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Yu T, Zhong X, Li D, Zhu J, Tuchin VV, Zhu D. Delivery and kinetics of immersion optical clearing agents in tissues: Optical imaging from ex vivo to in vivo. Adv Drug Deliv Rev 2024:115470. [PMID: 39481483 DOI: 10.1016/j.addr.2024.115470] [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: 08/01/2024] [Revised: 09/30/2024] [Accepted: 10/27/2024] [Indexed: 11/02/2024]
Abstract
Advanced optical imaging provides a powerful tool for the structural and functional analysis of tissues with high resolution and contrast, but the imaging performance decreases as light propagates deeper into the tissue. Tissue optical clearing technique demonstrates an innovative way to realize deep-tissue imaging and have emerged substantially in the last two decades. Here, we briefly reviewed the basic principles of tissue optical clearing techniques in the view of delivery strategies via either free diffusion or external forces-driven advection, and the commonly-used optical techniques for monitoring kinetics of clearing agents in tissue, as well as their ex vivo to in vivo applications in multiple biomedical research fields. With future efforts on the even distribution of both clearing agents and probes, excavation of more effective clearing agents, and automation of tissue clearing processes, tissue optical clearing should provide more insights into the fundamental questions in biological events clinical diagnostics.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Xiang Zhong
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China; School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Jingtan Zhu
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Valery V Tuchin
- Institute of Physics and Science Medical Center, Saratov State University, Saratov 410012, Russia; Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk 634050, Russia; Institute of Precision Mechanics and Control, FRS "Saratov Scientific Centre of the RAS", Saratov 410028, Russia
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
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2
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Zhu E, Li YR, Margolis S, Wang J, Wang K, Zhang Y, Wang S, Park J, Zheng C, Yang L, Chu A, Zhang Y, Gao L, Hsiai TK. Frontiers in artificial intelligence-directed light-sheet microscopy for uncovering biological phenomena and multi-organ imaging. VIEW 2024; 5:20230087. [PMID: 39478956 PMCID: PMC11521201 DOI: 10.1002/viw.20230087] [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: 04/02/2024] [Accepted: 07/18/2024] [Indexed: 11/02/2024] Open
Abstract
Light-sheet fluorescence microscopy (LSFM) introduces fast scanning of biological phenomena with deep photon penetration and minimal phototoxicity. This advancement represents a significant shift in 3-D imaging of large-scale biological tissues and 4-D (space + time) imaging of small live animals. The large data associated with LSFM requires efficient imaging acquisition and analysis with the use of artificial intelligence (AI)/machine learning (ML) algorithms. To this end, AI/ML-directed LSFM is an emerging area for multi-organ imaging and tumor diagnostics. This review will present the development of LSFM and highlight various LSFM configurations and designs for multi-scale imaging. Optical clearance techniques will be compared for effective reduction in light scattering and optimal deep-tissue imaging. This review will further depict a diverse range of research and translational applications, from small live organisms to multi-organ imaging to tumor diagnosis. In addition, this review will address AI/ML-directed imaging reconstruction, including the application of convolutional neural networks (CNNs) and generative adversarial networks (GANs). In summary, the advancements of LSFM have enabled effective and efficient post-imaging reconstruction and data analyses, underscoring LSFM's contribution to advancing fundamental and translational research.
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Affiliation(s)
- Enbo Zhu
- Department of Bioengineering, UCLA, California, 90095, USA
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
- Department of Medicine, Greater Los Angeles VA Healthcare System, California, 90073, USA
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, California, 90095, USA
| | - Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, California, 90095, USA
| | - Samuel Margolis
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
| | - Jing Wang
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Kaidong Wang
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
- Department of Medicine, Greater Los Angeles VA Healthcare System, California, 90073, USA
| | - Yaran Zhang
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Shaolei Wang
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Jongchan Park
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Charlie Zheng
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, California, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, California, 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, California, 90095, USA
- Molecular Biology Institute, UCLA, California, 90095, USA
| | - Alison Chu
- Division of Neonatology and Developmental Biology, Department of Pediatrics, David Geffen School of Medicine, UCLA, California, 90095, USA
| | - Yuhua Zhang
- Doheny Eye Institute, Department of Ophthalmology, UCLA, California, 90095, USA
| | - Liang Gao
- Department of Bioengineering, UCLA, California, 90095, USA
| | - Tzung K. Hsiai
- Department of Bioengineering, UCLA, California, 90095, USA
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, UCLA, California, 90095, USA
- Department of Medicine, Greater Los Angeles VA Healthcare System, California, 90073, USA
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3
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Zhang D, Cleveland AH, Krimitza E, Han K, Yi C, Stout AL, Zou W, Dorsey JF, Gong Y, Fan Y. Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy. Nat Protoc 2024; 19:1053-1082. [PMID: 38212641 DOI: 10.1038/s41596-023-00941-5] [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: 05/31/2023] [Accepted: 10/25/2023] [Indexed: 01/13/2024]
Abstract
The pathogenesis of cancer and cardiovascular diseases is subjected to spatiotemporal regulation by the tissue microenvironment. Multiplex visualization of the microenvironmental components, including immune cells, vasculature and tissue hypoxia, provides critical information underlying the disease progression and therapy resistance, which is often limited by imaging depth and resolution in large-volume tissues. To this end, light sheet fluorescence microscopy, following tissue clarification and immunostaining, may generate three-dimensional high-resolution images at a whole-organ level. Here we provide a detailed description of light sheet fluorescence microscopy imaging analysis of immune cell composition, vascularization, tissue perfusion and hypoxia in mouse normal brains and hearts, as well as brain tumors. We describe a procedure for visualizing tissue vascularization, perfusion and hypoxia with a transgenic vascular labeling system. We provide the procedures for tissue collection, tissue semi-clearing and immunostaining. We further describe standard methods for analyzing tissue immunity and vascularity. We anticipate that this method will facilitate the spatial illustration of structure and function of the tissue microenvironmental components in cancer and cardiovascular diseases. The procedure requires 1-2 weeks and can be performed by users with expertise in general molecular biology.
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Affiliation(s)
- Duo Zhang
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - Abigail H Cleveland
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - Elisavet Krimitza
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine Han
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - Chenlong Yi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrea L Stout
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei Zou
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jay F Dorsey
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yanqing Gong
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Yi Fan
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Jiang T, Gong H, Yuan J. Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level. Neurosci Bull 2023; 39:1840-1858. [PMID: 37715920 PMCID: PMC10661546 DOI: 10.1007/s12264-023-01112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 09/18/2023] Open
Abstract
The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve "optical sectioning" by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.
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Affiliation(s)
- Tao Jiang
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
| | - Hui Gong
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jing Yuan
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Zhan YJ, Zhang SW, Zhu S, Jiang N. Tissue Clearing and Its Application in the Musculoskeletal System. ACS OMEGA 2023; 8:1739-1758. [PMID: 36687066 PMCID: PMC9850472 DOI: 10.1021/acsomega.2c05180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The musculoskeletal system is an integral part of the human body. Currently, most skeletal muscle research is conducted through conventional histological sections due to technological limitations and the structure of skeletal muscles. For studying and observing bones and muscles, there is an urgent need for three-dimensional, objective imaging technologies. Optical tissue-clearing technologies seem to offer a novel and accessible approach to research of the musculoskeletal system. Using this approach, the components which cause refraction or prevent light from penetrating into the tissue are physically and chemically eliminated; then the liquid in the tissue is replaced with high-refractive-index chemicals. This innovative method, which allows three-dimensional reconstruction at the cellular and subcellular scale, significantly improves imaging depth and resolution. Nonetheless, this technology was not originally developed to image bones or muscles. When compared with brain and nerve organs which have attracted considerable attention in this field, the musculoskeletal system contains fewer lipids and has high levels of hemoglobin, collagen fibers, and inorganic hydroxyapatite crystals. Currently, three-dimensional imaging methods are widely used in the diagnosis and treatment of skeletal and muscular illnesses. In this regard, it is vitally important to review and evaluate the optical tissue-clearing technologies currently employed in the musculoskeletal system, so that researchers may make an informed decision. In the meantime, this study offers guidelines and recommendations for expanding the use of this technology in the musculoskeletal system.
