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McKenzie AT, Nnadi O, Slagell KD, Thorn EL, Farrell K, Crary JF. Fluid preservation in brain banking: a review. FREE NEUROPATHOLOGY 2024; 5:5-10. [PMID: 38690035 PMCID: PMC11058410 DOI: 10.17879/freeneuropathology-2024-5373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Fluid preservation is nearly universally used in brain banking to store fixed tissue specimens for future research applications. However, the effects of long-term immersion on neural circuitry and biomolecules are not well characterized. As a result, there is a need to synthesize studies investigating fluid preservation of brain tissue. We searched PubMed and other databases to identify studies measuring the effects of fluid preservation in nervous system tissue. We categorized studies based on the fluid preservative used: formaldehyde solutions, buffer solutions, alcohol solutions, storage after tissue clearing, and cryoprotectant solutions. We identified 91 studies containing 197 independent observations of the effects of long-term storage on cellular morphology. Most studies did not report any significant alterations due to long-term storage. When present, the most frequent alteration was decreased antigenicity, commonly attributed to progressive crosslinking by aldehydes that renders biomolecules increasingly inaccessible over time. To build a mechanistic understanding, we discuss biochemical aspects of long-term fluid preservation. A subset of lipids appears to be chemical altered or extracted over time due to incomplete retention in the crosslinked gel. Alternative storage fluids mitigate the problem of antigen masking but have not been extensively characterized and may have other downsides. We also compare fluid preservation to cryopreservation, paraffin embedding, and resin embedding. Overall, existing evidence suggests that fluid preservation provides maintenance of neural architecture for decades, including precise structural details. However, to avoid the well-established problem of overfixation caused by storage in high concentration formaldehyde solutions, fluid preservation procedures can use an initial fixation step followed by an alternative long-term storage fluid. Further research is warranted on optimizing protocols and characterizing the generalizability of the storage artifacts that have been identified.
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Affiliation(s)
| | - Oge Nnadi
- Brain Preservation Foundation, Ashburn, Virginia, USA
| | - Kat D. Slagell
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma L. Thorn
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kurt Farrell
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John F. Crary
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Friedman Brain Institute, Departments of Pathology, Neuroscience, and Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Neuropathology Brain Bank & Research Core and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Bos PR, Berentsen J, Wientjes E. Expansion microscopy resolves the thylakoid structure of spinach. PLANT PHYSIOLOGY 2023; 194:347-358. [PMID: 37792700 PMCID: PMC10756755 DOI: 10.1093/plphys/kiad526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
The light-harvesting reactions of photosynthesis take place on the thylakoid membrane inside chloroplasts. The thylakoid membrane is folded into appressed membranes, the grana, and nonappressed membranes that interconnect the grana, the stroma lamellae. This folding is essential for the correct functioning of photosynthesis. Electron microscopy and atomic force microscopy are commonly used to study the thylakoid membrane, but these techniques have limitations in visualizing a complete chloroplast and its organization. To overcome this limitation, we applied expansion microscopy (ExM) on isolated chloroplasts. ExM is a technique that involves physically expanding a sample in a swellable hydrogel to enhance the spatial resolution of fluorescence microscopy. Using all-protein staining, we visualized the 3D structure of spinach (Spinacia oleracea) thylakoids in detail. We were able to resolve stroma lamellae that were 60 nm apart and observe their helical wrapping around the grana. Furthermore, we accurately measured the dimensions of grana from top views of chloroplasts, which allow for precise determination of the granum diameter. Our results demonstrate that ExM is a fast and reliable technique for studying thylakoid organization in great detail.
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Affiliation(s)
- Peter R Bos
- Laboratory of Biophysics, Wageningen University & Research, Wageningen 6700 ET, The Netherlands
| | - Jarne Berentsen
- Laboratory of Biophysics, Wageningen University & Research, Wageningen 6700 ET, The Netherlands
| | - Emilie Wientjes
- Laboratory of Biophysics, Wageningen University & Research, Wageningen 6700 ET, The Netherlands
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Yuan PQ, Li T, Million M, Larauche M, Atmani K, Bellier JP, Taché Y. New insight on the enteric cholinergic innervation of the pig colon by central and peripheral nervous systems: reduction by repeated loperamide administration. Front Neurosci 2023; 17:1204233. [PMID: 37650102 PMCID: PMC10463754 DOI: 10.3389/fnins.2023.1204233] [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: 04/11/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Introduction The central and peripheral nervous systems provide cholinergic innervation in the colon. The ability to assess their neuroanatomical distinctions is still a challenge. The pig is regarded as a relevant translational model due to the close similarity of its enteric nervous system (ENS) with that of human. Opioid-induced constipation is one of the most common side effects of opioid therapy. Methods We developed an approach to differentiate the central and peripheral cholinergic innervation of the pig colon using double immunolabeling with a novel mouse anti-human peripheral type of choline acetyltransferase (hpChAT) antibody combined with a rabbit anti-common type of ChAT (cChAT) antibody, a reliable marker of cholinergic neurons in the central nervous system. We examined their spatial configurations in 3D images of the ENS generated from CLARITY-cleared colonic segments. The density was quantitated computationally using Imaris 9.7. We assessed changes in the distal colon induced by daily oral treatment for 4 weeks with the μ opioid receptor agonist, loperamide (0.4 or 3 mg/kg). Results The double labeling showed strong cChAT immunoreactive (ir) fibers in the cervical vagus nerve and neuronal somata and fibers in the ventral horn of the sacral (S2) cord while hpChAT immunoreactivity was visualized only in the ENS but not in the vagus or sacral neural structures indicating the selectivity of these two antibodies. In the colonic myenteric plexus, dense hpChAT-ir neurons and fibers and varicose cChAT-ir fibers surrounding hpChAT-ir neurons were simultaneously visualized in 3D. The density of cChAT-ir varicose fibers in the outer submucosal plexus of both males and females were higher in the transverse and distal colon than in the proximal colon and in the myenteric plexus compared to the outer submucosal plexus and there was no cChAT innervation in the inner submucosal plexus. The density of hpChAT in the ENS showed no segmental or plexus differences in both sexes. Loperamide at the highest dose significantly decreased the density hpChAT-ir fibers + somata in the myenteric plexus of the distal colon. Discussion These data showed the distinct density of central cholinergic innervation between myenteric and submucosal plexuses among colonic segments and the localization of cChAT-ir fibers around peripheral hpChAT neurons in 3D. The reduction of cholinergic myenteric innervation by chronic opiate treatment points to target altered prokinetic cholinergic pathway to counteract opiate constipation.
