101
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Scardigli M, Pesce L, Brady N, Mazzamuto G, Gavryusev V, Silvestri L, Hof PR, Destrieux C, Costantini I, Pavone FS. Comparison of Different Tissue Clearing Methods for Three-Dimensional Reconstruction of Human Brain Cellular Anatomy Using Advanced Imaging Techniques. Front Neuroanat 2021; 15:752234. [PMID: 34867215 PMCID: PMC8632656 DOI: 10.3389/fnana.2021.752234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/13/2021] [Indexed: 01/29/2023] Open
Abstract
The combination of tissue clearing techniques with advanced optical microscopy facilitates the achievement of three-dimensional (3D) reconstruction of macroscopic specimens at high resolution. Whole mouse organs or even bodies have been analyzed, while the reconstruction of the human nervous system remains a challenge. Although several tissue protocols have been proposed, the high autofluorescence and variable post-mortem conditions of human specimens negatively affect the quality of the images in terms of achievable transparency and staining contrast. Moreover, homogeneous staining of high-density epitopes, such as neuronal nuclear antigen (NeuN), creates an additional challenge. Here, we evaluated different tissue transformation approaches to find the best solution to uniformly clear and label all neurons in the human cerebral cortex using anti-NeuN antibodies in combination with confocal and light-sheet fluorescence microscopy (LSFM). Finally, we performed mesoscopic high-resolution 3D reconstruction of the successfully clarified and stained samples with LSFM.
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Affiliation(s)
- Marina Scardigli
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Luca Pesce
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Niamh Brady
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
- Department of Biology, University of Florence, Florence, Italy
| | - Francesco S. Pavone
- European Laboratory for Non-linear Spectroscopy, University of Florence, Florence, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
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102
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Kingston R, Amin D, Misra S, Gross JM, Kuwajima T. Serotonin transporter-mediated molecular axis regulates regional retinal ganglion cell vulnerability and axon regeneration after nerve injury. PLoS Genet 2021; 17:e1009885. [PMID: 34735454 PMCID: PMC8594818 DOI: 10.1371/journal.pgen.1009885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/16/2021] [Accepted: 10/17/2021] [Indexed: 11/19/2022] Open
Abstract
Molecular insights into the selective vulnerability of retinal ganglion cells (RGCs) in optic neuropathies and after ocular trauma can lead to the development of novel therapeutic strategies aimed at preserving RGCs. However, little is known about what molecular contexts determine RGC susceptibility. In this study, we show the molecular mechanisms underlying the regional differential vulnerability of RGCs after optic nerve injury. We identified RGCs in the mouse peripheral ventrotemporal (VT) retina as the earliest population of RGCs susceptible to optic nerve injury. Mechanistically, the serotonin transporter (SERT) is upregulated on VT axons after injury. Utilizing SERT-deficient mice, loss of SERT attenuated VT RGC death and led to robust retinal axon regeneration. Integrin β3, a factor mediating SERT-induced functions in other systems, is also upregulated in RGCs and axons after injury, and loss of integrin β3 led to VT RGC protection and axon regeneration. Finally, RNA sequencing analyses revealed that loss of SERT significantly altered molecular signatures in the VT retina after optic nerve injury, including expression of the transmembrane protein, Gpnmb. GPNMB is rapidly downregulated in wild-type, but not SERT- or integrin β3-deficient VT RGCs after injury, and maintaining expression of GPNMB in RGCs via AAV2 viruses even after injury promoted VT RGC survival and axon regeneration. Taken together, our findings demonstrate that the SERT-integrin β3-GPNMB molecular axis mediates selective RGC vulnerability and axon regeneration after optic nerve injury.
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Affiliation(s)
- Rody Kingston
- Department of Ophthalmology, The Louis J. Fox Center for Vision Restoration, Pittsburgh, Pennsylvania, United States of America
| | - Dwarkesh Amin
- Department of Ophthalmology, The Louis J. Fox Center for Vision Restoration, Pittsburgh, Pennsylvania, United States of America
| | - Sneha Misra
- Department of Ophthalmology, The Louis J. Fox Center for Vision Restoration, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey M. Gross
- Department of Ophthalmology, The Louis J. Fox Center for Vision Restoration, Pittsburgh, Pennsylvania, United States of America
- Department of Developmental Biology, The McGowan Institute for Regenerative Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Takaaki Kuwajima
- Department of Ophthalmology, The Louis J. Fox Center for Vision Restoration, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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103
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Endo M, Maruoka H, Okabe S. Advanced Technologies for Local Neural Circuits in the Cerebral Cortex. Front Neuroanat 2021; 15:757499. [PMID: 34803616 PMCID: PMC8595196 DOI: 10.3389/fnana.2021.757499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The neural network in the brain can be viewed as an integrated system assembled from a large number of local neural circuits specialized for particular brain functions. Activities of neurons in local neural circuits are thought to be organized both spatially and temporally under the rules optimized for their roles in information processing. It is well perceived that different areas of the mammalian neocortex have specific cognitive functions and distinct computational properties. However, the organizational principles of the local neural circuits in different cortical regions have not yet been clarified. Therefore, new research principles and related neuro-technologies that enable efficient and precise recording of large-scale neuronal activities and synaptic connections are necessary. Innovative technologies for structural analysis, including tissue clearing and expansion microscopy, have enabled super resolution imaging of the neural circuits containing thousands of neurons at a single synapse resolution. The imaging resolution and volume achieved by new technologies are beyond the limits of conventional light or electron microscopic methods. Progress in genome editing and related technologies has made it possible to label and manipulate specific cell types and discriminate activities of multiple cell types. These technologies will provide a breakthrough for multiscale analysis of the structure and function of local neural circuits. This review summarizes the basic concepts and practical applications of the emerging technologies and new insight into local neural circuits obtained by these technologies.
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Affiliation(s)
| | | | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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104
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Novel fluorescent staining protocol for thick sections of human osteochondral tissues to facilitate correlation with MRI and CT. Skeletal Radiol 2021; 50:2281-2288. [PMID: 33638655 PMCID: PMC8390588 DOI: 10.1007/s00256-021-03746-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To describe a novel fluorescent histochemical protocol to visualize osteoclasts, vasculature, and nerves in thick sections of human osteochondral tissues and to demonstrate its feasibility for use in radiologic-pathologic research correlation studies. MATERIALS AND METHODS Consecutive patients scheduled for total knee arthroplasty surgeries underwent pre-operative MRI. CT imaging was performed after tissue collection, and abnormal osteochondral regions were sectioned to 1-2 mm in thickness and decalcified. Fluorescent labeling of osteoclasts was performed by staining for tartrate-resistant alkaline phosphatase activity with a fluorescent substrate. Vascular structure was visualized with fluorescently labeled lectin Ulex europaeus Agglutinin I (UEA-I). Immunostaining was performed for proteins including smooth muscle actin expressed in smooth muscle cells surrounding arterioles and fibrotic myofibroblasts, as well as for neuropeptide Y expressed in sympathetic nerves. Sections were then recut at 5 μm and stained with hematoxylin and eosin (H&E). RESULTS Edema-like and cyst-like regions identified with MRI and CT were easily located in fluorescent images and appeared to have increased osteoclast activity. Fibrotic regions were identified with thickened arterioles and increased myofibroblasts. Sympathetic nerve fibers traveled alongside arborizing blood vessels. Stained sections became transparent in a water-based refractive index-matched medium, permitting deep 3D visualization of the elaborate neurovascular network in bone. Sequential staining procedures were successfully performed with the same sections, demonstrating the potential to compare multiple cellular markers from the same locations. Routine H&E staining could be performed after the fluorescent staining protocol. CONCLUSION We have developed a multimodal framework to facilitate comparisons between histology and clinical MRI and CT.
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105
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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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106
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Kim H, Roh H, Kim H, Park JK. Droplet contact-based spheroid transfer technique as a multi-step assay tool for spheroid arrays. LAB ON A CHIP 2021; 21:4155-4165. [PMID: 34515264 DOI: 10.1039/d1lc00581b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hanging drop plates and low-attachment well plates are suitable for a high throughput screening model of a spheroid, because each drop (or well) contains a single spheroid and the spheroid environment are separated from each other. However, uniform spheroid culture on these devices is difficult as the liquid around the spheroid is replaced by direct pipetting, which can cause spheroid damage or loss, and well-to-well variation. If spheroids need to be cultured for a long time or analyzed through chemical treatment of immunostaining, it becomes a more considerable problem as the number of pipetting action increases. To address these problems, we have developed a poly(dimethylsiloxane) (PDMS)-based drop array chip (DAC) and a pillar array chip (PAC) that can apply a droplet contact-based spheroid transfer (DCST) technique to multiple reagent change or washing steps of spheroid assays. Unlike previous DCST devices, 3D-printed mold-based DCST devices showed stable spheroid manipulation during repetitive drop contact and facile transfer of spheroid arrays to the next reagent-loaded DAC while minimizing cross-contamination of the reagents. Compared to the conventional manual or machine pipetting method, the DCST method showed lower user-to-user variation and a higher spheroid retention rate in the manipulation of the spheroid array. Live/dead staining, hypoxia staining, and immunofluorescence staining of the spheroid array were performed on a breast cancer cell line, BT-474. Furthermore, four clearing methods were applied to the spheroid array as a proof of concept, and we have identified the applicability of the DCST platform as a pretreatment platform for whole spheroid analysis.