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Affiliation(s)
- Yan-Jing Zhan
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Shi-Wen Zhang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - SongSong Zhu
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Nan Jiang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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Attuluri VPS, Sánchez López JF, Maier L, Paruch K, Robert HS. Comparing the efficiency of six clearing methods in developing seeds of Arabidopsis thaliana. PLANT REPRODUCTION 2022; 35:279-293. [PMID: 36378346 PMCID: PMC9705463 DOI: 10.1007/s00497-022-00453-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
ClearSee alpha and FAST9 were optimized for imaging Arabidopsis seeds up to the torpedo stages. The methods preserve the fluorescence of reporter proteins and seed shape, allowing phenotyping embryos in intact seeds. Tissue clearing methods eliminate the need for sectioning, thereby helping better understand the 3D organization of tissues and organs. In the past fifteen years, clearing methods have been developed to preserve endogenous fluorescent protein tags. Some of these methods (ClearSee, TDE, PEA-Clarity, etc.) were adapted to clear various plant species, with the focus on roots, leaves, shoot apical meristems, and floral parts. However, these methods have not been used in developing seeds beyond the early globular stage. Tissue clearing is problematic in post-globular seeds due to various apoplastic barriers and secondary metabolites. In this study, we compared six methods for their efficiency in clearing Arabidopsis thaliana seeds at post-globular embryonic stages. Three methods (TDE, ClearSee, and ClearSee alpha) have already been reported in plants, whereas the others (fsDISCO, FAST9, and CHAPS clear) are used in this context for the first time. These methods were assessed for seed morphological changes, clearing capacity, removal of tannins, and spectral properties. We tested each method in seeds from globular to mature stages. The pros and cons of each method are listed herein. ClearSee alpha appears to be the method of choice as it preserves seed morphology and prevents tannin oxidation. However, FAST9 with 60% iohexol as a mounting medium is faster, clears better, and appears suitable for embryonic shape imaging. Our results may guide plant researchers to choose a suitable method for imaging fluorescent protein-labeled embryos in intact Arabidopsis seeds.
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Affiliation(s)
- Venkata Pardha Saradhi Attuluri
- Mendel Centre for Genomics and Proteomics of Plants, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Juan Francisco Sánchez López
- Mendel Centre for Genomics and Proteomics of Plants, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lukáš Maier
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, 602 00, Brno, Czech Republic
| | - Kamil Paruch
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, 602 00, Brno, Czech Republic
| | - Hélène S Robert
- Mendel Centre for Genomics and Proteomics of Plants, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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Pichardo AH, Amadeo F, Wilm B, Lévy R, Ressel L, Murray P, Sée V. Optical Tissue Clearing to Study the Intra-Pulmonary Biodistribution of Intravenously Delivered Mesenchymal Stromal Cells and Their Interactions with Host Lung Cells. Int J Mol Sci 2022; 23:14171. [PMID: 36430651 PMCID: PMC9699424 DOI: 10.3390/ijms232214171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) injected intravenously are trapped in the capillaries of the lungs and die within the first 24 h. Studying the biodistribution and fate of labelled therapeutic cells in the 3D pulmonary context is important to understand their function in this organ and gain insights into their mechanisms of action. Optical tissue clearing enables volumetric cell tracking at single-cell resolution. Thus, we compared three optical tissue-clearing protocols (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis (CUBIC), modified stabilised 3D imaging of solvent-cleared organs (s-DISCO) and ethyl cinnamate (ECi)) to evaluate their potential to track the biodistribution of human umbilical cord MSCs expressing the tdTomato fluorescence reporter and investigate how they interact with host cells in the mouse lung. The results showed that although CUBIC clearing is the only method that enables direct imaging of fluorescently labelled MSCs, combining s-DISCO or ECi with immunofluorescence or dye labelling allows the interaction of MSCs with endothelial and immune cells to be studied. Overall, this comparative study offers guidance on selecting an optical tissue-clearing method for cell tracking applications.
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Affiliation(s)
- Alejandra Hernandez Pichardo
- Department of Molecular Physiology and Cell Signalling, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
- Centre for Preclinical Imaging, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Francesco Amadeo
- Department of Molecular Physiology and Cell Signalling, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
- Centre for Preclinical Imaging, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Bettina Wilm
- Department of Molecular Physiology and Cell Signalling, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
- Centre for Preclinical Imaging, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Raphaël Lévy
- INSERM, LVTS, Université Sorbonne Paris Nord, F-75018 Paris, France
| | - Lorenzo Ressel
- Department of Veterinary Anatomy Physiology and Pathology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Patricia Murray
- Department of Molecular Physiology and Cell Signalling, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
- Centre for Preclinical Imaging, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Violaine Sée
- CNRS UMR 5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), University Claude Bernard Lyon1, 69007 Lyon, France
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Lee EJ, Hong SK, Choi DH, Gum SI, Hwang MY, Kim DS, Oh JW, Lee ES. Three-dimensional visualization of cerebral blood vessels and neural changes in thick ischemic rat brain slices using tissue clearing. Sci Rep 2022; 12:15897. [PMID: 36151103 PMCID: PMC9508267 DOI: 10.1038/s41598-022-19575-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 08/31/2022] [Indexed: 11/08/2022] Open
Abstract
Blood vessels are three-dimensional (3D) in structure and precisely connected. Conventional histological methods are unsuitable for their analysis because of the destruction of functionally important topological 3D vascular structures. Tissue optical clearing techniques enable extensive volume imaging and data analysis without destroying tissue. This study therefore applied a tissue clearing technique to acquire high-resolution 3D images of rat brain vasculature using light-sheet and confocal microscopies. Rats underwent middle cerebral artery occlusion for 45 min followed by 24 h reperfusion with lectin injected directly into the heart for vascular staining. For acquiring 3D images of rat brain vasculature, 3-mm-thick brain slices were reconstructed using tissue clearing and light-sheet microscopy. Subsequently, after 3D rendering, the fitting of blood vessels to a filament model was used for analysis. The results revealed a significant reduction in vessel diameter and density in the ischemic region compared to those in contralesional non-ischemic regions. Immunostaining of 0.5-mm-thick brain slices revealed considerable neuronal loss and increased astrocyte fluorescence intensity in the ipsilateral region. Thus, these methods can provide more accurate data by broadening the scope of the analyzed regions of interest for examining the 3D cerebrovascular system and neuronal changes occurring in various brain disorders.
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Affiliation(s)
- Eun-Joo Lee
- Binaree, Inc., STE#608 Daegu Techbiz Center, Techno Gongwon-Ro 16, Dalseong-Gun, Daegu, 43017, South Korea
| | - Sung-Kuk Hong
- Department of Anatomy, School of Medicine, Kyungpook National University, Gukchaebosang-Ro 680, Jung-Gu, Daegu, 41944, South Korea
| | - Dong-Hwa Choi
- Biocenter, Gyeonggido Business & Science Accelerator, Gwanggyo-Ro 107, Yeongtong-Gu, Suwon, 16229, South Korea
| | - Sang-Il Gum
- Binaree, Inc., STE#608 Daegu Techbiz Center, Techno Gongwon-Ro 16, Dalseong-Gun, Daegu, 43017, South Korea
| | - Mee Yul Hwang
- Binaree, Inc., STE#608 Daegu Techbiz Center, Techno Gongwon-Ro 16, Dalseong-Gun, Daegu, 43017, South Korea
| | - Dong Sun Kim
- Department of Anatomy, School of Medicine, Kyungpook National University, Gukchaebosang-Ro 680, Jung-Gu, Daegu, 41944, South Korea
| | - Ji Won Oh
- Department of Anatomy, School of Medicine, Kyungpook National University, Gukchaebosang-Ro 680, Jung-Gu, Daegu, 41944, South Korea.
- Department of Anatomy, Yonsei University College of Medicine, Yonsei-Ro 50, Seodaemun-Gu, Seoul, 03722, South Korea.
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Yonsei-Ro 50, Seodaemun-Gu, Seoul, 03722, South Korea.
| | - Eun-Shil Lee
- Binaree, Inc., STE#608 Daegu Techbiz Center, Techno Gongwon-Ro 16, Dalseong-Gun, Daegu, 43017, South Korea.
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9
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Lu T, Shinozaki M, Nagoshi N, Nakamura M, Okano H. Long Preservation of AAV-Transduced Fluorescence by a Modified Organic Solvent-Based Clearing Method. Int J Mol Sci 2022; 23:ijms23179637. [PMID: 36077034 PMCID: PMC9455935 DOI: 10.3390/ijms23179637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
The development of tissue clearing technologies allows 3D imaging of whole tissues and organs, especially in studies of the central nervous system innervated throughout the body. Although the three-dimensional imaging of solvent-cleared organs (3DISCO) method provides a powerful clearing capacity and high transparency, the rapid quenching of endogenous fluorescence and peroxide removal process decreases its practicability. This study provides a modified method named tDISCO to solve these limitations. The tDISCO protocol can preserve AAV-transduced endogenous EGFP fluorescence for months and achieve high transparency in a fast and simple clearing process. In addition to the brain, tDISCO was applied to other organs and even hard bone tissue. tDISCO also enabled us to visualize the long projection neurons and axons with high resolution. This method provides a fast and simple clearing protocol for 3D visualization of the AAV- transduced long projection neurons throughout the brain and spinal cord.