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Affiliation(s)
- Pu-Qing Yuan
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
- VA GLAHS, Los Angeles, CA, United States
| | - Tao Li
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Mulugeta Million
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Muriel Larauche
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Karim Atmani
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Jean-Pierre Bellier
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Yvette Taché
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
- VA GLAHS, Los Angeles, CA, United States
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Wen G, Leen V, Rohand T, Sauer M, Hofkens J. Current Progress in Expansion Microscopy: Chemical Strategies and Applications. Chem Rev 2023; 123:3299-3323. [PMID: 36881995 DOI: 10.1021/acs.chemrev.2c00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Expansion microscopy (ExM) is a newly developed super-resolution technique, allowing visualization of biological targets at nanoscale resolution on conventional fluorescence microscopes. Since its introduction in 2015, many efforts have been dedicated to broaden its application range or increase the resolution that can be achieved. As a consequence, recent years have witnessed remarkable advances in ExM. This review summarizes recent progress in ExM, with the focus on the chemical aspects of the method, from chemistries for biomolecule grafting to polymer synthesis and the impact on biological analysis. The combination of ExM with other microscopy techniques, in search of additional resolution improvement, is also discussed. In addition, we compare pre- and postexpansion labeling strategies and discuss the impact of fixation methods on ultrastructure preservation. We conclude this review with a perspective on existing challenges and future directions. We believe that this review will provide a comprehensive understanding of ExM and facilitate its usage and further development.
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Affiliation(s)
- Gang Wen
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Volker Leen
- Chrometra Scientific, Kortenaken 3470, Belgium
| | - Taoufik Rohand
- Laboratory of Analytical and Molecular Chemistry, Faculty Polydisciplinaire of Safi, University Cadi Ayyad Marrakech, BP 4162, 46000 Safi, Morocco
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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Malkovskiy AV, Tom A, Joubert LM, Bao Z. Visualization of the distribution of covalently cross-linked hydrogels in CLARITY brain-polymer hybrids for different monomer concentrations. Sci Rep 2022; 12:13549. [PMID: 35941350 PMCID: PMC9360022 DOI: 10.1038/s41598-022-17687-x] [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: 04/08/2022] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
CLARITY is a tissue preservation and optical clearing technique whereby a hydrogel is formed directly within the architectural confines of ex vivo brain tissue. In this work, the extent of polymer gel formation and crosslinking within tissue was assessed using Raman spectroscopy and rheology on CLARITY samples prepared with a range of acrylamide monomer (AAm) concentrations (1%, 4%, 8%, 12% w/v). Raman spectroscopy of individual neurons within hybrids revealed the chemical presence and distribution of polyacrylamide within the mouse hippocampus. Consistent with rheological measurements, lower %AAm concentration decreased shear elastic modulus G', providing a practical correlation with sample permeability and protein retention. Permeability of F(ab)'2 secondary fluorescent antibody changes from 9.3 to 1.4 µm2 s-1 going from 1 to 12%. Notably, protein retention increased linearly relative to standard PFA-fixed tissue from 96.6% when AAm concentration exceeded 1%, with 12% AAm samples retaining up to ~ 99.3% native protein. This suggests that though 1% AAm offers high permeability, additional %AAm may be required to enhance protein. Our quantitative results on polymer distribution, stability, protein retention, and macromolecule permeability can be used to guide the design of future CLARITY-based tissue-clearing solutions, and establish protocols for characterization of novel tissue-polymer hybrid biomaterials using chemical spectroscopy and rheology.
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Affiliation(s)
| | - Ariane Tom
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Lydia-Marie Joubert
- Cell Sciences Imaging Facility (CSIF), Stanford University, Stanford, CA, 94305, USA
| | - Zhenan Bao
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA.
