1
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André M, Dinvaut S, Castellani V, Falk J. 3D exploration of gene expression in chicken embryos through combined RNA fluorescence in situ hybridization, immunofluorescence, and clearing. BMC Biol 2024; 22:131. [PMID: 38831263 PMCID: PMC11149291 DOI: 10.1186/s12915-024-01922-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Fine characterization of gene expression patterns is crucial to understand many aspects of embryonic development. The chicken embryo is a well-established and valuable animal model for developmental biology. The period spanning from the third to sixth embryonic days (E3 to E6) is critical for many organ developments. Hybridization chain reaction RNA fluorescent in situ hybridization (HCR RNA-FISH) enables multiplex RNA detection in thick samples including embryos of various animal models. However, its use is limited by tissue opacity. RESULTS We optimized HCR RNA-FISH protocol to efficiently label RNAs in whole mount chicken embryos from E3.5 to E5.5 and adapted it to ethyl cinnamate (ECi) tissue clearing. We show that light sheet imaging of HCR RNA-FISH after ECi clearing allows RNA expression analysis within embryonic tissues with good sensitivity and spatial resolution. Finally, whole mount immunofluorescence can be performed after HCR RNA-FISH enabling as exemplified to assay complex spatial relationships between axons and their environment or to monitor GFP electroporated neurons. CONCLUSIONS We could extend the use of HCR RNA-FISH to older chick embryos by optimizing HCR RNA-FISH and combining it with tissue clearing and 3D imaging. The integration of immunostaining makes possible to combine gene expression with classical cell markers, to correlate expressions with morphological differentiation and to depict gene expressions in gain or loss of function contexts. Altogether, this combined procedure further extends the potential of HCR RNA-FISH technique for chicken embryology.
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Affiliation(s)
- Maëlys André
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France.
| | - Sarah Dinvaut
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France
| | - Valérie Castellani
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France
| | - Julien Falk
- MeLiS, CNRS UMR 5284 - INSERM U1314, Université Claude Bernard Lyon 1, 8 avenue Rockefeller, 69008, Lyon, France.
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2
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Balcaen T, Benova A, de Jong F, de Oliveira Silva R, Cajka T, Sakellariou D, Tencerova M, Kerckhofs G, De Borggraeve W. Exploring contrast-enhancing staining agents for studying adipose tissue through contrast-enhanced computed tomography. J Lipid Res 2024:100572. [PMID: 38823780 DOI: 10.1016/j.jlr.2024.100572] [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: 03/25/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 06/03/2024] Open
Abstract
Contrast-enhanced computed tomography (CECT) offers a non-destructive approach to studying adipose tissue in 3D. Several contrast-enhancing staining agents (CESAs) have been explored, whereof osmium tetroxide (OsO4) is the most popular nowadays. However, due to the toxicity and volatility of the conventional OsO4, alternative CESAs with similar staining properties were desired. Hf-WD 1:2 POM and Hexabrix have proven effective for structural analysis of adipocytes using CECT, but fail to provide chemical information. This study introduces isotonic Lugol's iodine (IL) as an alternative CESA for adipose tissue analysis, comparing its staining potential with Hf-WD 1:2 POM and Hexabrix in murine caudal vertebrae (MCV) and bovine muscle tissue (BMT) strips. Single and sequential staining protocols were compared to assess the maximization of information extraction from each sample. The study investigated interactions, distribution, and reactivity of iodine species towards biomolecules using simplified model systems and assesses the potential of the CESA to provide chemical information. (Bio)chemical analyses on whole tissues revealed that differences in adipocyte grey values post-IL staining were associated with chemical distinctions between BMT and MCV. More specific, a difference in degree of unsaturation of fatty acids was identified as a likely contributor, though not the sole determinant of grey value differences. This research sheds light on the potential of IL as a CESA, offering both structural and chemical insights into adipose tissue composition.
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Affiliation(s)
- Tim Balcaen
- MolDesignS, Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, Leuven, Belgium; Institute of Mechanics, Materials and Civil Engineering, Mechatronic, Electrical Energy and Dynamic Systems, UCLouvain, Louvain-la-Neuve, Belgium; Pole of Morphology, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
| | - Andrea Benova
- Laboratory of Molecular Physiology of Bone, Institute of Physiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague, Czech Republic
| | - Flip de Jong
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Rodrigo de Oliveira Silva
- Membrane Separations, Adsorption, Catalysis, and Spectroscopy for Sustainable Solutions (cMACS), Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Tomas Cajka
- Laboratory of Translational Metabolism, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic
| | - Dimitrios Sakellariou
- Membrane Separations, Adsorption, Catalysis, and Spectroscopy for Sustainable Solutions (cMACS), Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Michaela Tencerova
- Laboratory of Molecular Physiology of Bone, Institute of Physiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Greet Kerckhofs
- Institute of Mechanics, Materials and Civil Engineering, Mechatronic, Electrical Energy and Dynamic Systems, UCLouvain, Louvain-la-Neuve, Belgium; Pole of Morphology, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium; Department Materials Engineering, KU Leuven, Leuven, Belgium.
