101
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Lu T, Shinozaki M, Nagoshi N, Nakamura M, Okano H. Long Preservation of AAV-Transduced Fluorescence by a Modified Organic Solvent-Based Clearing Method. Int J Mol Sci 2022; 23:ijms23179637. [PMID: 36077034 PMCID: PMC9455935 DOI: 10.3390/ijms23179637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
The development of tissue clearing technologies allows 3D imaging of whole tissues and organs, especially in studies of the central nervous system innervated throughout the body. Although the three-dimensional imaging of solvent-cleared organs (3DISCO) method provides a powerful clearing capacity and high transparency, the rapid quenching of endogenous fluorescence and peroxide removal process decreases its practicability. This study provides a modified method named tDISCO to solve these limitations. The tDISCO protocol can preserve AAV-transduced endogenous EGFP fluorescence for months and achieve high transparency in a fast and simple clearing process. In addition to the brain, tDISCO was applied to other organs and even hard bone tissue. tDISCO also enabled us to visualize the long projection neurons and axons with high resolution. This method provides a fast and simple clearing protocol for 3D visualization of the AAV- transduced long projection neurons throughout the brain and spinal cord.
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Affiliation(s)
- Tao Lu
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Munehisa Shinozaki
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Narihito Nagoshi
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masaya Nakamura
- Department of Orthopaedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Correspondence: (M.N.); (H.O.)
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- Correspondence: (M.N.); (H.O.)
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102
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Woo A, Botta A, Shi SSW, Paus T, Pausova Z. Obesity-Related Neuroinflammation: Magnetic Resonance and Microscopy Imaging of the Brain. Int J Mol Sci 2022; 23:8790. [PMID: 35955925 PMCID: PMC9368789 DOI: 10.3390/ijms23158790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/06/2022] [Indexed: 12/01/2022] Open
Abstract
Obesity is a major risk factor of Alzheimer's disease and related dementias. The principal feature of dementia is a loss of neurons and brain atrophy. The mechanistic links between obesity and the neurodegenerative processes of dementias are not fully understood, but recent research suggests that obesity-related systemic inflammation and subsequent neuroinflammation may be involved. Adipose tissues release multiple proinflammatory molecules (fatty acids and cytokines) that impact blood and vessel cells, inducing low-grade systemic inflammation that can transition to tissues, including the brain. Inflammation in the brain-neuroinflammation-is one of key elements of the pathobiology of neurodegenerative disorders; it is characterized by the activation of microglia, the resident immune cells in the brain, and by the structural and functional changes of other cells forming the brain parenchyma, including neurons. Such cellular changes have been shown in animal models with direct methods, such as confocal microscopy. In humans, cellular changes are less tangible, as only indirect methods such as magnetic resonance (MR) imaging are usually used. In these studies, obesity and low-grade systemic inflammation have been associated with lower volumes of the cerebral gray matter, cortex, and hippocampus, as well as altered tissue MR properties (suggesting microstructural variations in cellular and molecular composition). How these structural variations in the human brain observed using MR imaging relate to the cellular variations in the animal brain seen with microscopy is not well understood. This review describes the current understanding of neuroinflammation in the context of obesity-induced systemic inflammation, and it highlights need for the bridge between animal microscopy and human MR imaging studies.
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Affiliation(s)
- Anita Woo
- The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Amy Botta
- The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Sammy S. W. Shi
- The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Tomas Paus
- Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, QC H3T 1C5, Canada
- Departments of Psychiatry of Neuroscience, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON M5S 1A1, Canada
- ECOGENE-21, Chicoutimi, QC G7H 7K9, Canada
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A1, Canada
- ECOGENE-21, Chicoutimi, QC G7H 7K9, Canada
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103
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Yendiki A, Aggarwal M, Axer M, Howard AF, van Cappellen van Walsum AM, Haber SN. Post mortem mapping of connectional anatomy for the validation of diffusion MRI. Neuroimage 2022; 256:119146. [PMID: 35346838 PMCID: PMC9832921 DOI: 10.1016/j.neuroimage.2022.119146] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 03/02/2022] [Accepted: 03/23/2022] [Indexed: 01/13/2023] Open
Abstract
Diffusion MRI (dMRI) is a unique tool for the study of brain circuitry, as it allows us to image both the macroscopic trajectories and the microstructural properties of axon bundles in vivo. The Human Connectome Project ushered in an era of impressive advances in dMRI acquisition and analysis. As a result of these efforts, the quality of dMRI data that could be acquired in vivo improved substantially, and large collections of such data became widely available. Despite this progress, the main limitation of dMRI remains: it does not image axons directly, but only provides indirect measurements based on the diffusion of water molecules. Thus, it must be validated by methods that allow direct visualization of axons but that can only be performed in post mortem brain tissue. In this review, we discuss methods for validating the various features of connectional anatomy that are extracted from dMRI, both at the macro-scale (trajectories of axon bundles), and at micro-scale (axonal orientations and other microstructural properties). We present a range of validation tools, including anatomic tracer studies, Klingler's dissection, myelin stains, label-free optical imaging techniques, and others. We provide an overview of the basic principles of each technique, its limitations, and what it has taught us so far about the accuracy of different dMRI acquisition and analysis approaches.
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Affiliation(s)
- Anastasia Yendiki
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States,Corresponding author (A. Yendiki)
| | - Manisha Aggarwal
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Markus Axer
- Forschungszentrum Jülich, Institute of Neuroscience and Medicine, Jülich, Germany,Department of Physics, University of Wuppertal Germany
| | - Amy F.D. Howard
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Anne-Marie van Cappellen van Walsum
- Department of Medical Imaging, Anatomy, Radboud University Medical Center, Nijmegen, the Netherland,Cognition and Behaviour, Donders Institute for Brain, Nijmegen, the Netherland
| | - Suzanne N. Haber
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, United States,McLean Hospital, Belmont, MA, United States
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104
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Moffitt JR, Lundberg E, Heyn H. The emerging landscape of spatial profiling technologies. Nat Rev Genet 2022; 23:741-759. [PMID: 35859028 DOI: 10.1038/s41576-022-00515-3] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 01/04/2023]
Abstract
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein profiling methods as a major pillar for cellular atlas building of complex samples, from tissues to full organisms. Emerging methods yield omics measurements at resolutions covering the nano- to microscale, enabling the charting of cellular heterogeneity, complex tissue architectures and dynamic changes during development and disease. We present an overview of the developing landscape of in situ spatial genome, transcriptome and proteome technologies, exemplify their impact on cell biology and translational research, and discuss current challenges for their community-wide adoption. Among many transformative applications, we envision that spatial methods will map entire organs and enable next-generation pathology.
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Affiliation(s)
- Jeffrey R Moffitt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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105
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Mai H, Rong Z, Zhao S, Cai R, Steinke H, Bechmann I, Ertürk A. Scalable tissue labeling and clearing of intact human organs. Nat Protoc 2022; 17:2188-2215. [PMID: 35859136 DOI: 10.1038/s41596-022-00712-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/05/2022] [Indexed: 11/09/2022]
Abstract
Advances in tissue labeling and clearing methods include improvement of tissue transparency, better preservation of fluorescence signal, compatibility with immunostaining and large sample volumes. However, as existing methods share the common limitation that they can only be applied to human tissue slices, rendering intact human organs transparent remains a challenge. Here, we describe experimental details of the small-micelle-mediated human organ efficient clearing and labeling (SHANEL) pipeline, which can be applied for cellular mapping of intact human organs. We have successfully cleared multiple human organs, including kidney, pancreas, heart, lung, spleen and brain, as well as hard tissue like skull. We also describe an advanced volumetric imaging system using a commercial light-sheet fluorescence microscope that can accommodate most human organs and a pipeline for whole-organ imaging and visualization. The complete experimental process of labeling and clearing whole human organs takes months and the analysis process takes several weeks, depending on the organ types and sizes.
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Affiliation(s)
- Hongcheng Mai
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany.,Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,Munich Medical Research School (MMRS), Ludwig-Maximilians University Munich, Munich, Germany
| | - Zhouyi Rong
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany.,Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,Munich Medical Research School (MMRS), Ludwig-Maximilians University Munich, Munich, Germany
| | - Shan Zhao
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany.,Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,Munich Medical Research School (MMRS), Ludwig-Maximilians University Munich, Munich, Germany
| | - Ruiyao Cai
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany.,Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Hanno Steinke
- Institute of Anatomy, University of Leipzig, Leipzig, Germany
| | - Ingo Bechmann
- Institute of Anatomy, University of Leipzig, Leipzig, Germany
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center, Neuherberg, Munich, Germany. .,Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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106
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Wang W, Chan YH, Kwon S, Tandukar J, Gao R. Nanoscale fluorescence imaging of biological ultrastructure via molecular anchoring and physical expansion. NANO CONVERGENCE 2022; 9:30. [PMID: 35810234 PMCID: PMC9271151 DOI: 10.1186/s40580-022-00318-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/26/2022] [Indexed: 05/25/2023]
Abstract
Nanoscale imaging of biological samples can provide rich morphological and mechanistic information about biological functions and dysfunctions at the subcellular and molecular level. Expansion microscopy (ExM) is a recently developed nanoscale fluorescence imaging method that takes advantage of physical enlargement of biological samples. In ExM, preserved cells and tissues are embedded in a swellable hydrogel, to which the molecules and fluorescent tags in the samples are anchored. When the hydrogel swells several-fold, the effective resolution of the sample images can be improved accordingly via physical separation of the retained molecules and fluorescent tags. In this review, we focus on the early conception and development of ExM from a biochemical and materials perspective. We first examine the general workflow as well as the numerous variations of ExM developed to retain and visualize a broad range of biomolecules, such as proteins, nucleic acids, and membranous structures. We then describe a number of inherent challenges facing ExM, including those associated with expansion isotropy and labeling density, as well as the ongoing effort to address these limitations. Finally, we discuss the prospect and possibility of pushing the resolution and accuracy of ExM to the single-molecule scale and beyond.
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Affiliation(s)
- Wei Wang
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Yat Ho Chan
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - SoYoung Kwon
- Department of Biomedical and Health Information Sciences, College of Applied Health Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Jamuna Tandukar
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA
| | - Ruixuan Gao
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA.
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, USA.