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Affiliation(s)
- Hwisoo Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hyewon Roh
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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107
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Sun Q, Tiziana P, Khan AUM, Heuveline V, Gretz N. A simple optical tissue clearing pipeline for 3D vasculature imaging of the mediastinal organs in mice. Int J Exp Pathol 2021; 102:218-227. [PMID: 34613652 DOI: 10.1111/iep.12399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/23/2021] [Accepted: 04/06/2021] [Indexed: 12/23/2022] Open
Abstract
Optical tissue clearing (OTC) methods render tissue transparent by matching the refractive index within a sample to enable three-dimensional (3D) imaging with advanced microscopes. The application of OTC method in mediastinal organs in mice remains poorly understand. Our aim was to establish a simple protocol pipeline for 3D imaging of the mediastinal organs in mice. Trachea, oesophagus, thymus and heart were harvested from mice after retrograde perfusion via the abdominal aorta. We combined and optimized antibody labelling of thick tissue samples, OTC with cheap and non-toxic solvent ethyl cinnamate (ECi), and light-sheet fluorescence microscopy (LSFM) or laser confocal fluorescence microscopy (LCFM) to visualize the vasculature of those tissues. A high degree of optical transparency of trachea, oesophagus, thymus and heart was achieved after ECi-based OTC. With anti-CD31 antibody immunofluorescence labelling before ECi-based OTC, the vasculature of these tissues with their natural morphology, location and organizational network was imaged using LSFM or LCFM. This simple protocol pipeline provides an easy-to-setup and comprehensive way to study the vasculature of mediastinal organs in 3D without any special equipment. We anticipate that it will facilitate diverse applications in biomedical research of thoracic diseases and even other organs.
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Affiliation(s)
- Quanchao Sun
- Department of Thoracic Surgery, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, China.,Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Institute for Medical Technology, University of Heidelberg and University of Applied Sciences, Mannheim, Germany
| | - Picascia Tiziana
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Institute for Medical Technology, University of Heidelberg and University of Applied Sciences, Mannheim, Germany
| | - Arif Ul Maula Khan
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Institute for Medical Technology, University of Heidelberg and University of Applied Sciences, Mannheim, Germany
| | - Vincent Heuveline
- Director of the Computing Centre, Heidelberg University, Heidelberg, Germany
| | - Norbert Gretz
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Institute for Medical Technology, University of Heidelberg and University of Applied Sciences, Mannheim, Germany
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108
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Mizukami Y, Takahashi Y, Shimizu K, Konishi S, Takakura Y, Nishikawa M. Calcium Peroxide-Containing Polydimethylsiloxane-Based Microwells for Inhibiting Cell Death in Spheroids through Improved Oxygen Supply. Biol Pharm Bull 2021; 44:1458-1464. [PMID: 34602554 DOI: 10.1248/bpb.b21-00269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Multicellular spheroids are expected to be used for in vivo-like tissue models and cell transplantation. Microwell devices are useful for the fabrication of multicellular spheroids to improve productivity and regulate their size. However, the high cell density in microwell devices leads to accelerated cell death. In this study, we developed O2-generating microwells by incorporating calcium peroxide (CaO2) into polydimethylsiloxane (PDMS)-based microwells. The CaO2-containing PDMS was shown to generate O2 for 3 d. Then, CaO2-containing PDMS was used to fabricate O2-generating microwells using a micro-molding technique. When human hepatocellular carcinoma (HepG2) spheroids were prepared using the conventional microwells, the O2 concentration in the culture medium reduced to approx. 67% of the cell-free level. In contrast, the O2-generating microwells maintained O2 at constant levels. The HepG2 spheroids prepared using the O2-generating microwells had a larger number of live cells than those prepared using the conventional microwells. In addition, the O2-generating microwells rescued hypoxia in the HepG2 spheroids and increased cell viability. Lastly, the O2-generating microwells were also useful for the preparation of multicellular spheroids of other cell types (i.e., MIN6, B16-BL6, and adipose-derived stem cells) with high cell viability. These results showed that the O2-generating microwells are useful for preparing multicellular spheroids with high cell viability.
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Affiliation(s)
- Yuya Mizukami
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Kazunori Shimizu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
| | - Satoshi Konishi
- Department of Mechanical Engineering, Graduate School of Science and Engineering, Ritsumeikan University
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Makiya Nishikawa
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University.,Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science
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109
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Zhang Z, Yao X, Yin X, Ding Z, Huang T, Huo Y, Ji R, Peng H, Guo ZV. Multi-Scale Light-Sheet Fluorescence Microscopy for Fast Whole Brain Imaging. Front Neuroanat 2021; 15:732464. [PMID: 34630049 PMCID: PMC8497830 DOI: 10.3389/fnana.2021.732464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/12/2021] [Indexed: 12/23/2022] Open
Abstract
Whole-brain imaging has become an increasingly important approach to investigate neural structures, such as somata distribution, dendritic morphology, and axonal projection patterns. Different structures require whole-brain imaging at different resolutions. Thus, it is highly desirable to perform whole-brain imaging at multiple scales. Imaging a complete mammalian brain at synaptic resolution is especially challenging, as it requires continuous imaging from days to weeks because of the large number of voxels to sample, and it is difficult to acquire a constant quality of imaging because of light scattering during in toto imaging. Here, we reveal that light-sheet microscopy has a unique advantage over wide-field microscopy in multi-scale imaging because of its decoupling of illumination and detection. Based on this observation, we have developed a multi-scale light-sheet microscope that combines tiling of light-sheet, automatic zooming, periodic sectioning, and tissue expansion to achieve a constant quality of brain-wide imaging from cellular (3 μm × 3 μm × 8 μm) to sub-micron (0.3 μm × 0.3 μm × 1 μm) spatial resolution rapidly (all within a few hours). We demonstrated the strength of the system by testing it using mouse brains prepared using different clearing approaches. We were able to track electrode tracks as well as axonal projections at sub-micron resolution to trace the full morphology of single medial prefrontal cortex (mPFC) neurons that have remarkable diversity in long-range projections.
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Affiliation(s)
- Zhouzhou Zhang
- School of Medicine, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiao Yao
- School of Medicine, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Xinxin Yin
- School of Medicine, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Zhangcan Ding
- SEU-Allen Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Tianyi Huang
- School of Medicine, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Yan Huo
- School of Medicine, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Runan Ji
- School of Medicine, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Hanchuan Peng
- SEU-Allen Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Allen Institute for Brain Science, Seattle, WA, United States
| | - Zengcai V Guo
- School of Medicine, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
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110
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Multicolor 3D Confocal Imaging of Thick Tissue Sections. Methods Mol Biol 2021; 2350:95-104. [PMID: 34331281 DOI: 10.1007/978-1-0716-1593-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
In multicellular organisms, most physiological and pathological processes involve an interplay between various cells and molecules that act both locally and systemically. To understand how these complex and dynamic processes occur in time and space, imaging techniques are key. Advances in tissue processing techniques and microscopy now allow us to probe these processes at a large scale and at the same time at a level of detail previously unachievable. Indeed, it is now possible to reliably quantify multiple protein expression levels at single-cell resolution in whole organs using three-dimensional fluorescence imaging techniques. Here we describe a method to prepare adult mouse bone tissue for multiplexed confocal imaging of thick tissue sections. Up to eight different fluorophores can be multiplexed using this technique and spectrally resolved using standard confocal microscopy. The optical clearing method described allows detection of these fluorophores up to a depth of >700 μm in the far-red. Although the method was initially developed for bone tissue imaging, we have successfully applied it to several other tissue types.
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111
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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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112
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Dwyer J, Ramirez MD, Katz PS, Karlstrom RO, Bergan J. Accelerated clearing and molecular labeling of biological tissues using magnetohydrodynamic force. Sci Rep 2021; 11:16462. [PMID: 34385489 PMCID: PMC8360944 DOI: 10.1038/s41598-021-95692-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 07/22/2021] [Indexed: 11/09/2022] Open
Abstract
Techniques used to clear biological tissue for fluorescence microscopy are essential to connect anatomical principles at levels ranging from subcellular to the whole animal. Here we report a simple and straightforward approach to efficiently render opaque tissue samples transparent and show that this approach can be modified to rapidly label intact tissue samples with antibodies for large volume fluorescence microscopy. This strategy applies a magnetohydrodynamic (MHD) force to accelerate the removal of lipids from tissue samples at least as large as an intact adult mouse brain. We also show that MHD force can be used to accelerate antibody penetration into tissue samples. This strategy complements a growing array of tools that enable high-resolution 3-dimensional anatomical analyses in intact tissues using fluorescence microscopy. MHD-accelerated clearing is simple, fast, reliable, inexpensive, provides good thermal regulation, and is compatible with existing strategies for high-quality fluorescence microscopy of intact tissues.
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Affiliation(s)
- Joseph Dwyer
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, USA
| | - Paul S Katz
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, USA.,Department of Biology, University of Massachusetts Amherst, Amherst, USA
| | - Rolf O Karlstrom
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, USA.,Department of Biology, University of Massachusetts Amherst, Amherst, USA
| | - Joseph Bergan
- Neuroscience and Behavior Graduate Program, University of Massachusetts Amherst, Amherst, USA. .,Department of Psychological and Brain Sciences, University of Massachusetts Amherst, Amherst, USA.
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113
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Application of a Tissue Clearing Method for the Analysis of Dopaminergic Axonal Projections. Methods Mol Biol 2021. [PMID: 34043200 DOI: 10.1007/978-1-0716-1495-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized with the progressive loss of dopaminergic (DA) neurons within the substantia nigra pars compacta (SNc). Quantitative analysis of neuronal loss including neuronal processes, axons and dendrites, would advance the understanding of the pathogenesis of PD. ScaleS, an aqueous tissue clearing method, provides stable tissue preservation while maintaining potent clearing capability, allowing quantitative three-dimensional (3D) imaging of biological tissues. In this chapter, we describe detailed procedures for 3D imaging of brain slice tissues with ScaleS technique. These include brain slice preparation, tissue clarification, chemical and immunohistochemical labeling (ChemScale and AbScale), and observation of labeled tissues using a confocal laser scanning microscope (CLSM).