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Hofmann J, Keppler SJ. Tissue clearing and 3D imaging - putting immune cells into context. J Cell Sci 2021; 134:271108. [PMID: 34342351 DOI: 10.1242/jcs.258494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A better understanding of cell-cell and cell-niche interactions is crucial to comprehend the complexity of inflammatory or pathophysiological scenarios such as tissue damage during viral infections, the tumour microenvironment and neuroinflammation. Optical clearing and 3D volumetric imaging of large tissue pieces or whole organs is a rapidly developing methodology that holds great promise for the in-depth study of cells in their natural surroundings. These methods have mostly been applied to image structural components such as endothelial cells and neuronal architecture. Recent work now highlights the possibility of studying immune cells in detail within their respective immune niches. This Review summarizes recent developments in tissue clearing methods and 3D imaging, with a focus on the localization and quantification of immune cells. We first provide background to the optical challenges involved and their solutions before discussing published protocols for tissue clearing, the limitations of 3D imaging of immune cells and image analysis. Furthermore, we highlight possible applications for tissue clearing and propose future developments for the analysis of immune cells within homeostatic or inflammatory immune niches.
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Affiliation(s)
- Julian Hofmann
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, 81675 Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University Munich, 81675 Munich, Germany
| | - Selina J Keppler
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, 81675 Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University Munich, 81675 Munich, Germany
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7
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Zhao J, Lai HM, Qi Y, He D, Sun H. Current Status of Tissue Clearing and the Path Forward in Neuroscience. ACS Chem Neurosci 2021; 12:5-29. [PMID: 33326739 DOI: 10.1021/acschemneuro.0c00563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Due to the complexity and limited availability of human brain tissues, for decades, pathologists have sought to maximize information gained from individual samples, based on which (patho)physiological processes could be inferred. Recently, new understandings of chemical and physical properties of biological tissues and multiple chemical profiling have given rise to the development of scalable tissue clearing methods allowing superior optical clearing of across-the-scale samples. In the past decade, tissue clearing techniques, molecular labeling methods, advanced laser scanning microscopes, and data visualization and analysis have become commonplace. Combined, they have made 3D visualization of brain tissues with unprecedented resolution and depth widely accessible. To facilitate further advancements and applications, here we provide a critical appraisal of these techniques. We propose a classification system of current tissue clearing and expansion methods that allows users to judge the applicability of individual ones to their questions, followed by a review of the current progress in molecular labeling, optical imaging, and data processing to demonstrate the whole 3D imaging pipeline based on tissue clearing and downstream techniques for visualizing the brain. We also raise the path forward of tissue-clearing-based imaging technology, that is, integrating with state-of-the-art techniques, such as multiplexing protein imaging, in situ signal amplification, RNA detection and sequencing, super-resolution imaging techniques, multiomics studies, and deep learning, for drawing the complete atlas of the human brain and building a 3D pathology platform for central nervous system disorders.
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Affiliation(s)
- Jiajia Zhao
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Hei Ming Lai
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yuwei Qi
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Dian He
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Haitao Sun
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Clinical Biobank Center, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
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M'Saad O, Bewersdorf J. Light microscopy of proteins in their ultrastructural context. Nat Commun 2020; 11:3850. [PMID: 32737322 PMCID: PMC7395138 DOI: 10.1038/s41467-020-17523-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/03/2020] [Indexed: 11/09/2022] Open
Abstract
Resolving the distribution of specific proteins at the nanoscale in the ultrastructural context of the cell is a major challenge in fluorescence microscopy. We report the discovery of a new principle for an optical contrast equivalent to electron microscopy (EM) which reveals the ultrastructural context of the cells with a conventional confocal microscope. By decrowding the intracellular space through 13 to 21-fold physical expansion while simultaneously retaining the proteins, bulk (pan) labeling of the proteome resolves local protein densities and reveals the cellular nanoarchitecture by standard light microscopy.
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Affiliation(s)
- Ons M'Saad
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- Nanobiology Institute, Yale University, West Haven, CT, USA.
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9
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Ueda HR, Dodt HU, Osten P, Economo MN, Chandrashekar J, Keller PJ. Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy. Neuron 2020; 106:369-387. [PMID: 32380050 PMCID: PMC7213014 DOI: 10.1016/j.neuron.2020.03.004] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/11/2020] [Accepted: 03/04/2020] [Indexed: 01/12/2023]
Abstract
Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.
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Affiliation(s)
- Hiroki R Ueda
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN BDR, Suita, Osaka 565-0871, Japan.
| | - Hans-Ulrich Dodt
- Department of Bioelectronics, FKE, Vienna University of Technology-TU Wien, Vienna, Austria; Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Pavel Osten
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA
| | - Michael N Economo
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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10
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Lee TB, Lee J, Jun JH. Three-Dimensional Approaches in Histopathological Tissue Clearing System. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Tae Bok Lee
- Confocal Core Facility, Center for Medical Innovation, Seoul National University Hospital, Seoul, Korea
| | - Jaewang Lee
- Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam, Korea
| | - Jin Hyun Jun
- Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam, Korea
- Department of Senior Healthcare, BK21 Plus Program, Graduate School of Eulji University, Seongnam, Korea
- Eulji Medi-Bio Research Institute (EMBRI), Eulji University, Daejeon, Korea
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11
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Ueda HR, Ertürk A, Chung K, Gradinaru V, Chédotal A, Tomancak P, Keller PJ. Tissue clearing and its applications in neuroscience. Nat Rev Neurosci 2020; 21:61-79. [PMID: 31896771 PMCID: PMC8121164 DOI: 10.1038/s41583-019-0250-1] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2019] [Indexed: 02/06/2023]
Abstract
State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.