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107
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Mestre H, Verma N, Greene TD, Lin LA, Ladron-de-Guevara A, Sweeney AM, Liu G, Thomas VK, Galloway CA, de Mesy Bentley KL, Nedergaard M, Mehta RI. Periarteriolar spaces modulate cerebrospinal fluid transport into brain and demonstrate altered morphology in aging and Alzheimer's disease. Nat Commun 2022; 13:3897. [PMID: 35794106 PMCID: PMC9259669 DOI: 10.1038/s41467-022-31257-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 06/03/2022] [Indexed: 12/13/2022] Open
Abstract
Perivascular spaces (PVS) drain brain waste metabolites, but their specific flow paths are debated. Meningeal pia mater reportedly forms the outermost boundary that confines flow around blood vessels. Yet, we show that pia is perforated and permissive to PVS fluid flow. Furthermore, we demonstrate that pia is comprised of vascular and cerebral layers that coalesce in variable patterns along leptomeningeal arteries, often merging around penetrating arterioles. Heterogeneous pial architectures form variable sieve-like structures that differentially influence cerebrospinal fluid (CSF) transport along PVS. The degree of pial coverage correlates with macrophage density and phagocytosis of CSF tracer. In vivo imaging confirms transpial influx of CSF tracer, suggesting a role of pia in CSF filtration, but not flow restriction. Additionally, pial layers atrophy with age. Old mice also exhibit areas of pial denudation that are not observed in young animals, but pia is unexpectedly hypertrophied in a mouse model of Alzheimer's disease. Moreover, pial thickness correlates with improved CSF flow and reduced β-amyloid deposits in PVS of old mice. We show that PVS morphology in mice is variable and that the structure and function of pia suggests a previously unrecognized role in regulating CSF transport and amyloid clearance in aging and disease.
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Affiliation(s)
- Humberto Mestre
- grid.412750.50000 0004 1936 9166Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642 USA ,grid.412750.50000 0004 1936 9166Department of Neuroscience, University of Rochester Medical Center, Rochester, NY 14642 USA ,grid.25879.310000 0004 1936 8972Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Natasha Verma
- grid.412750.50000 0004 1936 9166Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Thom D. Greene
- grid.412750.50000 0004 1936 9166Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - LiJing A. Lin
- grid.412750.50000 0004 1936 9166Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Antonio Ladron-de-Guevara
- grid.412750.50000 0004 1936 9166Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Amanda M. Sweeney
- grid.412750.50000 0004 1936 9166Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Guojun Liu
- grid.412750.50000 0004 1936 9166Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - V. Kaye Thomas
- grid.412750.50000 0004 1936 9166Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Chad A. Galloway
- grid.412750.50000 0004 1936 9166Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Karen L. de Mesy Bentley
- grid.412750.50000 0004 1936 9166Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Maiken Nedergaard
- grid.412750.50000 0004 1936 9166Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642 USA ,grid.5254.60000 0001 0674 042XCenter for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rupal I. Mehta
- grid.412750.50000 0004 1936 9166Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642 USA ,grid.240684.c0000 0001 0705 3621Department of Pathology, Rush University Medical Center, Chicago, IL 60612 USA ,grid.240684.c0000 0001 0705 3621Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612 USA
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108
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Kazachkina NI, Zherdeva VV, Meerovich IG, Saydasheva AN, Solovyev ID, Tuchina DK, Savitsky AP, Tuchin VV, Bogdanov AA. MR and fluorescence imaging of gadobutrol-induced optical clearing of red fluorescent protein signal in an in vivo cancer model. NMR IN BIOMEDICINE 2022; 35:e4708. [PMID: 35106848 DOI: 10.1002/nbm.4708] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/15/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Multimodality registration of optical and MR images in the same tissue volume in vivo may be enabled by MR contrast agents with an optical clearing (OC) effect. The goals of this study were to (a) investigate the effects of clinical MR contrast agent gadobutrol (GB) and its combinations as a potential OC agent assisting in fluorescence intensity (FI) imaging in vivo and (b) evaluate MRI as a tool for imaging of topical or systemic application of GB for the purpose of OC. Subcutaneous tumor xenografts expressing red fluorescent marker protein were used as disease models. MRI was performed at 1 T 1 H MRI using T1 -weighted 3D gradient-echo (T1w-3D GRE) sequences to measure time-dependent MR signal intensity changes by region of interest analysis after image segmentation. Topical application of 1.0 M or 0.7 M GB-containing OC mixture with water and dimethyl sulfoxide showed similar 30-40% increases of tumor FI during the initial 15 min. Afterwards, the OC effect of GB on FI and tumor/background FI ratio showed a decrease over time in the case of 1.0 M GB, unlike the 0.7 M GB mixture, which resulted in a steady increase of FI and tumor/background ratio for 15-60 min. The use of T1w-3D GRE MR pulse sequences showed that concentrated 1.0 M GB resulted in MR signal loss of the skin due to high magnetic susceptibility and that signal loss coincided with the OC effect. Intravenous injection of 0.3 mmol GB/kg resulted in a rapid but transient 40% increase of FI of the tumors. Overall, 1 T MRI enabled tracking of GB-containing OC compositions on the skin surface and tumor tissue, supporting the observation of a time-dependent FI increase in vivo.
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Affiliation(s)
- Natalia I Kazachkina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Victoria V Zherdeva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Irina G Meerovich
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Asiya N Saydasheva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Ilya D Solovyev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Daria K Tuchina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
- Saratov State University, Saratov, Russian Federation
- National Research Tomsk State University, Tomsk, Russian Federation
| | - Alexander P Savitsky
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Valery V Tuchin
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
- Saratov State University, Saratov, Russian Federation
- National Research Tomsk State University, Tomsk, Russian Federation
- Institute of Precision Mechanics and Control of the Russian Academy of Sciences, Saratov, Russian Federation
| | - Alexei A Bogdanov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
- Department of Radiology, UMASS Chan Medical School, Worcester, Massachusetts, USA
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109
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Kim S, Kim YE, Song I, Ujihara Y, Kim N, Jiang YH, Yin HH, Lee TH, Kim IH. Neural circuit pathology driven by Shank3 mutation disrupts social behaviors. Cell Rep 2022; 39:110906. [PMID: 35675770 PMCID: PMC9210496 DOI: 10.1016/j.celrep.2022.110906] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 03/21/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022] Open
Abstract
Dysfunctional sociability is a core symptom in autism spectrum disorder (ASD) that may arise from neural-network dysconnectivity between multiple brain regions. However, pathogenic neural-network mechanisms underlying social dysfunction are largely unknown. Here, we demonstrate that circuit-selective mutation (ctMUT) of ASD-risk Shank3 gene within a unidirectional projection from the prefrontal cortex to the basolateral amygdala alters spine morphology and excitatory-inhibitory balance of the circuit. Shank3 ctMUT mice show reduced sociability as well as elevated neural activity and its amplitude variability, which is consistent with the neuroimaging results from human ASD patients. Moreover, the circuit hyper-activity disrupts the temporal correlation of socially tuned neurons to the events of social interactions. Finally, optogenetic circuit activation in wild-type mice partially recapitulates the reduced sociability of Shank3 ctMUT mice, while circuit inhibition in Shank3 ctMUT mice partially rescues social behavior. Collectively, these results highlight a circuit-level pathogenic mechanism of Shank3 mutation that drives social dysfunction.
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Affiliation(s)
- Sunwhi Kim
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Yong-Eun Kim
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Inuk Song
- Department of Psychology, Virginia Tech, Blacksburg, VA 24061, USA
| | - Yusuke Ujihara
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Namsoo Kim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Yong-Hui Jiang
- Department of Genetics, Pediatrics and Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Henry H Yin
- Department of Psychology and Neuroscience, Duke University, Durham, NC 27708, USA
| | - Tae-Ho Lee
- Department of Psychology, Virginia Tech, Blacksburg, VA 24061, USA
| | - Il Hwan Kim
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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110
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In situ identification of cellular drug targets in mammalian tissue. Cell 2022; 185:1793-1805.e17. [PMID: 35483372 PMCID: PMC9106931 DOI: 10.1016/j.cell.2022.03.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 02/01/2022] [Accepted: 03/28/2022] [Indexed: 12/24/2022]
Abstract
The lack of tools to observe drug-target interactions at cellular resolution in intact tissue has been a major barrier to understanding in vivo drug actions. Here, we develop clearing-assisted tissue click chemistry (CATCH) to optically image covalent drug targets in intact mammalian tissues. CATCH permits specific and robust in situ fluorescence imaging of target-bound drug molecules at subcellular resolution and enables the identification of target cell types. Using well-established inhibitors of endocannabinoid hydrolases and monoamine oxidases, direct or competitive CATCH not only reveals distinct anatomical distributions and predominant cell targets of different drug compounds in the mouse brain but also uncovers unexpected differences in drug engagement across and within brain regions, reflecting rare cell types, as well as dose-dependent target shifts across tissue, cellular, and subcellular compartments that are not accessible by conventional methods. CATCH represents a valuable platform for visualizing in vivo interactions of small molecules in tissue.
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111
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Pesce L, Scardigli M, Gavryusev V, Laurino A, Mazzamuto G, Brady N, Sancataldo G, Silvestri L, Destrieux C, Hof PR, Costantini I, Pavone FS. 3D molecular phenotyping of cleared human brain tissues with light-sheet fluorescence microscopy. Commun Biol 2022; 5:447. [PMID: 35551498 PMCID: PMC9098858 DOI: 10.1038/s42003-022-03390-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/21/2022] [Indexed: 12/17/2022] Open
Abstract
The combination of optical tissue transparency with immunofluorescence allows the molecular characterization of biological tissues in 3D. However, adult human organs are particularly challenging to become transparent because of the autofluorescence contributions of aged tissues. To meet this challenge, we optimized SHORT (SWITCH-H2O2-antigen Retrieval-TDE), a procedure based on standard histological treatments in combination with a refined clearing procedure to clear and label portions of the human brain. 3D histological characterization with multiple molecules is performed on cleared samples with a combination of multi-colors and multi-rounds labeling. By performing fast 3D imaging of the samples with a custom-made inverted light-sheet fluorescence microscope (LSFM), we reveal fine details of intact human brain slabs at subcellular resolution. Overall, we proposed a scalable and versatile technology that in combination with LSFM allows mapping the cellular and molecular architecture of the human brain, paving the way to reconstruct the entire organ.
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Affiliation(s)
- Luca Pesce
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Marina Scardigli
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Vladislav Gavryusev
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Annunziatina Laurino
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Niamh Brady
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
| | - Giuseppe Sancataldo
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
| | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy.
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy.
