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Ventura-Antunes L, Nackenoff A, Romero-Fernandez W, Bosworth AM, Prusky A, Wang E, Carvajal-Tapia C, Shostak A, Harmsen H, Mobley B, Maldonado J, Solopova E, Caleb Snider J, David Merryman W, Lippmann ES, Schrag M. Arteriolar degeneration and stiffness in cerebral amyloid angiopathy are linked to β-amyloid deposition and lysyl oxidase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583563. [PMID: 38659767 PMCID: PMC11042178 DOI: 10.1101/2024.03.08.583563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cerebral amyloid angiopathy (CAA) is a vasculopathy characterized by vascular β-amyloid (Aβ) deposition on cerebral blood vessels. CAA is closely linked to Alzheimer's disease (AD) and intracerebral hemorrhage. CAA is associated with the loss of autoregulation in the brain, vascular rupture, and cognitive decline. To assess morphological and molecular changes associated with the degeneration of penetrating arterioles in CAA, we analyzed post-mortem human brain tissue from 26 patients with mild, moderate, and severe CAA end neurological controls. The tissue was optically cleared for three-dimensional light sheet microscopy, and morphological features were quantified using surface volume rendering. We stained Aβ, vascular smooth muscle (VSM), lysyl oxidase (LOX), and vascular markers to visualize the relationship between degenerative morphological features, including vascular dilation, dolichoectasia (variability in lumenal diameter) and tortuosity, and the volumes of VSM, Aβ, and LOX in arterioles. Atomic force microscopy (AFM) was used to assess arteriolar wall stiffness, and we identified a pattern of morphological features associated with degenerating arterioles in the cortex. The volume of VSM associated with the arteriole was reduced by around 80% in arterioles with severe CAA and around 60% in cases with mild/moderate CAA. This loss of VSM correlated with increased arteriolar diameter and variability of diameter, suggesting VSM loss contributes to arteriolar laxity. These vascular morphological features correlated strongly with Aβ deposits. At sites of microhemorrhage, Aβ was consistently present, although the morphology of the deposits changed from the typical organized ring shape to sharply contoured shards with marked dilation of the vessel. AFM showed that arteriolar walls with CAA were more than 400% stiffer than those without CAA. Finally, we characterized the association of vascular degeneration with LOX, finding strong associations with VSM loss and vascular degeneration. These results show an association between vascular Aβ deposition, microvascular degeneration, and increased vascular stiffness, likely due to the combined effects of replacement of VSM by β-amyloid, cross-linking of extracellular matrices (ECM) by LOX, and possibly fibrosis. This advanced microscopic imaging study clarifies the association between Aβ deposition and vascular fragility. Restoration of physiologic ECM properties in penetrating arteries may yield a novel therapeutic strategy for CAA.
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Affiliation(s)
| | - Alex Nackenoff
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Allison M Bosworth
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Alex Prusky
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emmeline Wang
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Alena Shostak
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hannah Harmsen
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bret Mobley
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jose Maldonado
- Vanderbilt Neurovisualization Lab, Vanderbilt University, Nashville, TN, USA
| | - Elena Solopova
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - J. Caleb Snider
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - W. David Merryman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ethan S Lippmann
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Matthew Schrag
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN, USA
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
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2
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Koukalova L, Chmelova M, Amlerova Z, Vargova L. Out of the core: the impact of focal ischemia in regions beyond the penumbra. Front Cell Neurosci 2024; 18:1336886. [PMID: 38504666 PMCID: PMC10948541 DOI: 10.3389/fncel.2024.1336886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 02/08/2024] [Indexed: 03/21/2024] Open
Abstract
The changes in the necrotic core and the penumbra following induction of focal ischemia have been the focus of attention for some time. However, evidence shows, that ischemic injury is not confined to the primarily affected structures and may influence the remote areas as well. Yet many studies fail to probe into the structures beyond the penumbra, and possibly do not even find any significant results due to their short-term design, as secondary damage occurs later. This slower reaction can be perceived as a therapeutic opportunity, in contrast to the ischemic core defined as irreversibly damaged tissue, where the window for salvation is comparatively short. The pathologies in remote structures occur relatively frequently and are clearly linked to the post-stroke neurological outcome. In order to develop efficient therapies, a deeper understanding of what exactly happens in the exo-focal regions is necessary. The mechanisms of glia contribution to the ischemic damage in core/penumbra are relatively well described and include impaired ion homeostasis, excessive cell swelling, glutamate excitotoxic mechanism, release of pro-inflammatory cytokines and phagocytosis or damage propagation via astrocytic syncytia. However, little is known about glia involvement in post-ischemic processes in remote areas. In this literature review, we discuss the definitions of the terms "ischemic core", "penumbra" and "remote areas." Furthermore, we present evidence showing the array of structural and functional changes in the more remote regions from the primary site of focal ischemia, with a special focus on glia and the extracellular matrix. The collected information is compared with the processes commonly occurring in the ischemic core or in the penumbra. Moreover, the possible causes of this phenomenon and the approaches for investigation are described, and finally, we evaluate the efficacy of therapies, which have been studied for their anti-ischemic effect in remote areas in recent years.