| | - Wim De Borggraeve
- MolDesignS, Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, Leuven, Belgium
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3
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Zheng J, Wu YC, Phillips EH, Cai X, Wang X, Seung-Young Lee S. Increased Multiplexity in Optical Tissue Clearing-Based Three-Dimensional Immunofluorescence Microscopy of the Tumor Microenvironment by Light-Emitting Diode Photobleaching. J Transl Med 2024; 104:102072. [PMID: 38679160 DOI: 10.1016/j.labinv.2024.102072] [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: 01/24/2024] [Revised: 03/29/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024] Open
Abstract
Optical tissue clearing and three-dimensional (3D) immunofluorescence (IF) microscopy is transforming imaging of the complex tumor microenvironment (TME). However, current 3D IF microscopy has restricted multiplexity; only 3 or 4 cellular and noncellular TME components can be localized in cleared tumor tissue. Here we report a light-emitting diode (LED) photobleaching method and its application for 3D multiplexed optical mapping of the TME. We built a high-power LED light irradiation device and temperature-controlled chamber for completely bleaching fluorescent signals throughout optically cleared tumor tissues without compromise of tissue and protein antigen integrity. With newly developed tissue mounting and selected region-tracking methods, we established a cyclic workflow involving IF staining, tissue clearing, 3D confocal microscopy, and LED photobleaching. By registering microscope channel images generated through 3 work cycles, we produced 8-plex image data from individual 400 μm-thick tumor macrosections that visualize various vascular, immune, and cancer cells in the same TME at tissue-wide and cellular levels in 3D. Our method was also validated for quantitative 3D spatial analysis of cellular remodeling in the TME after immunotherapy. These results demonstrate that our LED photobleaching system and its workflow offer a novel approach to increase the multiplexing power of 3D IF microscopy for studying tumor heterogeneity and response to therapy.
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Affiliation(s)
- Jingtian Zheng
- Department of Pharmaceutical Sciences, University of Illinois, Chicago, Chicago, Illinois
| | - Yi-Chien Wu
- Department of Pharmaceutical Sciences, University of Illinois, Chicago, Chicago, Illinois
| | - Evan H Phillips
- Department of Pharmaceutical Sciences, University of Illinois, Chicago, Chicago, Illinois
| | - Xiaoying Cai
- Department of Pharmaceutical Sciences, University of Illinois, Chicago, Chicago, Illinois
| | - Xu Wang
- Department of Pharmaceutical Sciences, University of Illinois, Chicago, Chicago, Illinois
| | - Steve Seung-Young Lee
- Department of Pharmaceutical Sciences, University of Illinois, Chicago, Chicago, Illinois; University of Illinois Cancer Center, University of Illinois Chicago, Chicago, Illinois.
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4
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Cayrol B, Colella S, Uzest M. Coupling clearing and hybridization chain reaction approaches to investigate gene expression in organs inside intact insect heads. Microsc Res Tech 2024. [PMID: 38558482 DOI: 10.1002/jemt.24561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
Detecting RNA molecules within their natural environment inside intact arthropods has long been challenging, particularly in small organisms covered by a tanned and pigmented cuticle. Here, we have developed a methodology that enables high-resolution analysis of the spatial distribution of transcripts of interest without having to dissect tiny organs or tissues, thereby preserving their integrity. We have combined an in situ amplification approach based on hybridization chain reaction, which enhances the signal-to-noise ratio, and a clearing approach that allows the visualization of inner organs beneath the cuticle. We have implemented this methodology for the first time in Hemiptera, mapping two salivary aphid (Acyrthosiphon pisum) transcripts, the effector c002 and the salivary sheath protein SHP. With a multiplex approach, we could simultaneously detect different mRNAs in mounted pea aphid head-thorax samples and show that they were distributed in distinct secretory cells of salivary glands. RESEARCH HIGHLIGHTS: Combining hybridisation chain reaction and clearing allows the detection of transcripts in intact aphids heads. The transcripts of the two salivary proteins c002 and SHP are compartmentalized in distinct secretory cells of the principal glands.
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Affiliation(s)
- Bastien Cayrol
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Stefano Colella
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Marilyne Uzest
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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5
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Soumier A, Lio G, Demily C. Current and future applications of light-sheet imaging for identifying molecular and developmental processes in autism spectrum disorders. Mol Psychiatry 2024:10.1038/s41380-024-02487-8. [PMID: 38443634 DOI: 10.1038/s41380-024-02487-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Autism spectrum disorder (ASD) is identified by a set of neurodevelopmental divergences that typically affect the social communication domain. ASD is also characterized by heterogeneous cognitive impairments and is associated with cooccurring physical and medical conditions. As behaviors emerge as the brain matures, it is particularly essential to identify any gaps in neurodevelopmental trajectories during early perinatal life. Here, we introduce the potential of light-sheet imaging for studying developmental biology and cross-scale interactions among genetic, cellular, molecular and macroscale levels of circuitry and connectivity. We first report the core principles of light-sheet imaging and the recent progress in studying brain development in preclinical animal models and human organoids. We also present studies using light-sheet imaging to understand the development and function of other organs, such as the skin and gastrointestinal tract. We also provide information on the potential of light-sheet imaging in preclinical drug development. Finally, we speculate on the translational benefits of light-sheet imaging for studying individual brain-body interactions in advancing ASD research and creating personalized interventions.
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Affiliation(s)
- Amelie Soumier
- Le Vinatier Hospital Center, 95 boulevard Pinel, 69675, Bron cedex, France.
- iMIND, Center of Excellence for Autism, 95 boulevard Pinel, 69675, Bron cedex, France.
- Institute of Cognitive Science Marc Jeannerod, CNRS, UMR 5229, 67 boulevard Pinel, 69675, Bron cedex, France.
- University Claude Bernard Lyon 1, 43 boulevard du 11 Novembre 1918, 69622, Villeurbanne cedex, France.