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Affiliation(s)
- Tao Lu
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Munehisa Shinozaki
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Narihito Nagoshi
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masaya Nakamura
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Correspondence: (M.N.); (H.O.)
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Correspondence: (M.N.); (H.O.)
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10
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Ryu Y, Kim Y, Lim HR, Kim HJ, Park BS, Kim JG, Park SJ, Ha CM. Single-Step Fast Tissue Clearing of Thick Mouse Brain Tissue for Multi-Dimensional High-Resolution Imaging. Int J Mol Sci 2022; 23:ijms23126826. [PMID: 35743267 PMCID: PMC9224586 DOI: 10.3390/ijms23126826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 12/10/2022] Open
Abstract
Recent advances in optical clearing techniques have dramatically improved deep tissue imaging by reducing the obscuring effects of light scattering and absorption. However, these optical clearing methods require specialized equipment or a lengthy undertaking with complex protocols that can lead to sample volume changes and distortion. In addition, the imaging of cleared tissues has limitations, such as fluorescence bleaching, harmful and foul-smelling solutions, and the difficulty of handling samples in high-viscosity refractive index (RI) matching solutions. To address the various limitations of thick tissue imaging, we developed an Aqueous high refractive Index matching and tissue Clearing solution for Imaging (termed AICI) with a one-step tissue clearing protocol that was easily made at a reasonable price in our own laboratory without any equipment. AICI can rapidly clear a 1 mm thick brain slice within 90 min with simultaneous RI matching, low viscosity, and a high refractive index (RI = 1.466), allowing the imaging of the sample without additional processing. We compared AICI with commercially available RI matching solutions, including optical clear agents (OCAs), for tissue clearing. The viscosity of AICI is closer to that of water compared with other RI matching solutions, and there was a less than 2.3% expansion in the tissue linear morphology during 24 h exposure to AICI. Moreover, AICI remained fluid over 30 days of air exposure, and the EGFP fluorescence signal was only reduced to ~65% after 10 days. AICI showed a limited clearing of brain tissue >3 mm thick. However, fine neuronal structures, such as dendritic spines and axonal boutons, could still be imaged in thick brain slices treated with AICI. Therefore, AICI is useful not only for the three-dimensional (3D) high-resolution identification of neuronal structures, but also for the examination of multiple structural imaging by neuronal distribution, projection, and gene expression in deep brain tissue. AICI is applicable beyond the imaging of fluorescent antibodies and dyes, and can clear a variety of tissue types, making it broadly useful to researchers for optical imaging applications.
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Affiliation(s)
- Youngjae Ryu
- Research Strategy Office and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41068, Korea; (Y.R.); (Y.K.); (H.R.L.)
- Department of Histology, College of Veterinary Medicine, Kyungpook University, Daegu 41566, Korea;
| | - Yoonju Kim
- Research Strategy Office and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41068, Korea; (Y.R.); (Y.K.); (H.R.L.)
| | - Hye Ryeong Lim
- Research Strategy Office and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41068, Korea; (Y.R.); (Y.K.); (H.R.L.)
| | - Hyung-Joon Kim
- Dementia Research Group, Korea Brain Research Institute, Daegu 41068, Korea;
| | - Byong Seo Park
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (B.S.P.); (J.G.K.)
| | - Jae Geun Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (B.S.P.); (J.G.K.)
| | - Sang-Joon Park
- Department of Histology, College of Veterinary Medicine, Kyungpook University, Daegu 41566, Korea;
| | - Chang Man Ha
- Research Strategy Office and Brain Research Core Facilities of Korea Brain Research Institute, Daegu 41068, Korea; (Y.R.); (Y.K.); (H.R.L.)
- Correspondence:
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11
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Shi L, Wei M, Miao Y, Qian N, Shi L, Singer RA, Benninger RKP, Min W. Highly-multiplexed volumetric mapping with Raman dye imaging and tissue clearing. Nat Biotechnol 2022; 40:364-373. [PMID: 34608326 PMCID: PMC8930416 DOI: 10.1038/s41587-021-01041-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023]
Abstract
Mapping the localization of multiple proteins in their native three-dimensional (3D) context would be useful across many areas of biomedicine, but multiplexed fluorescence imaging has limited intrinsic multiplexing capability, and most methods for increasing multiplexity can only be applied to thin samples (<100 µm). Here, we harness the narrow spectrum of Raman spectroscopy and introduce Raman dye imaging and tissue clearing (RADIANT), an optical method that is capable of imaging multiple targets in thick samples in one shot. We expanded the range of suitable bioorthogonal Raman dyes and developed a tissue-clearing strategy for them (Raman 3D imaging of solvent-cleared organs (rDISCO)). We applied RADIANT to image up to 11 targets in millimeter-thick brain slices, extending the imaging depth 10- to 100-fold compared to prior multiplexed protein imaging methods. We showcased the utility of RADIANT in extracting systems information, including region-specific correlation networks and their topology in cerebellum development. RADIANT will facilitate the exploration of the intricate 3D protein interactions in complex systems.
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Affiliation(s)
- Lixue Shi
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Yupeng Miao
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Naixin Qian
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Lingyan Shi
- Department of Chemistry, Columbia University, New York, NY, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Ruth A Singer
- Graduate Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, NY, USA
- Laboratory of Molecular Neuro-oncology, Rockefeller University, New York, NY, USA
| | - Richard K P Benninger
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA.
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
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12
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Becker K, Saghafi S, Pende M, Hahn C, Dodt HU. Visualizing minute details in light-sheet and confocal microscopy data by combining 3D rolling ball filtering and deconvolution. JOURNAL OF BIOPHOTONICS 2022; 15:e202100290. [PMID: 34726837 DOI: 10.1002/jbio.202100290] [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: 09/14/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
We developed an open-source deconvolution software that stunningly increases the visibility of minute details, as for example, neurons or nerve fibers in light-sheet microscopy or confocal microscopy data by combining rolling ball background subtraction in three directions with deconvolution using a synthetic or measured point spread function. Via automatic block-wise processing image stacks of virtually unlimited size can be deconvolved even on small computers with 8 or 16 GB RAM. By parallelization and optional GPU-acceleration, the software works with high speed: On a PC equipped with a state-of-the-art NVidia graphic board a three dimensional (3D)-stack of about 1 billion voxels can be deconvolved within 5 to 10 minutes. The implemented variation of the Richardson-Lucy deconvolution algorithm preserves the photogrammetry of the image data by using flux-preserving regularization, an approach that to our knowledge has not been applied for deconvolving microscopy data before.
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Affiliation(s)
- Klaus Becker
- Department of Bioelectronics, FKE, Vienna University of Technology, Vienna, Austria
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Saiedeh Saghafi
- Department of Bioelectronics, FKE, Vienna University of Technology, Vienna, Austria
| | - Marko Pende
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Mount Desert Island Biological Laboratory (MDIBL), Bar Harbor, Maine, USA
| | - Christian Hahn
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Hans Ulrich Dodt
- Department of Bioelectronics, FKE, Vienna University of Technology, Vienna, Austria
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
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13
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Liu L, Xia X, Xiang F, Gao Y, Li X, Li H, Zheng W. F-CUBIC: a rapid optical clearing method optimized by quantitative evaluation. BIOMEDICAL OPTICS EXPRESS 2022; 13:237-251. [PMID: 35154867 PMCID: PMC8803013 DOI: 10.1364/boe.442976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
In recent decades, various powerful optical clearing methods have emerged to facilitate deep-tissue imaging. However, a rapid and safe protocol for millimeter-thick specimens is still desired. In this study, we propose a simple and economical chemical screening method that uses porcine small intestine tissue as the testing sample to quantify the clearing speed of different optical clearing reagents. By screening with this method, we developed a fast and versatile clearing protocol, termed F-CUBIC (adding formamide to CUBIC). F-CUBIC allows easy clearing of millimeter-thick tissues within 2-20 min by one-step immersion at room temperature. It introduces negligible tissue distortion and shows high compatibility with various fluorescent labeling techniques. Based on endoscopic human colon specimens, we successfully demonstrated the potential of F-CUBIC for nondestructive three-dimensional (3D) biopsy in combination with two-photon microscopy. This study would substantially benefit rapid 3D tissue mapping in biomedical research and clinics, such as instant histopathological examinations.