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114
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Hofmann J, Keppler SJ. Tissue clearing and 3D imaging - putting immune cells into context. J Cell Sci 2021; 134:271108. [PMID: 34342351 DOI: 10.1242/jcs.258494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A better understanding of cell-cell and cell-niche interactions is crucial to comprehend the complexity of inflammatory or pathophysiological scenarios such as tissue damage during viral infections, the tumour microenvironment and neuroinflammation. Optical clearing and 3D volumetric imaging of large tissue pieces or whole organs is a rapidly developing methodology that holds great promise for the in-depth study of cells in their natural surroundings. These methods have mostly been applied to image structural components such as endothelial cells and neuronal architecture. Recent work now highlights the possibility of studying immune cells in detail within their respective immune niches. This Review summarizes recent developments in tissue clearing methods and 3D imaging, with a focus on the localization and quantification of immune cells. We first provide background to the optical challenges involved and their solutions before discussing published protocols for tissue clearing, the limitations of 3D imaging of immune cells and image analysis. Furthermore, we highlight possible applications for tissue clearing and propose future developments for the analysis of immune cells within homeostatic or inflammatory immune niches.
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Affiliation(s)
- Julian Hofmann
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, 81675 Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University Munich, 81675 Munich, Germany
| | - Selina J Keppler
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, 81675 Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University Munich, 81675 Munich, Germany
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115
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Basic principles of hydrogel-based tissue transformation technologies and their applications. Cell 2021; 184:4115-4136. [PMID: 34358468 DOI: 10.1016/j.cell.2021.07.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/06/2021] [Accepted: 07/06/2021] [Indexed: 12/28/2022]
Abstract
Emerging tissue transformation technologies provide an unprecedented opportunity to investigate system-level molecular and anatomical features in situ. Hydrogel-based methods engineer physicochemical tissue properties to render intact organs optically transparent and size and shape adjustable while preserving biomolecules at their physiological locations. When combined with advanced molecular tools, labeling, and imaging techniques, tissue transformation enables three-dimensional (3D) mapping of molecules, cells, and their interrelationships at increasing speeds and resolutions. In this review, we discuss the basic engineering principles of tissue transformation and labeling techniques as well as their broad applications, current challenges, and future potential.
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116
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Bose SK, White BM, Kashyap MV, Dave A, De Bie FR, Li H, Singh K, Menon P, Wang T, Teerdhala S, Swaminathan V, Hartman HA, Jayachandran S, Chandrasekaran P, Musunuru K, Jain R, Frank DB, Zoltick P, Peranteau WH. In utero adenine base editing corrects multi-organ pathology in a lethal lysosomal storage disease. Nat Commun 2021; 12:4291. [PMID: 34257302 PMCID: PMC8277817 DOI: 10.1038/s41467-021-24443-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 06/09/2021] [Indexed: 01/19/2023] Open
Abstract
In utero base editing has the potential to correct disease-causing mutations before the onset of pathology. Mucopolysaccharidosis type I (MPS-IH, Hurler syndrome) is a lysosomal storage disease (LSD) affecting multiple organs, often leading to early postnatal cardiopulmonary demise. We assessed in utero adeno-associated virus serotype 9 (AAV9) delivery of an adenine base editor (ABE) targeting the Idua G→A (W392X) mutation in the MPS-IH mouse, corresponding to the common IDUA G→A (W402X) mutation in MPS-IH patients. Here we show efficient long-term W392X correction in hepatocytes and cardiomyocytes and low-level editing in the brain. In utero editing was associated with improved survival and amelioration of metabolic, musculoskeletal, and cardiac disease. This proof-of-concept study demonstrates the possibility of efficiently performing therapeutic base editing in multiple organs before birth via a clinically relevant delivery mechanism, highlighting the potential of this approach for MPS-IH and other genetic diseases.
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Affiliation(s)
- Sourav K Bose
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brandon M White
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Meghana V Kashyap
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Apeksha Dave
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Felix R De Bie
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Haiying Li
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kshitiz Singh
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Pallavi Menon
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tiankun Wang
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiva Teerdhala
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Vishal Swaminathan
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Heather A Hartman
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sowmya Jayachandran
- Division of Pediatric Cardiology, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Center for Pulmonary Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Prashant Chandrasekaran
- Division of Pediatric Cardiology, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Center for Pulmonary Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kiran Musunuru
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Rajan Jain
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - David B Frank
- Division of Pediatric Cardiology, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Center for Pulmonary Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Philip Zoltick
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - William H Peranteau
- Center for Fetal Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Division of General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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117
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Marquez J, Mann N, Arana K, Deniz E, Ji W, Konstantino M, Mis EK, Deshpande C, Jeffries L, McGlynn J, Hugo H, Widmeier E, Konrad M, Tasic V, Morotti R, Baptista J, Ellard S, Lakhani SA, Hildebrandt F, Khokha MK. DLG5 variants are associated with multiple congenital anomalies including ciliopathy phenotypes. J Med Genet 2021; 58:453-464. [PMID: 32631816 PMCID: PMC7785698 DOI: 10.1136/jmedgenet-2019-106805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/01/2020] [Accepted: 05/25/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Cilia are dynamic cellular extensions that generate and sense signals to orchestrate proper development and tissue homeostasis. They rely on the underlying polarisation of cells to participate in signalling. Cilia dysfunction is a well-known cause of several diseases that affect multiple organ systems including the kidneys, brain, heart, respiratory tract, skeleton and retina. METHODS Among individuals from four unrelated families, we identified variants in discs large 5 (DLG5) that manifested in a variety of pathologies. In our proband, we also examined patient tissues. We depleted dlg5 in Xenopus tropicalis frog embryos to generate a loss-of-function model. Finally, we tested the pathogenicity of DLG5 patient variants through rescue experiments in the frog model. RESULTS Patients with variants of DLG5 were found to have a variety of phenotypes including cystic kidneys, nephrotic syndrome, hydrocephalus, limb abnormalities, congenital heart disease and craniofacial malformations. We also observed a loss of cilia in cystic kidney tissue of our proband. Knockdown of dlg5 in Xenopus embryos recapitulated many of these phenotypes and resulted in a loss of cilia in multiple tissues. Unlike introduction of wildtype DLG5 in frog embryos depleted of dlg5, introduction of DLG5 patient variants was largely ineffective in restoring proper ciliation and tissue morphology in the kidney and brain suggesting that the variants were indeed detrimental to function. CONCLUSION These findings in both patient tissues and Xenopus shed light on how mutations in DLG5 may lead to tissue-specific manifestations of disease. DLG5 is essential for cilia and many of the patient phenotypes are in the ciliopathy spectrum.
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Affiliation(s)
- Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nina Mann
- Division of Nephrology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kathya Arana
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Engin Deniz
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emily K Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Julie McGlynn
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hannah Hugo
- Division of Nephrology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Division of Nephrology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Martin Konrad
- Department of General Pediatrics, University Hospital Münster, Münster, Germany
| | - Velibor Tasic
- Department of Pediatric Nephrology, University Children's Hospital, Skopje, North Macedonia
| | - Raffaella Morotti
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Julia Baptista
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
- Institute of Biomedical & Clinical Science, College of Medicine and Health, Exeter, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
- Institute of Biomedical & Clinical Science, College of Medicine and Health, Exeter, UK
| | - Saquib Ali Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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118
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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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119
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Lin LE, Miao K, Qian C, Wei L. High spatial-resolution imaging of label-free in vivo protein aggregates by VISTA. Analyst 2021; 146:4135-4145. [PMID: 33949430 PMCID: PMC8238904 DOI: 10.1039/d1an00060h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Amyloid aggregation, formed by aberrant proteins, is a pathological hallmark for neurodegenerative diseases, including Alzheimer's disease and Huntington's disease. High-resolution holistic mapping of the fine structures from these aggregates should facilitate our understanding of their pathological roles. Here, we achieved label-free high-resolution imaging of the polyQ and the amyloid-beta (Aβ) aggregates in cells and tissues utilizing a sample-expansion stimulated Raman strategy. We further focused on characterizing the Aβ plaques in 5XFAD mouse brain tissues. 3D volumetric imaging enabled visualization of the whole plaques, resolving both the fine protein filaments and the surrounding components. Coupling our expanded label-free Raman imaging with machine learning, we obtained specific segmentation of aggregate cores, peripheral filaments together with cell nuclei and blood vessels by pre-trained convolutional neural network models. Combining with 2-channel fluorescence imaging, we achieved a 6-color holistic view of the same sample. This ability for precise and multiplex high-resolution imaging of the protein aggregates and their micro-environment without the requirement of labeling would open new biomedical applications.
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Affiliation(s)
- Li-En Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
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Mano T, Murata K, Kon K, Shimizu C, Ono H, Shi S, Yamada RG, Miyamichi K, Susaki EA, Touhara K, Ueda HR. CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping. CELL REPORTS METHODS 2021; 1:100038. [PMID: 35475238 PMCID: PMC9017177 DOI: 10.1016/j.crmeth.2021.100038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/17/2021] [Accepted: 05/20/2021] [Indexed: 01/18/2023]
Abstract
Recent advancements in tissue clearing technologies have offered unparalleled opportunities for researchers to explore the whole mouse brain at cellular resolution. With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets. To that end, here we present CUBIC-Cloud, a cloud-based framework to quantify, visualize, and integrate mouse brain data. CUBIC-Cloud is a fully automated system where users can upload their whole-brain data, run analyses, and publish the results. We demonstrate the generality of CUBIC-Cloud by a variety of applications. First, we investigated the brain-wide distribution of five cell types. Second, we quantified Aβ plaque deposition in Alzheimer's disease model mouse brains. Third, we reconstructed a neuronal activity profile under LPS-induced inflammation by c-Fos immunostaining. Last, we show brain-wide connectivity mapping by pseudotyped rabies virus. Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.