| | - Guillaume Lio
- Le Vinatier Hospital Center, 95 boulevard Pinel, 69675, Bron cedex, France
- iMIND, Center of Excellence for Autism, 95 boulevard Pinel, 69675, Bron cedex, France
- Institute of Cognitive Science Marc Jeannerod, CNRS, UMR 5229, 67 boulevard Pinel, 69675, Bron cedex, France
| | - Caroline Demily
- Le Vinatier Hospital Center, 95 boulevard Pinel, 69675, Bron cedex, France
- iMIND, Center of Excellence for Autism, 95 boulevard Pinel, 69675, Bron cedex, France
- Institute of Cognitive Science Marc Jeannerod, CNRS, UMR 5229, 67 boulevard Pinel, 69675, Bron cedex, France
- University Claude Bernard Lyon 1, 43 boulevard du 11 Novembre 1918, 69622, Villeurbanne cedex, France
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6
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Folts L, Martinez AS, McKey J. Tissue clearing and imaging approaches for in toto analysis of the reproductive system. Biol Reprod 2023:ioad182. [PMID: 38159104 DOI: 10.1093/biolre/ioad182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Abstract
New microscopy techniques in combination with tissue clearing protocols and emerging analytical approaches have presented researchers with the tools to understand dynamic biological processes in a three-dimensional context. This paves the road for the exploration of new research questions in reproductive biology, for which previous techniques have provided only approximate resolution. These new methodologies now allow for contextualized analysis of far larger volumes than was previously possible. Tissue optical clearing and three-dimensional imaging techniques posit the bridging of molecular mechanisms, macroscopic morphogenic development, and maintenance of reproductive function into one cohesive and comprehensive understanding of the biology of the reproductive system. In this review, we present a survey of the various tissue clearing techniques and imaging systems, as they have been applied to the developing and adult reproductive system. We provide an overview of tools available for analysis of experimental data, giving particular attention to the emergence of AI-assisted methods and their applicability to image analysis. We conclude with an evaluation of how novel image analysis approaches which have been applied to other organ systems could be incorporated into future experimental evaluation of reproductive biology.
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Affiliation(s)
- Lillian Folts
- Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora CO 80045
| | - Anthony S Martinez
- Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora CO 80045
| | - Jennifer McKey
- Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora CO 80045
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7
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Zheng J, Wu YC, Phillips EH, Wang X, Lee SSY. Increased multiplexity in optical tissue clearing-based 3D immunofluorescence microscopy of the tumor microenvironment by LED photobleaching. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569277. [PMID: 38076864 PMCID: PMC10705380 DOI: 10.1101/2023.11.29.569277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Optical tissue clearing and three-dimensional (3D) immunofluorescence (IF) microscopy have been transforming imaging of the complex tumor microenvironment (TME). However, current 3D IF microscopy has restricted multiplexity; only three or four cellular and non-cellular TME components can be localized in a cleared tumor tissue. Here we report a LED photobleaching method and its application for 3D multiplexed optical mapping of the TME. We built a high-power LED light irradiation device and temperature-controlled chamber for completely bleaching fluorescent signals throughout optically cleared tumor tissues without compromise of tissue and protein antigen integrity. With newly developed tissue mounting and selected region-tracking methods, we established a cyclic workflow involving IF staining, tissue clearing, 3D confocal microscopy, and LED photobleaching. By registering microscope channel images generated through three work cycles, we produced 8-plex image data from individual 400 μm-thick tumor macrosections that visualize various vascular, immune, and cancer cells in the same TME at tissue-wide and cellular levels in 3D. Our method was also validated for quantitative 3D spatial analysis of cellular remodeling in the TME after immunotherapy. These results demonstrate that our LED photobleaching system and its workflow offer a novel approach to increase the multiplexing power of 3D IF microscopy for studying tumor heterogeneity and response to therapy.
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8
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Delage E, Guilbert T, Yates F. Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy. J Cell Biol 2023; 222:e202307143. [PMID: 37847528 PMCID: PMC10583220 DOI: 10.1083/jcb.202307143] [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: 07/28/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023] Open
Abstract
In parallel with the development of tissue-clearing methods, over the last decade, light sheet fluorescence microscopy has contributed to major advances in various fields, such as cell and developmental biology and neuroscience. While biologists are increasingly integrating three-dimensional imaging into their research projects, their experience with the technique is not always up to their expectations. In response to a survey of specific challenges associated with sample clearing and labeling, image acquisition, and data analysis, we have critically assessed the recent literature to characterize the difficulties inherent to light sheet fluorescence microscopy applied to cleared biological samples and to propose solutions to overcome them. This review aims to provide biologists interested in light sheet fluorescence microscopy with a primer for the development of their imaging pipeline, from sample preparation to image analysis. Importantly, we believe that issues could be avoided with better anticipation of image analysis requirements, which should be kept in mind while optimizing sample preparation and acquisition parameters.
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Affiliation(s)
- Elise Delage
- CellTechs Laboratory, SupBiotech, Villejuif, France
- Service d’Etude des Prions et des Infections Atypiques, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, Université Paris Saclay, Fontenay-aux-Roses, France
| | - Thomas Guilbert
- Institut Cochin, Institut national de la santé et de la recherche médicale (U1016), Centre National de la Recherche Scientifique (UMR 8104), Université de Paris (UMR-S1016), Paris, France
| | - Frank Yates
- CellTechs Laboratory, SupBiotech, Villejuif, France
- Service d’Etude des Prions et des Infections Atypiques, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, Université Paris Saclay, Fontenay-aux-Roses, France
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9
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Ćorić A, Stockinger AW, Schaffer P, Rokvić D, Tessmar-Raible K, Raible F. A Fast And Versatile Method for Simultaneous HCR, Immunohistochemistry And Edu Labeling (SHInE). Integr Comp Biol 2023; 63:372-381. [PMID: 36866518 PMCID: PMC10445416 DOI: 10.1093/icb/icad007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Access to newer, fast, and cheap sequencing techniques, particularly on the single-cell level, have made transcriptomic data of tissues or single cells accessible to many researchers. As a consequence, there is an increased need for in situ visualization of gene expression or encoded proteins to validate, localize, or help interpret such sequencing data, as well as put them in context with cellular proliferation. A particular challenge for labeling and imaging transcripts are complex tissues that are often opaque and/or pigmented, preventing easy visual inspection. Here, we introduce a versatile protocol that combines in situ hybridization chain reaction, immunohistochemistry, and proliferative cell labeling using 5-ethynyl-2'-deoxyuridine, and demonstrate its compatibility with tissue clearing. As a proof-of-concept, we show that our protocol allows for the parallel analysis of cell proliferation, gene expression, and protein localization in bristleworm heads and trunks.