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Affiliation(s)
- Hiroki R Ueda
- Department of Systems Pharmacology, University of Tokyo, Tokyo, Japan.
- Laboratory for Synthetic Biology, RIKEN BDR, Suita, Japan.
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University of Munich, Munich, Germany
- Institute of Tissue Engineering and Regenerative Medicine, Helmholtz Zentrum München, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Eli & Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for NanoMedicine, Institute for Basic Science, Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering, Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alain Chédotal
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- IT4Innovations, Technical University of Ostrava, Ostrava, Czech Republic
| | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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12
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Ren YX, Wu J, Lai QTK, Lai HM, Siu DMD, Wu W, Wong KKY, Tsia KK. Parallelized volumetric fluorescence microscopy with a reconfigurable coded incoherent light-sheet array. LIGHT, SCIENCE & APPLICATIONS 2020; 9:8. [PMID: 31993126 PMCID: PMC6971027 DOI: 10.1038/s41377-020-0245-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 12/23/2019] [Accepted: 01/06/2020] [Indexed: 05/12/2023]
Abstract
Parallelized fluorescence imaging has been a long-standing pursuit that can address the unmet need for a comprehensive three-dimensional (3D) visualization of dynamical biological processes with minimal photodamage. However, the available approaches are limited to incomplete parallelization in only two dimensions or sparse sampling in three dimensions. We hereby develop a novel fluorescence imaging approach, called coded light-sheet array microscopy (CLAM), which allows complete parallelized 3D imaging without mechanical scanning. Harnessing the concept of an "infinity mirror", CLAM generates a light-sheet array with controllable sheet density and degree of coherence. Thus, CLAM circumvents the common complications of multiple coherent light-sheet generation in terms of dedicated wavefront engineering and mechanical dithering/scanning. Moreover, the encoding of multiplexed optical sections in CLAM allows the synchronous capture of all sectioned images within the imaged volume. We demonstrate the utility of CLAM in different imaging scenarios, including a light-scattering medium, an optically cleared tissue, and microparticles in fluidic flow. CLAM can maximize the signal-to-noise ratio and the spatial duty cycle, and also provides a further reduction in photobleaching compared to the major scanning-based 3D imaging systems. The flexible implementation of CLAM regarding both hardware and software ensures compatibility with any light-sheet imaging modality and could thus be instrumental in a multitude of areas in biological research.
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Affiliation(s)
- Yu-Xuan Ren
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
| | - Jianglai Wu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
- Department of Physics, University of California, Berkeley, CA 94720 USA
| | - Queenie T. K. Lai
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
| | - Hei Ming Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR 999077 China
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR 999077 China
| | - Dickson M. D. Siu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
| | - Wutian Wu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR 999077 China
- GHM Institute of CNS Regeneration, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632 China
- Re-Stem Biotechnology, Suzhou, 215007 China
| | - Kenneth K. Y. Wong
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
| | - Kevin K. Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
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13
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Choi J, Lee E, Kim JH, Sun W. FxClear, A Free-hydrogel Electrophoretic Tissue Clearing Method for Rapid De-lipidation of Tissues with High Preservation of Immunoreactivity. Exp Neurobiol 2019; 28:436-445. [PMID: 31308802 PMCID: PMC6614074 DOI: 10.5607/en.2019.28.3.436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/19/2019] [Accepted: 05/10/2019] [Indexed: 01/11/2023] Open
Abstract
Over the last two decades, several tissue clearing methodologies have been established that render tissues optically transparent and allow imaging of unsectioned tissues of significant volumes, thus improving the capacity to study the relationships between cell and 3D tissue architecture. Despite these technical advances, the important unsolved challenges that these methods face include complexity, time, consistency of tissue size before and after clearing, and ability to immunolabel various antibodies in cleared tissue. Here, we established very simple and fast tissue clearing protocol, FxClear, which involves acrylamide-free electrophoretic tissue clearing (ETC). By removal of the acrylamide infusion step, we were able to achieve fast reaction time, smaller tissue expansion, and higher immunoreactivity. Especially, immunoreactivity and fluorescence intensity were increased in FxClear-processed tissues compared to un-cleared tissues. Our protocol may be suitable for small-sized biopsy samples for 3D pathological examinations.
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Affiliation(s)
- Jungyoon Choi
- Department of Anatomy and Division of Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul 02841, Korea
| | - Eunsoo Lee
- Department of Anatomy and Division of Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul 02841, Korea
| | - June Hoan Kim
- Department of Anatomy and Division of Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul 02841, Korea
| | - Woong Sun
- Department of Anatomy and Division of Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul 02841, Korea
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14
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Bernal L, Cisneros E, García-Magro N, Roza C. Immunostaining in whole-mount lipid-cleared peripheral nerves and dorsal root ganglia after neuropathy in mice. Sci Rep 2019; 9:8374. [PMID: 31182787 PMCID: PMC6558043 DOI: 10.1038/s41598-019-44897-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/23/2019] [Indexed: 12/31/2022] Open
Abstract
Immunohistochemical characterization of primary afferent fibers (intact or after nerve damage) is traditionally performed in thin sections from dorsal root ganglia (DRGs) or in teased fibers, as light scattering in whole-mounts compromises visualization. These procedures are time-consuming, require specific equipment and advanced experimental skills. Lipid-clearing techniques are increasing in popularity, but they have never been used for the peripheral nervous system. We established a modified, inexpensive clearing method based on lipid-removal protocols to make transparent peripheral nerve tissue (inCLARITY). We compared retrograde-labeling and free-floating immunostaining with cryo-sections. Confocal microscopy on whole-mount transparent DRGs showed neurons marked with retrograde tracers applied to experimental neuromas (Retrobeads, Fluoro-ruby, Fluoro-emerald, DiI, and Fluoro-gold). After immunostaining with calcitonin gene-related peptide (peptidergic) or isolectin IB4 (non-peptidergic), nociceptors were visualized. Immunostaining in transparent whole-mount nerves allows simultaneous evaluation of the axotomized branches containing the neuroma and neighboring intact branches as they can be mounted preserving their anatomical disposition and fiber integrity. The goal of our study was to optimize CLARITY for its application in peripheral nerve tissues. The protocol is compatible with the use of retrograde tracers and improves immunostaining outcomes when compared to classical cryo-sectioning, as lack of lipids maximizes antibody penetration within the tissue.