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Affiliation(s)
- Tomoyuki Mano
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Ken Murata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuhiro Kon
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Hiroaki Ono
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shoi Shi
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Kazunari Miyamichi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Etsuo A. Susaki
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroki R. Ueda
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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Qian C, Miao K, Lin LE, Chen X, Du J, Wei L. Super-resolution label-free volumetric vibrational imaging. Nat Commun 2021; 12:3648. [PMID: 34131146 PMCID: PMC8206358 DOI: 10.1038/s41467-021-23951-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/07/2021] [Indexed: 11/22/2022] Open
Abstract
Innovations in high-resolution optical imaging have allowed visualization of nanoscale biological structures and connections. However, super-resolution fluorescence techniques, including both optics-oriented and sample-expansion based, are limited in quantification and throughput especially in tissues from photobleaching or quenching of the fluorophores, and low-efficiency or non-uniform delivery of the probes. Here, we report a general sample-expansion vibrational imaging strategy, termed VISTA, for scalable label-free high-resolution interrogations of protein-rich biological structures with resolution down to 78 nm. VISTA achieves decent three-dimensional image quality through optimal retention of endogenous proteins, isotropic sample expansion, and deprivation of scattering lipids. Free from probe-labeling associated issues, VISTA offers unbiased and high-throughput tissue investigations. With correlative VISTA and immunofluorescence, we further validated the imaging specificity of VISTA and trained an image-segmentation model for label-free multi-component and volumetric prediction of nucleus, blood vessels, neuronal cells and dendrites in complex mouse brain tissues. VISTA could hence open new avenues for versatile biomedical studies.
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Affiliation(s)
- Chenxi Qian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Li-En Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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122
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Susaki EA, Takasato M. Perspective: Extending the Utility of Three-Dimensional Organoids by Tissue Clearing Technologies. Front Cell Dev Biol 2021; 9:679226. [PMID: 34195197 PMCID: PMC8236633 DOI: 10.3389/fcell.2021.679226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 01/06/2023] Open
Abstract
An organoid, a self-organizing organ-like tissue developed from stem cells, can exhibit a miniaturized three-dimensional (3D) structure and part of the physiological functions of the original organ. Due to the reproducibility of tissue complexity and ease of handling, organoids have replaced real organs and animals for a variety of uses, such as investigations of the mechanisms of organogenesis and disease onset, and screening of drug effects and/or toxicity. The recent advent of tissue clearing and 3D imaging techniques have great potential contributions to organoid studies by allowing the collection and analysis of 3D images of whole organoids with a reasonable throughput and thus can expand the means of examining the 3D architecture, cellular components, and variability among organoids. Genetic and histological cell-labeling methods, together with organoid clearing, also allow visualization of critical structures and cellular components within organoids. The collected 3D data may enable image analysis to quantitatively assess structures within organoids and sensitively/effectively detect abnormalities caused by perturbations. These capabilities of tissue/organoid clearing and 3D imaging techniques not only extend the utility of organoids in basic biology but can also be applied for quality control of clinical organoid production and large-scale drug screening.
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Affiliation(s)
- Etsuo A. Susaki
- Department of Biochemistry and Systems Biomedicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Minoru Takasato
- Laboratory for Human Organogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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Yu T, Li D, Zhu D. Tissue Optical Clearing for Biomedical Imaging: From In Vitro to In Vivo. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 3233:217-255. [PMID: 34053030 DOI: 10.1007/978-981-15-7627-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tissue optical clearing technique provides a prospective solution for the application of advanced optical methods in life sciences. This chapter firstly gives a brief introduction to mechanisms of tissue optical clearing techniques, from the physical mechanism to chemical mechanism, which is the most important foundation to develop tissue optical clearing methods. During the past years, in vitro and in vivo tissue optical clearing methods were developed. In vitro tissue optical clearing techniques, including the solvent-based clearing methods and the hydrophilic reagents-based clearing methods, combined with labeling technique and advanced microscopy, can be applied to image 3D microstructure of tissue blocks or whole organs such as brain and spinal cord with high resolution. In vivo skin or skull optical clearing, promise various optical imaging techniques to detect cutaneous or cortical cell and vascular structure and function without surgical window.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China. .,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Weiss KR, Voigt FF, Shepherd DP, Huisken J. Tutorial: practical considerations for tissue clearing and imaging. Nat Protoc 2021; 16:2732-2748. [PMID: 34021294 PMCID: PMC10542857 DOI: 10.1038/s41596-021-00502-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/18/2021] [Indexed: 02/06/2023]
Abstract
Tissue clearing has become a powerful technique for studying anatomy and morphology at scales ranging from entire organisms to subcellular features. With the recent proliferation of tissue-clearing methods and imaging options, it can be challenging to determine the best clearing protocol for a particular tissue and experimental question. The fact that so many clearing protocols exist suggests there is no one-size-fits-all approach to tissue clearing and imaging. Even in cases where a basic level of clearing has been achieved, there are many factors to consider, including signal retention, staining (labeling), uniformity of transparency, image acquisition and analysis. Despite reviews citing features of clearing protocols, it is often unknown a priori whether a protocol will work for a given experiment, and thus some optimization is required by the end user. In addition, the capabilities of available imaging setups often dictate how the sample needs to be prepared. After imaging, careful evaluation of volumetric image data is required for each combination of clearing protocol, tissue type, biological marker, imaging modality and biological question. Rather than providing a direct comparison of the many clearing methods and applications available, in this tutorial we address common pitfalls and provide guidelines for designing, optimizing and imaging in a successful tissue-clearing experiment with a focus on light-sheet fluorescence microscopy (LSFM).
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Affiliation(s)
- Kurt R Weiss
- Morgridge Institute for Research, Madison, WI, USA
| | - Fabian F Voigt
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich & ETH Zurich, Zurich, Switzerland
| | - Douglas P Shepherd
- Department of Physics, Arizona State University, Tempe, AZ, USA
- Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Jan Huisken
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA.
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Chou SM, Li KX, Huang MY, Chen C, Lin King YH, Li GG, Zhou W, Teo CF, Jan YN, Jan LY, Yang SB. Kv1.1 channels regulate early postnatal neurogenesis in mouse hippocampus via the TrkB signaling pathway. eLife 2021; 10:e58779. [PMID: 34018923 PMCID: PMC8208815 DOI: 10.7554/elife.58779] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
In the postnatal brain, neurogenesis occurs only within a few regions, such as the hippocampal sub-granular zone (SGZ). Postnatal neurogenesis is tightly regulated by factors that balance stem cell renewal with differentiation, and it gives rise to neurons that participate in learning and memory formation. The Kv1.1 channel, a voltage-gated potassium channel, was previously shown to suppress postnatal neurogenesis in the SGZ in a cell-autonomous manner. In this study, we have clarified the physiological and molecular mechanisms underlying Kv1.1-dependent postnatal neurogenesis. First, we discovered that the membrane potential of neural progenitor cells is highly dynamic during development. We further established a multinomial logistic regression model for cell-type classification based on the biophysical characteristics and corresponding cell markers. We found that the loss of Kv1.1 channel activity causes significant depolarization of type 2b neural progenitor cells. This depolarization is associated with increased tropomyosin receptor kinase B (TrkB) signaling and proliferation of neural progenitor cells; suppressing TrkB signaling reduces the extent of postnatal neurogenesis. Thus, our study defines the role of the Kv1.1 potassium channel in regulating the proliferation of postnatal neural progenitor cells in mouse hippocampus.
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Affiliation(s)
- Shu-Min Chou
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Ke-Xin Li
- Howard Hughes Medical Institute, Departments of Physiology, Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | | | - Chao Chen
- Howard Hughes Medical Institute, Departments of Physiology, Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Yuan-Hung Lin King
- Howard Hughes Medical Institute, Departments of Physiology, Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Neuroscience Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | | | - Wei Zhou
- Department of Anesthesia and Perioperative Care, University of California, San FranciscoSan FranciscoUnited States
| | - Chin Fen Teo
- Howard Hughes Medical Institute, Departments of Physiology, Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Yuh Nung Jan
- Howard Hughes Medical Institute, Departments of Physiology, Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Lily Yeh Jan
- Howard Hughes Medical Institute, Departments of Physiology, Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Shi-Bing Yang
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Neuroscience Program of Academia Sinica, Academia SinicaTaipeiTaiwan
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126
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Schedin-Weiss S, Nilsson P, Sandebring-Matton A, Axenhus M, Sekiguchi M, Saito T, Winblad B, Saido T, Tjernberg LO. Proteomics Time-Course Study of App Knock-In Mice Reveals Novel Presymptomatic Aβ42-Induced Pathways to Alzheimer's Disease Pathology. J Alzheimers Dis 2021; 75:321-335. [PMID: 32280097 PMCID: PMC7902969 DOI: 10.3233/jad-200028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background: The 42 amino acids long amyloid-β peptide, Aβ42, may initiate a cascade of events leading to the severe neurodegeneration observed in Alzheimer’s disease (AD) brain. However, the underlying molecular mechanisms remain to be established. Objective: To find early Aβ42-induced AD related mechanisms, we performed a brain proteomics time-course study on a novel App knock-in AD mouse model, AppNL-F, expressing high levels of Aβ42 without AβPP overexpression artifacts. Methods: Hippocampus and cortex were analyzed separately by using 18O-labelling mass spectrometry to reveal alterations in protein levels. Pathway analysis of proteomics data was used to identify altered biological functions. Immunohistochemistry was used to further investigate a significant key regulatory protein. Results: Around 100 proteins were differently expressed in AppNL-F mice at each time point (3, 6, 9, and 18 months of age) as compared to wild type mice. Strikingly, already at 3 months of age—long before Aβ plaque development and memory impairment—several pathways, including long-term potentiation and synaptic plasticity, were downregulated, and neuritogenesis was increased. Huntingtin (HTT) was identified as an upstream regulator, i.e., a key protein affecting the levels of several proteins. Increased levels of HTT in hippocampus of AppNL-F mice was supported by immunofluorescence microscopy. Conclusion: Notably, the proteome was significantly altered already at 3 months of age, 6 months before the development of plaques. Differentially expressed proteins varied over time, indicating that increased Aβ42 levels initiate a cascade of events that eventually manifests in amyloid depositions, inflammation, and decline in memory.