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Affiliation(s)
- Aida Ćorić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Alexander W Stockinger
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Research Platform “Single-Cell Regulation of Stem Cells,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Petra Schaffer
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Dunja Rokvić
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Carl-von-Ossietzky University, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria
- Research Platform “Rhythms of Life,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
- Research Platform “Single-Cell Regulation of Stem Cells,” University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, A-1030, Vienna, Austria
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10
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Rai MR, Li C, Ghashghaei HT, Greenbaum A. Deep learning-based adaptive optics for light sheet fluorescence microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:2905-2919. [PMID: 37342701 PMCID: PMC10278610 DOI: 10.1364/boe.488995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
Abstract
Light sheet fluorescence microscopy (LSFM) is a high-speed imaging technique that is often used to image intact tissue-cleared specimens with cellular or subcellular resolution. Like other optical imaging systems, LSFM suffers from sample-induced optical aberrations that decrement imaging quality. Optical aberrations become more severe when imaging a few millimeters deep into tissue-cleared specimens, complicating subsequent analyses. Adaptive optics are commonly used to correct sample-induced aberrations using a deformable mirror. However, routinely used sensorless adaptive optics techniques are slow, as they require multiple images of the same region of interest to iteratively estimate the aberrations. In addition to the fading of fluorescent signal, this is a major limitation as thousands of images are required to image a single intact organ even without adaptive optics. Thus, a fast and accurate aberration estimation method is needed. Here, we used deep-learning techniques to estimate sample-induced aberrations from only two images of the same region of interest in cleared tissues. We show that the application of correction using a deformable mirror greatly improves image quality. We also introduce a sampling technique that requires a minimum number of images to train the network. Two conceptually different network architectures are compared; one that shares convolutional features and another that estimates each aberration independently. Overall, we have presented an efficient way to correct aberrations in LSFM and to improve image quality.
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Affiliation(s)
- Mani Ratnam Rai
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - Chen Li
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
| | - H. Troy Ghashghaei
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Alon Greenbaum
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC 27695, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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11
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Gu Q, Sarkar S, Raymick B, Kanungo J. Combining tissue clearing and Fluoro-Jade C labeling for neurotoxicity assessments. Exp Biol Med (Maywood) 2023; 248:605-611. [PMID: 37208909 PMCID: PMC10350804 DOI: 10.1177/15353702231165009] [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: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 05/21/2023] Open
Abstract
Tissue clearing refers to laboratory methods that make tissue transparent by chemical means. This approach allows the labeling, visualization, and analysis of specific targets without cutting the tissue into sections, thereby maintaining three-dimensional architecture. More than two dozen tissue-clearing methods have been developed by different research teams to date. While tissue clearing has been successfully applied in several studies concerning basic science or diseases, little is known about the utilization of tissue clearing for neurotoxicity evaluation. In this study, several tissue-clearing methods were combined with Fluoro-Jade C (FJ-C), a standard marker of neurodegeneration. The results suggest that some but not all tissue-clearing media are compatible with the FJ-C fluorophore. By utilizing a neurotoxicity animal model, the results further suggest that FJ-C labeling can be combined with tissue clearing for neurotoxicity assessments. This approach has the potential to be expanded further by combining multicolor labeling of molecular targets involved in the development and/or mechanisms of neurotoxicity and neurodegeneration.
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Affiliation(s)
- Qiang Gu
- Division of Neurotoxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Sumit Sarkar
- Division of Neurotoxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Bryan Raymick
- Division of Neurotoxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Jyotshna Kanungo
- Division of Neurotoxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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12
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Timin G, Milinkovitch MC. High-resolution confocal and light-sheet imaging of collagen 3D network architecture in very large samples. iScience 2023; 26:106452. [PMID: 37020961 PMCID: PMC10067766 DOI: 10.1016/j.isci.2023.106452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/06/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
Although notoriously difficult, imaging collagen network architecture, a key element affecting tissue mechanical properties, is of paramount importance in developmental and cancer biology. Here, we introduce a simple and robust method of whole-mount collagen staining with the 'Fast Green' dye that provides unmatched visualization of collagen 3D network architecture, via confocal or light-sheet microscopy, compatible with solvent-based tissue clearing and immunostaining.
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13
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Weiss K, Huisken J, Bakalov V, Engle M, Gridley L, Krzyzanowski MC, Madden T, Maiese D, Waterfield J, Williams D, Wu X, Hamilton CM, Huggins W. T-CLEARE: A Pilot Community-Driven Tissue-Clearing Protocol Repository. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.531970. [PMID: 36945489 PMCID: PMC10028991 DOI: 10.1101/2023.03.09.531970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Selecting and implementing a tissue-clearing protocol is challenging. Established more than 100 years ago, tissue clearing is still a rapidly evolving field of research. There are currently many published protocols to choose from, and each performs better or worse across a range of key evaluation factors (e.g., speed, cost, tissue stability, fluorescence quenching). Additionally, tissue-clearing protocols are often optimized for specific experimental contexts, and applying an existing protocol to a new problem can require a lengthy period of adaptation by trial and error. Although the primary literature and review articles provide a useful starting point for optimization, there is growing recognition that many articles do not provide sufficient detail to replicate or reproduce experimental results. To help address this issue, we have developed a novel, freely available repository of tissue-clearing protocols named T-CLEARE (Tissue CLEAring protocol REpository; https://doryworkspace.org/doryviz). T-CLEARE incorporates community responses to an open survey designed to capture details not commonly found in the scientific literature, including modifications to published protocols required for specific use cases and instances when tissue-clearing protocols did not perform well (negative results). The goal of T-CLEARE is to provide a forum for the community to share evaluations and modifications of tissue-clearing protocols for various tissue types and potentially identify best-in-class methods for a given application.