- Department of Biology, University of Florence, Florence, Italy.
| | - Francesco S Pavone
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
- National Institute of Optics (INO), National Research Council (CNR), Sesto Fiorentino, Italy
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112
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Seo J, Sim Y, Kim J, Kim H, Cho I, Nam H, Yoon YG, Chang JB. PICASSO allows ultra-multiplexed fluorescence imaging of spatially overlapping proteins without reference spectra measurements. Nat Commun 2022; 13:2475. [PMID: 35513404 PMCID: PMC9072354 DOI: 10.1038/s41467-022-30168-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 04/20/2022] [Indexed: 12/19/2022] Open
Abstract
Ultra-multiplexed fluorescence imaging requires the use of spectrally overlapping fluorophores to label proteins and then to unmix the images of the fluorophores. However, doing this remains a challenge, especially in highly heterogeneous specimens, such as the brain, owing to the high degree of variation in the emission spectra of fluorophores in such specimens. Here, we propose PICASSO, which enables more than 15-color imaging of spatially overlapping proteins in a single imaging round without using any reference emission spectra. PICASSO requires an equal number of images and fluorophores, which enables such advanced multiplexed imaging, even with bandpass filter-based microscopy. We show that PICASSO can be used to achieve strong multiplexing capability in diverse applications. By combining PICASSO with cyclic immunofluorescence staining, we achieve 45-color imaging of the mouse brain in three cycles. PICASSO provides a tool for multiplexed imaging with high accessibility and accuracy for a broad range of researchers.
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Affiliation(s)
- Junyoung Seo
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Yeonbo Sim
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Korea
| | - Jeewon Kim
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Hyunwoo Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - In Cho
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Hoyeon Nam
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Young-Gyu Yoon
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
| | - Jae-Byum Chang
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
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113
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Roy DS, Park YG, Kim ME, Zhang Y, Ogawa SK, DiNapoli N, Gu X, Cho JH, Choi H, Kamentsky L, Martin J, Mosto O, Aida T, Chung K, Tonegawa S. Brain-wide mapping reveals that engrams for a single memory are distributed across multiple brain regions. Nat Commun 2022; 13:1799. [PMID: 35379803 PMCID: PMC8980018 DOI: 10.1038/s41467-022-29384-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/10/2022] [Indexed: 11/28/2022] Open
Abstract
Neuronal ensembles that hold specific memory (memory engrams) have been identified in the hippocampus, amygdala, or cortex. However, it has been hypothesized that engrams of a specific memory are distributed among multiple brain regions that are functionally connected, referred to as a unified engram complex. Here, we report a partial map of the engram complex for contextual fear conditioning memory by characterizing encoding activated neuronal ensembles in 247 regions using tissue phenotyping in mice. The mapping was aided by an engram index, which identified 117 cFos+ brain regions holding engrams with high probability, and brain-wide reactivation of these neuronal ensembles by recall. Optogenetic manipulation experiments revealed engram ensembles, many of which were functionally connected to hippocampal or amygdala engrams. Simultaneous chemogenetic reactivation of multiple engram ensembles conferred a greater level of memory recall than reactivation of a single engram ensemble, reflecting the natural memory recall process. Overall, our study supports the unified engram complex hypothesis for memory storage.
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Affiliation(s)
- Dheeraj S Roy
- RIKEN-MIT Laboratory for Neural Circuit Genetics at the Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Young-Gyun Park
- Institute for Medical Engineering and Science, Picower Institute for Learning and Memory, Department of Chemical Engineering and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Minyoung E Kim
- Institute for Medical Engineering and Science, Picower Institute for Learning and Memory, Department of Chemical Engineering and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ying Zhang
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sachie K Ogawa
- RIKEN-MIT Laboratory for Neural Circuit Genetics at the Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nicholas DiNapoli
- Institute for Medical Engineering and Science, Picower Institute for Learning and Memory, Department of Chemical Engineering and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Xinyi Gu
- Institute for Medical Engineering and Science, Picower Institute for Learning and Memory, Department of Chemical Engineering and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jae H Cho
- Institute for Medical Engineering and Science, Picower Institute for Learning and Memory, Department of Chemical Engineering and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Heejin Choi
- Institute for Medical Engineering and Science, Picower Institute for Learning and Memory, Department of Chemical Engineering and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lee Kamentsky
- Institute for Medical Engineering and Science, Picower Institute for Learning and Memory, Department of Chemical Engineering and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jared Martin
- RIKEN-MIT Laboratory for Neural Circuit Genetics at the Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Olivia Mosto
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tomomi Aida
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kwanghun Chung
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Institute for Medical Engineering and Science, Picower Institute for Learning and Memory, Department of Chemical Engineering and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Yonsei-IBS Institute, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Susumu Tonegawa
- RIKEN-MIT Laboratory for Neural Circuit Genetics at the Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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114
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Qian N, Min W. Super-multiplexed vibrational probes: Being colorful makes a difference. Curr Opin Chem Biol 2022; 67:102115. [PMID: 35077919 PMCID: PMC8940683 DOI: 10.1016/j.cbpa.2021.102115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/03/2022]
Abstract
Biological systems with intrinsic complexity require multiplexing techniques to comprehensively describe the phenotype, interaction, and heterogeneity. Recent years have witnessed the development of super-multiplexed vibrational microscopy, overcoming the 'color barrier' of fluorescence-based optical techniques. Here, we will review the recent progress in the design and applications of super-multiplexed vibrational probes. We hope to illustrate how rainbow-like vibrational colors can be generated from systematic studies on structure-spectroscopy relationships and how being colorful makes a difference to various biomedical applications.
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Affiliation(s)
- Naixin Qian
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
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115
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Nudell V, Wang Y, Pang Z, Lal NK, Huang M, Shaabani N, Kanim W, Teijaro J, Maximov A, Ye L. HYBRiD: hydrogel-reinforced DISCO for clearing mammalian bodies. Nat Methods 2022; 19:479-485. [PMID: 35347322 PMCID: PMC9337799 DOI: 10.1038/s41592-022-01427-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 02/17/2022] [Indexed: 11/08/2022]
Abstract
The recent development of solvent- and polymer-based brain-clearing techniques has advanced our ability to visualize the mammalian nervous system in three dimensions. However, it remains challenging to image the mammalian body en bloc. Here we developed HYBRiD (hydrogel-based reinforcement of three-dimensional imaging solvent-cleared organs (DISCO)), by recombining components of organic- and polymer-based clearing pipelines. We achieved high transparency and protein retention, as well as compatibility with direct fluorescent imaging and immunostaining in cleared mammalian bodies. Using parvalbumin- and somatostatin-Cre models, we demonstrated the utility of HYBRiD for whole-body imaging of genetically encoded fluorescent reporters without antibody enhancement of signals in newborn and juvenile mice. Using K18-hACE2 transgenic mice, HYBRiD enabled perfusion-free clearing and visualization of SARS-CoV-2 infection in a whole mouse chest, revealing macroscopic and microscopic features of viral pathology in the same sample. HYBRiD offers a simple and universal solution to visualize large heterogeneous body parts or entire animals for basic and translational research.
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Affiliation(s)
- Victoria Nudell
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - Yu Wang
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - Zhengyuan Pang
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - Neeraj K Lal
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - Min Huang
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - Namir Shaabani
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wesam Kanim
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - John Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anton Maximov
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - Li Ye
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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116
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Cheng W, Su YL, Hsu HH, Lin YH, Chu LA, Huang WC, Lu YJ, Chiang CS, Hu SH. Rabies Virus Glycoprotein-Mediated Transportation and T Cell Infiltration to Brain Tumor by Magnetoelectric Gold Yarnballs. ACS NANO 2022; 16:4014-4027. [PMID: 35225594 DOI: 10.1021/acsnano.1c09601] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
T lymphocyte infiltration with immunotherapy potentially suppresses most devastating brain tumors. However, local immune privilege and tumor heterogeneity usually limit the penetration of immune cells and therapeutic agents into brain tumors, leading to tumor recurrence after treatment. Here, a rabies virus glycoprotein (RVG)-camouflaged gold yarnball (RVG@GY) that can boost the targeting efficiency at a brain tumor via dual hierarchy- and RVG-mediated spinal cord transportation, facilitating the decrease of tumor heterogeneity for T cell infiltration, is developed. Upon magnetoelectric irradiation, the electron current generated on the GYs activates the electrolytic penetration of palbociclib-loaded dendrimer (Den[Pb]) deep into tumors. In addition, the high-density GYs at brain tumors also induces the disruption of cell-cell interactions and T cell infiltration. The integration of the electrolytic effects and T cell infiltration promoted by drug-loaded RVG@GYs deep in the brain tumor elicits sufficient T cell numbers and effectively prolongs the survival rate of mice with orthotopic brain tumors.
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Affiliation(s)
| | | | | | | | | | - Wei-Chen Huang
- Department of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Yu-Jen Lu
- Department of Neurosurgery, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan 33305, Taiwan
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117
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Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods 2022; 19:284-295. [PMID: 34811556 PMCID: PMC9264278 DOI: 10.1038/s41592-021-01316-y] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
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Affiliation(s)
- John W Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Rebecca T Beuschel
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Alexandre Albanese
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Boston Children's Hospital, Division of Hematology/Oncology, Boston, MA, USA
| | | | - Julia Hatler
- Antibody Development Department, Bio-Techne, Minneapolis, MN, USA
| | - Anne E Wiblin
- Department of Research and Development, Abcam, Cambridge, UK
| | - Jeremy Fisher
- Department of Research and Development, Cell Signaling Technology, Danvers, MA, USA
| | - Josh Croteau
- Department of Applications Science, BioLegend, San Diego, CA, USA
| | | | | | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - R Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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118
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Shi L, Wei M, Miao Y, Qian N, Shi L, Singer RA, Benninger RKP, Min W. Highly-multiplexed volumetric mapping with Raman dye imaging and tissue clearing. Nat Biotechnol 2022; 40:364-373. [PMID: 34608326 PMCID: PMC8930416 DOI: 10.1038/s41587-021-01041-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 07/29/2021] [Indexed: 02/08/2023]
Abstract
Mapping the localization of multiple proteins in their native three-dimensional (3D) context would be useful across many areas of biomedicine, but multiplexed fluorescence imaging has limited intrinsic multiplexing capability, and most methods for increasing multiplexity can only be applied to thin samples (<100 µm). Here, we harness the narrow spectrum of Raman spectroscopy and introduce Raman dye imaging and tissue clearing (RADIANT), an optical method that is capable of imaging multiple targets in thick samples in one shot. We expanded the range of suitable bioorthogonal Raman dyes and developed a tissue-clearing strategy for them (Raman 3D imaging of solvent-cleared organs (rDISCO)). We applied RADIANT to image up to 11 targets in millimeter-thick brain slices, extending the imaging depth 10- to 100-fold compared to prior multiplexed protein imaging methods. We showcased the utility of RADIANT in extracting systems information, including region-specific correlation networks and their topology in cerebellum development. RADIANT will facilitate the exploration of the intricate 3D protein interactions in complex systems.