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Affiliation(s)
- Sophia Schedin-Weiss
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Per Nilsson
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Anna Sandebring-Matton
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden.,Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Michael Axenhus
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Misaki Sekiguchi
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan.,Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Science, Nagoya, Japan
| | - Bengt Winblad
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Takaomi Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
| | - Lars O Tjernberg
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
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127
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Chen Y, Li X, Zhang D, Wang C, Feng R, Li X, Wen Y, Xu H, Zhang XS, Yang X, Chen Y, Feng Y, Zhou B, Chen BC, Lei K, Cai S, Jia JM, Gao L. A Versatile Tiling Light Sheet Microscope for Imaging of Cleared Tissues. Cell Rep 2021; 33:108349. [PMID: 33147464 DOI: 10.1016/j.celrep.2020.108349] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/13/2020] [Accepted: 10/13/2020] [Indexed: 01/14/2023] Open
Abstract
We present a tiling light sheet microscope compatible with all tissue clearing methods for rapid multicolor 3D imaging of cleared tissues with micron-scale (4 × 4 × 10 μm3) to submicron-scale (0.3 × 0.3 × 1 μm3) spatial resolution. The resolving ability is improved to sub-100 nm (70 × 70 × 200 nm3) via tissue expansion. The microscope uses tiling light sheets to achieve higher spatial resolution and better optical sectioning ability than conventional light sheet microscopes. The illumination light is phase modulated to adjust the position and intensity profile of the light sheet based on the desired spatial resolution and imaging speed and to keep the microscope aligned. The ability of the microscope to align via phase modulation alone also ensures its accuracy for multicolor 3D imaging and makes the microscope reliable and easy to operate. Here we describe the working principle and design of the microscope. We demonstrate its utility by imaging various cleared tissues.
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Affiliation(s)
- Yanlu Chen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Xiaoliang Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Dongdong Zhang
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Chunhui Wang
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Ruili Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Xuzhao Li
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Yao Wen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Hao Xu
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Xinyi Shirley Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yongyi Chen
- Department of Clinical laboratory, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310000, China
| | - Yi Feng
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Bo Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kai Lei
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Shang Cai
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.
| | - Jie-Min Jia
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.
| | - Liang Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.
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128
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Kolesová H, Olejníčková V, Kvasilová A, Gregorovičová M, Sedmera D. Tissue clearing and imaging methods for cardiovascular development. iScience 2021; 24:102387. [PMID: 33981974 PMCID: PMC8086021 DOI: 10.1016/j.isci.2021.102387] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tissue imaging in 3D using visible light is limited and various clearing techniques were developed to increase imaging depth, but none provides universal solution for all tissues at all developmental stages. In this review, we focus on different tissue clearing methods for 3D imaging of heart and vasculature, based on chemical composition (solvent-based, simple immersion, hyperhydration, and hydrogel embedding techniques). We discuss in detail compatibility of various tissue clearing techniques with visualization methods: fluorescence preservation, immunohistochemistry, nuclear staining, and fluorescent dyes vascular perfusion. We also discuss myocardium visualization using autofluorescence, tissue shrinking, and expansion. Then we overview imaging methods used to study cardiovascular system and live imaging. We discuss heart and vessels segmentation methods and image analysis. The review covers the whole process of cardiovascular system 3D imaging, starting from tissue clearing and its compatibility with various visualization methods to the types of imaging methods and resulting image analysis.
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Affiliation(s)
- Hana Kolesová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - Veronika Olejníčková
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - Alena Kvasilová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martina Gregorovičová
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
| | - David Sedmera
- Institute of Anatomy, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Physiology, Czech Academy of Science, Prague, Czech Republic
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129
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Nowzari F, Wang H, Khoradmehr A, Baghban M, Baghban N, Arandian A, Muhaddesi M, Nabipour I, Zibaii MI, Najarasl M, Taheri P, Latifi H, Tamadon A. Three-Dimensional Imaging in Stem Cell-Based Researches. Front Vet Sci 2021; 8:657525. [PMID: 33937378 PMCID: PMC8079735 DOI: 10.3389/fvets.2021.657525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/19/2021] [Indexed: 12/14/2022] Open
Abstract
Stem cells have an important role in regenerative therapies, developmental biology studies and drug screening. Basic and translational research in stem cell technology needs more detailed imaging techniques. The possibility of cell-based therapeutic strategies has been validated in the stem cell field over recent years, a more detailed characterization of the properties of stem cells is needed for connectomics of large assemblies and structural analyses of these cells. The aim of stem cell imaging is the characterization of differentiation state, cellular function, purity and cell location. Recent progress in stem cell imaging field has included ultrasound-based technique to study living stem cells and florescence microscopy-based technique to investigate stem cell three-dimensional (3D) structures. Here, we summarized the fundamental characteristics of stem cells via 3D imaging methods and also discussed the emerging literatures on 3D imaging in stem cell research and the applications of both classical 2D imaging techniques and 3D methods on stem cells biology.
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Affiliation(s)
- Fariborz Nowzari
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Huimei Wang
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mandana Baghban
- Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Baghban
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Alireza Arandian
- Laser and Plasma Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Mahdi Muhaddesi
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohammad I. Zibaii
- Laser and Plasma Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Mostafa Najarasl
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Payam Taheri
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Hamid Latifi
- Laser and Plasma Research Institute, Shahid Beheshti University, Tehran, Iran
- Department of Physics, Shahid Beheshti University, Tehran, Iran
| | - Amin Tamadon
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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130
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Lee K, Lai HM, Soerensen MH, Hui ES, Ma VW, Cho WC, Ho Y, Chang RC. Optimised tissue clearing minimises distortion and destruction during tissue delipidation. Neuropathol Appl Neurobiol 2021; 47:441-453. [PMID: 33107057 PMCID: PMC8048831 DOI: 10.1111/nan.12673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/04/2020] [Accepted: 10/15/2020] [Indexed: 01/24/2023]
Abstract
AIMS A variety of tissue clearing techniques have been developed to render intact tissue transparent. For thicker samples, additional partial tissue delipidation is required before immersion into the final refractive index (RI)-matching solution, which alone is often inadequate to achieve full tissue transparency. However, it is difficult to determine a sufficient degree of tissue delipidation, excess of which can result in tissue distortion and protein loss. Here, we aim to develop a clearing strategy that allows better monitoring and more precise determination of delipidation progress. METHODS We combined the detergent sodium dodecyl sulphate (SDS) with OPTIClear, a RI-matching solution, to form a strategy termed Accurate delipidation with Optimal Clearing (Accu-OptiClearing). Accu-OptiClearing allows for a better preview of the final tissue transparency achieved when immersed in OPTIClear alone just before imaging. We assessed for the changes in clearing rate, protein loss, degree of tissue distortion, and preservation of antigens. RESULTS Partial delipidation using Accu-OptiClearing accelerated tissue clearing and better preserved tissue structure and antigens than delipidation with SDS alone. Despite achieving similar transparency in the final OPTIClear solution, more lipids were retained in samples cleared with Accu-OptiClearing compared to SDS. CONCLUSIONS Combining the RI-matching solution OPTIClear with detergents, Accu-OptiClearing, can avoid excessive delipidation, leading to accelerated tissue clearing, less tissue damage and better preserved antigens.
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Affiliation(s)
- Krit Lee
- Laboratory of Neurodegenerative DiseasesSchool of Biomedical SciencesLKS Faculty of MedicineThe University of Hong KongPokfulam, Hong Kong SARChina
| | - Hei Ming Lai
- School of Biomedical SciencesLKS Faculty of MedicineThe University of Hong KongPokfulam, Hong Kong SARChina
- Department of PsychiatryFaculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Maja Hoejvang Soerensen
- Laboratory of Neurodegenerative DiseasesSchool of Biomedical SciencesLKS Faculty of MedicineThe University of Hong KongPokfulam, Hong Kong SARChina
| | - Edward Sai‐Kam Hui
- Department of Diagnostic RadiologyLKS Faculty of MedicineThe University of Hong KongPokfulam, Hong Kong SARChina
| | - Victor Wan‐San Ma
- Department of Clinical OncologyQueen Elizabeth HospitalKowloon, Hong Kong SARChina
| | | | - Yuen‐Shan Ho
- School of NursingThe Hong Kong Polytechnic UniversityHung Hom, Hong Kong SARChina
| | - Raymond Chuen‐Chung Chang
- Laboratory of Neurodegenerative DiseasesSchool of Biomedical SciencesLKS Faculty of MedicineThe University of Hong KongPokfulam, Hong Kong SARChina
- State Key Laboratory of Brain and Cognitive SciencesThe University of Hong KongPokfulam, Hong Kong SARChina
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Abstract
Advanced optical methods combined with various probes pave the way toward molecular imaging within living cells. However, major challenges are associated with the need to enhance the imaging resolution even further to the subcellular level for the imaging of larger tissues, as well as for in vivo studies. High scattering and absorption of opaque tissues limit the penetration of light into deep tissues and thus the optical imaging depth. Tissue optical clearing technique provides an innovative way to perform deep-tissue imaging. Recently, various optical clearing methods have been developed, which provide tissue clearing based on similar physical principles via different chemical approaches. Here, we introduce the mechanisms of the current clearing methods from fundamental physical and chemical perspectives, including the main physical principle, refractive index matching via various chemical approaches, such as dissociation of collagen, delipidation, decalcification, dehydration, and hyperhydration, to reduce scattering, as well as decolorization to reduce absorption.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - 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
| | - 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
| | - 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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Ogawa T, Matsumura Y. Revealing 3D structure of gluten in wheat dough by optical clearing imaging. Nat Commun 2021; 12:1708. [PMID: 33731714 PMCID: PMC7969737 DOI: 10.1038/s41467-021-22019-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/19/2021] [Indexed: 11/09/2022] Open
Abstract
Gluten, which makes up 85% of endosperm wheat protein, is considered a crucial quality determinant of wheat-based food products. During wheat dough manufacture, the molecular packing of gluten causes formation of large structures that exceed the millimetre scale. However, due to lack of imaging techniques for complex systems composed of giant macromolecules, the entire gluten structure remains unknown. Here, we develop an optical clearing reagent (termed SoROCS) that makes wheat-based products transparent. Combined with two-photon microscopy, we image the three-dimensional (3D) structure of gluten at the size in the millimetre scale and at submicron resolution. Further, we demonstrate how the 3D structure of gluten dramatically changes from a honeycomb-shaped network to sparse large clumps in wheat noodles, depending on the salt added during dough making, thereby reducing stress when compressing the noodle. Moreover, we show that SoROCS can be used for noodle imaging using confocal laser scanning microscopy.