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Affiliation(s)
- Lina Liu
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Authors contributed equally to this work
| | - Xianyuan Xia
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Authors contributed equally to this work
| | - Feng Xiang
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yufeng Gao
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xi Li
- Department of Gastroenterology, Peking University Shenzhen Hospital, Shen Zhen 518036, China
| | - Hui Li
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei Zheng
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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14
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Richardson DS, Guan W, Matsumoto K, Pan C, Chung K, Ertürk A, Ueda HR, Lichtman JW. TISSUE CLEARING. NATURE REVIEWS. METHODS PRIMERS 2021; 1:84. [PMID: 35128463 PMCID: PMC8815095 DOI: 10.1038/s43586-021-00080-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2021] [Indexed: 12/16/2022]
Abstract
Tissue clearing of gross anatomical samples was first described over a century ago and has only recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Many biological relationships between structure and function require investigation in three dimensions and tissue clearing therefore has the potential to enable broad discoveries in the biological sciences. Unfortunately, the current literature is complex and could confuse researchers looking to begin a clearing project. The goal of this Primer is to outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest. Further, the Primer outlines the required imaging and computational infrastructure needed to perform tissue clearing at scale, gives an overview of current applications, discusses limitations and provides an outlook on future advances in the field.
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Affiliation(s)
- Douglas S. Richardson
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Webster Guan
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Katsuhiko Matsumoto
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Chenchen Pan
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Kwanghun Chung
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Nano Biomedical Engineering (Nano BME) Graduate Program, Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Jeff W. Lichtman
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
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15
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Boulan B, Ravanello C, Peyrel A, Bosc C, Delphin C, Appaix F, Denarier E, Kraut A, Jacquier-Sarlin M, Fournier A, Andrieux A, Gory-Fauré S, Deloulme JC. CRMP4-mediated fornix development involves Semaphorin-3E signaling pathway. eLife 2021; 10:e70361. [PMID: 34860155 PMCID: PMC8683083 DOI: 10.7554/elife.70361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 12/25/2022] Open
Abstract
Neurodevelopmental axonal pathfinding plays a central role in correct brain wiring and subsequent cognitive abilities. Within the growth cone, various intracellular effectors transduce axonal guidance signals by remodeling the cytoskeleton. Semaphorin-3E (Sema3E) is a guidance cue implicated in development of the fornix, a neuronal tract connecting the hippocampus to the hypothalamus. Microtubule-associated protein 6 (MAP6) has been shown to be involved in the Sema3E growth-promoting signaling pathway. In this study, we identified the collapsin response mediator protein 4 (CRMP4) as a MAP6 partner and a crucial effector in Sema3E growth-promoting activity. CRMP4-KO mice displayed abnormal fornix development reminiscent of that observed in Sema3E-KO mice. CRMP4 was shown to interact with the Sema3E tripartite receptor complex within detergent-resistant membrane (DRM) domains, and DRM domain integrity was required to transduce Sema3E signaling through the Akt/GSK3 pathway. Finally, we showed that the cytoskeleton-binding domain of CRMP4 is required for Sema3E's growth-promoting activity, suggesting that CRMP4 plays a role at the interface between Sema3E receptors, located in DRM domains, and the cytoskeleton network. As the fornix is affected in many psychiatric diseases, such as schizophrenia, our results provide new insights to better understand the neurodevelopmental components of these diseases.
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Affiliation(s)
- Benoît Boulan
- Univ. Grenoble Alpes, Inserm, U1216, CEA, Grenoble Institut NeurosciencesGrenobleFrance
| | - Charlotte Ravanello
- Univ. Grenoble Alpes, Inserm, U1216, CEA, Grenoble Institut NeurosciencesGrenobleFrance
| | - Amandine Peyrel
- Univ. Grenoble Alpes, Inserm, U1216, CEA, Grenoble Institut NeurosciencesGrenobleFrance
| | - Christophe Bosc
- Univ. Grenoble Alpes, Inserm, U1216, CEA, Grenoble Institut NeurosciencesGrenobleFrance
| | - Christian Delphin
- Univ. Grenoble Alpes, Inserm, U1216, CEA, Grenoble Institut NeurosciencesGrenobleFrance
| | - Florence Appaix
- Univ. Grenoble Alpes, Inserm, U1216, CEA, Grenoble Institut NeurosciencesGrenobleFrance
| | - Eric Denarier
- Univ. Grenoble Alpes, Inserm, U1216, CEA, Grenoble Institut NeurosciencesGrenobleFrance
| | - Alexandra Kraut
- Univ. Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEAGrenobleFrance
| | | | - Alyson Fournier
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill UniversityMontréalCanada
| | - Annie Andrieux
- Univ. Grenoble Alpes, Inserm, U1216, CEA, Grenoble Institut NeurosciencesGrenobleFrance
| | - Sylvie Gory-Fauré
- Univ. Grenoble Alpes, Inserm, U1216, CEA, Grenoble Institut NeurosciencesGrenobleFrance
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16
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Kosmidis S, Negrean A, Dranovsky A, Losonczy A, Kandel ER. A fast, aqueous, reversible three-day tissue clearing method for adult and embryonic mouse brain and whole body. CELL REPORTS METHODS 2021; 1:100090. [PMID: 34966901 PMCID: PMC8713566 DOI: 10.1016/j.crmeth.2021.100090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/13/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022]
Abstract
Optical clearing methods serve as powerful tools to study intact organs and neuronal circuits. We developed an aqueous clearing protocol, Fast 3D Clear, that relies on tetrahydrofuran for tissue delipidation and iohexol for clearing, such that tissues can be imaged under immersion oil in light-sheet imaging systems. Fast 3D Clear requires 3 days to achieve high transparency of adult and embryonic mouse tissues while maintaining their anatomical integrity and preserving a vast array of transgenic and viral/dye fluorophores. A unique advantage of Fast 3D Clear is its complete reversibility and thus compatibility with tissue sectioning and immunohistochemistry. Fast 3D Clear can be easily and quickly applied to a wide range of biomedical studies, facilitating the acquisition of high-resolution two- and three-dimensional images.
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Affiliation(s)
- Stylianos Kosmidis
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Adrian Negrean
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Alex Dranovsky
- New York State Psychiatric Institute, New York, NY 10032, USA; Department of Psychiatry, Columbia University, New York, NY 10032, USA
| | - Attila Losonczy
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Eric R. Kandel
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
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17
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Almagro J, Messal HA, Zaw Thin M, van Rheenen J, Behrens A. Tissue clearing to examine tumour complexity in three dimensions. Nat Rev Cancer 2021; 21:718-730. [PMID: 34331034 DOI: 10.1038/s41568-021-00382-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
The visualization of whole organs and organisms through tissue clearing and fluorescence volumetric imaging has revolutionized the way we look at biological samples. Its application to solid tumours is changing our perception of tumour architecture, revealing signalling networks and cell interactions critical in tumour progression, and provides a powerful new strategy for cancer diagnostics. This Review introduces the latest advances in tissue clearing and three-dimensional imaging, examines the challenges in clearing epithelia - the tissue of origin of most malignancies - and discusses the insights that tissue clearing has brought to cancer research, as well as the prospective applications to experimental and clinical oncology.
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Affiliation(s)
- Jorge Almagro
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Hendrik A Messal
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - May Zaw Thin
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK
| | - Jacco van Rheenen
- Department of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK.
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK.
- Convergence Science Centre and Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK.
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18
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Zhu J, Liu X, Deng Y, Li D, Yu T, Zhu D. Tissue optical clearing for 3D visualization of vascular networks: A review. Vascul Pharmacol 2021; 141:106905. [PMID: 34506969 DOI: 10.1016/j.vph.2021.106905] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/01/2022]
Abstract
Reconstruction of the vasculature of intact tissues/organs down to the capillary level is essential for understanding the development and remodeling of vascular networks under physiological and pathological conditions. Optical imaging techniques can provide sufficient resolution to distinguish small vessels with several microns, but the imaging depth is somewhat limited due to the high light scattering of opaque tissue. Recently, various tissue optical clearing methods have been developed to overcome light attenuation and improve the imaging depth both for ex-vivo and in-vivo visualizations. Tissue clearing combined with vessel labeling techniques and advanced optical tomography enables successful mapping of the vasculature of different tissues/organs, as well as dynamically monitoring vessel function under normal and pathological conditions. Here, we briefly introduce the commonly-used labeling strategies for entire vascular networks, the current tissue optical clearing techniques available for various tissues, as well as the advanced optical imaging techniques for fast, high-resolution structural and functional imaging for blood vessels. We also discuss the applications of these techniques in the 3D visualization of vascular networks in normal tissues, and the vascular remodeling in several typical pathological models in clinical research. This review is expected to provide valuable insights for researchers to study the potential mechanisms of various vessel-associated diseases using tissue optical clearing pipeline.