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Affiliation(s)
- Ludmila Koukalova
- Department of Neuroscience, Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Martina Chmelova
- Department of Neuroscience, Second Faculty of Medicine, Charles University, Prague, Czechia
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Zuzana Amlerova
- Department of Neuroscience, Second Faculty of Medicine, Charles University, Prague, Czechia
| | - Lydia Vargova
- Department of Neuroscience, Second Faculty of Medicine, Charles University, Prague, Czechia
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
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3
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Baek S, Jang J, Jung HJ, Lee H, Choe Y. Advanced Immunolabeling Method for Optical Volumetric Imaging Reveals Dystrophic Neurites of Dopaminergic Neurons in Alzheimer's Disease Mouse Brain. Mol Neurobiol 2023:10.1007/s12035-023-03823-9. [PMID: 38049707 DOI: 10.1007/s12035-023-03823-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023]
Abstract
Optical brain clearing combined with immunolabeling is valuable for analyzing molecular tissue structures, including complex synaptic connectivity. However, the presence of aberrant lipid deposition due to aging and brain disorders poses a challenge for achieving antibody penetration throughout the entire brain volume. Herein, we present an efficient brain-wide immunolabeling method, the immuno-active clearing technique (iACT). The treatment of brain tissues with a zwitterionic detergent, specifically SB3-12, significantly enhanced tissue permeability by effectively mitigating lipid barriers. Notably, Quadrol treatment further refines the methodology by effectively eliminating residual detergents from cleared brain tissues, subsequently amplifying volumetric fluorescence signals. Employing iACT, we uncover disrupted axonal projections within the mesolimbic dopaminergic (DA) circuits in 5xFAD mice. Subsequent characterization of DA neural circuits in 5xFAD mice revealed proximal axonal swelling and misrouting of distal axonal compartments in proximity to amyloid-beta plaques. Importantly, these structural anomalies in DA axons correlate with a marked reduction in DA release within the nucleus accumbens. Collectively, our findings highlight the efficacy of optical volumetric imaging with iACT in resolving intricate structural alterations in deep brain neural circuits. Furthermore, we unveil the compromised integrity of DA pathways, contributing to the underlying neuropathology of Alzheimer's disease. The iACT technique thus holds significant promise as a valuable asset for advancing our understanding of complex neurodegenerative disorders and may pave the way for targeted therapeutic interventions. The axonal projection of DA neurons in the septum and the NAc showed dystrophic phenotypes such as growth cone-like enlargement of the axonal terminus and aggregated neurites. Brain-wide imaging of structural defects in the neural circuits was facilitated with brain clearing and antibody penetration assisted with SB3-12 and Quadrol pre-treatment. The whole volumetric imaging process could be completed in a week with the robust iACT method. Created with https://www.biorender.com/ .
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Affiliation(s)
- Soonbong Baek
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea
| | - Jaemyung Jang
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea
| | - Hyun Jin Jung
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea
| | - Hyeyoung Lee
- Division of Applied Bioengineering, Dong-eui University, Busanjin-gu, Busan, 47340, Republic of Korea
| | - Youngshik Choe
- Developmental Disorders & Rare Diseases Research Group, Korea Brain Research Institute, 61 Cheomdan-ro, Daegu, 41062, Republic of Korea.
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4
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Delage E, Guilbert T, Yates F. Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy. J Cell Biol 2023; 222:e202307143. [PMID: 37847528 PMCID: PMC10583220 DOI: 10.1083/jcb.202307143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023] Open
Abstract
In parallel with the development of tissue-clearing methods, over the last decade, light sheet fluorescence microscopy has contributed to major advances in various fields, such as cell and developmental biology and neuroscience. While biologists are increasingly integrating three-dimensional imaging into their research projects, their experience with the technique is not always up to their expectations. In response to a survey of specific challenges associated with sample clearing and labeling, image acquisition, and data analysis, we have critically assessed the recent literature to characterize the difficulties inherent to light sheet fluorescence microscopy applied to cleared biological samples and to propose solutions to overcome them. This review aims to provide biologists interested in light sheet fluorescence microscopy with a primer for the development of their imaging pipeline, from sample preparation to image analysis. Importantly, we believe that issues could be avoided with better anticipation of image analysis requirements, which should be kept in mind while optimizing sample preparation and acquisition parameters.
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Affiliation(s)
- Elise Delage
- CellTechs Laboratory, SupBiotech, Villejuif, France
- Service d’Etude des Prions et des Infections Atypiques, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, Université Paris Saclay, Fontenay-aux-Roses, France
| | - Thomas Guilbert
- Institut Cochin, Institut national de la santé et de la recherche médicale (U1016), Centre National de la Recherche Scientifique (UMR 8104), Université de Paris (UMR-S1016), Paris, France
| | - Frank Yates
- CellTechs Laboratory, SupBiotech, Villejuif, France
- Service d’Etude des Prions et des Infections Atypiques, Institut François Jacob, Commissariat à l’Energie Atomique et aux Energies Alternatives, Université Paris Saclay, Fontenay-aux-Roses, France
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5
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Terstege DJ, Epp JR. Network Neuroscience Untethered: Brain-Wide Immediate Early Gene Expression for the Analysis of Functional Connectivity in Freely Behaving Animals. BIOLOGY 2022; 12:biology12010034. [PMID: 36671727 PMCID: PMC9855808 DOI: 10.3390/biology12010034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
Abstract
Studying how spatially discrete neuroanatomical regions across the brain interact is critical to advancing our understanding of the brain. Traditional neuroimaging techniques have led to many important discoveries about the nature of these interactions, termed functional connectivity. However, in animal models these traditional neuroimaging techniques have generally been limited to anesthetized or head-fixed setups or examination of small subsets of neuroanatomical regions. Using the brain-wide expression density of immediate early genes (IEG), we can assess brain-wide functional connectivity underlying a wide variety of behavioural tasks in freely behaving animal models. Here, we provide an overview of the necessary steps required to perform IEG-based analyses of functional connectivity. We also outline important considerations when designing such experiments and demonstrate the implications of these considerations using an IEG-based network dataset generated for the purpose of this review.