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Affiliation(s)
- Lixue Shi
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Yupeng Miao
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Naixin Qian
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Lingyan Shi
- Department of Chemistry, Columbia University, New York, NY, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Ruth A Singer
- Graduate Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, NY, USA
- Laboratory of Molecular Neuro-oncology, Rockefeller University, New York, NY, USA
| | - Richard K P Benninger
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA.
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
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119
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Ghosh S, Li N, Schwalm M, Bartelle BB, Xie T, Daher JI, Singh UD, Xie K, DiNapoli N, Evans NB, Chung K, Jasanoff A. Functional dissection of neural circuitry using a genetic reporter for fMRI. Nat Neurosci 2022; 25:390-398. [PMID: 35241803 PMCID: PMC9203076 DOI: 10.1038/s41593-022-01014-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 01/14/2022] [Indexed: 12/16/2022]
Abstract
The complex connectivity of the mammalian brain underlies its function, but understanding how interconnected brain regions interact in neural processing remains a formidable challenge. Here we address this problem by introducing a genetic probe that permits selective functional imaging of distributed neural populations defined by viral labeling techniques. The probe is an engineered enzyme that transduces cytosolic calcium dynamics of probe-expressing cells into localized hemodynamic responses that can be specifically visualized by functional magnetic resonance imaging. Using a viral vector that undergoes retrograde transport, we apply the probe to characterize a brain-wide network of presynaptic inputs to the striatum activated in a deep brain stimulation paradigm in rats. The results reveal engagement of surprisingly diverse projection sources and inform an integrated model of striatal function relevant to reward behavior and therapeutic neurostimulation approaches. Our work thus establishes a strategy for mechanistic analysis of multiregional neural systems in the mammalian brain.
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Affiliation(s)
- Souparno Ghosh
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Nan Li
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Miriam Schwalm
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Benjamin B. Bartelle
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Tianshu Xie
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Jade I. Daher
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139,Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Urvashi D. Singh
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Katherine Xie
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Nicholas DiNapoli
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Nicholas B. Evans
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Kwanghun Chung
- Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139,Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139,Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139
| | - Alan Jasanoff
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139,Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139,Department of Nuclear Science & Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139,Correspondence to AJ, phone: 617-452-2538,
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120
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Paulsen B, Velasco S, Kedaigle AJ, Pigoni M, Quadrato G, Deo AJ, Adiconis X, Uzquiano A, Sartore R, Yang SM, Simmons SK, Symvoulidis P, Kim K, Tsafou K, Podury A, Abbate C, Tucewicz A, Smith SN, Albanese A, Barrett L, Sanjana NE, Shi X, Chung K, Lage K, Boyden ES, Regev A, Levin JZ, Arlotta P. Autism genes converge on asynchronous development of shared neuron classes. Nature 2022; 602:268-273. [PMID: 35110736 PMCID: PMC8852827 DOI: 10.1038/s41586-021-04358-6] [Citation(s) in RCA: 178] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/14/2021] [Indexed: 02/08/2023]
Abstract
Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions1-6. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals7,8. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes-SUV420H1 (also known as KMT5B), ARID1B and CHD8-in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages-γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons-but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology.
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Affiliation(s)
- Bruna Paulsen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvia Velasco
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia.
| | - Amanda J Kedaigle
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martina Pigoni
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Giorgia Quadrato
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anthony J Deo
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
- Rutgers University Behavioral Health Care, Piscataway, NJ, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ana Uzquiano
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rafaela Sartore
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sung Min Yang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Panagiotis Symvoulidis
- MIT Center for Neurobiological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Kwanho Kim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kalliopi Tsafou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Archana Podury
- MIT Center for Neurobiological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Harvard-MIT Health Sciences & Technology Program (HST), Harvard Medical School, Boston, MA, USA
| | - Catherine Abbate
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashley Tucewicz
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha N Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandre Albanese
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Lindy Barrett
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neville E Sanjana
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Xi Shi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Picower Institute for Learning and Memory, Departments of Chemical Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- New York Genome Center, New York, NY, USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Edward S Boyden
- MIT Center for Neurobiological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Harvard-MIT Health Sciences & Technology Program (HST), Harvard Medical School, Boston, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
- Department of Brain of Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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121
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Chen S, Liu Z, Li A, Gong H, Long B, Li X. High-Throughput Strategy for Profiling Sequential Section With Multiplex Staining of Mouse Brain. Front Neuroanat 2022; 15:771229. [PMID: 35002637 PMCID: PMC8732995 DOI: 10.3389/fnana.2021.771229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/29/2021] [Indexed: 12/04/2022] Open
Abstract
The brain modulates specific functions in its various regions. Understanding the organization of different cells in the whole brain is crucial for investigating brain functions. Previous studies have focused on several regions and have had difficulty analyzing serial tissue samples. In this study, we introduced a pipeline to acquire anatomical and histological information quickly and efficiently from serial sections. First, we developed a serial brain-slice-staining method to stain serial sections and obtained more than 98.5% of slices with high integrity. Subsequently, using the self-developed analysis software, we registered and quantified the signals of imaged sections to the Allen Mouse Brain Common Coordinate Framework, which is compatible with multimodal images and slant section planes. Finally, we validated the pipeline with immunostaining by analyzing the activity variance in the whole brain during acute stress in aging and young mice. By removing the problems resulting from repeated manual operations, this pipeline is widely applicable to serial brain slices from multiple samples in a rapid and convenient manner, which benefits to facilitate research in life sciences.
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Affiliation(s)
- Siqi Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Zhixiang Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China.,HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China.,HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Ben Long
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China.,HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
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Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, Zhao Y. Neurophotonic tools for microscopic measurements and manipulation: status report. NEUROPHOTONICS 2022; 9:013001. [PMID: 35493335 PMCID: PMC9047450 DOI: 10.1117/1.nph.9.s1.013001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.
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Affiliation(s)
- Ahmed S. Abdelfattah
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Sapna Ahuja
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Srinivasa Rao Allu
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Joshua Brake
- Harvey Mudd College, Department of Engineering, Claremont, California, United States
| | - David A. Boas
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Erin M. Buckley
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Emory University, Department of Pediatrics, Atlanta, Georgia, United States
| | - Robert E. Campbell
- University of Tokyo, Department of Chemistry, Tokyo, Japan
- University of Alberta, Department of Chemistry, Edmonton, Alberta, Canada
| | - Anderson I. Chen
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Xiaojun Cheng
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Irene Costantini
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Biology, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Massimo De Vittorio
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Anna Devor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Patrick R. Doran
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Mirna El Khatib
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | | | - Natalie Fomin-Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Yeshaiahu Fainman
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Tomas Fernandez-Alfonso
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Christopher G. L. Ferri
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Ariel Gilad
- The Hebrew University of Jerusalem, Institute for Medical Research Israel–Canada, Department of Medical Neurobiology, Faculty of Medicine, Jerusalem, Israel
| | - Xue Han
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Andrew Harris
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | | | - Ute Hochgeschwender
- Central Michigan University, Department of Neuroscience, Mount Pleasant, Michigan, United States
| | - Matthew G. Holt
- University of Porto, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal
| | - Na Ji
- University of California Berkeley, Department of Physics, Berkeley, California, United States
| | - Kıvılcım Kılıç
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evelyn M. R. Lake
- Yale School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, Connecticut, United States
| | - Lei Li
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Tianqi Li
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Philipp Mächler
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evan W. Miller
- University of California Berkeley, Departments of Chemistry and Molecular & Cell Biology and Helen Wills Neuroscience Institute, Berkeley, California, United States
| | | | | | - U. Valentin Nägerl
- Interdisciplinary Institute for Neuroscience University of Bordeaux & CNRS, Bordeaux, France
| | - Yusuke Nasu
- University of Tokyo, Department of Chemistry, Tokyo, Japan
| | - Axel Nimmerjahn
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, California, United States
| | - Petra Ondráčková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Francesco S. Pavone
- National Institute of Optics, National Research Council, Rome, Italy
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Physics, Florence, Italy
| | - Citlali Perez Campos
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Darcy S. Peterka
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Filippo Pisano
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Francesca Puppo
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Bernardo L. Sabatini
- Harvard Medical School, Howard Hughes Medical Institute, Department of Neurobiology, Boston, Massachusetts, United States
| | - Sanaz Sadegh
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Sava Sakadzic
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Shy Shoham
- New York University Grossman School of Medicine, Tech4Health and Neuroscience Institutes, New York, New York, United States
| | - Sanaya N. Shroff
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - R. Angus Silver
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Ruth R. Sims
- Sorbonne University, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Spencer L. Smith
- University of California Santa Barbara, Department of Electrical and Computer Engineering, Santa Barbara, California, United States
| | - Vivek J. Srinivasan
- New York University Langone Health, Departments of Ophthalmology and Radiology, New York, New York, United States
| | - Martin Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Lei Tian
- Boston University, Departments of Electrical Engineering and Biomedical Engineering, Boston, Massachusetts, United States
| | - Lin Tian
- University of California Davis, Department of Biochemistry and Molecular Medicine, Davis, California, United States
| | - Thomas Troxler
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Antoine Valera
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Alipasha Vaziri
- Rockefeller University, Laboratory of Neurotechnology and Biophysics, New York, New York, United States
- The Rockefeller University, The Kavli Neural Systems Institute, New York, New York, United States
