa.2023.102369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Fluorescence microscopy is indispensable in live cell studies of fluorescently-labeled proteins, but has limited resolution and context. Electron microscopy offers high-resolution imaging of cellular ultrastructure, including membranes, organelles, and other nanoscale features. However, identifying proteins by EM remains a substantial challenge. There is potential to combine the strengths of both FM and EM through correlative light and EM (CLEM), and bridging the two modalities enables new discoveries and biological insights. CLEM enables cellular proteins to be observed dynamically, across size scales, and in relationship to sub-cellular structures. A central limitation to using CLEM is the scarcity of methods for labeling proteins with CLEM reporters. This review will describe the characteristics of genetic tags for CLEM that are available today, including fixation-resistant fluorescent proteins, 3,3'-diaminobenzidine (DAB)-based tags, metal-chelating tags, DNA origami tags, and VIP tags.
Collapse
Affiliation(s)
- Kimberly E Beatty
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
| | - Claudia S López
- Department of Biomedical Engineering Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
| |
Collapse
|
2
|
López CS, Devlin K, Stempinski ES, Beatty KE. Novel Genetically Encoded Peptide Tags for Correlative Imaging: Lessons Learned. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2099. [PMID: 37612994 DOI: 10.1093/micmic/ozad067.1086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Claudia S López
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | - Kaylyn Devlin
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University Portland, Oregon, USA
| | - Erin S Stempinski
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, Oregon, USA
| | - Kimberly E Beatty
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University Portland, Oregon, USA
| |
Collapse
|
3
|
Parlanti P, Cappello V. Microscopes, tools, probes, and protocols: A guide in the route of correlative microscopy for biomedical investigation. Micron 2021; 152:103182. [PMID: 34801960 DOI: 10.1016/j.micron.2021.103182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 12/11/2022]
Abstract
In the last decades, the advancements of microscopes technology, together with the development of new imaging approaches, are trying to address some biological questions that have been unresolved in the past: the need to combine in the same analysis temporal, functional and morphological information on the biological sample has become pressing. For this reason, the use of correlative microscopy, in which two or more imaging techniques are combined in the same analysis, is getting increasingly widespread. In fact, correlative microscopy can overcome limitations of a single imaging method, giving access to a larger amount of information from the same specimen. However, correlative microscopy can be challenging, and appropriate protocols for sample preparation and imaging methods must be selected. Here we review the state of the art of correlating electron microscopy with different imaging methods, focusing on sample preparation, tools, and labeling methods, with the aim to provide a comprehensive guide for those scientists who are approaching the field of correlative methods.
Collapse
Affiliation(s)
- Paola Parlanti
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
| | - Valentina Cappello
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
| |
Collapse
|
4
|
Lawson MJ, Katsamenis OL, Chatelet D, Alzetani A, Larkin O, Haig I, Lackie P, Warner J, Schneider P. Immunofluorescence-guided segmentation of three-dimensional features in micro-computed tomography datasets of human lung tissue. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211067. [PMID: 34737879 PMCID: PMC8564621 DOI: 10.1098/rsos.211067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Micro-computed tomography (µCT) provides non-destructive three-dimensional (3D) imaging of soft tissue microstructures. Specific features in µCT images can be identified using correlated two-dimensional (2D) histology images allowing manual segmentation. However, this is very time-consuming and requires specialist knowledge of the tissue and imaging modalities involved. Using a custom-designed µCT system optimized for imaging unstained formalin-fixed paraffin-embedded soft tissues, we imaged human lung tissue at isotropic voxel sizes less than 10 µm. Tissue sections were stained with haematoxylin and eosin or cytokeratin 18 in columnar airway epithelial cells using immunofluorescence (IF), as an exemplar of this workflow. Novel utilization of tissue autofluorescence allowed automatic alignment of 2D microscopy images to the 3D µCT data using scripted co-registration and automated image warping algorithms. Warped IF images, which were accurately aligned with the µCT datasets, allowed 3D segmentation of immunoreactive tissue microstructures in the human lung. Blood vessels were segmented semi-automatically using the co-registered µCT datasets. Correlating 2D IF and 3D µCT data enables accurate identification, localization and segmentation of features in fixed soft lung tissue. Our novel correlative imaging workflow provides faster and more automated 3D segmentation of µCT datasets. This is applicable to the huge range of formalin-fixed paraffin-embedded tissues held in biobanks and archives.