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6
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Mahmud N, Eisner C, Purushothaman S, Storer MA, Kaplan DR, Miller FD. Nail-associated mesenchymal cells contribute to and are essential for dorsal digit tip regeneration. Cell Rep 2022; 41:111853. [PMID: 36543145 DOI: 10.1016/j.celrep.2022.111853] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/05/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Here, we ask why the nail base is essential for mammalian digit tip regeneration, focusing on the inductive nail mesenchyme. We identify a transcriptional signature for these cells that includes Lmx1b and show that the Lmx1b-expressing nail mesenchyme is essential for blastema formation. We use a combination of Lmx1bCreERT2-based lineage-tracing and single-cell transcriptional analyses to show that the nail mesenchyme contributes cells for two pro-regenerative mechanisms. One group of cells maintains their identity and regenerates the new nail mesenchyme. A second group contributes specifically to the dorsal blastema, loses their nail mesenchyme phenotype, acquires a blastema transcriptional state that is highly similar to blastema cells of other origins, and ultimately contributes to regeneration of the dorsal but not ventral dermis and bone. Thus, the regenerative necessity for an intact nail base is explained, at least in part, by a requirement for the inductive nail mesenchyme.
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Affiliation(s)
- Neemat Mahmud
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, ON M5G 1A8, Canada
| | - Christine Eisner
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sruthi Purushothaman
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mekayla A Storer
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - David R Kaplan
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z, Canada
| | - Freda D Miller
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, ON M5G 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z, Canada.
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7
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Lopes MM, Paysan J, Rino J, Lopes SM, Pereira de Almeida L, Cortes L, Nobre RJ. A new protocol for whole-brain biodistribution analysis of AAVs by tissue clearing, light-sheet microscopy and semi-automated spatial quantification. Gene Ther 2022; 29:665-679. [PMID: 36316447 DOI: 10.1038/s41434-022-00372-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 12/23/2022]
Abstract
Recombinant adeno-associated virus (rAAV) has become one of the most promising gene delivery systems for both in vitro and in vivo applications. However, a key challenge is the lack of suitable imaging technologies to evaluate delivery, biodistribution and tropism of rAAVs and efficiently monitor disease amelioration promoted by AAV-based therapies at a whole-organ level with single-cell resolution. Therefore, we aimed to establish a new pipeline for the biodistribution analysis of natural and new variants of AAVs at a whole-brain level by tissue clearing and light-sheet fluorescence microscopy (LSFM). To test this platform, neonatal C57BL/6 mice were intravenously injected with rAAV9 encoding EGFP and, after sacrifice, brains were processed by standard immunohistochemistry and a recently released aqueous-based clearing procedure. This clearing technique required no dedicated equipment and rendered highly cleared brains, while simultaneously preserving endogenous fluorescence. Moreover, three-dimensional imaging by LSFM allowed the quantitative analysis of EGFP at a whole-brain level, as well as the reconstruction of Purkinje cells for the retrieval of valuable morphological information inaccessible by standard immunohistochemistry. In conclusion, the pipeline herein described takes the AAVs to a new level when coupled to LSFM, proving its worth as a bioimaging tool in tropism and gene therapy studies.
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Affiliation(s)
- Miguel M Lopes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | | | - José Rino
- iMM - Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sara M Lopes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Luís Pereira de Almeida
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal. .,ViraVector - Viral Vectors for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal. .,FFUC - Faculty of Pharmacy of the University of Coimbra, Coimbra, Portugal.
| | - Luísa Cortes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal. .,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal. .,MICC-CNC - Microscopy Imaging Center of Coimbra - CNC, University of Coimbra, Coimbra, Portugal.
| | - Rui Jorge Nobre
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal. .,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal. .,ViraVector - Viral Vectors for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal.
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Kim JJH, Parajuli S, Sinha A, Mahamdeh M, van den Boomen M, Coll-Font J, Chen LS, Fan Y, Eder RA, Phipps K, Yuan S, Nguyen C. Pocket CLARITY enables distortion-mitigated cardiac microstructural tissue characterization of large-scale specimens. Front Cardiovasc Med 2022; 9:1037500. [PMID: 36451924 PMCID: PMC9701703 DOI: 10.3389/fcvm.2022.1037500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
Molecular phenotyping by imaging of intact tissues has been used to reveal 3D molecular and structural coherence in tissue samples using tissue clearing techniques. However, clearing and imaging of cardiac tissue remains challenging for large-scale (>100 mm3) specimens due to sample distortion. Thus, directly assessing tissue microstructural geometric properties confounded by distortion such as cardiac helicity has been limited. To combat sample distortion, we developed a passive CLARITY technique (Pocket CLARITY) that utilizes a permeable cotton mesh pocket to encapsulate the sample to clear large-scale cardiac swine samples with minimal tissue deformation and protein loss. Combined with light sheet auto-fluorescent and scattering microscopy, Pocket CLARITY enabled the characterization of myocardial microstructural helicity of cardiac tissue from control, heart failure, and myocardial infarction in swine. Pocket CLARITY revealed with high fidelity that transmural microstructural helicity of the heart is significantly depressed in cardiovascular disease (CVD), thereby revealing new insights at the tissue level associated with impaired cardiac function.