| | - Sergei A. Vinogradov
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Flavia Vitale
- Center for Neuroengineering and Therapeutics, Departments of Neurology, Bioengineering, Physical Medicine and Rehabilitation, Philadelphia, Pennsylvania, United States
| | - Lihong V. Wang
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Chris Xu
- Cornell University, School of Applied and Engineering Physics, Ithaca, New York, United States
| | - Changhuei Yang
- California Institute of Technology, Departments of Electrical Engineering, Bioengineering and Medical Engineering, Pasadena, California, United States
| | - Mu-Han Yang
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Gary Yellen
- Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, United States
| | - Ofer Yizhar
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | - Yongxin Zhao
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States
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Furuta T, Yamauchi K, Okamoto S, Takahashi M, Kakuta S, Ishida Y, Takenaka A, Yoshida A, Uchiyama Y, Koike M, Isa K, Isa T, Hioki H. Multi-scale light microscopy/electron microscopy neuronal imaging from brain to synapse with a tissue clearing method, ScaleSF. iScience 2022; 25:103601. [PMID: 35106459 PMCID: PMC8786651 DOI: 10.1016/j.isci.2021.103601] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/19/2021] [Accepted: 12/06/2021] [Indexed: 12/02/2022] Open
Abstract
The mammalian brain is organized over sizes that span several orders of magnitude, from synapses to the entire brain. Thus, a technique to visualize neural circuits across multiple spatial scales (multi-scale neuronal imaging) is vital for deciphering brain-wide connectivity. Here, we developed this technique by coupling successive light microscopy/electron microscopy (LM/EM) imaging with a glutaraldehyde-resistant tissue clearing method, ScaleSF. Our multi-scale neuronal imaging incorporates (1) brain-wide macroscopic observation, (2) mesoscopic circuit mapping, (3) microscopic subcellular imaging, and (4) EM imaging of nanoscopic structures, allowing seamless integration of structural information from the brain to synapses. We applied this technique to three neural circuits of two different species, mouse striatofugal, mouse callosal, and marmoset corticostriatal projection systems, and succeeded in simultaneous interrogation of their circuit structure and synaptic connectivity in a targeted way. Our multi-scale neuronal imaging will significantly advance the understanding of brain-wide connectivity by expanding the scales of objects. Successive light microscopy/electron microscopy in optically cleared tissues Multi-scale neuronal imaging from the entire brain to individual synapses Simultaneous interrogation of neural circuit structure and synaptic connectivity Zooming-in to scarce synaptic contacts with the successive imaging
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Affiliation(s)
- Takahiro Furuta
- Department of Oral Anatomy and Neurobiology, Graduate School of Dentistry, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kenta Yamauchi
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Advanced Research Institute for Health Sciences, Juntendo University, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Shinichiro Okamoto
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Advanced Research Institute for Health Sciences, Juntendo University, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Megumu Takahashi
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Department of Neuroscience, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Soichiro Kakuta
- Laboratory of Morphology and Image Analysis, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Yoko Ishida
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Advanced Research Institute for Health Sciences, Juntendo University, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Aya Takenaka
- Department of Oral Anatomy and Neurobiology, Graduate School of Dentistry, Osaka University, Suita, Osaka 565-0871, Japan
| | - Atsushi Yoshida
- Department of Oral Anatomy and Neurobiology, Graduate School of Dentistry, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasuo Uchiyama
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Advanced Research Institute for Health Sciences, Juntendo University, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Kaoru Isa
- Department of Neuroscience, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Tadashi Isa
- Department of Neuroscience, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Hiroyuki Hioki
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Department of Multi-Scale Brain Structure Imaging, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
- Corresponding author
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124
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Rusch H, Brammerloh M, Stieler J, Sonntag M, Mohammadi S, Weiskopf N, Arendt T, Kirilina E, Morawski M. Finding the best clearing approach - Towards 3D wide-scale multimodal imaging of aged human brain tissue. Neuroimage 2021; 247:118832. [PMID: 34929383 DOI: 10.1016/j.neuroimage.2021.118832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
The accessibility of new wide-scale multimodal imaging techniques led to numerous clearing techniques emerging over the last decade. However, clearing mesoscopic-sized blocks of aged human brain tissue remains an extremely challenging task. Homogenizing refractive indices and reducing light absorption and scattering are the foundation of tissue clearing. Due to its dense and highly myelinated nature, especially in white matter, the human brain poses particular challenges to clearing techniques. Here, we present a comparative study of seven tissue clearing approaches and their impact on aged human brain tissue blocks (> 5 mm). The goal was to identify the most practical and efficient method in regards to macroscopic transparency, brief clearing time, compatibility with immunohistochemical processing and wide-scale multimodal microscopic imaging. We successfully cleared 26 × 26 × 5 mm3-sized human brain samples with two hydrophilic and two hydrophobic clearing techniques. Optical properties as well as light and antibody penetration depths highly vary between these methods. In addition to finding the best clearing approach, we compared three microscopic imaging setups (the Zeiss Laser Scanning Microscope (LSM) 880 , the Miltenyi Biotec Ultramicroscope ll (UM ll) and the 3i Marianas LightSheet microscope) regarding optimal imaging of large-scale tissue samples. We demonstrate that combining the CLARITY technique (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging compatible Tissue hYdrogel) with the Zeiss LSM 880 and combining the iDISCO technique (immunolabeling-enabled three-dimensional imaging of solvent-cleared organs) with the Miltenyi Biotec UM ll are the most practical and efficient approaches to sufficiently clear aged human brain tissue and generate 3D microscopic images. Our results point out challenges that arise from seven clearing and three imaging techniques applied to non-standardized tissue samples such as aged human brain tissue.
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Affiliation(s)
- Henriette Rusch
- Paul Flechsig Institute of Brain Research, Medical Faculty, University of Leipzig, Liebigstraße 19, Leipzig 04103, Germany
| | - Malte Brammerloh
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Science, Stephanstraße 1a, Leipzig 04103, Germany; Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth Sciences, University of Leipzig, Linnéstraße 5, Leipzig 04103, Germany; International Max Planck Research School on Neuroscience of Communication: Function, Structure, and Plasticity, Stephanstraße 1a, Leipzig 04103, Germany
| | - Jens Stieler
- Paul Flechsig Institute of Brain Research, Medical Faculty, University of Leipzig, Liebigstraße 19, Leipzig 04103, Germany
| | - Mandy Sonntag
- Paul Flechsig Institute of Brain Research, Medical Faculty, University of Leipzig, Liebigstraße 19, Leipzig 04103, Germany
| | - Siawoosh Mohammadi
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Science, Stephanstraße 1a, Leipzig 04103, Germany; Institute of Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg 20246, Germany
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Science, Stephanstraße 1a, Leipzig 04103, Germany; Felix Bloch Institute for Solid State Physics, Faculty of Physics and Earth Sciences, University of Leipzig, Linnéstraße 5, Leipzig 04103, Germany
| | - Thomas Arendt
- Paul Flechsig Institute of Brain Research, Medical Faculty, University of Leipzig, Liebigstraße 19, Leipzig 04103, Germany
| | - Evgeniya Kirilina
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Science, Stephanstraße 1a, Leipzig 04103, Germany; Center for Cognitive Neuroscience Berlin, Free University Berlin, Habelschwerdter Allee 45, Berlin 14195, Germany
| | - Markus Morawski
- Paul Flechsig Institute of Brain Research, Medical Faculty, University of Leipzig, Liebigstraße 19, Leipzig 04103, Germany; Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Science, Stephanstraße 1a, Leipzig 04103, Germany.
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125
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Vulders RCM, van Hoogenhuizen RC, van der Giessen E, van der Zaag PJ. Clearing-induced tisssue shrinkage: A novel observation of a thickness size effect. PLoS One 2021; 16:e0261417. [PMID: 34914768 PMCID: PMC8675714 DOI: 10.1371/journal.pone.0261417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 12/01/2021] [Indexed: 11/18/2022] Open
Abstract
The use of clearing agents has provided new insights in various fields of medical research (developmental biology, neurology) by enabling examination of tissue architecture in 3D. One of the challenges is that clearing agents induce tissue shrinkage and the shrinkage rates reported in the literature are incoherent. Here, we report that for a classical clearing agent, benzyl-alcohol benzyl-benzoate (BABB), the shrinkage decreases significantly with increasing sample size, and present an analytical formula describing this.
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Affiliation(s)
| | | | - E. van der Giessen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
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126
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Germain RN, Radtke AJ, Thakur N, Schrom EC, Hor JL, Ichise H, Arroyo-Mejias AJ, Chu CJ, Grant S. Understanding immunity in a tissue-centric context: Combining novel imaging methods and mathematics to extract new insights into function and dysfunction. Immunol Rev 2021; 306:8-24. [PMID: 34918351 DOI: 10.1111/imr.13052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/20/2021] [Accepted: 11/24/2021] [Indexed: 02/02/2023]
Abstract
A central question in immunology is what features allow the immune system to respond in a timely manner to a variety of pathogens encountered at unanticipated times and diverse body sites. Two decades of advanced and static dynamic imaging methods have now revealed several major principles facilitating host defense. Suborgan spatial prepositioning of distinct cells promotes time-efficient interactions upon pathogen sensing. Such pre-organization also provides an effective barrier to movement of pathogens from parenchymal tissues into the blood circulation. Various molecular mechanisms maintain effective intercellular communication among otherwise rapidly moving cells. These and related discoveries have benefited from recent increases in the number of parameters that can be measured simultaneously in a single tissue section and the extension of such multiplex analyses to 3D tissue volumes. The application of new computational methods to such imaging data has provided a quantitative, in vivo context for cell trafficking and signaling pathways traditionally explored in vitro or with dissociated cell preparations. Here, we summarize our efforts to devise and employ diverse imaging tools to probe immune system organization and function, concluding with a commentary on future developments, which we believe will reveal even more about how the immune system operates in health and disease.
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Affiliation(s)
- Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA.,Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Andrea J Radtke
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA.,Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Nishant Thakur
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA.,Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Edward C Schrom
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Jyh Liang Hor
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Hiroshi Ichise
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Armando J Arroyo-Mejias
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Colin J Chu
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA.,Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Spencer Grant
- Lymphocyte Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA.,Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, Maryland, USA
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127
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Richardson DS, Guan W, Matsumoto K, Pan C, Chung K, Ertürk A, Ueda HR, Lichtman JW. TISSUE CLEARING. NATURE REVIEWS. METHODS PRIMERS 2021; 1:84. [PMID: 35128463 PMCID: PMC8815095 DOI: 10.1038/s43586-021-00080-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2021] [Indexed: 12/16/2022]
Abstract
Tissue clearing of gross anatomical samples was first described over a century ago and has only recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Many biological relationships between structure and function require investigation in three dimensions and tissue clearing therefore has the potential to enable broad discoveries in the biological sciences. Unfortunately, the current literature is complex and could confuse researchers looking to begin a clearing project. The goal of this Primer is to outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest. Further, the Primer outlines the required imaging and computational infrastructure needed to perform tissue clearing at scale, gives an overview of current applications, discusses limitations and provides an outlook on future advances in the field.