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Affiliation(s)
- L Bernal
- Department of System's Biology, Medical School, University of Alcala, Alcalá de Henares, 28871, Madrid, Spain
| | - E Cisneros
- Department of System's Biology, Medical School, University of Alcala, Alcalá de Henares, 28871, Madrid, Spain.,Centro Universitario Internacional de Madrid (CUNIMAD), Madrid, Spain
| | - N García-Magro
- Department of Anatomy, Histology and Neuroscience, Medical School, Autonoma University of Madrid, 28029, Madrid, Spain
| | - C Roza
- Department of System's Biology, Medical School, University of Alcala, Alcalá de Henares, 28871, Madrid, Spain.
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15
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Gradinaru V, Treweek J, Overton K, Deisseroth K. Hydrogel-Tissue Chemistry: Principles and Applications. Annu Rev Biophys 2019; 47:355-376. [PMID: 29792820 PMCID: PMC6359929 DOI: 10.1146/annurev-biophys-070317-032905] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.
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Affiliation(s)
- Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Jennifer Treweek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Kristin Overton
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA;
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA; .,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, USA.,H oward Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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16
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Wang H, Khoradmehr A, Tamadon A. FACT or PACT: A Comparison between Free-Acrylamide and Acrylamide-Based Passive Sodium Dodecyl Sulfate Tissue Clearing for whole Tissue Imaging. CELL JOURNAL 2019; 21:103-114. [PMID: 30825283 PMCID: PMC6397597 DOI: 10.22074/cellj.2019.5989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/26/2018] [Indexed: 01/13/2023]
Abstract
Major biological processes rely on the spatial organization of cells in complex, highly orchestrated three-dimensional (3D)
tissues. Until the recent decade, most of information on spatial neural representation primarily came from microscopic imaging
of “2D” (5-50 μm) tissue using traditional immunohistochemical techniques. However, serially sectioned and imaged tissue
sections for tissue visualization can lead to unique non-linear deformations, which dramatically hinders scientists’ insight into
the structural organization of intact organs. An emerging technique known as CLARITY renders large-scale biological tissues
transparent for 3D phenotype mapping and thereby, greatly facilitates structure-function relationships analyses. Since then,
numerous modifications and improvements have been reported to push the boundaries of knowledge on tissue clearing
techniques in research on assembled biological systems. This review aims to outline our current knowledge on next-generation
protocols of fast free-of-acrylamide clearing tissue (FACT) and passive CLARITY (PACT). The most important question is what
method we should select for tissue clearing, FACT or PACT. This review also highlights how FACT differs from PACT on
spanning multiple dimensions of the workflow. We systematically compared a number of factors including hydrogel formation,
clearing solution, and clearing temperatures between free-acrylamide and acrylamide-based passive sodium dodecyl sulfate
(SDS) tissue clearing and discussed negative effects of polyacrylamide on clearing, staining, and imaging in detail. Such
information may help to gain a perspective for interrogating neural circuits spatial interactions between molecules and cells
and provide guidance for developing novel tissue clearing strategies to probe deeply into intact organ.
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Affiliation(s)
- Huimei Wang
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Arezoo Khoradmehr
- Research and Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Amin Tamadon
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran. Electronic Address:
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17
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Pende M, Becker K, Wanis M, Saghafi S, Kaur R, Hahn C, Pende N, Foroughipour M, Hummel T, Dodt HU. High-resolution ultramicroscopy of the developing and adult nervous system in optically cleared Drosophila melanogaster. Nat Commun 2018; 9:4731. [PMID: 30413688 PMCID: PMC6226481 DOI: 10.1038/s41467-018-07192-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/13/2018] [Indexed: 11/21/2022] Open
Abstract
The fruit fly, Drosophila melanogaster, is an important experimental model to address central questions in neuroscience at an organismic level. However, imaging of neural circuits in intact fruit flies is limited due to structural properties of the cuticle. Here we present a novel approach combining tissue clearing, ultramicroscopy, and data analysis that enables the visualisation of neuronal networks with single-cell resolution from the larval stage up to the adult Drosophila. FlyClear, the signal preserving clearing technique we developed, stabilises tissue integrity and fluorescence signal intensity for over a month and efficiently removes the overall pigmentation. An aspheric ultramicroscope set-up utilising an improved light-sheet generator allows us to visualise long-range connections of peripheral sensory and central neurons in the visual and olfactory system. High-resolution 3D reconstructions with isotropic resolution from entire GFP-expressing flies are obtained by applying image fusion from orthogonal directions. This methodological integration of novel chemical, optical, and computational techniques allows a major advance in the analysis of global neural circuit organisation.