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Affiliation(s)
- Joan J. H. Kim
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Shestruma Parajuli
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Aman Sinha
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Mohammed Mahamdeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | - Maaike van den Boomen
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Radiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Jaume Coll-Font
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Lily Shi Chen
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Yiling Fan
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Robert A. Eder
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Kellie Phipps
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Shiaulou Yuan
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Christopher Nguyen
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States,Division of Health Science Technology, Harvard-Massachusetts Institute of Technology, Cambridge, MA, United States,Cardiovascular Innovation Research Center, Heart, Vascular, and Thoracic Institute, Cleveland Clinic, Cleveland, OH, United States,*Correspondence: Christopher Nguyen,
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9
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Malkovskiy AV, Tom A, Joubert LM, Bao Z. Visualization of the distribution of covalently cross-linked hydrogels in CLARITY brain-polymer hybrids for different monomer concentrations. Sci Rep 2022; 12:13549. [PMID: 35941350 PMCID: PMC9360022 DOI: 10.1038/s41598-022-17687-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
CLARITY is a tissue preservation and optical clearing technique whereby a hydrogel is formed directly within the architectural confines of ex vivo brain tissue. In this work, the extent of polymer gel formation and crosslinking within tissue was assessed using Raman spectroscopy and rheology on CLARITY samples prepared with a range of acrylamide monomer (AAm) concentrations (1%, 4%, 8%, 12% w/v). Raman spectroscopy of individual neurons within hybrids revealed the chemical presence and distribution of polyacrylamide within the mouse hippocampus. Consistent with rheological measurements, lower %AAm concentration decreased shear elastic modulus G', providing a practical correlation with sample permeability and protein retention. Permeability of F(ab)'2 secondary fluorescent antibody changes from 9.3 to 1.4 µm2 s-1 going from 1 to 12%. Notably, protein retention increased linearly relative to standard PFA-fixed tissue from 96.6% when AAm concentration exceeded 1%, with 12% AAm samples retaining up to ~ 99.3% native protein. This suggests that though 1% AAm offers high permeability, additional %AAm may be required to enhance protein. Our quantitative results on polymer distribution, stability, protein retention, and macromolecule permeability can be used to guide the design of future CLARITY-based tissue-clearing solutions, and establish protocols for characterization of novel tissue-polymer hybrid biomaterials using chemical spectroscopy and rheology.
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Affiliation(s)
| | - Ariane Tom
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Lydia-Marie Joubert
- Cell Sciences Imaging Facility (CSIF), Stanford University, Stanford, CA, 94305, USA
| | - Zhenan Bao
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA.
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10
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MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. Sci Data 2022; 9:230. [PMID: 35614082 PMCID: PMC9133120 DOI: 10.1038/s41597-022-01338-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/13/2022] [Indexed: 11/08/2022] Open
Abstract
Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase ( www.facebase.org , https://doi.org/10.25550/3-HXMC ) and GitHub ( https://github.com/jaydevine/MusMorph ).
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11
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Tadokoro T, Bravo-Hernandez M, Agashkov K, Kobayashi Y, Platoshyn O, Navarro M, Marsala S, Miyanohara A, Yoshizumi T, Shigyo M, Krotov V, Juhas S, Juhasova J, Nguyen D, Kupcova Skalnikova H, Motlik J, Studenovska H, Proks V, Reddy R, Driscoll SP, Glenn TD, Kemthong T, Malaivijitnond S, Tomori Z, Vanicky I, Kakinohana M, Pfaff SL, Ciacci J, Belan P, Marsala M. Precision spinal gene delivery-induced functional switch in nociceptive neurons reverses neuropathic pain. Mol Ther 2022; 30:2722-2745. [PMID: 35524407 PMCID: PMC9372322 DOI: 10.1016/j.ymthe.2022.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/31/2022] [Accepted: 04/29/2022] [Indexed: 11/17/2022] Open
Abstract
Second-order spinal cord excitatory neurons play a key role in spinal processing and transmission of pain signals to the brain. Exogenously-induced change in developmentally-imprinted excitatory neurotransmitter phenotype of these neurons to inhibitory has not yet been achieved. Here we use a subpial dorsal horn-targeted delivery of AAV (adeno-associated virus) vector(s) encoding GABA (gamma-Aminobutyric acid,) synthesizing-releasing inhibitory machinery in mice with neuropathic pain. Treated animals showed a progressive and complete reversal of neuropathic pain (tactile and brush-evoked pain behavior) which persisted for minimum 2.5 months post-treatment. The mechanism of this treatment effect results from the switch of excitatory to preferential inhibitory neurotransmitter phenotype in dorsal horn nociceptive neurons and a resulting increase in inhibitory activity in regional spinal circuitry after peripheral nociceptive stimulation. No detectable side effects (such as sedation, motor weakness or loss of normal sensation) were seen between 2-13 months post-treatment in naive adult mice, pigs and non-human primates. The use of this treatment approach may represent a potent and safe treatment modality in patients suffering from spinal cord- or peripheral nerve-injury induced neuropathic pain.