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Affiliation(s)
- Douglas S. Richardson
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Webster Guan
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Katsuhiko Matsumoto
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Chenchen Pan
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Kwanghun Chung
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Nano Biomedical Engineering (Nano BME) Graduate Program, Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Jeff W. Lichtman
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
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128
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Nobre RJ, Lobo DD, Henriques C, Duarte SP, Lopes SM, Silva AC, Lopes MM, Mariet F, Schwarz LK, Baatje MS, Ferreira V, Vallès A, Pereira de Almeida L, Evers MM, Toonen LJA. MiRNA-Mediated Knockdown of ATXN3 Alleviates Molecular Disease Hallmarks in a Mouse Model for Spinocerebellar Ataxia Type 3. Nucleic Acid Ther 2021; 32:194-205. [PMID: 34878314 PMCID: PMC9221165 DOI: 10.1089/nat.2021.0020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3) is a neurodegenerative disorder caused by the expansion of a CAG repeat in the ATXN3 gene. This mutation leads to a toxic gain of function of the ataxin-3 protein, resulting in neuronal dysfunction and atrophy of specific brain regions over time. As ataxin-3 is a dispensable protein in rodents, ataxin-3 knockdown by gene therapy may be a powerful approach for the treatment of SCA3. In this study, we tested the feasibility of an adeno-associated viral (AAV) vector carrying a previously described artificial microRNA against ATXN3 in a striatal mouse model of SCA3. Striatal injection of the AAV resulted in good distribution throughout the striatum, with strong dose-dependent ataxin-3 knockdown. The hallmark intracellular ataxin-3 inclusions were almost completely alleviated by the microRNA-induced ATXN3 knockdown. In addition, the striatal lesion of dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) in the SCA3 mice was rescued by ATXN3 knockdown, indicating functional rescue of neuronal signaling and health upon AAV treatment. Together, these data suggest that microRNA-induced ataxin-3 knockdown is a promising therapeutic strategy in the treatment of SCA3.
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Affiliation(s)
- Rui Jorge Nobre
- Center for Neuroscience and Cell Biology (CNC), Molecular Therapy of Brain Disorders Group, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, Coimbra, Portugal.,ViraVector-Viral Vector for Gene Transfer Core Facility and University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research (III), University of Coimbra, Coimbra, Portugal
| | - Diana D Lobo
- Center for Neuroscience and Cell Biology (CNC), Molecular Therapy of Brain Disorders Group, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research (III), University of Coimbra, Coimbra, Portugal
| | - Carina Henriques
- Center for Neuroscience and Cell Biology (CNC), Molecular Therapy of Brain Disorders Group, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, Coimbra, Portugal.,ViraVector-Viral Vector for Gene Transfer Core Facility and University of Coimbra, Coimbra, Portugal.,Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Sonia P Duarte
- Center for Neuroscience and Cell Biology (CNC), Molecular Therapy of Brain Disorders Group, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research (III), University of Coimbra, Coimbra, Portugal
| | - Sara M Lopes
- Center for Neuroscience and Cell Biology (CNC), Molecular Therapy of Brain Disorders Group, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research (III), University of Coimbra, Coimbra, Portugal
| | - Ana C Silva
- Center for Neuroscience and Cell Biology (CNC), Molecular Therapy of Brain Disorders Group, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research (III), University of Coimbra, Coimbra, Portugal
| | - Miguel M Lopes
- Center for Neuroscience and Cell Biology (CNC), Molecular Therapy of Brain Disorders Group, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research (III), University of Coimbra, Coimbra, Portugal
| | - Fanny Mariet
- uniQure Biopharma b.v., Amsterdam, the Netherlands
| | | | - M S Baatje
- uniQure Biopharma b.v., Amsterdam, the Netherlands
| | | | | | - Luis Pereira de Almeida
- Center for Neuroscience and Cell Biology (CNC), Molecular Therapy of Brain Disorders Group, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), Vectors, Gene and Cell Therapy Group, University of Coimbra, Coimbra, Portugal.,ViraVector-Viral Vector for Gene Transfer Core Facility and University of Coimbra, Coimbra, Portugal.,Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
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129
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Lee M, Woo J, Kim DH, Yang YM, Lee EY, Kim JH, Kang SG, Shim JK, Park JY. A novel paper MAP method for rapid high resolution histological analysis. Sci Rep 2021; 11:23340. [PMID: 34857810 PMCID: PMC8639998 DOI: 10.1038/s41598-021-02632-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022] Open
Abstract
Three-dimensional visualization of cellular and subcellular-structures in histological-tissues is essential for understanding the complexities of biological-phenomena, especially with regards structural and spatial relationships and pathologlical-diagnosis. Recent advancements in tissue-clearing technology, such as Magnified Analysis of Proteome (MAP), have significantly improved our ability to study biological-structures in three-dimensional space; however, their wide applicability to a variety of tissues is limited by long incubation-times and a need for advanced imaging-systems that are not readily available in most-laboratories. Here, we present optimized MAP-based method for paper-thin samples, Paper-MAP, which allow for rapid clearing and subsequent imaging of three-dimensional sections derived from various tissues using conventional confocal-microscopy. Paper-MAP successfully clear tissues within 1-day, compared to the original-MAP, without significant differences in achieved optical-transparency. As a proof-of-concept, we investigated the vasculature and neuronal-networks of a variety of human and rodent tissues processed via Paper-MAP, in both healthy and diseased contexts, including Alzheimer’s disease and glioma.
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Affiliation(s)
- Mirae Lee
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.,Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
| | - Jiwon Woo
- The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.,Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.,Biomedical Research Institute, Biohedron Therapeutics Co., Ltd, Seoul, 06273, Republic of Korea
| | - Doh-Hee Kim
- Research Institute, Seoul Medical Center, Seoul, 02053, Republic of Korea
| | - Yu-Mi Yang
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.,Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea
| | - Eunice Yoojin Lee
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Jung-Hee Kim
- Research Institute, Seoul Medical Center, Seoul, 02053, Republic of Korea
| | - Seok-Gu Kang
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Department of Medical Sciences, Yonsei University Graduate School, Seoul, 03722, Republic of Korea
| | - Jin-Kyung Shim
- Department of Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jeong-Yoon Park
- Department of Neurosurgery, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea. .,The Spine and Spinal Cord Institute, Department of Neurosurgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea. .,Biomedical Research Center, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 06273, Republic of Korea.
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130
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PSD-93 up-regulates the synaptic activity of corticotropin-releasing hormone neurons in the paraventricular nucleus in depression. Acta Neuropathol 2021; 142:1045-1064. [PMID: 34536123 DOI: 10.1007/s00401-021-02371-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/28/2022]
Abstract
Since the discovery of ketamine anti-depressant effects in last decade, it has effectively revitalized interest in investigating excitatory synapses hypothesis in the pathogenesis of depression. In the present study, we aimed to reveal the excitatory synaptic regulation of corticotropin-releasing hormone (CRH) neuron in the hypothalamus, which is the driving force in hypothalamic-pituitary-adrenal (HPA) axis regulation. This study constitutes the first observation of an increased density of PSD-93-CRH co-localized neurons in the hypothalamic paraventricular nucleus (PVN) of patients with major depression. PSD-93 overexpression in CRH neurons in the PVN induced depression-like behaviors in mice, accompanied by increased serum corticosterone level. PSD-93 knockdown relieved the depression-like phenotypes in a lipopolysaccharide (LPS)-induced depression model. Electrophysiological data showed that PSD-93 overexpression increased CRH neurons synaptic activity, while PSD-93 knockdown decreased CRH neurons synaptic activity. Furthermore, we found that LPS induced increased the release of glutamate from microglia to CRH neurons resulted in depression-like behaviors using fiber photometry recordings. Together, these results show that PSD-93 is involved in the pathogenesis of depression via increasing the synaptic activity of CRH neurons in the PVN, leading to the hyperactivity of the HPA axis that underlies depression-like behaviors.
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131
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Minami Y, Yuan Y, Ueda HR. Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling. Biophys Rev 2021; 13:1113-1126. [PMID: 35059031 PMCID: PMC8724464 DOI: 10.1007/s12551-021-00859-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/18/2021] [Indexed: 02/06/2023] Open
Abstract
The system-level identification and analysis of molecular and cellular networks in mammals can be accelerated by "next-generation" genetics, which is defined as genetics that can achieve desired genetic makeup in a single generation without any animal crossing. We recently established a highly efficient procedure for producing knock-out (KO) mice using the "Triple-CRISPR" method, which targets a single gene by triple gRNAs in the CRISPR/Cas9 system. This procedure achieved an almost perfect KO efficiency (96-100%). We also established a highly efficient procedure, the "ES-mouse" method, for producing knock-in (KI) mice within a single generation. In this method, ES cells were treated with three inhibitors to keep their potency and then injected into 8-cell-stage embryos. These procedures dramatically shortened the time required to produce KO or KI mice from years down to about 3 months. The produced KO and KI mice can also be systematically profiled at a single-cell resolution by the "whole-organ cell profiling," which was realized by tissue-clearing methods, such as CUBIC, and an advanced light-sheet microscopy. The review describes the establishment and application of these technologies above in analyzing the three states (NREM sleep, REM sleep, and awake) of mammalian brains. It also discusses the role of calcium and muscarinic receptors in these states as well as the current challenges and future opportunities in the next-generation mammalian genetics and whole-organ cell profiling for organism-level systems biology.
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Affiliation(s)
- Yoichi Minami
- Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yufei Yuan
- Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
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132
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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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133
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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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134
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Li Q, Shen L. Neuron segmentation using 3D wavelet integrated encoder-decoder network. Bioinformatics 2021; 38:809-817. [PMID: 34647994 PMCID: PMC8756182 DOI: 10.1093/bioinformatics/btab716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 10/12/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION 3D neuron segmentation is a key step for the neuron digital reconstruction, which is essential for exploring brain circuits and understanding brain functions. However, the fine line-shaped nerve fibers of neuron could spread in a large region, which brings great computational cost to the neuron segmentation. Meanwhile, the strong noises and disconnected nerve fibers bring great challenges to the task. RESULTS In this article, we propose a 3D wavelet and deep learning-based 3D neuron segmentation method. The neuronal image is first partitioned into neuronal cubes to simplify the segmentation task. Then, we design 3D WaveUNet, the first 3D wavelet integrated encoder-decoder network, to segment the nerve fibers in the cubes; the wavelets could assist the deep networks in suppressing data noises and connecting the broken fibers. We also produce a Neuronal Cube Dataset (NeuCuDa) using the biggest available annotated neuronal image dataset, BigNeuron, to train 3D WaveUNet. Finally, the nerve fibers segmented in cubes are assembled to generate the complete neuron, which is digitally reconstructed using an available automatic tracing algorithm. The experimental results show that our neuron segmentation method could completely extract the target neuron in noisy neuronal images. The integrated 3D wavelets can efficiently improve the performance of 3D neuron segmentation and reconstruction. AVAILABILITYAND IMPLEMENTATION The data and codes for this work are available at https://github.com/LiQiufu/3D-WaveUNet. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qiufu Li
- Computer Vision Institute, College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China,AI Research Center for Medical Image Analysis and Diagnosis, Shenzhen University, Shenzhen 518060, China,Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen University, Shenzhen 518060, China
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135
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Krupa O, Fragola G, Hadden-Ford E, Mory JT, Liu T, Humphrey Z, Rees BW, Krishnamurthy A, Snider WD, Zylka MJ, Wu G, Xing L, Stein JL. NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images. Cell Rep 2021; 37:109802. [PMID: 34644582 PMCID: PMC8530274 DOI: 10.1016/j.celrep.2021.109802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 07/07/2021] [Accepted: 09/15/2021] [Indexed: 01/18/2023] Open
Abstract
Tissue-clearing methods allow every cell in the mouse brain to be imaged without physical sectioning. However, the computational tools currently available for cell quantification in cleared tissue images have been limited to counting sparse cell populations in stereotypical mice. Here, we introduce NuMorph, a group of analysis tools to quantify all nuclei and nuclear markers within the mouse cortex after clearing and imaging by light-sheet microscopy. We apply NuMorph to investigate two distinct mouse models: a Topoisomerase 1 (Top1) model with severe neurodegenerative deficits and a Neurofibromin 1 (Nf1) model with a more subtle brain overgrowth phenotype. In each case, we identify differential effects of gene deletion on individual cell-type counts and distribution across cortical regions that manifest as alterations of gross brain morphology. These results underline the value of whole-brain imaging approaches, and the tools are widely applicable for studying brain structure phenotypes at cellular resolution.