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Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaomei Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yating Deng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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19
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Abstract
Tissue clearing increases the transparency of late developmental stages and enables deep imaging in fixed organisms. Successful implementation of these methodologies requires a good grasp of sample processing, imaging and the possibilities offered by image analysis. In this Primer, we highlight how tissue clearing can revolutionize the histological analysis of developmental processes and we advise on how to implement effective clearing protocols, imaging strategies and analysis methods for developmental biology.
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Affiliation(s)
| | - Nicolas Renier
- Sorbonne Université, Paris Brain Institute – ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
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20
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Zhu J, Ma Y, Xu J, Li Y, Wan P, Qi Y, Yu T, Zhu D. Dec-DISCO: decolorization DISCO clearing for seeing through the biological architectures of heme-rich organs. BIOMEDICAL OPTICS EXPRESS 2021; 12:5499-5513. [PMID: 34692197 PMCID: PMC8515970 DOI: 10.1364/boe.431397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/11/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
The tissue optical clearing technique plays an important role in three-dimensional (3D) visualization of large tissues. As a typical solvent-based clearing method, 3DISCO can achieve the highest level of tissue transparency with favorable clearing speed. However, 3DISCO cannot deal with the residual blood within tissues, leading to tissue brownness or redness after clearing, thus greatly influencing the tissue transparency and image quality due to the strong absorption of residual blood. To address this problem, we proposed an optimized clearing method by introducing CUBIC-L solution combined with 3DISCO for effective decolorization, termed Dec-DISCO (Decolorization DISCO). Dec-DISCO achieves better transparency than 3DISCO for various heme-rich tissues and performs enhanced fluorescence preservation capability. Dec-DISCO allows high-quality 3D imaging of fluorescently labeled heme-rich organs, as well as pathological tissue with severe hemorrhage. Dec-DISCO is expected to provide a powerful tool for histological analysis of kinds of heme-rich tissues in various medical conditions.
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Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yilin Ma
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jianyi Xu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yusha Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Peng Wan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yisong Qi
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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21
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Wan P, Li Y, Zhu J, Xu J, Liu X, Yu T, Zhu D. FDISCO+: a clearing method for robust fluorescence preservation of cleared samples. NEUROPHOTONICS 2021; 8:035007. [PMID: 34514032 PMCID: PMC8427119 DOI: 10.1117/1.nph.8.3.035007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/24/2021] [Indexed: 05/05/2023]
Abstract
Significance: The recently reported solvent-based optical clearing method FDISCO can preserve various fluorescent signals very well. However, the strict low-temperature storage condition of FDISCO is not conducive to long-time or repetitive imaging usually conducted at room temperature. Therefore, it is important to solve the contradiction between fluorescence preservation and imaging condition. Aim: We develop a modified FDISCO clearing method, termed FDISCO+, to change the preservation condition from low temperature to room temperature. Approach: Two alternative antioxidants were screened out to effectively inhibit the peroxide generation in the clearing agent at room temperature, enabling robust fluorescence preservation of cleared samples. Results: FDISCO+ achieves comparable fluorescence preservation with the original FDISCO protocol and allows long-time storage at room temperature, making it easier for researchers to image and preserve the samples. Conclusions: FDISCO+ is expected to be widely used due to its loose operation requirements.
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Affiliation(s)
- Peng Wan
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Yusha Li
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Jingtan Zhu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Jianyi Xu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Xiaomei Liu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
| | - Tingting Yu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
- Address all correspondence to Tingting Yu,
| | - Dan Zhu
- Huazhong University of Science and Technology, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Wuhan, China
- Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Wuhan, China
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22
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Matryba P, Łukasiewicz K, Pawłowska M, Tomczuk J, Gołąb J. Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging? Int J Mol Sci 2021; 22:ijms22136730. [PMID: 34201632 PMCID: PMC8268743 DOI: 10.3390/ijms22136730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.
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Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
- The Doctoral School of the Medical University of Warsaw, Medical University of Warsaw, 02-097 Warsaw, Poland
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Correspondence:
| | - Kacper Łukasiewicz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
| | - Monika Pawłowska
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Tomczuk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
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23
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Khouri K, Xie DF, Crouzet C, Bahani AW, Cribbs DH, Fisher MJ, Choi B. Simple methodology to visualize whole-brain microvasculature in three dimensions. NEUROPHOTONICS 2021; 8:025004. [PMID: 33884280 PMCID: PMC8056070 DOI: 10.1117/1.nph.8.2.025004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Significance: To explore brain architecture and pathology, a consistent and reliable methodology to visualize the three-dimensional cerebral microvasculature is beneficial. Perfusion-based vascular labeling is quick and easily deliverable. However, the quality of vascular labeling can vary with perfusion-based labels due to aggregate formation, leakage, rapid photobleaching, and incomplete perfusion. Aim: We describe a simple, two-day protocol combining perfusion-based labeling with a two-day clearing step that facilitates whole-brain, three-dimensional microvascular imaging and characterization. Approach: The combination of retro-orbital injection of Lectin-Dylight-649 to label the vasculature, the clearing process of a modified iDISCO+ protocol, and light-sheet imaging collectively enables a comprehensive view of the cerebrovasculature. Results: We observed ∼ threefold increase in contrast-to-background ratio of Lectin-Dylight-649 vascular labeling over endogenous green fluorescent protein fluorescence from a transgenic mouse model. With light-sheet microscopy, we demonstrate sharp visualization of cerebral microvasculature throughout the intact mouse brain. Conclusions: Our tissue preparation protocol requires fairly routine processing steps and is compatible with multiple types of optical microscopy.
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Affiliation(s)
- Katiana Khouri
- University of California, Irvine, Beckman Laser Institute and Medical Clinic, Irvine, California, United States
- University of California, Irvine, Graduate Program in Mathematical, Computational, and Systems Biology, Irvine, California, United States
| | - Danny F. Xie
- University of California, Irvine, Beckman Laser Institute and Medical Clinic, Irvine, California, United States
- University of California, Irvine, Department of Biomedical Engineering, Irvine, California, United States
| | - Christian Crouzet
- University of California, Irvine, Beckman Laser Institute and Medical Clinic, Irvine, California, United States
- University of California, Irvine, Department of Biomedical Engineering, Irvine, California, United States
| | - Adrian W. Bahani
- University of California, Irvine, Beckman Laser Institute and Medical Clinic, Irvine, California, United States
- University of California, Irvine, Department of Biomedical Engineering, Irvine, California, United States
| | - David H. Cribbs
- University of California, Irvine, Institute for Memory Impairments and Neurological Disorders, Irvine, California, United States
| | - Mark J. Fisher
- University of California, Irvine, Beckman Laser Institute and Medical Clinic, Irvine, California, United States
- University of California, Irvine, Department of Neurology, Orange, California, United States
- University of California, Irvine, Department of Pathology and Laboratory Medicine, Irvine, California, United States
- University of California, Irvine, Department of Anatomy and Neurobiology, Irvine, California, United States
| | - Bernard Choi
- University of California, Irvine, Beckman Laser Institute and Medical Clinic, Irvine, California, United States
- University of California, Irvine, Graduate Program in Mathematical, Computational, and Systems Biology, Irvine, California, United States
- University of California, Irvine, Department of Biomedical Engineering, Irvine, California, United States
- University of California, Irvine, Edwards Lifesciences Center for Advanced Cardiovascular Technology, Irvine, California, United States
- University of California, Irvine, Department of Surgery, Irvine, California, United States
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24
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Zhan Y, Wu H, Liu L, Lin J, Zhang S. Organic solvent-based tissue clearing techniques and their applications. JOURNAL OF BIOPHOTONICS 2021; 14:e202000413. [PMID: 33715302 DOI: 10.1002/jbio.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023]
Abstract
Revealing the true structure of tissues and organs with tissue slicing technology is difficult since images reconstructed in three dimensions are easily distorted. To address the limitations in tissue slicing technology, tissue clearing has been invented and has recently achieved significant progress in three-dimensional imaging. Currently, this technology can mainly be divided into two types: aqueous clearing methods and solvent-based clearing methods. As one of the important parts of this technology, organic solvent-based tissue clearing techniques have been widely applied because of their efficient clearing speed and high clearing intensity. This review introduces the primary organic solvent-based tissue clearing techniques and their applications.