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Affiliation(s)
- Takenobu Ogawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
| | - Yasuki Matsumura
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan.
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133
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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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134
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Kronschläger MT, Siegert ASM, Resch FJ, Rajendran PS, Khakh BS, Sandkühler J. Lamina-specific properties of spinal astrocytes. Glia 2021; 69:1749-1766. [PMID: 33694249 PMCID: PMC8252791 DOI: 10.1002/glia.23990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/19/2022]
Abstract
Astrocytes are indispensable for proper neuronal functioning. Given the diverse needs of neuronal circuits and the variety of tasks astrocytes perform, the perceived homogeneous nature of astrocytes has been questioned. In the spinal dorsal horn, complex neuronal circuitries regulate the integration of sensory information of different modalities. The dorsal horn is organized in a distinct laminar manner based on termination patterns of high‐ and low‐threshold afferent fibers and neuronal properties. Neurons in laminae I (L1) and II (L2) integrate potentially painful, nociceptive information, whereas neurons in lamina III (L3) and deeper laminae integrate innocuous, tactile information from the periphery. Sensory information is also integrated by an uncharacterized network of astrocytes. How these lamina‐specific characteristics of neuronal circuits of the dorsal horn are of functional importance for properties of astrocytes is currently unknown. We addressed if astrocytes in L1, L2, and L3 of the upper dorsal horn of mice are differentially equipped for the needs of neuronal circuits that process sensory information of different modalities. We found that astrocytes in L1 and L2 were characterized by a higher density, higher expression of GFAP, Cx43, and GLAST and a faster coupling speed than astrocytes located in L3. L1 astrocytes were more responsive to Kir4.1 blockade and had higher levels of AQP4 compared to L3 astrocytes. In contrast, basic membrane properties, network formation, and somatic intracellular calcium signaling were similar in L1–L3 astrocytes. Our data indicate that the properties of spinal astrocytes are fine‐tuned for the integration of nociceptive versus tactile information.
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Affiliation(s)
- Mira T Kronschläger
- Department of Neurophysiology, Center for Brain Research, Medical University of Vienna, Vienna, Austria.,Department of Physiology, David Geffen Schoof of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Anna S M Siegert
- Department of Neurophysiology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Felix J Resch
- Department of Neurophysiology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Pradeep S Rajendran
- UCLA Cardiac Arrhythmia Center, Neurocardiology Research Program of Excellence, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Baljit S Khakh
- Department of Physiology, David Geffen Schoof of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Jürgen Sandkühler
- Department of Neurophysiology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
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135
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Costamagna G, Comi GP, Corti S. Advancing Drug Discovery for Neurological Disorders Using iPSC-Derived Neural Organoids. Int J Mol Sci 2021; 22:ijms22052659. [PMID: 33800815 PMCID: PMC7961877 DOI: 10.3390/ijms22052659] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
In the last decade, different research groups in the academic setting have developed induced pluripotent stem cell-based protocols to generate three-dimensional, multicellular, neural organoids. Their use to model brain biology, early neural development, and human diseases has provided new insights into the pathophysiology of neuropsychiatric and neurological disorders, including microcephaly, autism, Parkinson’s disease, and Alzheimer’s disease. However, the adoption of organoid technology for large-scale drug screening in the industry has been hampered by challenges with reproducibility, scalability, and translatability to human disease. Potential technical solutions to expand their use in drug discovery pipelines include Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) to create isogenic models, single-cell RNA sequencing to characterize the model at a cellular level, and machine learning to analyze complex data sets. In addition, high-content imaging, automated liquid handling, and standardized assays represent other valuable tools toward this goal. Though several open issues still hamper the full implementation of the organoid technology outside academia, rapid progress in this field will help to prompt its translation toward large-scale drug screening for neurological disorders.
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Affiliation(s)
- Gianluca Costamagna
- Dino Ferrari Centre, Department of Pathophysiology and Transplantation (DEPT), Neuroscience Section, University of Milan, 20122 Milan, Italy; (G.C.); (G.P.C.)
- IRCCS Foundation Ca’ Granda Ospedale Maggiore Policlinico, Neurology Unit, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Giacomo Pietro Comi
- Dino Ferrari Centre, Department of Pathophysiology and Transplantation (DEPT), Neuroscience Section, University of Milan, 20122 Milan, Italy; (G.C.); (G.P.C.)
- IRCCS Foundation Ca’ Granda Ospedale Maggiore Policlinico, Neurology Unit, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Stefania Corti
- Dino Ferrari Centre, Department of Pathophysiology and Transplantation (DEPT), Neuroscience Section, University of Milan, 20122 Milan, Italy; (G.C.); (G.P.C.)
- IRCCS Foundation Ca’ Granda Ospedale Maggiore Policlinico, Neurology Unit, Via Francesco Sforza 35, 20122 Milan, Italy
- Correspondence:
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Kim MS, Ahn JH, Mo JE, Song HY, Cheon D, Yoo SH, Choi HJ. Optimizing tissue clearing and imaging methods for human brain tissue. J Int Med Res 2021; 49:3000605211001729. [PMID: 33771067 PMCID: PMC8166401 DOI: 10.1177/03000605211001729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/16/2021] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES To identify optimum sample conditions for human brains, we compared the clearing efficiency, antibody staining efficiency, and artifacts between fresh and cadaver samples. METHODS Fresh and cadaver samples were cleared using X-CLARITY™. Clearing efficiency and artifact levels were calculated using ImageJ, and antibody staining efficiency was evaluated after confocal microscopy imaging. Three staining methods were compared: 4-day staining (4DS), 11-day staining (11DS), and 4-day staining with a commercial kit (4DS-C). The optimum staining method was then selected by evaluating staining time, depth, method complexity, contamination, and cost. RESULTS Fresh samples outperformed cadaver samples in terms of the time and quality of clearing, artifacts, and 4',6-diamidino-2-phenylindole (DAPI) staining efficiency, but had a glial fibrillary acidic protein (GFAP) staining efficiency that was similar to that of cadaver samples. The penetration depth and DAPI staining improved in fresh samples as the incubation period lengthened. 4DS-C was the best method, with the deepest penetration. Human brain images containing blood vessels, cell nuclei, and astrocytes were visualized three-dimensionally. The chemical dye staining depth reached 800 µm and immunostaining depth exceeded 200 µm in 4 days. CONCLUSIONS We present optimized sample preparation and staining protocols for the visualization of three-dimensional macrostructure in the human brain.
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Affiliation(s)
- Min Sun Kim
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
| | - Jang Ho Ahn
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
| | - Ji Eun Mo
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
| | - Ha Young Song
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
| | - Deokhyeon Cheon
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
| | - Seong Ho Yoo
- Institute of Forensic Medicine and Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyung Jin Choi
- Functional Neuroanatomy of Metabolism Regulation Laboratory, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
- BK21Plus Biomedical Science Project Team, Seoul National University College of Medicine, Seoul, South Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea
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137
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Liu JTC, Glaser AK, Bera K, True LD, Reder NP, Eliceiri KW, Madabhushi A. Harnessing non-destructive 3D pathology. Nat Biomed Eng 2021; 5:203-218. [PMID: 33589781 PMCID: PMC8118147 DOI: 10.1038/s41551-020-00681-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/17/2020] [Indexed: 02/08/2023]
Abstract
High-throughput methods for slide-free three-dimensional (3D) pathological analyses of whole biopsies and surgical specimens offer the promise of modernizing traditional histology workflows and delivering improvements in diagnostic performance. Advanced optical methods now enable the interrogation of orders of magnitude more tissue than previously possible, where volumetric imaging allows for enhanced quantitative analyses of cell distributions and tissue structures that are prognostic and predictive. Non-destructive imaging processes can simplify laboratory workflows, potentially reducing costs, and can ensure that samples are available for subsequent molecular assays. However, the large size of the feature-rich datasets that they generate poses challenges for data management and computer-aided analysis. In this Perspective, we provide an overview of the imaging technologies that enable 3D pathology, and the computational tools-machine learning, in particular-for image processing and interpretation. We also discuss the integration of various other diagnostic modalities with 3D pathology, along with the challenges and opportunities for clinical adoption and regulatory approval.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Kaustav Bera
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nicholas P Reder
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kevin W Eliceiri
- Department of Medical Physics, University of Wisconsin, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, OH, USA.
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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: 43] [Impact Index Per Article: 14.3] [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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139
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Slomianka L. Basic quantitative morphological methods applied to the central nervous system. J Comp Neurol 2021; 529:694-756. [PMID: 32639600 PMCID: PMC7818269 DOI: 10.1002/cne.24976] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022]
Abstract
Generating numbers has become an almost inevitable task associated with studies of the morphology of the nervous system. Numbers serve a desire for clarity and objectivity in the presentation of results and are a prerequisite for the statistical evaluation of experimental outcomes. Clarity, objectivity, and statistics make demands on the quality of the numbers that are not met by many methods. This review provides a refresher of problems associated with generating numbers that describe the nervous system in terms of the volumes, surfaces, lengths, and numbers of its components. An important aim is to provide comprehensible descriptions of the methods that address these problems. Collectively known as design-based stereology, these methods share two features critical to their application. First, they are firmly based in mathematics and its proofs. Second and critically underemphasized, an understanding of their mathematical background is not necessary for their informed and productive application. Understanding and applying estimators of volume, surface, length or number does not require more of an organizational mastermind than an immunohistochemical protocol. And when it comes to calculations, square roots are the gravest challenges to overcome. Sampling strategies that are combined with stereological probes are efficient and allow a rational assessment if the numbers that have been generated are "good enough." Much may be unfamiliar, but very little is difficult. These methods can no longer be scapegoats for discrepant results but faithfully produce numbers on the material that is assessed. They also faithfully reflect problems that associated with the histological material and the anatomically informed decisions needed to generate numbers that are not only valid in theory. It is within reach to generate practically useful numbers that must integrate with qualitative knowledge to understand the function of neural systems.