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Affiliation(s)
- Oleh Krupa
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27514, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Giulia Fragola
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ellie Hadden-Ford
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica T Mory
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tianyi Liu
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zachary Humphrey
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin W Rees
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ashok Krishnamurthy
- Renaissance Computing Institute, Chapel Hill, NC 27517, USA; Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William D Snider
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark J Zylka
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Guorong Wu
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Lei Xing
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jason L Stein
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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136
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Foster NN, Barry J, Korobkova L, Garcia L, Gao L, Becerra M, Sherafat Y, Peng B, Li X, Choi JH, Gou L, Zingg B, Azam S, Lo D, Khanjani N, Zhang B, Stanis J, Bowman I, Cotter K, Cao C, Yamashita S, Tugangui A, Li A, Jiang T, Jia X, Feng Z, Aquino S, Mun HS, Zhu M, Santarelli A, Benavidez NL, Song M, Dan G, Fayzullina M, Ustrell S, Boesen T, Johnson DL, Xu H, Bienkowski MS, Yang XW, Gong H, Levine MS, Wickersham I, Luo Q, Hahn JD, Lim BK, Zhang LI, Cepeda C, Hintiryan H, Dong HW. The mouse cortico-basal ganglia-thalamic network. Nature 2021; 598:188-194. [PMID: 34616074 PMCID: PMC8494639 DOI: 10.1038/s41586-021-03993-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/03/2021] [Indexed: 12/05/2022]
Abstract
The cortico–basal ganglia–thalamo–cortical loop is one of the fundamental network motifs in the brain. Revealing its structural and functional organization is critical to understanding cognition, sensorimotor behaviour, and the natural history of many neurological and neuropsychiatric disorders. Classically, this network is conceptualized to contain three information channels: motor, limbic and associative1–4. Yet this three-channel view cannot explain the myriad functions of the basal ganglia. We previously subdivided the dorsal striatum into 29 functional domains on the basis of the topography of inputs from the entire cortex5. Here we map the multi-synaptic output pathways of these striatal domains through the globus pallidus external part (GPe), substantia nigra reticular part (SNr), thalamic nuclei and cortex. Accordingly, we identify 14 SNr and 36 GPe domains and a direct cortico-SNr projection. The striatonigral direct pathway displays a greater convergence of striatal inputs than the more parallel striatopallidal indirect pathway, although direct and indirect pathways originating from the same striatal domain ultimately converge onto the same postsynaptic SNr neurons. Following the SNr outputs, we delineate six domains in the parafascicular and ventromedial thalamic nuclei. Subsequently, we identify six parallel cortico–basal ganglia–thalamic subnetworks that sequentially transduce specific subsets of cortical information through every elemental node of the cortico–basal ganglia–thalamic loop. Thalamic domains relay this output back to the originating corticostriatal neurons of each subnetwork in a bona fide closed loop. Mesoscale connectomic mapping of the cortico–basal ganglia–thalamic network reveals key architectural and information processing features.
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Affiliation(s)
- Nicholas N Foster
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA. .,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Joshua Barry
- Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Laura Korobkova
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Luis Garcia
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lei Gao
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Marlene Becerra
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yasmine Sherafat
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bo Peng
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China.,HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Jun-Hyeok Choi
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lin Gou
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Brian Zingg
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sana Azam
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Darrick Lo
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Neda Khanjani
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bin Zhang
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jim Stanis
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ian Bowman
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kaelan Cotter
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chunru Cao
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Seita Yamashita
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Amanda Tugangui
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China.,HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Science, Shanghai, China
| | - Tao Jiang
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Xueyan Jia
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Zhao Feng
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Sarvia Aquino
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hyun-Seung Mun
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Muye Zhu
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anthony Santarelli
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nora L Benavidez
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Monica Song
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Gordon Dan
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Marina Fayzullina
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sarah Ustrell
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tyler Boesen
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David L Johnson
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hanpeng Xu
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael S Bienkowski
- Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - X William Yang
- Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience, Los Angeles, CA, USA
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China.,HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Science, Shanghai, China
| | - Michael S Levine
- Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ian Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China.,HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China.,School of Biomedical Engineering, Hainan University, Haikou, China
| | - Joel D Hahn
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Byung Kook Lim
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Li I Zhang
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Carlos Cepeda
- Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Houri Hintiryan
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hong-Wei Dong
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA. .,Mark and Mary Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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137
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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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138
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Zhu J, Liu X, Deng Y, Li D, Yu T, Zhu D. Tissue optical clearing for 3D visualization of vascular networks: A review. Vascul Pharmacol 2021; 141:106905. [PMID: 34506969 DOI: 10.1016/j.vph.2021.106905] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/01/2022]
Abstract
Reconstruction of the vasculature of intact tissues/organs down to the capillary level is essential for understanding the development and remodeling of vascular networks under physiological and pathological conditions. Optical imaging techniques can provide sufficient resolution to distinguish small vessels with several microns, but the imaging depth is somewhat limited due to the high light scattering of opaque tissue. Recently, various tissue optical clearing methods have been developed to overcome light attenuation and improve the imaging depth both for ex-vivo and in-vivo visualizations. Tissue clearing combined with vessel labeling techniques and advanced optical tomography enables successful mapping of the vasculature of different tissues/organs, as well as dynamically monitoring vessel function under normal and pathological conditions. Here, we briefly introduce the commonly-used labeling strategies for entire vascular networks, the current tissue optical clearing techniques available for various tissues, as well as the advanced optical imaging techniques for fast, high-resolution structural and functional imaging for blood vessels. We also discuss the applications of these techniques in the 3D visualization of vascular networks in normal tissues, and the vascular remodeling in several typical pathological models in clinical research. This review is expected to provide valuable insights for researchers to study the potential mechanisms of various vessel-associated diseases using tissue optical clearing pipeline.
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Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaomei Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yating Deng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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139
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Exploring the human cerebral cortex using confocal microscopy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 168:3-9. [PMID: 34536443 PMCID: PMC8992370 DOI: 10.1016/j.pbiomolbio.2021.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/07/2021] [Indexed: 01/12/2023]
Abstract
Cover-all mapping of the distribution of neurons in the human brain would have a significant impact on the deep understanding of brain function. Therefore, complete knowledge of the structural organization of different human brain regions at the cellular level would allow understanding their role in the functions of specific neural networks. Recent advances in tissue clearing techniques have allowed important advances towards this goal. These methods use specific chemicals capable of dissolving lipids, making the tissue completely transparent by homogenizing the refractive index. However, labeling and clearing human brain samples is still challenging. Here, we present an approach to perform the cellular mapping of the human cerebral cortex coupling immunostaining with SWITCH/TDE clearing and confocal microscopy. A specific evaluation of the contributions of the autofluorescence signals generated from the tissue fixation is provided as well as an assessment of lipofuscin pigments interference. Our evaluation demonstrates the possibility of obtaining an efficient clearing and labeling process of parts of adult human brain slices, making it an excellent method for morphological classification and antibody validation of neuronal and non-neuronal markers.
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140
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Abstract
Tissue clearing increases the transparency of late developmental stages and enables deep imaging in fixed organisms. Successful implementation of these methodologies requires a good grasp of sample processing, imaging and the possibilities offered by image analysis. In this Primer, we highlight how tissue clearing can revolutionize the histological analysis of developmental processes and we advise on how to implement effective clearing protocols, imaging strategies and analysis methods for developmental biology.
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Affiliation(s)
| | - Nicolas Renier
- Sorbonne Université, Paris Brain Institute – ICM, INSERM, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
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141
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Shi X, Li Q, Dai Z, Tran AA, Feng S, Ramirez AD, Lin Z, Wang X, Chow TT, Chen J, Kumar D, McColloch AR, Reiter JF, Huang EJ, Seiple IB, Huang B. Label-retention expansion microscopy. J Cell Biol 2021; 220:e202105067. [PMID: 34228783 PMCID: PMC8266563 DOI: 10.1083/jcb.202105067] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 11/28/2022] Open
Abstract
Expansion microscopy (ExM) increases the effective resolving power of any microscope by expanding the sample with swellable hydrogel. Since its invention, ExM has been successfully applied to a wide range of cell, tissue, and animal samples. Still, fluorescence signal loss during polymerization and digestion limits molecular-scale imaging using ExM. Here, we report the development of label-retention ExM (LR-ExM) with a set of trifunctional anchors that not only prevent signal loss but also enable high-efficiency labeling using SNAP and CLIP tags. We have demonstrated multicolor LR-ExM for a variety of subcellular structures. Combining LR-ExM with superresolution stochastic optical reconstruction microscopy (STORM), we have achieved molecular resolution in the visualization of polyhedral lattice of clathrin-coated pits in situ.