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Affiliation(s)
- Takahiro Tadokoro
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA; Department of Anesthesiology, University of Ryukyus, Okinawa, Japan; Neurgain Technologies, 9620 Towne Centre Drive, Suite 100, San Diego, CA 92121, USA
| | - Mariana Bravo-Hernandez
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Kirill Agashkov
- Departments of Sensory Signaling and Molecular Biophysics, Bogomoletz Institute of Physiology, Kyiv, Ukraine
| | - Yoshiomi Kobayashi
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Oleksandr Platoshyn
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Michael Navarro
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Silvia Marsala
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA; Neurgain Technologies, 9620 Towne Centre Drive, Suite 100, San Diego, CA 92121, USA
| | - Atsushi Miyanohara
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA; Vector Core Laboratory, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Tetsuya Yoshizumi
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Michiko Shigyo
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Volodymyr Krotov
- Departments of Sensory Signaling and Molecular Biophysics, Bogomoletz Institute of Physiology, Kyiv, Ukraine
| | - Stefan Juhas
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Jana Juhasova
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Duong Nguyen
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Helena Kupcova Skalnikova
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Jan Motlik
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Hana Studenovska
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Department of Biomaterials and Bioanalogous Systems, Heyrovsky Square 2,162 06 Prague 6, Czech Republic
| | - Vladimir Proks
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Department of Biomaterials and Bioanalogous Systems, Heyrovsky Square 2,162 06 Prague 6, Czech Republic
| | - Rajiv Reddy
- Department of Anesthesiology, Pain Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shawn P Driscoll
- Gene Expression Laboratory and the Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Thomas D Glenn
- Gene Expression Laboratory and the Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Taratorn Kemthong
- National Primate Research Center of Thailand, Chulalongkorn University, Kaengkhoi District, Saraburi 18110, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Kaengkhoi District, Saraburi 18110, Thailand
| | - Zoltan Tomori
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Ivo Vanicky
- Institute of Neurobiology, Biomedical Research Center, Slovak Academy of Sciences, Kosice, Slovakia
| | | | - Samuel L Pfaff
- Gene Expression Laboratory and the Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph Ciacci
- Department of Neurosurgery, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Pavel Belan
- Departments of Sensory Signaling and Molecular Biophysics, Bogomoletz Institute of Physiology, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
| | - Martin Marsala
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA; Institute of Neurobiology, Biomedical Research Center, Slovak Academy of Sciences, Kosice, Slovakia.
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12
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FASTMAP: Open-Source Flexible Atlas Segmentation Tool for Multi-Area Processing of Biological Images. eNeuro 2022; 9:ENEURO.0325-21.2022. [PMID: 35228311 PMCID: PMC8938980 DOI: 10.1523/eneuro.0325-21.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 12/03/2022] Open
Abstract
To better understand complex systems, such as the brain, studying the interactions between multiple brain regions is imperative. Such experiments often require delineation of multiple brain regions on microscopic images based on preexisting brain atlases. Experiments examining the relationships of multiple regions across the brain have traditionally relied on manual plotting of regions. This process is very intensive and becomes untenable with a large number of regions of interest (ROIs). To reduce the amount of time required to process multi-region datasets, several tools for atlas registration have been developed; however, these tools are often inflexible to tissue type, only supportive of a limited number of atlases and orientation, require considerable computational expertise, or are only compatible with certain types of microscopy. To address the need for a simple yet extensible atlas registration tool, we have developed FASTMAP, a Flexible Atlas Segmentation Tool for Multi-Area Processing. We demonstrate its ability to register images efficiently and flexibly to custom mouse brain atlas plates, to detect differences in the regional numbers of labels of interest, and to conduct densitometry analyses. This open-source and user-friendly tool will facilitate the atlas registration of diverse tissue types, unconventional atlas organizations, and a variety of tissue preparations.
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13
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Molina LM, Krutsenko Y, Jenkins NE, Smith MC, Tao J, Wheeler TB, Watkins SC, Watson AM, Monga SP. LiverClear: A versatile protocol for mouse liver tissue clearing. STAR Protoc 2022; 3:101178. [PMID: 35243370 PMCID: PMC8857608 DOI: 10.1016/j.xpro.2022.101178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Although there are numerous tissue clearing protocols, most are inadequate for clearing liver tissue. Here we present a flexible protocol for mouse liver tissue; we combine strategies from several previously published protocols for delipidation, decolorization, staining, and refractive index matching. LiverClear is sufficiently versatile to allow clearing of healthy and diseased mouse liver followed by immunofluorescence staining and imaging to visualize intact 3D structures such as bile ducts and hepatocyte canaliculi. We also adapted this protocol for clearing human livers. For complete details on the use and execution of this protocol, please refer to Molina et al. (2021).