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Affiliation(s)
- Marko Pende
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria.
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria.
| | - Klaus Becker
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Martina Wanis
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria
- Department of Neurobiology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Saiedeh Saghafi
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria
| | - Rashmit Kaur
- Department of Neurobiology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Christian Hahn
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Nika Pende
- Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Massih Foroughipour
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Thomas Hummel
- Department of Neurobiology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Hans-Ulrich Dodt
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria.
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria.
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18
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Wong HS, Yeung PKK, Lai HM, Lam KSL, Wutian W, Chung SK. Simple and Rapid Tissue Clearing Method for Three‐Dimensional Histology of the Pancreas. ACTA ACUST UNITED AC 2018; 77:19.20.1-19.20.10. [DOI: 10.1002/cpcb.34] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Hang Sheung Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Patrick Ka Kit Yeung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Hei Ming Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Karen Siu Ling Lam
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong Hong Kong China
- Department of Medicine, The University of Hong Kong Hong Kong China
| | - Wu Wutian
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
- State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong Hong Kong SAR China
- Research Centre of Heart, Brain, Hormone and Healthy Aging, Li Ka Shing Faculty of Medicine, The University of Hong Kong Hong Kong SAR China
- Joint Laboratory of Jinan University and The University of Hong Kong, GHM Institute of CNS Regeneration, Jinan University Guangzhou China
| | - Sookja Kim Chung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
- Research Centre of Heart, Brain, Hormone and Healthy Aging, Li Ka Shing Faculty of Medicine, The University of Hong Kong Hong Kong SAR China
- State Key Laboratory of Pharmaceutical Biotechnology, Li Ka Shing Faculty of Medicine, The University of Hong Kong Hong Kong SAR China
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19
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Yu T, Qi Y, Gong H, Luo Q, Zhu D. Optical clearing for multiscale biological tissues. JOURNAL OF BIOPHOTONICS 2018; 11. [PMID: 29024450 DOI: 10.1002/jbio.201700187] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/08/2017] [Indexed: 05/03/2023]
Abstract
Three-dimensional reconstruction of tissue structures is essential for biomedical research. The development of light microscopes and various fluorescent labeling techniques provides powerful tools for this motivation. However, optical imaging depth suffers from strong light scattering due to inherent heterogeneity of biological tissues. Tissue optical clearing technology provides a distinct solution and permits us to image large volumes with high resolution. Until now, various clearing methods have been developed. In this study, from the perspective of the end users, we review in vitro tissue optical clearing techniques based on the sample features in terms of size and age, enumerate the methods suitable for immunostaining and lipophilic dyes and summarize the combinations with various imaging techniques. We hope this review will be helpful for researchers to choose the most suitable clearing method from a variety of protocols to meet their specific needs.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yisong Qi
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China
- MOE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
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20
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Kassem MS, Fok SY, Smith KL, Kuligowski M, Balleine BW. A novel, modernized Golgi-Cox stain optimized for CLARITY cleared tissue. J Neurosci Methods 2018; 294:102-110. [DOI: 10.1016/j.jneumeth.2017.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 10/18/2022]
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21
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Hu W, Tamadon A, Hsueh AJW, Feng Y. Three-dimensional Reconstruction of the Vascular Architecture of the Passive CLARITY-cleared Mouse Ovary. J Vis Exp 2017. [PMID: 29286393 DOI: 10.3791/56141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ovary is the main organ of the female reproductive system and is essential for the production of female gametes and for controlling the endocrine system, but the complex structural relationships and three-dimensional (3D) vasculature architectures of the ovary are not well described. In order to visualize the 3D connections and architecture of blood vessels in the intact ovary, the first important step is to make the ovary optically clear. In order to avoid tissue shrinkage, we used the hydrogel fixation-based passive CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging/ Immunostaining/In situ-hybridization-compatible Tissue Hydrogel) protocol method to clear an intact ovary. Immunostaining, advanced multiphoton confocal microscopy, and 3D image-reconstructions were then used for the visualization of ovarian vessels and follicular capillaries. Using this approach, we showed a significant positive correlation (P <0.01) between the length of the follicular capillaries and volume of the follicular wall.