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Affiliation(s)
- Yanjing Zhan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Haoyan Wu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Linfeng Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jie Lin
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shiwen Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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25
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Avilov SV. Navigating across multi-dimensional space of tissue clearing parameters. Methods Appl Fluoresc 2021; 9:022001. [PMID: 33592593 DOI: 10.1088/2050-6120/abe6fb] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Optical tissue clearing refers to physico-chemical treatments which make thick biological samples transparent by removal of refractive index gradients and light absorbing substances. Although tissue clearing was first reported in 1914, it was not widely used in light microscopy until 21th century, because instrumentation of that time did not permit to acquire and handle images of thick (mm to cm) samples as whole. Rapid progress in optical instrumentation, computers and software over the last decades made micrograph acquisition of centimeter-thick samples feasible. This boosted tissue clearing use and development. Numerous diverse protocols have been developed. They use organic solvents or water-miscible substances, such as detergents and chaotropic agents; some protocols require application of electric field or perfusion with special devices. There is no 'best-for-all' tissue clearing method. Depending on the case, one or another protocol is more suitable. Most of protocols require days or even weeks to complete, thus choosing an unsuitable protocol may cause an important waste of time. Several inter-dependent parameters should be taken into account to choose a tissue clearing protocol, such as: (1) required image quality (resolution, contrast, signal to noise ratio etc), (2) nature and size of the sample, (3) type of labels, (4) characteristics of the available instrumentation, (5) budget, (6) time budget, and (7) feasibility. Present review focusses on the practical aspects of various tissue clearing techniques. It is aimed to help non-experts to choose tissue clearing techniques which are optimal for their particular cases.
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Affiliation(s)
- Sergiy V Avilov
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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26
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Molbay M, Kolabas ZI, Todorov MI, Ohn T, Ertürk A. A guidebook for DISCO tissue clearing. Mol Syst Biol 2021; 17:e9807. [PMID: 33769689 PMCID: PMC7995442 DOI: 10.15252/msb.20209807] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/29/2020] [Accepted: 01/14/2021] [Indexed: 12/14/2022] Open
Abstract
Histological analysis of biological tissues by mechanical sectioning is significantly time-consuming and error-prone due to loss of important information during sample slicing. In the recent years, the development of tissue clearing methods overcame several of these limitations and allowed exploring intact biological specimens by rendering tissues transparent and subsequently imaging them by laser scanning fluorescence microscopy. In this review, we provide a guide for scientists who would like to perform a clearing protocol from scratch without any prior knowledge, with an emphasis on DISCO clearing protocols, which have been widely used not only due to their robustness, but also owing to their relatively straightforward application. We discuss diverse tissue-clearing options and propose solutions for several possible pitfalls. Moreover, after surveying more than 30 researchers that employ tissue clearing techniques in their laboratories, we compiled the most frequently encountered issues and propose solutions. Overall, this review offers an informative and detailed guide through the growing literature of tissue clearing and can help with finding the easiest way for hands-on implementation.
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Affiliation(s)
- Muge Molbay
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
- Munich Medical Research School (MMRS)MunichGermany
| | - Zeynep Ilgin Kolabas
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
- Graduate School for Systemic Neurosciences (GSN)MunichGermany
| | - Mihail Ivilinov Todorov
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
- Graduate School for Systemic Neurosciences (GSN)MunichGermany
| | - Tzu‐Lun Ohn
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM)Helmholtz CenterNeuherberg, MunichGermany
- Institute for Stroke and Dementia ResearchKlinikum der Universität MünchenLudwig‐Maximilians‐University MunichMunichGermany
- Munich Cluster for Systems Neurology (SyNergy)MunichGermany
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27
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Epigenetics and Communication Mechanisms in Microglia Activation with a View on Technological Approaches. Biomolecules 2021; 11:biom11020306. [PMID: 33670563 PMCID: PMC7923060 DOI: 10.3390/biom11020306] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 12/13/2022] Open
Abstract
Microglial cells, the immune cells of the central nervous system (CNS), play a crucial role for the proper brain development and function and in CNS homeostasis. While in physiological conditions, microglia continuously check the state of brain parenchyma, in pathological conditions, microglia can show different activated phenotypes: In the early phases, microglia acquire the M2 phenotype, increasing phagocytosis and releasing neurotrophic and neuroprotective factors. In advanced phases, they acquire the M1 phenotype, becoming neurotoxic and contributing to neurodegeneration. Underlying this phenotypic change, there is a switch in the expression of specific microglial genes, in turn modulated by epigenetic changes, such as DNA methylation, histones post-translational modifications and activity of miRNAs. New roles are attributed to microglial cells, including specific communication with neurons, both through direct cell–cell contact and by release of many different molecules, either directly or indirectly, through extracellular vesicles. In this review, recent findings on the bidirectional interaction between neurons and microglia, in both physiological and pathological conditions, are highlighted, with a focus on the complex field of microglia immunomodulation through epigenetic mechanisms and/or released factors. In addition, advanced technologies used to study these mechanisms, such as microfluidic, 3D culture and in vivo imaging, are presented.
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28
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Tian T, Yang Z, Li X. Tissue clearing technique: Recent progress and biomedical applications. J Anat 2021; 238:489-507. [PMID: 32939792 PMCID: PMC7812135 DOI: 10.1111/joa.13309] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/19/2020] [Accepted: 08/24/2020] [Indexed: 02/03/2023] Open
Abstract
Organisms are inherently three dimensional, thus comprehensive understanding of the complicated biological system requires analysis of organs or even whole bodies in the context of three dimensions. However, this is a tremendous task since the biological specimens are naturally opaque, a major obstacle in whole-body and whole-organ imaging. Tissue clearing technique provides a prospective solution and has become a powerful tool for three-dimensional imaging and quantification of organisms. Tissue clearing technique aims to make tissue transparent by minimizing light scattering and light absorption, thus allowing deep imaging of large volume samples. When combined with diverse molecular labeling methods and high-throughput optical sectioning microscopes, tissue clearing technique enables whole-body and whole-organ imaging at cellular or subcellular resolution, providing detailed and comprehensive information about the intact biological systems. Here, we give an overview of recent progress and biomedical applications of tissue clearing technique. We introduce the mechanisms and basic principles of tissue clearing, and summarize the current tissue clearing methods. Moreover, the available imaging techniques and software packages for data processing are also presented. Finally, we introduce the recent advances in applications of tissue clearing in biomedical fields. Tissue clearing contributes to the investigation of structure-function relationships in intact mammalian organs, and opens new avenues for cellular and molecular mapping of intact human organs. We hope this review contributes to a better understanding of tissue clearing technique and can help researchers to select the best-suited clearing protocol for their experiments.
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Affiliation(s)
- Ting Tian
- Beijing Key Laboratory for Biomaterials and Neural RegenerationSchool of Biological Science and Medical EngineeringBeihang UniversityBeijingChina
| | - Zhaoyang Yang
- Department of NeurobiologySchool of Basic Medical SciencesCapital Medical UniversityBeijingChina,Beijing International Cooperation Bases for Science and Technology on Biomaterials and Neural RegenerationBeijing Advanced Innovation Center for Biomedical EngineeringBeihang UniversityBeijingChina
| | - Xiaoguang Li
- Beijing Key Laboratory for Biomaterials and Neural RegenerationSchool of Biological Science and Medical EngineeringBeihang UniversityBeijingChina,Department of NeurobiologySchool of Basic Medical SciencesCapital Medical UniversityBeijingChina,Beijing International Cooperation Bases for Science and Technology on Biomaterials and Neural RegenerationBeijing Advanced Innovation Center for Biomedical EngineeringBeihang UniversityBeijingChina
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29
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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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30
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Liang X, Luo H. Optical Tissue Clearing: Illuminating Brain Function and Dysfunction. Theranostics 2021; 11:3035-3051. [PMID: 33537072 PMCID: PMC7847687 DOI: 10.7150/thno.53979] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
Tissue optical clearing technology has been developing rapidly in the past decade due to advances in microscopy equipment and various labeling techniques. Consistent modification of primary methods for optical tissue transparency has allowed observation of the whole mouse body at single-cell resolution or thick tissue slices at the nanoscale level, with the final aim to make intact primate and human brains or thick human brain tissues optically transparent. Optical clearance combined with flexible large-volume tissue labeling technology can not only preserve the anatomical structure but also visualize multiple molecular information from intact samples in situ. It also provides a new strategy for studying complex tissues, which is of great significance for deciphering the functional structure of healthy brains and the mechanisms of neurological pathologies. In this review, we briefly introduce the existing optical clearing technology and discuss its application in deciphering connection and structure, brain development, and brain diseases. Besides, we discuss the standard computational analysis tools for large-scale imaging dataset processing and information extraction. In general, we hope that this review will provide a valuable reference for researchers who intend to use optical clearing technology in studying the brain.