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Affiliation(s)
- Laura M. Molina
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA,Division of Experimental Pathology, Department of Pathology, UPMC, Pittsburgh, PA 15213, USA
| | - Yekaterina Krutsenko
- Division of Experimental Pathology, Department of Pathology, UPMC, Pittsburgh, PA 15213, USA
| | - Nathaniel E.C. Jenkins
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Megan C. Smith
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Junyan Tao
- Division of Experimental Pathology, Department of Pathology, UPMC, Pittsburgh, PA 15213, USA,Pittsburgh Liver Research Center, UPMC, Pittsburgh, PA 15213, USA
| | - Travis B. Wheeler
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Simon C. Watkins
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Alan M. Watson
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA,Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA,Corresponding author
| | - Satdarshan P. Monga
- Division of Experimental Pathology, Department of Pathology, UPMC, Pittsburgh, PA 15213, USA,Pittsburgh Liver Research Center, UPMC, Pittsburgh, PA 15213, USA,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, UPMC, Pittsburgh, PA 15213, USA,Corresponding author
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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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15
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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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16
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Sands GB, Ashton JL, Trew ML, Baddeley D, Walton RD, Benoist D, Efimov IR, Smith NP, Bernus O, Smaill BH. It's clearly the heart! Optical transparency, cardiac tissue imaging, and computer modelling. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 168:18-32. [PMID: 34126113 DOI: 10.1016/j.pbiomolbio.2021.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/10/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022]
Abstract
Recent developments in clearing and microscopy enable 3D imaging with cellular resolution up to the whole organ level. These methods have been used extensively in neurobiology, but their uptake in other fields has been much more limited. Application of this approach to the human heart and effective use of the data acquired present challenges of scale and complexity. Four interlinked issues need to be addressed: 1) efficient clearing and labelling of heart tissue, 2) fast microscopic imaging of human-scale samples, 3) handling and processing of multi-terabyte 3D images, and 4) extraction of structural information in computationally tractable structure-based models of cardiac function. Preliminary studies show that each of these requirements can be achieved with the appropriate application and development of existing technologies.
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Affiliation(s)
- Gregory B Sands
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand.
| | - Jesse L Ashton
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - Mark L Trew
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - David Baddeley
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand; Department of Cell Biology, Yale University, New Haven CT, 06520, USA
| | - Richard D Walton
- IHU Liryc, Fondation Bordeaux Université, Bordeaux, France; Univ. Bordeaux, Inserm, Centre de Recherche Cardio-Thoracique, U1045, 33000, Bordeaux, France
| | - David Benoist
- IHU Liryc, Fondation Bordeaux Université, Bordeaux, France; Univ. Bordeaux, Inserm, Centre de Recherche Cardio-Thoracique, U1045, 33000, Bordeaux, France
| | - Igor R Efimov
- IHU Liryc, Fondation Bordeaux Université, Bordeaux, France; Department of Biomedical Engineering, The George Washington University, Washington DC, 20052, USA
| | - Nicolas P Smith
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand; Queensland University of Technology, Brisbane 4000, Australia
| | - Olivier Bernus
- IHU Liryc, Fondation Bordeaux Université, Bordeaux, France; Univ. Bordeaux, Inserm, Centre de Recherche Cardio-Thoracique, U1045, 33000, Bordeaux, France
| | - Bruce H Smaill
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
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17
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Yu T, Li D, Zhu D. Tissue Optical Clearing for Biomedical Imaging: From In Vitro to In Vivo. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 3233:217-255. [PMID: 34053030 DOI: 10.1007/978-981-15-7627-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tissue optical clearing technique provides a prospective solution for the application of advanced optical methods in life sciences. This chapter firstly gives a brief introduction to mechanisms of tissue optical clearing techniques, from the physical mechanism to chemical mechanism, which is the most important foundation to develop tissue optical clearing methods. During the past years, in vitro and in vivo tissue optical clearing methods were developed. In vitro tissue optical clearing techniques, including the solvent-based clearing methods and the hydrophilic reagents-based clearing methods, combined with labeling technique and advanced microscopy, can be applied to image 3D microstructure of tissue blocks or whole organs such as brain and spinal cord with high resolution. In vivo skin or skull optical clearing, promise various optical imaging techniques to detect cutaneous or cortical cell and vascular structure and function without surgical window.
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Affiliation(s)
- Tingting Yu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dongyu Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, China. .,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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18
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Weiss KR, Voigt FF, Shepherd DP, Huisken J. Tutorial: practical considerations for tissue clearing and imaging. Nat Protoc 2021; 16:2732-2748. [PMID: 34021294 PMCID: PMC10542857 DOI: 10.1038/s41596-021-00502-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/18/2021] [Indexed: 02/06/2023]
Abstract
Tissue clearing has become a powerful technique for studying anatomy and morphology at scales ranging from entire organisms to subcellular features. With the recent proliferation of tissue-clearing methods and imaging options, it can be challenging to determine the best clearing protocol for a particular tissue and experimental question. The fact that so many clearing protocols exist suggests there is no one-size-fits-all approach to tissue clearing and imaging. Even in cases where a basic level of clearing has been achieved, there are many factors to consider, including signal retention, staining (labeling), uniformity of transparency, image acquisition and analysis. Despite reviews citing features of clearing protocols, it is often unknown a priori whether a protocol will work for a given experiment, and thus some optimization is required by the end user. In addition, the capabilities of available imaging setups often dictate how the sample needs to be prepared. After imaging, careful evaluation of volumetric image data is required for each combination of clearing protocol, tissue type, biological marker, imaging modality and biological question. Rather than providing a direct comparison of the many clearing methods and applications available, in this tutorial we address common pitfalls and provide guidelines for designing, optimizing and imaging in a successful tissue-clearing experiment with a focus on light-sheet fluorescence microscopy (LSFM).
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Affiliation(s)
- Kurt R Weiss
- Morgridge Institute for Research, Madison, WI, USA
| | - Fabian F Voigt
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich & ETH Zurich, Zurich, Switzerland
| | - Douglas P Shepherd
- Department of Physics, Arizona State University, Tempe, AZ, USA
- Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Jan Huisken
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA.