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Affiliation(s)
- Wei Hu
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences; Institutes of Brain Science, Brain Science Collaborative Innovation Center, State Key Laboratory of Medical Neurobiology, Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative Medicine, Fudan University
| | - Amin Tamadon
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences; Institutes of Brain Science, Brain Science Collaborative Innovation Center, State Key Laboratory of Medical Neurobiology, Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative Medicine, Fudan University
| | - Aaron J W Hsueh
- Program of Reproductive and Stem Cell Biology, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford University
| | - Yi Feng
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences; Institutes of Brain Science, Brain Science Collaborative Innovation Center, State Key Laboratory of Medical Neurobiology, Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative Medicine, Fudan University;
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22
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Jensen KHR, Berg RW. Advances and perspectives in tissue clearing using CLARITY. J Chem Neuroanat 2017; 86:19-34. [DOI: 10.1016/j.jchemneu.2017.07.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/12/2017] [Accepted: 07/12/2017] [Indexed: 12/16/2022]
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23
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Kaufman JA, Castro MJ, Sandoval-Skeet N, Al-Nakkash L. Optical clearing of small intestine for three-dimensional visualization of cellular proliferation within crypts. J Anat 2017; 232:152-157. [PMID: 28967147 DOI: 10.1111/joa.12711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2017] [Indexed: 12/31/2022] Open
Abstract
New methods on optical clearing provide a valuable alternative to traditional physical section histology. Optical clearing allows investigation of relatively large tissue samples at histological resolution while maintaining the three-dimensional architecture of the intact system. There is significant potential for applying optical clearing to gastrointestinal tissues. In particular, intestinal crypts contain high concentrations of stem cells, making these structures especially important for research on cellular proliferation in the intestinal epithelium. The objective of our study is to demonstrate an optical clearing method that is easy to implement and is compatible with mitotic fluorescent labeling. The optical clearing method we present utilizes a Triton/DMSO delipidization step followed by refractive index matching, rendering the tissue nearly transparent. We use EdU click chemistry to fluorescently label mitotic cell nuclei. Our results demonstrate successful clearing of jejunal samples with readily visible EdU staining by means of confocal microscopy. Three-dimensional reconstruction of labeled samples reveals preservation of intestinal cytoarchitecture including muscular, submucosal, and mucosal layers. Additionally, the morphology of intestinal crypts and individual EdU-positive mitotic nuclei are visible in sharp detail within their intact three-dimensional organization. In summary, we present an optical clearing method that is easy to implement and has the potential to provide more accurate assessment of cellular proliferation within the gastrointestinal tract in both healthy and disease states.
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Affiliation(s)
- Jason A Kaufman
- Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Monica J Castro
- Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Noemy Sandoval-Skeet
- Masters of Biomedical Science Program, College of Health Sciences, Midwestern University, Glendale, AZ, USA
| | - Layla Al-Nakkash
- Department of Physiology, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
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24
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Nojima S, Susaki EA, Yoshida K, Takemoto H, Tsujimura N, Iijima S, Takachi K, Nakahara Y, Tahara S, Ohshima K, Kurashige M, Hori Y, Wada N, Ikeda JI, Kumanogoh A, Morii E, Ueda HR. CUBIC pathology: three-dimensional imaging for pathological diagnosis. Sci Rep 2017; 7:9269. [PMID: 28839164 PMCID: PMC5571108 DOI: 10.1038/s41598-017-09117-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/21/2017] [Indexed: 12/11/2022] Open
Abstract
The examination of hematoxylin and eosin (H&E)-stained tissues on glass slides by conventional light microscopy is the foundation for histopathological diagnosis. However, this conventional method has some limitations in x-y axes due to its relatively narrow range of observation area and in z-axis due to its two-dimensionality. In this study, we applied a CUBIC pipeline, which is the most powerful tissue-clearing and three-dimensional (3D)-imaging technique, to clinical pathology. CUBIC was applicable to 3D imaging of both normal and abnormal patient-derived, human lung and lymph node tissues. Notably, the combination of deparaffinization and CUBIC enabled 3D imaging of specimens derived from paraffin-embedded tissue blocks, allowing quantitative evaluation of nuclear and structural atypia of an archival malignant lymphoma tissue. Furthermore, to examine whether CUBIC can be applied to practical use in pathological diagnosis, we performed a histopathological screening of a lymph node metastasis based on CUBIC, which successfully improved the sensitivity in detecting minor metastatic carcinoma nodules in lymph nodes. Collectively, our results indicate that CUBIC significantly contributes to retrospective and prospective clinicopathological diagnosis, which might lead to the establishment of a novel field of medical science based on 3D histopathology.
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Affiliation(s)
- Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Etsuo A Susaki
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Kyotaro Yoshida
- Department of Pathology, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Hiroyoshi Takemoto
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Naoto Tsujimura
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Shohei Iijima
- Department of Nutrition Oncology, Osaka International Cancer Institute, 3-1-69, Otemae, Chuo-ku, Osaka-shi, Osaka, 541-8567, Japan
| | - Ko Takachi
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Yujiro Nakahara
- Department of Surgery, Kinki Central Hospital, 3-1 Kurumazuka, Itami, Hyogo, 664-8533, Japan
| | - Shinichiro Tahara
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kenji Ohshima
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masako Kurashige
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yumiko Hori
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naoki Wada
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun-Ichiro Ikeda
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Atsushi Kumanogoh
- Department of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Respiratory Medicine, Allergy and Rheumatic Disease, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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Abstract
Newly developed tissue clearing techniques can be used to render intact tissues transparent. When combined with fluorescent labeling technologies and optical sectioning microscopy, this allows visualization of fine structure in three dimensions. Gene-transfection techniques have proved very useful in visualizing cellular structures in animal models, but they are not applicable to human brain tissue. Here, we discuss the characteristics of an ideal chemical fluorescent probe for use in brain and other cleared tissues, and offer a comprehensive overview of currently available chemical probes. We describe their working principles and compare their performance with the goal of simplifying probe selection for neuropathologists and stimulating probe development by chemists. We propose several approaches for the development of innovative chemical labeling methods which, when combined with tissue clearing, have the potential to revolutionize how we study the structure and function of the human brain.