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Affiliation(s)
- Xiaohan Liang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, 430074, 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, 430074, Wuhan, Hubei, China
| | - Haiming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, 430074, 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, 430074, Wuhan, Hubei, China
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31
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Sabdyusheva Litschauer I, Becker K, Saghafi S, Ballke S, Bollwein C, Foroughipour M, Gaugeler J, Foroughipour M, Schavelová V, László V, Döme B, Brostjan C, Weichert W, Dodt HU. 3D histopathology of human tumours by fast clearing and ultramicroscopy. Sci Rep 2020; 10:17619. [PMID: 33077794 PMCID: PMC7572501 DOI: 10.1038/s41598-020-71737-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/02/2020] [Indexed: 12/31/2022] Open
Abstract
Here, we describe a novel approach that allows pathologists to three-dimensionally analyse malignant tissues, including the tumour-host tissue interface. Our visualization technique utilizes a combination of ultrafast chemical tissue clearing and light-sheet microscopy to obtain virtual slices and 3D reconstructions of up to multiple centimetre sized tumour resectates. For the clearing of tumours we propose a preparation technique comprising three steps: (a) Fixation and enhancement of tissue autofluorescence with formalin/5-sulfosalicylic acid. (b) Ultrafast active chemical dehydration with 2,2-dimethoxypropane and (c) refractive index matching with dibenzyl ether at up to 56 °C. After clearing, the tumour resectates are imaged. The images are computationally post-processed for contrast enhancement and artefact removal and then 3D reconstructed. Importantly, the sequence a–c is fully reversible, allowing the morphological correlation of one and the same histological structures, once visualized with our novel technique and once visualized by standard H&E- and IHC-staining. After reverting the clearing procedure followed by standard H&E processing, the hallmarks of ductal carcinoma in situ (DCIS) found in the cleared samples could be successfully correlated with the corresponding structures present in H&E and IHC staining. Since the imaging of several thousands of optical sections is a fast process, it is possible to analyse a larger part of the tumour than by mechanical slicing. As this also adds further information about the 3D structure of malignancies, we expect that our technology will become a valuable addition for histological diagnosis in clinical pathology.
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Affiliation(s)
- Inna Sabdyusheva Litschauer
- Department of Bioelectronics, TU Wien, Vienna, Austria. .,Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| | - Klaus Becker
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Saiedeh Saghafi
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Simone Ballke
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Christine Bollwein
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Meraaj Foroughipour
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Julia Gaugeler
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Massih Foroughipour
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Viktória Schavelová
- Department of Bioelectronics, TU Wien, Vienna, Austria.,Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Viktória László
- Department of Surgery, Anna Spiegel Center of Translational Research, Medical University of Vienna, Vienna, Austria
| | - Balazs Döme
- Department of Surgery, Anna Spiegel Center of Translational Research, Medical University of Vienna, Vienna, Austria
| | - Christine Brostjan
- Department of Surgery, Anna Spiegel Center of Translational Research, Medical University of Vienna, Vienna, Austria
| | - Wilko Weichert
- Institute of Pathology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Hans-Ulrich Dodt
- Department of Bioelectronics, TU Wien, Vienna, Austria. .,Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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32
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Tian T, Li X. Applications of tissue clearing in the spinal cord. Eur J Neurosci 2020; 52:4019-4036. [DOI: 10.1111/ejn.14938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/22/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ting Tian
- Beijing Key Laboratory for Biomaterials and Neural Regeneration School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Xiaoguang Li
- Beijing Key Laboratory for Biomaterials and Neural Regeneration School of Biological Science and Medical Engineering Beihang University Beijing China
- Beijing International Cooperation Bases for Science and Technology on Biomaterials and Neural Regeneration Beijing Advanced Innovation Center for Biomedical Engineering Beihang University Beijing China
- Department of Neurobiology School of Basic Medical Sciences Capital Medical University Beijing China
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33
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Gómez-Gaviro MV, Sanderson D, Ripoll J, Desco M. Biomedical Applications of Tissue Clearing and Three-Dimensional Imaging in Health and Disease. iScience 2020; 23:101432. [PMID: 32805648 PMCID: PMC7452225 DOI: 10.1016/j.isci.2020.101432] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/27/2022] Open
Abstract
Three-dimensional (3D) optical imaging techniques can expand our knowledge about physiological and pathological processes that cannot be fully understood with 2D approaches. Standard diagnostic tests frequently are not sufficient to unequivocally determine the presence of a pathological condition. Whole-organ optical imaging requires tissue transparency, which can be achieved by using tissue clearing procedures enabling deeper image acquisition and therefore making possible the analysis of large-scale biological tissue samples. Here, we review currently available clearing agents, methods, and their application in imaging of physiological or pathological conditions in different animal and human organs. We also compare different optical tissue clearing methods discussing their advantages and disadvantages and review the use of different 3D imaging techniques for the visualization and image acquisition of cleared tissues. The use of optical tissue clearing resources for large-scale biological tissues 3D imaging paves the way for future applications in translational and clinical research.
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Affiliation(s)
- Maria Victoria Gómez-Gaviro
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain.
| | - Daniel Sanderson
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Jorge Ripoll
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Manuel Desco
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain; Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
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34
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Henschke JU, Pakan JM. Disynaptic cerebrocerebellar pathways originating from multiple functionally distinct cortical areas. eLife 2020; 9:59148. [PMID: 32795386 PMCID: PMC7428308 DOI: 10.7554/elife.59148] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/28/2020] [Indexed: 12/31/2022] Open
Abstract
The cerebral cortex and cerebellum both play important roles in sensorimotor processing, however, precise connections between these major brain structures remain elusive. Using anterograde mono-trans-synaptic tracing, we elucidate cerebrocerebellar pathways originating from primary motor, sensory, and association cortex. We confirm a highly organized topography of corticopontine projections in mice; however, we found no corticopontine projections originating from primary auditory cortex and detail several potential extra-pontine cerebrocerebellar pathways. The cerebellar hemispheres were the major target of resulting disynaptic mossy fiber terminals, but we also found at least sparse cerebrocerebellar projections to every lobule of the cerebellum. Notably, projections originating from association cortex resulted in less laterality than primary sensory/motor cortices. Within molecularly defined cerebellar modules we found spatial overlap of mossy fiber terminals, originating from functionally distinct cortical areas, within crus I, paraflocculus, and vermal regions IV/V and VI - highlighting these regions as potential hubs for multimodal cortical influence.
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Affiliation(s)
- Julia U Henschke
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke-University, Magdeburg, Germany.,German Centre for Neurodegenerative Diseases, Magdeburg, Germany
| | - Janelle Mp Pakan
- Institute of Cognitive Neurology and Dementia Research, Otto-von-Guericke-University, Magdeburg, Germany.,German Centre for Neurodegenerative Diseases, Magdeburg, Germany.,Center for Behavioral Brain Sciences, Universitätsplatz, Magdeburg, Germany
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35
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Matryba P, Wolny A, Pawłowska M, Sosnowska A, Rydzyńska Z, Jasiński M, Stefaniuk M, Gołąb J. Tissue clearing-based method for unobstructed three-dimensional imaging of mouse penis with subcellular resolution. JOURNAL OF BIOPHOTONICS 2020; 13:e202000072. [PMID: 32352207 DOI: 10.1002/jbio.202000072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/16/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Although mice are widely used to elucidate factors contributing to penile disorders and develop treatment options, quantification of tissue changes upon intervention is either limited to minuscule tissue volume (histology) or acquired with limited spatial resolution (MRI/CT). Thus, imaging method suitable for expeditious acquisition of the entire mouse penis with subcellular resolution is described that relies on both aqueous- (clear, unobstructed brain imaging cocktails and computational analysis) and solvent-based (fluorescence-preserving capability imaging of solvent-cleared organs) tissue optical clearing (TOC). The combined TOC approach allows to image mouse penis innervation and vasculature with unprecedented detail and, for the first time, reveals the three-dimensional structure of murine penis fibrocartilage.