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19
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Chen Y, Li X, Zhang D, Wang C, Feng R, Li X, Wen Y, Xu H, Zhang XS, Yang X, Chen Y, Feng Y, Zhou B, Chen BC, Lei K, Cai S, Jia JM, Gao L. A Versatile Tiling Light Sheet Microscope for Imaging of Cleared Tissues. Cell Rep 2021; 33:108349. [PMID: 33147464 DOI: 10.1016/j.celrep.2020.108349] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/13/2020] [Accepted: 10/13/2020] [Indexed: 01/14/2023] Open
Abstract
We present a tiling light sheet microscope compatible with all tissue clearing methods for rapid multicolor 3D imaging of cleared tissues with micron-scale (4 × 4 × 10 μm3) to submicron-scale (0.3 × 0.3 × 1 μm3) spatial resolution. The resolving ability is improved to sub-100 nm (70 × 70 × 200 nm3) via tissue expansion. The microscope uses tiling light sheets to achieve higher spatial resolution and better optical sectioning ability than conventional light sheet microscopes. The illumination light is phase modulated to adjust the position and intensity profile of the light sheet based on the desired spatial resolution and imaging speed and to keep the microscope aligned. The ability of the microscope to align via phase modulation alone also ensures its accuracy for multicolor 3D imaging and makes the microscope reliable and easy to operate. Here we describe the working principle and design of the microscope. We demonstrate its utility by imaging various cleared tissues.
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Affiliation(s)
- Yanlu Chen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Xiaoliang Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Dongdong Zhang
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Chunhui Wang
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Ruili Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Xuzhao Li
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Yao Wen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Hao Xu
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Xinyi Shirley Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yongyi Chen
- Department of Clinical laboratory, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310000, China
| | - Yi Feng
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Bo Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kai Lei
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Shang Cai
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.
| | - Jie-Min Jia
- Key Laboratory of Growth Regulation and Translation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.
| | - Liang Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.
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20
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Avilov SV. Navigating across multi-dimensional space of tissue clearing parameters. Methods Appl Fluoresc 2021; 9:022001. [PMID: 33592593 DOI: 10.1088/2050-6120/abe6fb] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Optical tissue clearing refers to physico-chemical treatments which make thick biological samples transparent by removal of refractive index gradients and light absorbing substances. Although tissue clearing was first reported in 1914, it was not widely used in light microscopy until 21th century, because instrumentation of that time did not permit to acquire and handle images of thick (mm to cm) samples as whole. Rapid progress in optical instrumentation, computers and software over the last decades made micrograph acquisition of centimeter-thick samples feasible. This boosted tissue clearing use and development. Numerous diverse protocols have been developed. They use organic solvents or water-miscible substances, such as detergents and chaotropic agents; some protocols require application of electric field or perfusion with special devices. There is no 'best-for-all' tissue clearing method. Depending on the case, one or another protocol is more suitable. Most of protocols require days or even weeks to complete, thus choosing an unsuitable protocol may cause an important waste of time. Several inter-dependent parameters should be taken into account to choose a tissue clearing protocol, such as: (1) required image quality (resolution, contrast, signal to noise ratio etc), (2) nature and size of the sample, (3) type of labels, (4) characteristics of the available instrumentation, (5) budget, (6) time budget, and (7) feasibility. Present review focusses on the practical aspects of various tissue clearing techniques. It is aimed to help non-experts to choose tissue clearing techniques which are optimal for their particular cases.
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Affiliation(s)
- Sergiy V Avilov
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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21
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Leuze C, Goubran M, Barakovic M, Aswendt M, Tian Q, Hsueh B, Crow A, Weber EMM, Steinberg GK, Zeineh M, Plowey ED, Daducci A, Innocenti G, Thiran JP, Deisseroth K, McNab JA. Comparison of diffusion MRI and CLARITY fiber orientation estimates in both gray and white matter regions of human and primate brain. Neuroimage 2021; 228:117692. [PMID: 33385546 PMCID: PMC7953593 DOI: 10.1016/j.neuroimage.2020.117692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 11/30/2022] Open
Abstract
Diffusion MRI (dMRI) represents one of the few methods for mapping brain fiber orientations non-invasively. Unfortunately, dMRI fiber mapping is an indirect method that relies on inference from measured diffusion patterns. Comparing dMRI results with other modalities is a way to improve the interpretation of dMRI data and help advance dMRI technologies. Here, we present methods for comparing dMRI fiber orientation estimates with optical imaging of fluorescently labeled neurofilaments and vasculature in 3D human and primate brain tissue cuboids cleared using CLARITY. The recent advancements in tissue clearing provide a new opportunity to histologically map fibers projecting in 3D, which represents a captivating complement to dMRI measurements. In this work, we demonstrate the capability to directly compare dMRI and CLARITY in the same human brain tissue and assess multiple approaches for extracting fiber orientation estimates from CLARITY data. We estimate the three-dimensional neuronal fiber and vasculature orientations from neurofilament and vasculature stained CLARITY images by calculating the tertiary eigenvector of structure tensors. We then extend CLARITY orientation estimates to an orientation distribution function (ODF) formalism by summing multiple sub-voxel structure tensor orientation estimates. In a sample containing part of the human thalamus, there is a mean angular difference of 19o±15o between the primary eigenvectors of the dMRI tensors and the tertiary eigenvectors from the CLARITY neurofilament stain. We also demonstrate evidence that vascular compartments do not affect the dMRI orientation estimates by showing an apparent lack of correspondence (mean angular difference = 49o±23o) between the orientation of the dMRI tensors and the structure tensors in the vasculature stained CLARITY images. In a macaque brain dataset, we examine how the CLARITY feature extraction depends on the chosen feature extraction parameters. By varying the volume of tissue over which the structure tensor estimates are derived, we show that orientation estimates are noisier with more spurious ODF peaks for sub-voxels below 30 µm3 and that, for our data, the optimal gray matter sub-voxel size is between 62.5 µm3 and 125 µm3. The example experiments presented here represent an important advancement towards robust multi-modal MRI-CLARITY comparisons.