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Affiliation(s)
- Kurt Weiss
- Morgridge Institute for Research, 330 N Orchard Street, Madison, WI, 53715, USA
| | - Jan Huisken
- Morgridge Institute for Research, 330 N Orchard Street, Madison, WI, 53715, USA
| | - Vesselina Bakalov
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Michelle Engle
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Lauren Gridley
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Michelle C Krzyzanowski
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Tom Madden
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Deborah Maiese
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Justin Waterfield
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - David Williams
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Xin Wu
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Carol M Hamilton
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Wayne Huggins
- Bioinformatics and Computational Biology Program, RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC, 27709, USA
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14
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Kiemen AL, Damanakis AI, Braxton AM, He J, Laheru D, Fishman EK, Chames P, Pérez CA, Wu PH, Wirtz D, Wood LD, Hruban RH. Tissue clearing and 3D reconstruction of digitized, serially sectioned slides provide novel insights into pancreatic cancer. MED 2023; 4:75-91. [PMID: 36773599 PMCID: PMC9922376 DOI: 10.1016/j.medj.2022.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/06/2022] [Accepted: 11/23/2022] [Indexed: 01/26/2023]
Abstract
Pancreatic cancer is currently the third leading cause of cancer death in the United States. The clinical hallmarks of this disease include abdominal pain that radiates to the back, the presence of a hypoenhancing intrapancreatic lesion on imaging, and widespread liver metastases. Technologies such as tissue clearing and three-dimensional (3D) reconstruction of digitized serially sectioned hematoxylin and eosin-stained slides can be used to visualize large (up to 2- to 3-centimeter cube) tissues at cellular resolution. When applied to human pancreatic cancers, these 3D visualization techniques have provided novel insights into the basis of a number of the clinical characteristics of this disease. Here, we describe the clinical features of pancreatic cancer, review techniques for clearing and the 3D reconstruction of digitized microscope slides, and provide examples that illustrate how 3D visualization of human pancreatic cancer at the microscopic level has revealed features not apparent in 2D microscopy and, in so doing, has closed the gap between bench and bedside. Compared with animal models and 2D microscopy, studies of human tissues in 3D can reveal the difference between what can happen and what does happen in human cancers.
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Affiliation(s)
- Ashley L Kiemen
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Chemical & Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Alexander Ioannis Damanakis
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of General, Visceral, Cancer and Transplant Surgery, University Hospital of Cologne, Cologne, Germany
| | - Alicia M Braxton
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jin He
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Daniel Laheru
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elliot K Fishman
- Department of Radiology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Patrick Chames
- Antibody Therapeutics and Immunotargeting Team, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Cristina Almagro Pérez
- Department of Chemical & Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Pei-Hsun Wu
- Department of Chemical & Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Denis Wirtz
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Chemical & Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
| | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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15
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Rakhilin N, Yang B, Spilker ME, Manzuk LK, Montgomery MK, Shin E, Prashad N, Hwang J, Song Y, Loganzo F, Giddabasappa A, Ram S. Volumetric imaging of optically cleared and fluorescently labeled animal tissue (VIOLA) for quantifying the 3D biodistribution of nanoparticles at cellular resolution in tumor tissue. J Control Release 2023; 354:244-259. [PMID: 36596340 DOI: 10.1016/j.jconrel.2022.12.060] [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: 09/23/2022] [Revised: 12/17/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Nanoparticle (NP) technology holds significant promise to mediate targeted drug delivery to specific organs in the body. Understanding the 3D biodistribution of NPs in heterogeneous environments such as the tumor tissue can provide crucial information on efficacy, safety and potential clinical outcomes. Here we present a novel end-to-end workflow, VIOLA, which makes use of tissue clearing methodology in conjunction with high resolution imaging and advanced 3D image processing to quantify the spatiotemporal 3D biodistribution of fluorescently labeled ACCURIN® NPs. Specifically, we investigate the spatiotemporal biodistribution of NPs in three different murine tumor models (CT26, EMT6, and KPC-GEM) of increasing complexity and translational relevance. We have developed new endpoints to characterize NP biodistribution at multiple length scales. Our observations reveal that the macroscale NP biodistribution is spatially heterogeneous and exhibits a gradient with relatively high accumulation at the tumor periphery that progressively decreases towards the tumor core in all the tumor models. Microscale analysis revealed that NP extravasation from blood vessels increases in a time dependent manner and plateaus at 72 h post injection. Volumetric analysis and pharmacokinetic modeling of NP biodistribution in the vicinity of the blood vessels revealed that the local NP density exhibits a distance dependent spatiotemporal biodistribution which provide insights into the dynamics of NP extravasation in the tumor tissue. Our data represents a comprehensive analysis of NP biodistribution at multiple length scales in different tumor models providing unique insights into their spatiotemporal dynamics. Specifically, our results show that NPs exhibit a dynamic equilibrium with macroscale heterogeneity combined with microscale homogeneity.
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Affiliation(s)
| | - Bing Yang
- Comparative Medicine, Pfizer Inc., United States
| | - Mary E Spilker
- Medicine Design - Translational Modeling and Simulation, Pfizer Inc., United States
| | | | | | - Eyoung Shin
- Oncology Research Unit, Pfizer Inc., United States
| | | | | | - Youngho Song
- Oncology Research Unit, Pfizer Inc., United States
| | | | | | - Sripad Ram
- Drug Safety R&D, Pfizer Inc., United States.