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Affiliation(s)
- Lutz Slomianka
- University of Zürich, Institute of AnatomyZürichSwitzerland
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140
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Szabo-Pardi TA, Syed UM, Castillo ZW, Burton MD. Use of Integrated Optical Clearing and 2-Photon Imaging to Investigate Sex Differences in Neuroimmune Interactions After Peripheral Nerve Injury. Front Cell Dev Biol 2021; 9:624201. [PMID: 34178976 PMCID: PMC8221108 DOI: 10.3389/fcell.2021.624201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/12/2021] [Indexed: 12/02/2022] Open
Abstract
Peripheral nerve injury induces a myriad of immune-derived symptoms that negatively impacts pain, depression, and overall quality of life. Neuroimmune differences underlie sexual dimorphisms in various pain states. The innate immune system is a source of these sex differences, which promotes inflammation and pro-nociception through bidirectional signaling with the nervous system. Spatiotemporal interactions between leukocytes and sensory neurons could hold the key to explain ascribed differences between sexes. To date, studies have found it difficult to display these interactions. We are poised to answer important questions regarding the recruitment of peripheral leukocytes to key tissues of the pain system, the dorsal root ganglia (DRG) and sciatic nerve after nerve injury. We optically clear whole DRGs and sciatic nerves and concomitantly use multi-photon microscopy and transgenic reporter lines, to visualize leukocyte dynamics involved in neuropathic pain development following nerve injury. We observed robust sexual dimorphisms in leukocyte recruitment to the lumbar DRGs after nerve injury. We also assessed immune cell size and morphology to understand activation states in the context of nervous tissue inflammation. The altered mechanisms by which the male and female immune systems respond to nerve injury are still topics of further research, however; the continued use of next-generation imaging with advanced whole tissue image analysis remains an important tool in understanding the reciprocal interactions between neuronal and non-neuronal cells.
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Affiliation(s)
| | | | | | - Michael D. Burton
- Neuroimmunology and Behavior Laboratory, Department of Neuroscience, Center for Advanced Pain Studies (CAPS), School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, TX, United States
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141
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Rybin MJ, Ivan ME, Ayad NG, Zeier Z. Organoid Models of Glioblastoma and Their Role in Drug Discovery. Front Cell Neurosci 2021; 15:605255. [PMID: 33613198 PMCID: PMC7892608 DOI: 10.3389/fncel.2021.605255] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is a devastating adult brain cancer with high rates of recurrence and treatment resistance. Cellular heterogeneity and extensive invasion of surrounding brain tissues are characteristic features of GBM that contribute to its intractability. Current GBM model systems do not recapitulate some of the complex features of GBM and have not produced sufficiently-effective treatments. This has cast doubt on the effectiveness of current GBM models and drug discovery paradigms. In search of alternative pre-clinical GBM models, various 3D organoid-based GBM model systems have been developed using human cells. The scalability of these systems and potential to more accurately model characteristic features of GBM, provide promising new avenues for pre-clinical GBM research and drug discovery efforts. Here, we review the current suite of organoid-GBM models, their individual strengths and weaknesses, and discuss their future applications with an emphasis on compound screening.
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Affiliation(s)
- Matthew J. Rybin
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Michael E. Ivan
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Nagi G. Ayad
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Zane Zeier
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
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Ogawa K, Kato N, Kawakami S. Recent Strategies for Targeted Brain Drug Delivery. Chem Pharm Bull (Tokyo) 2021; 68:567-582. [PMID: 32611994 DOI: 10.1248/cpb.c20-00041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Because the brain is the most important human organ, many brain disorders can cause severe symptoms. For example, glioma, one type of brain tumor, is progressive and lethal, while neurodegenerative diseases cause severe disability. Nevertheless, medical treatment for brain diseases remains unsatisfactory, and therefore innovative therapies are desired. However, the development of therapies to treat some cerebral diseases is difficult because the blood-brain barrier (BBB) or blood-brain tumor barrier prevents drugs from entering the brain. Hence, drug delivery system (DDS) strategies are required to deliver therapeutic agents to the brain. Recently, brain-targeted DDS have been developed, which increases the quality of therapy for cerebral disorders. This review gives an overview of recent brain-targeting DDS strategies. First, it describes strategies to cross the BBB. This includes BBB-crossing ligand modification or temporal BBB permeabilization. Strategies to avoid the BBB using local administration are also summarized. Intrabrain drug distribution is a crucial factor that directly determines the therapeutic effect, and thus it is important to evaluate drug distribution using optimal methods. We introduce some methods for evaluating drug distribution in the brain. Finally, applications of brain-targeted DDS for the treatment of brain tumors, Alzheimer's disease, Parkinson's disease, and stroke are explained.
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Affiliation(s)
- Koki Ogawa
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University
| | - Naoya Kato
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University
| | - Shigeru Kawakami
- Department of Pharmaceutical Informatics, Graduate School of Biomedical Sciences, Nagasaki University
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143
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Jager P, Moore G, Calpin P, Durmishi X, Salgarella I, Menage L, Kita Y, Wang Y, Kim DW, Blackshaw S, Schultz SR, Brickley S, Shimogori T, Delogu A. Dual midbrain and forebrain origins of thalamic inhibitory interneurons. eLife 2021; 10:e59272. [PMID: 33522480 PMCID: PMC7906600 DOI: 10.7554/elife.59272] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 01/31/2021] [Indexed: 12/12/2022] Open
Abstract
The ubiquitous presence of inhibitory interneurons in the thalamus of primates contrasts with the sparsity of interneurons reported in mice. Here, we identify a larger than expected complexity and distribution of interneurons across the mouse thalamus, where all thalamic interneurons can be traced back to two developmental programmes: one specified in the midbrain and the other in the forebrain. Interneurons migrate to functionally distinct thalamocortical nuclei depending on their origin: the abundant, midbrain-derived class populates the first and higher order sensory thalamus while the rarer, forebrain-generated class is restricted to some higher order associative regions. We also observe that markers for the midbrain-born class are abundantly expressed throughout the thalamus of the New World monkey marmoset. These data therefore reveal that, despite the broad variability in interneuron density across mammalian species, the blueprint of the ontogenetic organisation of thalamic interneurons of larger-brained mammals exists and can be studied in mice.
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Affiliation(s)
- Polona Jager
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College LondonLondonUnited Kingdom
| | - Gerald Moore
- Department of Bioengineering, Imperial College LondonLondonUnited Kingdom
- Department of Life Sciences and Centre for Neurotechnology, Imperial College LondonLondonUnited Kingdom
| | - Padraic Calpin
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
| | - Xhuljana Durmishi
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College LondonLondonUnited Kingdom
| | - Irene Salgarella
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College LondonLondonUnited Kingdom
| | - Lucy Menage
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College LondonLondonUnited Kingdom
| | | | - Yan Wang
- RIKEN, Center for Brain Science (CBS)SaitamaJapan
| | - Dong Won Kim
- The Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins UniversityBaltimoreUnited States
| | - Seth Blackshaw
- The Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins UniversityBaltimoreUnited States
| | - Simon R Schultz
- Department of Bioengineering, Imperial College LondonLondonUnited Kingdom
| | - Stephen Brickley
- Department of Life Sciences and Centre for Neurotechnology, Imperial College LondonLondonUnited Kingdom
| | | | - Alessio Delogu
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College LondonLondonUnited Kingdom
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Geng J, Zhang X, Prabhu S, Shahoei SH, Nelson ER, Swanson KS, Anastasio MA, Smith AM. 3D microscopy and deep learning reveal the heterogeneity of crown-like structure microenvironments in intact adipose tissue. SCIENCE ADVANCES 2021; 7:7/8/eabe2480. [PMID: 33597245 PMCID: PMC7888944 DOI: 10.1126/sciadv.abe2480] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/24/2020] [Indexed: 05/12/2023]
Abstract
Crown-like structures (CLSs) are adipose microenvironments of macrophages engulfing adipocytes. Their histological density in visceral adipose tissue (VAT) predicts metabolic disorder progression in obesity and is believed to initiate obesity comorbidities. Here, we use three-dimensional (3D) light sheet microscopy and deep learning to quantify 3D features of VAT CLSs in lean and obese states. Obese CLS densities are significantly higher, composing 3.9% of tissue volume compared with 0.46% in lean tissue. Across the states, individual CLS structural characteristics span similar ranges; however, subpopulations are distinguishable. Obese VAT contains large CLSs absent from lean tissues, located near the tissue center, while lean CLSs have higher volumetric cell densities and prolate shapes. These features are consistent with inefficient adipocyte elimination in obesity that contributes to chronic inflammation, representing histological biomarkers to assess adipose pathogenesis. This tissue processing, imaging, and analysis pipeline can be applied to quantitatively classify 3D microenvironments across diverse tissues.