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Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
- The Doctoral School of the Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Artur Wolny
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Monika Pawłowska
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Anna Sosnowska
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Zuzanna Rydzyńska
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Jasiński
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Marzena Stefaniuk
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
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36
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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: 129] [Impact Index Per Article: 32.3] [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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37
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Pende M, Vadiwala K, Schmidbaur H, Stockinger AW, Murawala P, Saghafi S, Dekens MPS, Becker K, Revilla-i-Domingo R, Papadopoulos SC, Zurl M, Pasierbek P, Simakov O, Tanaka EM, Raible F, Dodt HU. A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity. SCIENCE ADVANCES 2020; 6:eaba0365. [PMID: 32523996 PMCID: PMC7259959 DOI: 10.1126/sciadv.aba0365] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Tissue clearing combined with deep imaging has emerged as a powerful alternative to classical histological techniques. Whereas current techniques have been optimized for imaging selected nonpigmented organs such as the mammalian brain, natural pigmentation remains challenging for most other biological specimens of larger volume. We have developed a fast DEpigmEntation-Plus-Clearing method (DEEP-Clear) that is easily incorporated in existing workflows and combines whole system labeling with a spectrum of detection techniques, ranging from immunohistochemistry to RNA in situ hybridization, labeling of proliferative cells (EdU labeling) and visualization of transgenic markers. With light-sheet imaging of whole animals and detailed confocal studies on pigmented organs, we provide unprecedented insight into eyes, whole nervous systems, and subcellular structures in animal models ranging from worms and squids to axolotls and zebrafish. DEEP-Clear thus paves the way for the exploration of species-rich clades and developmental stages that are largely inaccessible by regular imaging approaches.
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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 for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Karim Vadiwala
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hannah Schmidbaur
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander W. Stockinger
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Saiedeh Saghafi
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Marcus P. S. Dekens
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Klaus Becker
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Roger Revilla-i-Domingo
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Sofia-Christina Papadopoulos
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Martin Zurl
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Pawel Pasierbek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Elly M. Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Florian Raible
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hans-Ulrich Dodt
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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38
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Zhu J, Yu T, Li Y, Xu J, Qi Y, Yao Y, Ma Y, Wan P, Chen Z, Li X, Gong H, Luo Q, Zhu D. MACS: Rapid Aqueous Clearing System for 3D Mapping of Intact Organs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903185. [PMID: 32328422 PMCID: PMC7175264 DOI: 10.1002/advs.201903185] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/16/2020] [Indexed: 05/21/2023]
Abstract
Tissue optical clearing techniques have provided important tools for large-volume imaging. Aqueous-based clearing methods are known for good fluorescence preservation and scalable size maintenance, but are limited by long incubation time, insufficient clearing performance, or requirements for specialized devices. Additionally, few clearing methods are compatible with widely used lipophilic dyes while maintaining high clearing performance. Here, to address these issues, m-xylylenediamine (MXDA) is firstly introduced into tissue clearing and used to develop a rapid, highly efficient aqueous clearing method with robust lipophilic dyes compatibility, termed MXDA-based Aqueous Clearing System (MACS). MACS can render whole adult brains highly transparent within 2.5 days and is also applicable for other intact organs. Meanwhile, MACS possesses ideal compatibility with multiple probes, especially for lipophilic dyes. MACS achieves 3D imaging of the intact neural structures labeled by various techniques. Combining MACS with DiI labeling, MACS allows reconstruction of the detailed vascular structures of various organs and generates 3D pathology of glomeruli tufts in healthy and diabetic kidneys. Therefore, MACS provides a useful method for 3D mapping of intact tissues and is expected to facilitate morphological, physiological, and pathological studies of various organs.
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Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Tingting Yu
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Yusha Li
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Jianyi Xu
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Yisong Qi
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Yingtao Yao
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Yilin Ma
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Peng Wan
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Zhilong Chen
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Xiangning Li
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Hui Gong
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Qingming Luo
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Dan Zhu
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
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39
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Asteriti S, Ricci V, Cangiano L. Two simple criteria to estimate an objective’s performance when imaging in non design tissue clearing solutions. J Neurosci Methods 2020; 332:108564. [DOI: 10.1016/j.jneumeth.2019.108564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 01/12/2023]
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40
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Matryba P, Sosnowska A, Wolny A, Bozycki L, Greig A, Grzybowski J, Stefaniuk M, Nowis D, Gołąb J. Systematic Evaluation of Chemically Distinct Tissue Optical Clearing Techniques in Murine Lymph Nodes. THE JOURNAL OF IMMUNOLOGY 2020; 204:1395-1407. [PMID: 31953352 DOI: 10.4049/jimmunol.1900847] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
Activation of adaptive immunity is a complex process coordinated at multiple levels in both time and the three-dimensional context of reactive lymph nodes (LNs). Although microscopy-based visualization of its spatiotemporal dynamics unravels complexities of developing immune response, such approach is highly limited by light-obstructing nature of tissue components. Recently, tissue optical clearing (TOC) techniques were established to bypass this obstacle and now allow to image and quantify the entire murine organs with cellular resolution. However, the spectrum of TOC is represented by wide variety of chemically distinct methods, each having certain advantages and disadvantages that were unsatisfactorily compared for suitability to LNs clearing. In this study, we have systematically tested 13 typical TOC techniques and assessed their impact on a number of critical factors such as LN transparency, imaging depth, change in size, compatibility with proteinaceous fluorophores, immunostaining, H&E staining, and light-sheet fluorescence microscopy. Based on the detailed data specific to TOC process of murine LNs, we provide a reliable reference for most suitable methods in an application-dependent manner.
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Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; .,Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Anna Sosnowska
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Artur Wolny
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Lukasz Bozycki
- Laboratory of Biochemistry of Lipids, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Alan Greig
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1 6DE, United Kingdom
| | - Jakub Grzybowski
- Department of Pathology, Medical University of Warsaw, 02-004 Warsaw, Poland
| | - Marzena Stefaniuk
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Dominika Nowis
- Department of Genomic Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland; and.,Laboratory of Experimental Medicine, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland;
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41
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Porter DDL, Morton PD. Clearing techniques for visualizing the nervous system in development, injury, and disease. J Neurosci Methods 2020; 334:108594. [PMID: 31945400 PMCID: PMC10674098 DOI: 10.1016/j.jneumeth.2020.108594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 01/05/2023]
Abstract
Modern clearing techniques enable high resolution visualization and 3D reconstruction of cell populations and their structural details throughout large biological samples, including intact organs and even entire organisms. In the past decade, these methods have become more tractable and are now being utilized to provide unforeseen insights into the complexities of the nervous system. While several iterations of optical clearing techniques have been developed, some are more suitable for specific applications than others depending on the type of specimen under study. Here we review findings from select studies utilizing clearing methods to visualize the developing, injured, and diseased nervous system within numerous model systems and species. We note trends and imbalances in the types of research questions being addressed with clearing methods across these fields in neuroscience. In addition, we discuss restrictions in applying optical clearing methods for postmortem tissue from humans and large animals and emphasize the lack in continuity between studies of these species. We aim for this review to serve as a key outline of available tissue clearing methods used successfully to address issues across neuronal development, injury/repair, and aging/disease.
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Affiliation(s)
- Demisha D L Porter
- Virginia Tech Graduate Program in Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Paul D Morton
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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42
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Becker K, Saghafi S, Pende M, Sabdyusheva-Litschauer I, Hahn CM, Foroughipour M, Jährling N, Dodt HU. Deconvolution of light sheet microscopy recordings. Sci Rep 2019; 9:17625. [PMID: 31772375 PMCID: PMC6879637 DOI: 10.1038/s41598-019-53875-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/04/2019] [Indexed: 02/01/2023] Open
Abstract
We developed a deconvolution software for light sheet microscopy that uses a theoretical point spread function, which we derived from a model of image formation in a light sheet microscope. We show that this approach provides excellent blur reduction and enhancement of fine image details for image stacks recorded with low magnification objectives of relatively high NA and high field numbers as e.g. 2x NA 0.14 FN 22, or 4x NA 0.28 FN 22. For these objectives, which are widely used in light sheet microscopy, sufficiently resolved point spread functions that are suitable for deconvolution are difficult to measure and the results obtained by common deconvolution software developed for confocal microscopy are usually poor. We demonstrate that the deconvolutions computed using our point spread function model are equivalent to those obtained using a measured point spread function for a 10x objective with NA 0.3 and for a 20x objective with NA 0.45.
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Affiliation(s)
- Klaus Becker
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria.
- Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| | | | - Marko Pende
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Inna Sabdyusheva-Litschauer
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Christian M Hahn
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Massih Foroughipour
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Nina Jährling
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Hans-Ulrich Dodt
- TU Wien, FKE, Dept. of Bioelectronics, Vienna, Austria
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
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