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16
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Godefroy D, Boukhzar L, Mallouki BY, Carpentier E, Dubessy C, Chigr F, Tillet Y, Anouar Y. SELENOT Deficiency in the Mouse Brain Impacts Catecholaminergic Neuron Density: An Immunohistochemical, in situ Hybridization and 3D Light-Sheet Imaging Study. Neuroendocrinology 2023; 113:193-207. [PMID: 35066506 DOI: 10.1159/000522091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/11/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Selenoprotein T (SELENOT), a PACAP-regulated thioredoxin-like protein, plays a role in catecholamine secretion and protects dopaminergic neurons. However, the role of SELENOT in the establishment of the catecholaminergic (CA) neuronal system is not known yet. METHODS We analyzed by immunohistochemistry and RNAscope in situ hybridization the distribution of SELENOT and the expression of its mRNA, respectively. In addition, 3D imaging involving immunostaining in toto, clearing through the iDISCO+ method, acquisitions by light-sheet microscopy, and processing of 3D images was performed to map the CA neuronal system. A semi-automatic quantification of 3D images was carried out. RESULTS SELENOT protein and mRNA are widely distributed in the mouse brain, with important local variations. Three-dimensional mapping, through tyrosine hydroxylase (TH) labeling, and semi-automated quantification of CA neurons in brain-specific SELENOT knockout mice showed a significant decrease in the number of TH-positive neurons in the area postrema (AP-A2), the A11 cell group (A11), and the zona incerta (ZI-A13) of SELENOT-deficient females, and in the hypothalamus (Hyp-A12-A14-A15) of SELENOT-deficient females and males. CONCLUSION These results showed that SELENOT is diffusely expressed in the mouse brain and that its deficiency impacts CA neuron distribution in different brain areas including Hyp-A12-A14-A15, in both male and female mice.
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Affiliation(s)
- David Godefroy
- UNIROUEN, INSERM U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Institute for Research and Innovation in Biomedicine (IRIB), Normandie Univsity, Rouen, France
| | - Loubna Boukhzar
- UNIROUEN, INSERM U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Institute for Research and Innovation in Biomedicine (IRIB), Normandie Univsity, Rouen, France
| | - Ben Yamine Mallouki
- UNIROUEN, INSERM U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Institute for Research and Innovation in Biomedicine (IRIB), Normandie Univsity, Rouen, France
| | - Emmanuelle Carpentier
- UNIROUEN, INSERM U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Institute for Research and Innovation in Biomedicine (IRIB), Normandie Univsity, Rouen, France
| | - Christophe Dubessy
- UNIROUEN, INSERM U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Institute for Research and Innovation in Biomedicine (IRIB), Normandie Univsity, Rouen, France
| | - Fatiha Chigr
- Bioengineering Laboratory, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Yves Tillet
- Physiologie de la Reproduction et des Comportements, UMR 085 INRAE, CNRS 7247, IFCE, Centre INRAE Val de Loire, Université de Tours, Nouzilly, France
| | - Youssef Anouar
- UNIROUEN, INSERM U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Institute for Research and Innovation in Biomedicine (IRIB), Normandie Univsity, Rouen, France
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17
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Chai W, Hao W, Liu J, Han Z, Chang S, Cheng L, Sun M, Yan G, Liu Z, Liu Y, Zhang G, Xing L, Chen H, Liu P. Visualizing Cathepsin K-Cre Expression at the Single-Cell Level with GFP Reporters. JBMR Plus 2022; 7:e10706. [PMID: 36699636 PMCID: PMC9850439 DOI: 10.1002/jbm4.10706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 11/10/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
The Cre/lox system is a fundamental tool for functional genomic studies, and a number of Cre lines have been generated to target genes of interest spatially and temporally in defined cells or tissues; this approach has greatly expanded our knowledge of gene functions. However, the limitations of this system have recently been recognized, and we must address the challenge of so-called nonspecific/off-target effects when a Cre line is utilized to investigate a gene of interest. For example, cathepsin K (Ctsk) has been used as a specific osteoclast marker, and Cre driven by its promoter is widely utilized for osteoclast investigations. However, Ctsk-Cre expression has recently been identified in other cell types, such as osteocytes, periosteal stem cells, and tenocytes. To better understand Ctsk-Cre expression and ensure appropriate use of this Cre line, we performed a comprehensive analysis of Ctsk-Cre expression at the single-cell level in major organs and tissues using two green fluorescent protein (GFP) reporters (ROSA nT-nG and ROSA tdT) and a tissue clearing technique in young and aging mice. The expression profile was further verified by immunofluorescence staining and droplet digital RT-PCR. The results demonstrate that Ctsk-Cre is expressed not only in osteoclasts but also at various levels in osteoblast lineage cells and other major organs/tissues, particularly in the brain, kidney, pancreas, and blood vessels. Furthermore, Ctsk-Cre expression increases markedly in the bone marrow, skeletal muscle, and intervertebral discs in aging mice. These data will be valuable for accurately interpreting data obtained from in vivo studies using Ctsk-Cre mice to avoid potentially misleading conclusions. © 2022 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Wenhuan Chai
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Weiwei Hao
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Jintao Liu
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Zhenglin Han
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Shiyu Chang
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Liben Cheng
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Mingxin Sun
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Guofang Yan
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Zemin Liu
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Yin Liu
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Guodong Zhang
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Li Xing
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Hongqian Chen
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
| | - Peng Liu
- Laboratory of Bone & Adipose BiologyShanxi Medical UniversityTaiyuanChina
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18
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He Y, Gao Y, Ma Q, Zhang X, Zhang Y, Song W. Nanotopographical cues for regulation of macrophages and osteoclasts: emerging opportunities for osseointegration. J Nanobiotechnology 2022; 20:510. [PMID: 36463225 PMCID: PMC9719660 DOI: 10.1186/s12951-022-01721-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Nanotopographical cues of bone implant surface has direct influences on various cell types during the establishment of osseointegration, a prerequisite of implant bear-loading. Given the important roles of monocyte/macrophage lineage cells in bone regeneration and remodeling, the regulation of nanotopographies on macrophages and osteoclasts has arisen considerable attentions recently. However, compared to osteoblastic cells, how nanotopographies regulate macrophages and osteoclasts has not been properly summarized. In this review, the roles and interactions of macrophages, osteoclasts and osteoblasts at different stages of bone healing is firstly presented. Then, the diversity and preparation methods of nanotopographies are summarized. Special attentions are paid to the regulation characterizations of nanotopographies on macrophages polarization and osteoclast differentiation, as well as the focal adhesion-cytoskeleton mediated mechanism. Finally, an outlook is indicated of coordinating nanotopographies, macrophages and osteoclasts to achieve better osseointegration. These comprehensive discussions may not only help to guide the optimization of bone implant surface nanostructures, but also provide an enlightenment to the osteoimmune response to external implant.