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Affiliation(s)
- Junlong Geng
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Xiaohui Zhang
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Suma Prabhu
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Sayyed Hamed Shahoei
- Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Erik R Nelson
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Division of Nutritional Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Kelly S Swanson
- Department of Animal Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Division of Nutritional Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Mark A Anastasio
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Department of Materials Science and Engineering, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, Urbana, IL 61801, USA
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145
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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: 58] [Impact Index Per Article: 19.3] [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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146
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Hofmann J, Gadjalova I, Mishra R, Ruland J, Keppler SJ. Efficient Tissue Clearing and Multi-Organ Volumetric Imaging Enable Quantitative Visualization of Sparse Immune Cell Populations During Inflammation. Front Immunol 2021; 11:599495. [PMID: 33569052 PMCID: PMC7869862 DOI: 10.3389/fimmu.2020.599495] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/04/2020] [Indexed: 12/19/2022] Open
Abstract
Spatial information of cells in their tissue microenvironment is necessary to understand the complexity of pathophysiological processes. Volumetric imaging of cleared organs provides this information; however, current protocols are often elaborate, expensive, and organ specific. We developed a simplified, cost-effective, non-hazardous approach for efficient tissue clearing and multi-organ volumetric imaging (EMOVI). EMOVI enabled multiplexed antibody-based immunolabeling, provided adequate tissue transparency, maintained cellular morphology and preserved fluorochromes. Exemplarily, EMOVI allowed the detection and quantification of scarce cell populations during pneumonitis. EMOVI also permitted histo-cytometric analysis of MHC-II expressing cells, revealing distinct populations surrounding or infiltrating glomeruli of nephritic kidneys. Using EMOVI, we found widefield microscopy with real-time computational clearing as a valuable option for rapid image acquisition and detection of rare cellular events in cleared organs. EMOVI has the potential to make tissue clearing and volumetric imaging of immune cells applicable for a broad audience by facilitating flexibility in organ, fluorochrome and microscopy usage.
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Affiliation(s)
- Julian Hofmann
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technische Universität München, München, Germany
| | - Iana Gadjalova
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technische Universität München, München, Germany
| | - Ritu Mishra
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technische Universität München, München, Germany
| | - Jürgen Ruland
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technische Universität München, München, Germany
| | - Selina J Keppler
- Institute for Clinical Chemistry and Pathobiochemistry, München rechts der Isar (MRI), Technical University Munich, Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technische Universität München, München, Germany
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147
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Adhya D, Chennell G, Crowe JA, Valencia-Alarcón EP, Seyforth J, Hosny NA, Yasvoina MV, Forster R, Baron-Cohen S, Vernon AC, Srivastava DP. Application of Airy beam light sheet microscopy to examine early neurodevelopmental structures in 3D hiPSC-derived human cortical spheroids. Mol Autism 2021; 12:4. [PMID: 33482917 PMCID: PMC7821651 DOI: 10.1186/s13229-021-00413-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The inability to observe relevant biological processes in vivo significantly restricts human neurodevelopmental research. Advances in appropriate in vitro model systems, including patient-specific human brain organoids and human cortical spheroids (hCSs), offer a pragmatic solution to this issue. In particular, hCSs are an accessible method for generating homogenous organoids of dorsal telencephalic fate, which recapitulate key aspects of human corticogenesis, including the formation of neural rosettes-in vitro correlates of the neural tube. These neurogenic niches give rise to neural progenitors that subsequently differentiate into neurons. Studies differentiating induced pluripotent stem cells (hiPSCs) in 2D have linked atypical formation of neural rosettes with neurodevelopmental disorders such as autism spectrum conditions. Thus far, however, conventional methods of tissue preparation in this field limit the ability to image these structures in three-dimensions within intact hCS or other 3D preparations. To overcome this limitation, we have sought to optimise a methodological approach to process hCSs to maximise the utility of a novel Airy-beam light sheet microscope (ALSM) to acquire high resolution volumetric images of internal structures within hCS representative of early developmental time points. RESULTS Conventional approaches to imaging hCS by confocal microscopy were limited in their ability to image effectively into intact spheroids. Conversely, volumetric acquisition by ALSM offered superior imaging through intact, non-clarified, in vitro tissues, in both speed and resolution when compared to conventional confocal imaging systems. Furthermore, optimised immunohistochemistry and optical clearing of hCSs afforded improved imaging at depth. This permitted visualization of the morphology of the inner lumen of neural rosettes. CONCLUSION We present an optimized methodology that takes advantage of an ALSM system that can rapidly image intact 3D brain organoids at high resolution while retaining a large field of view. This imaging modality can be applied to both non-cleared and cleared in vitro human brain spheroids derived from hiPSCs for precise examination of their internal 3D structures. This process represents a rapid, highly efficient method to examine and quantify in 3D the formation of key structures required for the coordination of neurodevelopmental processes in both health and disease states. We posit that this approach would facilitate investigation of human neurodevelopmental processes in vitro.
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Affiliation(s)
- Dwaipayan Adhya
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - George Chennell
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - James A Crowe
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Eva P Valencia-Alarcón
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - James Seyforth
- M Squared Life Ltd., The Surrey Technology Centre, 40 Occam Road, Guildford, UK
| | - Neveen A Hosny
- M Squared Life Ltd., The Surrey Technology Centre, 40 Occam Road, Guildford, UK
| | - Marina V Yasvoina
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Robert Forster
- M Squared Life Ltd., The Surrey Technology Centre, 40 Occam Road, Guildford, UK
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Anthony C Vernon
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Deepak P Srivastava
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.
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148
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Kariyama N, Sakata-Haga H, Tsukada T, Shimada H, Taniguchi M, Hatta T. Rapid bone staining with hair removal (RAP-B/HR): a non-destructive and rapid whole-mount bone staining protocol optimized for adult hairy mice. Sci Rep 2021; 11:1950. [PMID: 33479385 PMCID: PMC7820006 DOI: 10.1038/s41598-021-81616-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/01/2021] [Indexed: 11/16/2022] Open
Abstract
We developed a non-destructive and rapid whole-mount bone staining method for small fish, Xenopus laevis, and rodent fetuses (RAP-B). RAP-B does not require skin or soft tissue removal. However, RAP-B requires hair removal from hairy animals, such as adult mice and rats. In the present study, we investigated hair removal chemical treatments that did not result in soft tissue destruction. The hair removal effectiveness was investigated using a calcium mercaptoacetate or sodium mercaptoacetate solution on skin fragments obtained from the back of adult mice. A mixture of 2% sodium mercaptoacetate in 3% potassium hydroxide was found to be the most effective in complete hair removal from the skin. Using this hair removal treatment as a pretreatment for RAP-B, the preparation of fast-acting artifact-free whole-mount bone staining was possible without skin and soft tissue removal (RAP-B/HR). We performed a seamless observation from a low magnification wide-view to a high magnification without artifactacting artifacts using fluorescence zoom microscopy. Therefore, the combination of RAP-B/HR and fluorescent zoom microscopy is a novel platform for three-dimensional, wide-field, high-resolution pathological anatomical analysis.
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Affiliation(s)
- Nobuo Kariyama
- Department of Anatomy, Kanazawa Medical University, Ishikawa, Japan.,Department of Physical Therapy, Kanazawa Rehabilitation Academy, Ishikawa, Japan
| | | | - Tsuyoshi Tsukada
- Department of Anatomy, Kanazawa Medical University, Ishikawa, Japan.,Department of Neurosurgery, Kanazawa Medical University, Ishikawa, Japan
| | - Hiroki Shimada
- Department of Medical Science, Kanazawa Medical University, Ishikawa, Japan
| | - Makoto Taniguchi
- Department of Life Science, Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan
| | - Toshihisa Hatta
- Department of Anatomy, Kanazawa Medical University, Ishikawa, Japan.
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149
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Urea-based amino sugar agent clears murine liver and preserves protein fluorescence and lipophilic dyes. Biotechniques 2021; 70:72-80. [PMID: 33467918 PMCID: PMC7983039 DOI: 10.2144/btn-2020-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Five established clearing protocols were compared with a modified and simplified method to determine an optimal clearing reagent for three-dimensionally visualizing fluorophores in the murine liver, a challenging organ to clear. We report successful clearing of whole liver lobes by modification of an established protocol (UbasM) using only Ub-1, a urea-based amino sugar reagent, in a simpler protocol that requires only a 24-h processing time. With Ub-1 alone, we observed sufficiently preserved liver tissue structure in three dimensions along with excellent preservation of fluorophore emissions from endogenous protein reporters and lipophilic tracer dyes. This streamlined technique can be used for 3D cell lineage tracing and fluoroprobe-based reporter gene expression to compare various experimental conditions. This study presents a simplified protocol for optically clearing murine liver tissue in only 24 h using one simple urea-based amino sugar solution and a single incubation. This method preserves fluorescence of transgenically expressed proteins and lipophilic tracer dyes within the context of native spatial morphology.
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150
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Suppression of Peritoneal Fibrosis by Sonoporation of Hepatocyte Growth Factor Gene-Encoding Plasmid DNA in Mice. Pharmaceutics 2021; 13:pharmaceutics13010115. [PMID: 33477422 PMCID: PMC7829751 DOI: 10.3390/pharmaceutics13010115] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Gene therapy is expected to be used for the treatment of peritoneal fibrosis, which is a serious problem associated with long-term peritoneal dialysis. Hepatocyte growth factor (HGF) is a well-known anti-fibrotic gene. We developed an ultrasound and nanobubble-mediated (sonoporation) gene transfection system, which selectively targets peritoneal tissues. Thus, we attempted to treat peritoneal fibrosis by sonoporation-based human HGF (hHGF) gene transfection in mice. To prepare a model of peritoneal fibrosis, mice were intraperitoneally injected with chlorhexidine digluconate. We evaluated the preventive and curative effects of sonoporation-based hHGF transfection by analyzing the following factors: hydroxyproline level, peritoneum thickness, and the peritoneal equilibration test. The transgene expression characteristics of sonoporation were also evaluated using multicolor deep imaging. In early-stage fibrosis in mice, transgene expression by sonoporation was observed in the submesothelial layer. Sonoporation-based hHGF transfection showed not only a preventive effect but also a curative effect for early-stage peritoneal fibrosis. Sonoporation-based hHGF transfection may be suitable for the treatment of peritoneal fibrosis regarding the transfection characteristics of transgene expression in the peritoneum under fibrosis.
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