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Affiliation(s)
- Xiaoyu Shi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA
| | - Qi Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | - Zhipeng Dai
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
| | - Arthur A. Tran
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA
| | - Siyu Feng
- University of California, Berkeley–University of California, San Francisco Joint Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA
| | - Alejandro D. Ramirez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Zixi Lin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Xiaomeng Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Tracy T. Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Jiapei Chen
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Dhivya Kumar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Andrew R. McColloch
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA
| | - Jeremy F. Reiter
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Eric J. Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Ian B. Seiple
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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142
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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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143
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Olianti C, Giardini F, Lazzeri E, Costantini I, Silvestri L, Coppini R, Cerbai E, Pavone FS, Sacconi L. Optical clearing in cardiac imaging: A comparative study. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 168:10-17. [PMID: 34358555 DOI: 10.1016/j.pbiomolbio.2021.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
The optical clearing of the cardiac tissue has always been a challenging goal to obtain successful three-dimensional reconstructions of entire hearts. Typically, the developed protocols are targeted at the clearing of the brain; cardiac tissue requires proper arrangements to the original protocols, which are usually tough and time-consuming to figure out. Here, we present the application of three different clearing methodologies on mouse hearts: uDISCO, CLARITY, and SHIELD. For each approach, we describe the required optimizations that we have developed to improve the outcome; in particular, we focus on comparing the features of the tissue after the application of each methodology, especially in terms of tissue preservation, transparency, and staining. We found that the uDISCO protocol induces strong fiber delamination of the cardiac tissue, thus reducing the reliability of structural analyses. The CLARITY protocol confers a high level of transparency to the heart and allows deep penetration of the fluorescent dyes; however, it requires long times for the clearing and the tissue loses its robustness. The SHIELD methodology, indeed, is very promising for tissue maintenance since it preserves its consistency and provides ideal transparency, but further approaches are needed to obtain homogeneous staining of the whole heart. Since the CLARITY procedure, despite the disadvantages in terms of tissue preservation and timings, is actually the most suitable approach to image labeled samples in depth, we optimized and performed the methodology also on human cardiac tissue from control hearts and hearts with hypertrophic cardiomyopathy.
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Affiliation(s)
- Camilla Olianti
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
| | - Francesco Giardini
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
| | - Erica Lazzeri
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy
| | - Irene Costantini
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; National Institute of Optics, National Research Council, Florence, 50125, Italy; Department of Biology, University of Florence, Sesto Fiorentino, 50019, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; National Institute of Optics, National Research Council, Florence, 50125, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, 50019, Italy
| | - Raffaele Coppini
- Department of Neurosciences, Psychology, Drugs and Child Health, University of Florence, Italy
| | - Elisabetta Cerbai
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; Department of Neurosciences, Psychology, Drugs and Child Health, University of Florence, Italy
| | - Francesco S Pavone
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; National Institute of Optics, National Research Council, Florence, 50125, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, 50019, Italy
| | - Leonardo Sacconi
- European Laboratory for Non-Linear Spectroscopy, Sesto Fiorentino, 50019, Italy; National Institute of Optics, National Research Council, Florence, 50125, Italy; Institute for Experimental Cardiovascular Medicine, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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144
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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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145
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Benavidez NL, Bienkowski MS, Zhu M, Garcia LH, Fayzullina M, Gao L, Bowman I, Gou L, Khanjani N, Cotter KR, Korobkova L, Becerra M, Cao C, Song MY, Zhang B, Yamashita S, Tugangui AJ, Zingg B, Rose K, Lo D, Foster NN, Boesen T, Mun HS, Aquino S, Wickersham IR, Ascoli GA, Hintiryan H, Dong HW. Organization of the inputs and outputs of the mouse superior colliculus. Nat Commun 2021; 12:4004. [PMID: 34183678 PMCID: PMC8239028 DOI: 10.1038/s41467-021-24241-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022] Open
Abstract
The superior colliculus (SC) receives diverse and robust cortical inputs to drive a range of cognitive and sensorimotor behaviors. However, it remains unclear how descending cortical input arising from higher-order associative areas coordinate with SC sensorimotor networks to influence its outputs. Here, we construct a comprehensive map of all cortico-tectal projections and identify four collicular zones with differential cortical inputs: medial (SC.m), centromedial (SC.cm), centrolateral (SC.cl) and lateral (SC.l). Further, we delineate the distinctive brain-wide input/output organization of each collicular zone, assemble multiple parallel cortico-tecto-thalamic subnetworks, and identify the somatotopic map in the SC that displays distinguishable spatial properties from the somatotopic maps in the neocortex and basal ganglia. Finally, we characterize interactions between those cortico-tecto-thalamic and cortico-basal ganglia-thalamic subnetworks. This study provides a structural basis for understanding how SC is involved in integrating different sensory modalities, translating sensory information to motor command, and coordinating different actions in goal-directed behaviors.
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Affiliation(s)
- Nora L Benavidez
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael S Bienkowski
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Muye Zhu
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Luis H Garcia
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Marina Fayzullina
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lei Gao
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ian Bowman
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lin Gou
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Neda Khanjani
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kaelan R Cotter
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Laura Korobkova
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Marlene Becerra
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chunru Cao
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Monica Y Song
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Bin Zhang
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Seita Yamashita
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Amanda J Tugangui
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Brian Zingg
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kasey Rose
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
| | - Darrick Lo
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nicholas N Foster
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Tyler Boesen
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Hyun-Seung Mun
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Sarvia Aquino
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Giorgio A Ascoli
- Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Houri Hintiryan
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Hong-Wei Dong
- Stevens Neuroimaging and Informatics Institute, Laboratory of Neuro Imaging, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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146
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Matryba P, Łukasiewicz K, Pawłowska M, Tomczuk J, Gołąb J. Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging? Int J Mol Sci 2021; 22:ijms22136730. [PMID: 34201632 PMCID: PMC8268743 DOI: 10.3390/ijms22136730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.
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Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
- The Doctoral School of the Medical University of Warsaw, Medical University of Warsaw, 02-097 Warsaw, Poland
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Correspondence:
| | - Kacper Łukasiewicz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
| | - Monika Pawłowska
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland;
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Jacek Tomczuk
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (J.T.); (J.G.)
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147
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Mao Y, Wang X, Huang P, Tian R. Spatial proteomics for understanding the tissue microenvironment. Analyst 2021; 146:3777-3798. [PMID: 34042124 DOI: 10.1039/d1an00472g] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human body comprises rich populations of cells, which are arranged into tissues and organs with diverse functionalities. These cells exhibit a broad spectrum of phenotypes and are often organized as a heterogeneous but sophisticatedly regulated ecosystem - tissue microenvironment, inside which every cell interacts with and is reciprocally influenced by its surroundings through its life span. Therefore, it is critical to comprehensively explore the cellular machinery and biological processes in the tissue microenvironment, which is best exemplified by the tumor microenvironment (TME). The past decade has seen increasing advances in the field of spatial proteomics, the main purpose of which is to characterize the abundance and spatial distribution of proteins and their post-translational modifications in the microenvironment of diseased tissues. Herein, we outline the achievements and remaining challenges of mass spectrometry-based tissue spatial proteomics. Exciting technology developments along with important biomedical applications of spatial proteomics are highlighted. In detail, we focus on high-quality resources built by scalpel macrodissection-based region-resolved proteomics, method development of sensitive sample preparation for laser microdissection-based spatial proteomics, and antibody recognition-based multiplexed tissue imaging. In the end, critical issues and potential future directions for spatial proteomics are also discussed.
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Affiliation(s)
- Yiheng Mao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China. and Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xi Wang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China and Shenzhen People's Hospital, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Peiwu Huang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
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148
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Myers A, Ford J, Decker S, Crawford F, Tzekov R. Volumetric histological characterization of optic nerve degeneration using tissue clearing: literature review and practical study. J Histotechnol 2021; 44:206-216. [PMID: 34132156 DOI: 10.1080/01478885.2021.1938808] [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: 10/21/2022]
Abstract
Tissue clearing technologies can greatly improve the depth and accuracy with which the three-dimensional structure of tissues, especially those of the nervous system, can be visualized. A review of the present literature suggests that the growing diversity and sophistication of various approaches have contributed to the expansion of this method to a greater variety of tissue types, experimental conditions, and imaging modalities. In the proof-of-concept study presented in this paper, a simplified and modified version of the tissue clearing method CUBIC (clear, unobstructed brain imaging cocktails and computational analysis) was used in conjunction with fluorescent staining and immunohistochemistry to illustrate the three-dimensional structure and molecular characteristics of inflammatory and degenerative activity in the mouse optic nerve. Based on the studies summarized in this mini-review, and our impression from using the mCUBIC method, it appears that tissue clearing could be a viable approach revealing three-dimensional histological features of myelin-rich tissues under normal conditions and after injury.
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Affiliation(s)
- April Myers
- Vision Research Program, The Roskamp Institute, Sarasota, FL, USA.,Department of Neurobiology, New College of Florida, Sarasota, FL, USA.,Vision Science Graduate Program, University of California Berkeley, Berkeley, CA, USA
| | - Jonathan Ford
- Department of Radiology, University of South Florida, Tampa, FL, USA
| | - Summer Decker
- Department of Radiology, University of South Florida, Tampa, FL, USA
| | - Fiona Crawford
- Vision Research Program, The Roskamp Institute, Sarasota, FL, USA.,James A. Haley Veterans' Administration Hospital, Tampa, FL, USA
| | - Radouil Tzekov
- Vision Research Program, The Roskamp Institute, Sarasota, FL, USA.,James A. Haley Veterans' Administration Hospital, Tampa, FL, USA.,Department of Ophthalmology, University of South Florida, Tampa, FL, USA
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149
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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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150
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Luchsinger JR, Fetterly TL, Williford KM, Salimando GJ, Doyle MA, Maldonado J, Simerly RB, Winder DG, Centanni SW. Delineation of an insula-BNST circuit engaged by struggling behavior that regulates avoidance in mice. Nat Commun 2021; 12:3561. [PMID: 34117229 PMCID: PMC8196075 DOI: 10.1038/s41467-021-23674-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 05/07/2021] [Indexed: 12/31/2022] Open
Abstract
Active responses to stressors involve motor planning, execution, and feedback. Here we identify an insular cortex to BNST (insula→BNST) circuit recruited during restraint stress-induced active struggling that modulates affective behavior. We demonstrate that activity in this circuit tightly follows struggling behavioral events and that the size of the fluorescent sensor transient reports the duration of the struggle event, an effect that fades with repeated exposure to the homotypic stressor. Struggle events are associated with enhanced glutamatergic- and decreased GABAergic signaling in the insular cortex, indicating the involvement of a larger circuit. We delineate the afferent network for this pathway, identifying substantial input from motor- and premotor cortex, somatosensory cortex, and the amygdala. To begin to dissect these incoming signals, we examine the motor cortex input, and show that the cells projecting from motor regions to insular cortex are engaged shortly before struggle event onset. This study thus demonstrates a role for the insula→BNST pathway in monitoring struggling activity and regulating affective behavior.
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Affiliation(s)
- Joseph R Luchsinger
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt J.F. Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tracy L Fetterly
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt J.F. Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kellie M Williford
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt J.F. Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gregory J Salimando
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt J.F. Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Marie A Doyle
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt J.F. Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jose Maldonado
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt J.F. Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Richard B Simerly
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt J.F. Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Danny G Winder
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt J.F. Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Samuel W Centanni
- Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA.
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