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Affiliation(s)
- Yide He
- grid.233520.50000 0004 1761 4404State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, 710032 China
| | - Yuanxue Gao
- grid.233520.50000 0004 1761 4404State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, 710032 China
| | - Qianli Ma
- grid.5510.10000 0004 1936 8921Department of Biomaterials, Institute of Clinical Dentistry, University of Oslo, 0317 Oslo, Norway
| | - Xige Zhang
- grid.233520.50000 0004 1761 4404State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, Department of Periodontology, School of Stomatology, The Fourth Military Medical University, Shaanxi Xi’an, 710032 China
| | - Yumei Zhang
- grid.233520.50000 0004 1761 4404State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, 710032 China
| | - Wen Song
- grid.233520.50000 0004 1761 4404State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi’an, 710032 China
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19
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Hereditary spastic paraplegia type 56: what a mouse can tell – a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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20
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Hériché M, Arnould C, Wipf D, Courty PE. Imaging plant tissues: advances and promising clearing practices. TRENDS IN PLANT SCIENCE 2022; 27:601-615. [PMID: 35339361 DOI: 10.1016/j.tplants.2021.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The study of the organ structure of plants and understanding their physiological complexity requires 3D imaging with subcellular resolution. Most plant organs are highly opaque to light, and their study under optical sectioning microscopes is therefore difficult. In animals, many protocols have been developed to make organs transparent to light using clearing protocols (CPs). By contrast, clearing plant tissues is challenging because of the presence of fibers and pigments. We describe progress in the development of plant CPs over the past 20 years through a modified taxonomy of CPs based on their physical and optical parameters that affect tissue properties. We also discuss successful approaches that combine CPs with new microscopy methods and their future applications in plant science research.
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Affiliation(s)
- Mathilde Hériché
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Arnould
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France.
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21
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Johnson CD, Zhou LY, Kopinke D. A Guide to Examining Intramuscular Fat Formation and its Cellular Origin in Skeletal Muscle. JOURNAL OF VISUALIZED EXPERIMENTS : JOVE 2022:10.3791/63996. [PMID: 35695517 PMCID: PMC9741761 DOI: 10.3791/63996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fibro-adipogenic progenitors (FAPs) are mesenchymal stromal cells that play a crucial role during skeletal muscle homeostasis and regeneration. FAPs build and maintain the extracellular matrix that acts as a molecular myofiber scaffold. In addition, FAPs are indispensable for myofiber regeneration as they secrete a multitude of beneficial factors sensed by the muscle stem cells (MuSCs). In diseased states, however, FAPs are the cellular origin of intramuscular fat and fibrotic scar tissue. This fatty fibrosis is a hallmark of sarcopenia and neuromuscular diseases, such as Duchenne Muscular Dystrophy. One significant barrier in determining why and how FAPs differentiate into intramuscular fat is effective preservation and subsequent visualization of adipocytes, especially in frozen tissue sections. Conventional methods of skeletal muscle tissue processing, such as snap-freezing, do not properly preserve the morphology of individual adipocytes, thereby preventing accurate visualization and quantification. To overcome this hurdle, a rigorous protocol was developed that preserves adipocyte morphology in skeletal muscle sections allowing visualization, imaging, and quantification of intramuscular fat. The protocol also outlines how to process a portion of muscle tissue for RT-qPCR, enabling users to confirm observed changes in fat formation by viewing differences in the expression of adipogenic genes. Additionally, it can be adapted to visualize adipocytes by whole-mount immunofluorescence of muscle samples. Finally, this protocol outlines how to perform genetic lineage tracing of Pdgfrα-expressing FAPs to study the adipogenic conversion of FAPs. This protocol consistently yields high-resolution and morphologically accurate immunofluorescent images of adipocytes, along with confirmation by RT-qPCR, allowing for robust, rigorous, and reproducible visualization and quantification of intramuscular fat. Together, the analysis pipeline described here is the first step to improving our understanding of how FAPs differentiate into intramuscular fat, and provides a framework to validate novel interventions to prevent fat formation.
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Affiliation(s)
- Connor D. Johnson
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine
| | - Lylybell Y. Zhou
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine,Myology Institute, University of Florida College of Medicine
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22
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Novel insights into embryonic cardiac macrophages. Dev Biol 2022; 488:1-10. [DOI: 10.1016/j.ydbio.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 11/19/2022]
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23
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Perens J, Hecksher-Sørensen J. Digital Brain Maps and Virtual Neuroscience: An Emerging Role for Light-Sheet Fluorescence Microscopy in Drug Development. Front Neurosci 2022; 16:866884. [PMID: 35516798 PMCID: PMC9067159 DOI: 10.3389/fnins.2022.866884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
The mammalian brain is by far the most advanced organ to have evolved and the underlying biology is extremely complex. However, with aging populations and sedentary lifestyles, the prevalence of neurological disorders is increasing around the world. Consequently, there is a dire need for technologies that can help researchers to better understand the complexity of the brain and thereby accelerate therapies for diseases with origin in the central nervous system. One such technology is light-sheet fluorescence microscopy (LSFM) which in combination with whole organ immunolabelling has made it possible to visualize an intact mouse brain with single cell resolution. However, the price for this level of detail comes in form of enormous datasets that often challenges extraction of quantitative information. One approach for analyzing whole brain data is to align the scanned brains to a reference brain atlas. Having a fixed spatial reference provides each voxel of the sample brains with x-, y-, z-coordinates from which it is possible to obtain anatomical information on the observed fluorescence signal. An additional and important benefit of aligning light sheet data to a reference brain is that the aligned data provides a digital map of gene expression or cell counts which can be deposited in databases or shared with other scientists. This review focuses on the emerging field of virtual neuroscience using digital brain maps and discusses some of challenges incurred when registering LSFM recorded data to a standardized brain template.