Collapse
Affiliation(s)
- Matthew J. Lawson
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Orestis L. Katsamenis
- μ-VIS X-ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - David Chatelet
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Aiman Alzetani
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Oliver Larkin
- Bioengineering Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - Ian Haig
- Nikon X-Tek Systems Ltd, Tring, UK
| | - Peter Lackie
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jane Warner
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Philipp Schneider
- Bioengineering Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
- High-Performance Vision Systems, Center for Vision, Automation and Control, AIT Austrian Institute of Technology, Vienna, Austria
| |
Collapse
|
5
|
Reactive oxygen FIB spin milling enables correlative workflow for 3D super-resolution light microscopy and serial FIB/SEM of cultured cells. Sci Rep 2021; 11:13162. [PMID: 34162977 PMCID: PMC8222390 DOI: 10.1038/s41598-021-92608-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/08/2021] [Indexed: 12/28/2022] Open
Abstract
Correlative light and electron microscopy (CLEM) is a powerful tool for defining the ultrastructural context of molecularly-labeled biological specimens, particularly when superresolution fluorescence microscopy (SRM) is used for CLEM. Current CLEM, however, is limited by the stark differences in sample preparation requirements between the two modalities. For CLEM using SRM, the small region of interest (ROI) of either or both modalities also leads to low success rate and imaging throughput. To overcome these limitations, here we present a CLEM workflow based on a novel focused ion beam/scanning electron microscope (FIB/SEM) compatible with common SRM for imaging biological specimen with ultrahigh 3D resolution and improved imaging throughput. By using a reactive oxygen source in a plasma FIB (PFIB) and a rotating sample stage, the novel FIB/SEM was able to achieve several hundreds of micrometer large area 3D analysis of resin embedded cells through a process named oxygen serial spin mill (OSSM). Compared with current FIB mechanisms, OSSM offers gentle erosion, highly consistent slice thickness, reduced charging during SEM imaging, and improved SEM contrast without increasing the dose of post-staining and fixation. These characteristics of OSSM-SEM allowed us to pair it with interferometric photoactivated localization microscopy (iPALM), a recent SRM technique that affords 10–20 nm isotropic spatial resolution on hydrated samples, for 3D CLEM imaging. We demonstrate a CLEM workflow generalizable to using other SRM strategies using mitochondria in human osteosarcoma (U2OS) cells as a model system, where immunostained TOM20, a marker for the mitochondrial outer membrane, was used for iPALM. Owing to the large scan area of OSSM-SEM, it is now possible to select as many FOVs as needed for iPALM and conveniently re-locate them in EM, this improving the imaging throughput. The significantly reduced dose of post-fixation also helped to better preserve the sample ultrastructures as evidenced by the excellent 3D registration between OSSM-SEM and iPALM images and by the accurate localization of TOM20 (by iPALM) to the peripheries of mitochondria (by OSSM-SEM). These advantages make OSSM-SEM an ideal modality for CLEM applications. As OSSM-SEM is still in development, we also discuss some of the remaining issues and the implications to biological imaging with SEM alone or with CLEM.
Collapse
|
6
|
Kagan J, Moritz RL, Mazurchuk R, Lee JH, Kharchenko PV, Rozenblatt-Rosen O, Ruppin E, Edfors F, Ginty F, Goltsev Y, Wells JA, LaCava J, Riesterer JL, Germain RN, Shi T, Chee MS, Budnik BA, Yates JR, Chait BT, Moffitt JR, Smith RD, Srivastava S. National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions. J Proteome Res 2020; 19:1900-1912. [PMID: 32163288 DOI: 10.1021/acs.jproteome.0c00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts' opinion on the development and application of multiomic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, and prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular, and functional aberrations within the lesion and within individual cells. Single-cell proteomic data will be essential for the establishment of new tools with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included (i) The best way/s to analyze single-cells from fresh and preserved tissue; (ii) Detection and analysis of secreted molecules and from single cells, especially from a tissue slice; (iii) Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment; (iv) Multiomic integration of data to support and inform proteomic measurements; (v) Subcellular organelles-identifying abnormal structure, function, distribution, and location within individual premalignant and malignant cells; (vi) How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post-translational modifications (PTM); (vii) The depth of coverage measured concurrently using single-cell techniques; (viii) Quantitation - absolute or semiquantitative? (ix) Single methodology or multiplexed combinations? (x) Application of analytical methods for identification of biologically significant subsets; (xi) Data visualization of N-dimensional data sets; (xii) How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME); (xiii) Associations between intrinsic cellular processes and extrinsic stimuli; (xiv) How to predict cellular responses to stress-inducing stimuli; (xv) Identification of new markers for prediction of progression from precursor, benign, and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells; (xvi) Identification of new targets for immunoprevention or immunotherapy-identification of neoantigens and surfactome of individual cells within a lesion.