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Affiliation(s)
- Hei Ming Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Neuropathology Unit, Division of Brain Sciences, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Wai-Lung Ng
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Steve M Gentleman
- Neuropathology Unit, Division of Brain Sciences, Department of Medicine, Imperial College London, London W12 0NN, UK.
| | - Wutian Wu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Research Center of Reproduction, Development and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Joint Laboratory of Jinan University and The University of Hong Kong, GHM Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China.
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26
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Free-of-Acrylamide SDS-based Tissue Clearing (FASTClear) for three dimensional visualization of myocardial tissue. Sci Rep 2017; 7:5188. [PMID: 28701763 PMCID: PMC5507863 DOI: 10.1038/s41598-017-05406-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/31/2017] [Indexed: 01/19/2023] Open
Abstract
Several pathologic conditions of the heart lead to cardiac structural remodelling. Given the high density and the opaque nature of the myocardium, deep three dimensional (3D) imaging is difficult to achieve and structural analysis of pathological myocardial structure is often limited to two dimensional images and of thin myocardial sections. Efficient methods to obtain optical clearing of the tissue for 3D visualisation are therefore needed. Here we describe a rapid, simple and versatile Free-of-Acrylamide SDS-based Tissue Clearing (FASTClear) protocol specifically designed for cardiac tissue. With this method 3D information regarding collagen content, collagen localization and distribution could be easily obtained across a whole 300 µm-thick myocardial slice. FASTClear does not induce structural or microstructural distortion and it can be combined with immunostaining to identify the micro- and macrovascular networks. In summary, we have obtained decolorized myocardial tissue suitable for high resolution 3D imaging, with implications for the study of complex cardiac tissue structure and its changes during pathology.
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27
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Liu AKL, Lai HM, Chang RCC, Gentleman SM. Free of acrylamide sodium dodecyl sulphate (SDS)-based tissue clearing (FASTClear): a novel protocol of tissue clearing for three-dimensional visualization of human brain tissues. Neuropathol Appl Neurobiol 2017; 43:346-351. [PMID: 27627784 PMCID: PMC5485160 DOI: 10.1111/nan.12361] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/25/2016] [Accepted: 09/07/2016] [Indexed: 01/13/2023]
Affiliation(s)
- A K L Liu
- Neuropathology Unit, Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK.,Laboratory of Neurodegenerative Diseases, LKS Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - H M Lai
- Neuropathology Unit, Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - R C-C Chang
- Laboratory of Neurodegenerative Diseases, LKS Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR.,LKS Faculty of Medicine, Research Centre of Heart, Brain, Hormone, and Healthy Aging, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - S M Gentleman
- Neuropathology Unit, Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
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28
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Lai HM, Ng HM, Wu W. Three-dimensional histology: new visual approaches to morphological changes during neural regeneration. Neural Regen Res 2017; 12:53-55. [PMID: 28250740 PMCID: PMC5319234 DOI: 10.4103/1673-5374.198974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Three-dimensional (3D) histology utilizes tissue clearing techniques to turn intact tissues transparent, allowing rapid interrogation of tissue architecture in three dimensions. In this article, we summarized the available tissue clearing methods and classified them according to their physicochemical principles of operation, which provided a framework for one to choose the best techniques for various research settings. Recent attempts in addressing various questions regarding the degenerating and regenerating nervous system have been promising with the use of 3D histological techniques.
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Affiliation(s)
- Hei Ming Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ho Man Ng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wutian Wu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Research Center of Reproduction, Development and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong Province, China
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Neckel PH, Mattheus U, Hirt B, Just L, Mack AF. Large-scale tissue clearing (PACT): Technical evaluation and new perspectives in immunofluorescence, histology, and ultrastructure. Sci Rep 2016; 6:34331. [PMID: 27680942 PMCID: PMC5041186 DOI: 10.1038/srep34331] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/12/2016] [Indexed: 12/27/2022] Open
Abstract
Novel techniques, like CLARITY and PACT, render large tissue specimens transparent and thereby suitable for microscopic analysis. We used these techniques to evaluate their potential in the intestine as an exemplary organ with a complex tissue composition. Immunohistochemistry, light sheet-, and confocal scanning-microscopy enabled us to follow complex three-dimensional structures, like nerve fibers, vessels, and epithelial barriers throughout the entire organ. Moreover, in a systematic electron microscopic study, we analyzed the morphology and preservation of tissue on ultrastructural level during the clearing process. We also connect tissue clearing with classical histology and demonstrate that cleared tissues can be stained with Hematoxylin-Eosin and Heidenhain's Azan stain, suggesting potential use in histopathology. These experiments showed that a neutral pH during the clearing process results in much better preservation of tissue ultrastructure and standard stainability. Volume changes of specimens were monitored and quantified during the course of the protocol. Additionally, we employed the technique to visualize the enteric nervous system and the epithelial barrier in post mortem human gut preparations. Our data show the high potential of tissue clearing throughout different tissue types supporting its usefulness in research and diagnosis, and contribute to the technical discussion of ultrastructural tissue-retention.
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Affiliation(s)
- Peter H. Neckel
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Tübingen, Germany
| | - Ulrich Mattheus
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Tübingen, Germany
| | - Bernhard Hirt
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Tübingen, Germany
| | - Lothar Just
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Tübingen, Germany
| | - Andreas F. Mack
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Tübingen, Germany
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