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24
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Kim HJ, Kim J, Choi J, Sun W. Chemical fluorescence-based dye staining for 3-dimensional histopathology analysis. Anim Cells Syst (Seoul) 2022; 26:45-51. [PMID: 35479512 PMCID: PMC9037194 DOI: 10.1080/19768354.2022.2049641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Tissue clearing for 3-dimensional (3D) imaging is increasingly utilized in many biomedical applications, including the pathological examination of human biopsy specimens. Although many protocols offer rapid and efficient tissue clearing (>1 d), immunofluorescence labeling of thick specimens is a highly time-consuming process. The use of low molecular weight chemical dyes has potential benefits in terms of speed and quality of 3D labeling. Accordingly, we tested several chemical dyes to assess their potential applications in 3D imaging. The combination of SYTO 16 and eosin (S&E) was found to be a potential fluorescent version of the hematoxylin–eosin (H&E) stain. Furthermore, picrosirius red (for collagen), Congo red (for senile plaques), and fluorescent Nissl (for neurons in the normal brain or blood vessels in the injured brain) stains can be used alone or in combination with antibody labeling. As chemical labeling requires a relatively short incubation time (<1 d), fluorescent chemical dyes could expedite the 3D imaging process.
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Affiliation(s)
- Hyun Jung Kim
- Department of Anatomy, College of Medicine, Korea University, Seoul, Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Jeongah Kim
- Department of Anatomy, College of Medicine, Korea University, Seoul, Korea
| | - Jungyoon Choi
- Department of Anatomy, College of Medicine, Korea University, Seoul, Korea
| | - Woong Sun
- Department of Anatomy, College of Medicine, Korea University, Seoul, Korea
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Flip-Flap: A Simple Dual-View Imaging Method for 3D Reconstruction of Thick Plant Samples. PLANTS 2022; 11:plants11040506. [PMID: 35214839 PMCID: PMC8875395 DOI: 10.3390/plants11040506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/02/2022]
Abstract
Plant development is a complex process that relies on molecular and cellular events being co-ordinated in space and time. Microscopy is one of the most powerful tools available to investigate this spatiotemporal complexity. One step towards a better understanding of complexity in plants would be the acquisition of 3D images of entire organs. However, 3D imaging of intact plant samples is not always simple and often requires expensive and/or non-trivial approaches. In particular, the inner tissues of thick samples are challenging to image. Here, we present the Flip-Flap method, a simple imaging protocol to produce 3D images of cleared plant samples at the organ scale. This method allows full 3D reconstruction of plant organs suitable for 3D segmentation and further related analysis and can be easily handled by relatively inexperienced microscopists.
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26
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Woo J, Lee EY, Lee M, Ku S, Park JY, Cho YE. Comparative Analyses of Clearing Efficacies of Tissue Clearing Protocols by Using a Punching Assisted Clarity Analysis. Front Bioeng Biotechnol 2022; 9:784626. [PMID: 35155401 PMCID: PMC8831720 DOI: 10.3389/fbioe.2021.784626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/30/2021] [Indexed: 02/03/2023] Open
Abstract
The advent of tissue clearing methods, in conjunction with novel high-resolution imaging techniques, has enabled the visualization of three-dimensional structures with unprecedented depth and detail. Although a variety of clearing protocols have been developed, little has been done to quantify their efficacies in a systematic, reproducible fashion. Here, we present two simple assays, Punching-Assisted Clarity Analysis (PACA)-Light and PACA-Glow, which use easily accessible spectroscopy and gel documentation systems to quantify the transparency of multiple cleared tissues simultaneously. We demonstrate the use of PACA-Light and PACA-Glow to compare twenty-eight tissue clearing protocols on rodent brains. We also show that regional differences exist in tissue transparency in the rodent brain, with cerebellar tissue consistently achieving lower clearing levels compared to the prefrontal or cerebral cortex across all protocols. This represents the largest comparative study of tissue clearing protocols to date, made possible by the high-throughput nature of our PACA platforms.
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Affiliation(s)
- Jiwon Woo
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Institute, Biohedron Therapeutics Co., Ltd., Seoul, South Korea
| | - Eunice Yoojin Lee
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Mirae Lee
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Seockmo Ku
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Jeong-Yoon Park
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Yong Eun Cho
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- *Correspondence: Yong Eun Cho,
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Abstract
The Tabula Gallus is a proposed project that aims to create a map of every cell type in the chicken body and chick embryos. Chickens (Gallus gallus) are one of the most recognized model animals that recapitulate the development and physiology of mammals. The Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus, characterize each cell type, and provide tools for the study of the biology of this species, similar to other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and humans, respectively). The Tabula Gallus will potentially become an international collaboration between many researchers. This project will be useful for the basic scientific study of Gallus gallus and other birds (e.g., cell biology, molecular biology, developmental biology, neuroscience, physiology, oncology, virology, behavior, ecology, and evolution). It will eventually be beneficial for a better understanding of human health and diseases.
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28
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Stower MJ, Srinivas S. Advances in live imaging early mouse development: exploring the researcher's interdisciplinary toolkit. Development 2021; 148:dev199433. [PMID: 34897401 PMCID: PMC7615354 DOI: 10.1242/dev.199433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Live imaging is an important part of the developmental biologist's armoury of methods. In the case of the mouse embryo, recent advances in several disciplines including embryo culture, microscopy hardware and computational analysis have all contributed to our ability to probe dynamic events during early development. Together, these advances have provided us with a versatile and powerful 'toolkit', enabling us not only to image events during mouse embryogenesis, but also to intervene with them. In this short Spotlight article, we summarise advances and challenges in using live imaging specifically for understanding early mouse embryogenesis.
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Affiliation(s)
- Matthew J. Stower
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Shankar Srinivas
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
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