Collapse
Affiliation(s)
- Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington, United States
| | - Richard Mazurchuk
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Je Hyuk Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Peter Vasili Kharchenko
- Blavatnik Institute for Biomedical Information, Harvard Medical School, Boston, Massachusetts, United States
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fiona Ginty
- Life Sciences and Molecular Diagnostics Laboratory, GE Global Research Center, Niskayuna, New York, United States
| | - Yury Goltsev
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford Medical School, Stanford, California, United States
| | - James A Wells
- Department of Pharmaceutical Sciences, University of California, San Francisco, California, United States
| | - John LaCava
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York, United States
| | - Jessica L Riesterer
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Ronald N Germain
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Mark S Chee
- Encodia, Inc., San Diego, California, United States
| | - Bogdan A Budnik
- Faculty of Arts & Sciences, Division of Science. Harvard University, Boston, Massachusetts, United States
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, United States
| | - Jeffery R Moffitt
- Boston Children's Hospital and Harvard University Medical School, Boston, Massachusetts, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| |
Collapse
|
7
|
Riesterer JL, López CS, Stempinski ES, Williams M, Loftis K, Stoltz K, Thibault G, Lanicault C, Williams T, Gray JW. A workflow for visualizing human cancer biopsies using large-format electron microscopy. Methods Cell Biol 2020; 158:163-181. [PMID: 32423648 DOI: 10.1016/bs.mcb.2020.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Recent developments in large format electron microscopy have enabled generation of images that provide detailed ultrastructural information on normal and diseased cells and tissues. Analyses of these images increase our understanding of cellular organization and interactions and disease-related changes therein. In this manuscript, we describe a workflow for two-dimensional (2D) and three-dimensional (3D) imaging, including both optical and scanning electron microscopy (SEM) methods, that allow pathologists and cancer biology researchers to identify areas of interest from human cancer biopsies. The protocols and mounting strategies described in this workflow are compatible with 2D large format EM mapping, 3D focused ion beam-SEM and serial block face-SEM. The flexibility to use diverse imaging technologies available at most academic institutions makes this workflow useful and applicable for most life science samples. Volumetric analysis of the biopsies studied here revealed morphological, organizational and ultrastructural aspects of the tumor cells and surrounding environment that cannot be revealed by conventional 2D EM imaging. Our results indicate that although 2D EM is still an important tool in many areas of diagnostic pathology, 3D images of ultrastructural relationships between both normal and cancerous cells, in combination with their extracellular matrix, enables cancer researchers and pathologists to better understand the progression of the disease and identify potential therapeutic targets.
Collapse
Affiliation(s)
- Jessica L Riesterer
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States; Multiscale Microscopy Core, Oregon Health and Sciences University, Portland, OR, United States.
| | - Claudia S López
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States; Multiscale Microscopy Core, Oregon Health and Sciences University, Portland, OR, United States; Pacific Northwest Center for CryoEM, Oregon Health and Sciences University, Portland, OR, United States.
| | - Erin S Stempinski
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States; Multiscale Microscopy Core, Oregon Health and Sciences University, Portland, OR, United States
| | - Melissa Williams
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States; Multiscale Microscopy Core, Oregon Health and Sciences University, Portland, OR, United States
| | - Kevin Loftis
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States
| | - Kevin Stoltz
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States
| | - Guillaume Thibault
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States
| | - Christian Lanicault
- Department of Pathology, Oregon Health and Sciences University, Portland, OR, United States
| | - Todd Williams
- Department of Pathology, Oregon Health and Sciences University, Portland, OR, United States
| | - Joe W Gray
- OHSU Center for Spatial Systems Biomedicine, Oregon Health and Sciences University, Portland, OR, United States.
| |
Collapse
|
8
|
Page MJ, Thomson GJA, Nunes JM, Engelbrecht AM, Nell TA, de Villiers WJS, de Beer MC, Engelbrecht L, Kell DB, Pretorius E. Serum amyloid A binds to fibrin(ogen), promoting fibrin amyloid formation. Sci Rep 2019; 9:3102. [PMID: 30816210 PMCID: PMC6395759 DOI: 10.1038/s41598-019-39056-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/16/2019] [Indexed: 12/15/2022] Open
Abstract
Complex associations exist between inflammation and thrombosis, with the inflammatory state tending to promote coagulation. Fibrinogen, an acute phase protein, has been shown to interact with the amyloidogenic ß-amyloid protein of Alzheimer’s disease. However, little is known about the association between fibrinogen and serum amyloid A (SAA), a highly fibrillogenic protein that is one of the most dramatically changing acute phase reactants in the circulation. To study the role of SAA in coagulation and thrombosis, in vitro experiments were performed where purified human SAA, in concentrations resembling a modest acute phase response, was added to platelet-poor plasma (PPP) and whole blood (WB), as well as purified and fluorescently labelled fibrinogen. Results from thromboelastography (TEG) suggest that SAA causes atypical coagulation with a fibrin(ogen)-mediated increase in coagulation, but a decreased platelet/fibrin(ogen) interaction. In WB scanning electron microscopy analysis, SAA mediated red blood cell (RBC) agglutination, platelet activation and clumping, but not platelet spreading. Following clot formation in PPP, the presence of SAA increased amyloid formation of fibrin(ogen) as determined both with auto-fluorescence and with fluorogenic amyloid markers, under confocal microcopy. SAA also binds to fibrinogen, as determined with a fluorescent-labelled SAA antibody and correlative light electron microscopy (CLEM). The data presented here indicate that SAA can affect coagulation by inducing amyloid formation in fibrin(ogen), as well as by propelling platelets to a more prothrombotic state. The discovery of these multiple and complex effects of SAA on coagulation invite further mechanistic analyses.
Collapse
Affiliation(s)
- Martin J Page
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, Stellenbosch, South Africa
| | - Greig J A Thomson
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, Stellenbosch, South Africa
| | - J Massimo Nunes
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, Stellenbosch, South Africa
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, Stellenbosch, South Africa
| | - Theo A Nell
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, Stellenbosch, South Africa
| | - Willem J S de Villiers
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, Stellenbosch, South Africa.,Department of Internal Medicine, Stellenbosch University, Stellenbosch, South Africa
| | - Maria C de Beer
- Department of Physiology, Saha Cardiovascular Research Center and Barnstable Brown Diabetes Center, University of Kentucky, Lexington, KY, USA
| | - Lize Engelbrecht
- Fluorescence Microscopy Unit, Central Analytical Facilities, Stellenbosch University, Stellenbosch, South Africa
| | - Douglas B Kell
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, Stellenbosch, South Africa. .,School of Chemistry, The University of Manchester, 131 Princess St, MANCHESTER M1 7DN, Lancs, UK. .,The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, MANCHESTER M1 7DN, Lancs, UK. .,Department of Biochemistry, Institute of integrative Biology, Biosciences Building., University of Liverpool, Crown St, Liverpool, L69 7ZB, UK.
| | - Etheresia Pretorius
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, Stellenbosch, South Africa.
| |
Collapse
|
9
|
|
10
|
VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy. Proc Natl Acad Sci U S A 2018; 115:12961-12966. [PMID: 30518560 DOI: 10.1073/pnas.1808626115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many discoveries in cell biology rely on making specific proteins visible within their native cellular environment. There are various genetically encoded tags, such as fluorescent proteins, developed for fluorescence microscopy (FM). However, there are almost no genetically encoded tags that enable cellular proteins to be observed by both FM and electron microscopy (EM). Herein, we describe a technology for labeling proteins with diverse chemical reporters, including bright organic fluorophores for FM and electron-dense nanoparticles for EM. Our technology uses versatile interacting peptide (VIP) tags, a class of genetically encoded tag. We present VIPER, which consists of a coiled-coil heterodimer formed between the genetic tag, CoilE, and a probe-labeled peptide, CoilR. Using confocal FM, we demonstrate that VIPER can be used to highlight subcellular structures or to image receptor-mediated iron uptake. Additionally, we used VIPER to image the iron uptake machinery by correlative light and EM (CLEM). VIPER compared favorably with immunolabeling for imaging proteins by CLEM, and is an enabling technology for protein targets that cannot be immunolabeled. VIPER is a versatile peptide tag that can be used to label and track proteins with diverse chemical reporters observable by both FM and EM instrumentation.
Collapse
|
11
|
de Waal GM, Engelbrecht L, Davis T, de Villiers WJS, Kell DB, Pretorius E. Correlative Light-Electron Microscopy detects lipopolysaccharide and its association with fibrin fibres in Parkinson's Disease, Alzheimer's Disease and Type 2 Diabetes Mellitus. Sci Rep 2018; 8:16798. [PMID: 30429533 PMCID: PMC6235901 DOI: 10.1038/s41598-018-35009-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/27/2018] [Indexed: 02/06/2023] Open
Abstract
Many chronic diseases, including those classified as cardiovascular, neurodegenerative, or autoimmune, are characterized by persistent inflammation. The origin of this inflammation is mostly unclear, but it is typically mediated by inflammatory biomarkers, such as cytokines, and affected by both environmental and genetic factors. Recently circulating bacterial inflammagens such as lipopolysaccharide (LPS) have been implicated. We used a highly selective mouse monoclonal antibody to detect bacterial LPS in whole blood and/or platelet poor plasma of individuals with Parkinson’s Disease, Alzheimer’s type dementia, or Type 2 Diabetes Mellitus. Our results showed that staining is significantly enhanced (P < 0.0001) compared to healthy controls. Aberrant blood clots in these patient groups are characterized by amyloid formation as shown by the amyloid-selective stains thioflavin T and Amytracker™ 480 or 680. Correlative Light-Electron Microscopy (CLEM) illustrated that the LPS antibody staining is located in the same places as where amyloid fibrils may be observed. These data are consistent with the Iron Dysregulation and Dormant Microbes (IDDM) hypothesis in which bacterial inflammagens such as LPS are responsible for anomalous blood clotting as part of the aetiology of these chronic inflammatory diseases.
Collapse
Affiliation(s)
- Greta M de Waal
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Lize Engelbrecht
- Central Analytical Facilities, Fluorescence Microscopy Unit, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Tanja Davis
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Willem J S de Villiers
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa.,Department of Internal Medicine, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Douglas B Kell
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa.,School of Chemistry, The University of Manchester, 131 Princess St, Manchester, Lancs, M1 7DN, UK.,Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, Lancs, M1 7DN, UK
| | - Etheresia Pretorius
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa.
| |
Collapse
|
12
|
Li S, Ji G, Shi Y, Klausen LH, Niu T, Wang S, Huang X, Ding W, Zhang X, Dong M, Xu W, Sun F. High-vacuum optical platform for cryo-CLEM (HOPE): A new solution for non-integrated multiscale correlative light and electron microscopy. J Struct Biol 2018; 201:63-75. [PMID: 29113848 DOI: 10.1016/j.jsb.2017.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/28/2017] [Accepted: 11/03/2017] [Indexed: 12/28/2022]
Abstract
Cryo-correlative light and electron microscopy (cryo-CLEM) offers a unique way to analyze the high-resolution structural information of cryo-vitrified specimen by cryo-electron microscopy (cryo-EM) with the guide of the search for unique events by cryo-fluorescence microscopy (cryo-FM). To achieve cryo-FM, a trade-off must be made between the temperature and performance of objective lens. The temperature of specimen should be kept below devitrification while the distance between the objective lens and specimen should be short enough for high resolution imaging. Although special objective lens was designed in many current cryo-FM approaches, the unavoided frosting and ice contamination are still affecting the efficiency of cryo-CLEM. In addition, the correlation accuracy between cryo-FM and cryo-EM would be reduced during the current specimen transfer procedure. Here, we report an improved cryo-CLEM technique (high-vacuum optical platform for cryo-CLEM, HOPE) based on a high-vacuum optical stage and a commercial cryo-EM holder. The HOPE stage comprises of a special adapter to suit the cryo-EM holder and a high-vacuum chamber with an anti-contamination system. It provides a clean and enduring environment for cryo specimen, while the normal dry objective lens in room temperature can be used via the optical windows. The 'touch-free' specimen transfer via cryo-EM holder allows least specimen deformation and thus maximizes the correlation accuracy between cryo-FM and cryo-EM. Besides, we developed a software to perform semi-automatic cryo-EM acquisition of the target region localized by cryo-FM. Our work provides a new solution for cryo-CLEM and can be adapted for different commercial fluorescence microscope and electron microscope.
Collapse
Affiliation(s)
- Shuoguo Li
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Gang Ji
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Yang Shi
- University of Chinese Academy of Sciences, Beijing, China; National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lasse Hyldgaard Klausen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Tongxin Niu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengliu Wang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojun Huang
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China
| | - Wei Ding
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China
| | - Xiang Zhang
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Wei Xu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China
| | - Fei Sun
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, CAS, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|