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Affiliation(s)
- C Leuze
- Department of Radiology, Stanford University, Stanford, CA, USA.
| | - M Goubran
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - M Barakovic
- Department of Radiology, Stanford University, Stanford, CA, USA; Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - M Aswendt
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Q Tian
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - B Hsueh
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - A Crow
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - E M M Weber
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - G K Steinberg
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - M Zeineh
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - E D Plowey
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - A Daducci
- Department of Computer Science, University of Verona, Verona, Italy
| | - G Innocenti
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden; Brain and Mind Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - J-P Thiran
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - K Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - J A McNab
- Department of Radiology, Stanford University, Stanford, CA, USA
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22
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Somuncu ÖS, Berns HM, Sanchez JG. New Pioneers of Optogenetics in Neuroscience. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1288:47-60. [PMID: 31983055 DOI: 10.1007/5584_2019_473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Optogenetics have recently increased in popularity as tools to study behavior in response to the brain and how these trends relate back to a neuronal circuit. Additionally, the high demand for human cerebral tissue in research has led to the generation of a new model to investigate human brain development and disease. Human Pluripotent Stem Cells (hPSCs) have been previously used to recapitulate the development of several tissues such as intestine, stomach and liver and to model disease in a human context, recently new improvements have been made in the field of hPSC-derived brain organoids to better understand overall brain development but more specifically, to mimic inter-neuronal communication. This review aims to highlight the recent advances in these two separate approaches of brain research and to emphasize the need for overlap. These two novel approaches would combine the study of behavior along with the specific circuits required to produce the signals causing such behavior. This review is focused on the current state of the field, as well as the development of novel optogenetic technologies and their potential for current scientific study and potential therapeutic use.
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Affiliation(s)
- Ö Sezin Somuncu
- Department of Medical Biology, Bahçeşehir University Faculty of Medicine, İstanbul, Turkey.
| | - H Matthew Berns
- Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, USA
| | - J Guillermo Sanchez
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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23
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Oh MS, Khawar IA, Lee DW, Park JK, Kuh HJ. Three-Dimensional Imaging for Multiplex Phenotypic Analysis of Pancreatic Microtumors Grown on a Minipillar Array Chip. Cancers (Basel) 2020; 12:E3662. [PMID: 33297288 PMCID: PMC7762293 DOI: 10.3390/cancers12123662] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/13/2022] Open
Abstract
Three-dimensional (3D) culture of tumor spheroids (TSs) within the extracellular matrix (ECM) represents a microtumor model that recapitulates human solid tumors in vivo, and is useful for 3D multiplex phenotypic analysis. However, the low efficiency of 3D culture and limited 3D visualization of microtumor specimens impose technical hurdles for the evaluation of TS-based phenotypic analysis. Here, we report a 3D microtumor culture-to-3D visualization system using a minipillar array chip combined with a tissue optical clearing (TOC) method for high-content phenotypic analysis of microtumors. To prove the utility of this method, phenotypic changes in TSs of human pancreatic cancer cells were determined by co-culture with cancer-associated fibroblasts and M2-type tumor-associated macrophages. Significant improvement was achieved in immunostaining and optical transmission in each TS as well as the entire microtumor specimen, enabling optimization in image-based analysis of the morphology, structural organization, and protein expression in cancer cells and the ECM. Changes in the invasive phenotype, including cellular morphology and expression of epithelial-mesenchymal transition-related proteins and drug-induced apoptosis under stromal cell co-culture were also successfully analyzed. Overall, our study demonstrates that a minipillar array chip combined with TOC offers a novel system for 3D culture-to-3D visualization of microtumors to facilitate high-content phenotypic analysis.
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Affiliation(s)
- Min-Suk Oh
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea;
| | - Iftikhar Ali Khawar
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
- Department of Urology, Samsung Advanced Institute of Health Science and Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University, Seoul 06351, Korea
| | - Dong Woo Lee
- Departments of Biomedical Engineering, Konyang University, Daejeon 35365, Korea;
| | - Jong Kook Park
- Department of Biomedical Science, Research Institute for Bioscience & Biotechnology, Hallym University, Chuncheon 24252, Korea;
| | - Hyo-Jeong Kuh
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea;
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
- Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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24
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Bouchery T, Moyat M, Sotillo J, Silverstein S, Volpe B, Coakley G, Tsourouktsoglou TD, Becker L, Shah K, Kulagin M, Guiet R, Camberis M, Schmidt A, Seitz A, Giacomin P, Le Gros G, Papayannopoulos V, Loukas A, Harris NL. Hookworms Evade Host Immunity by Secreting a Deoxyribonuclease to Degrade Neutrophil Extracellular Traps. Cell Host Microbe 2020; 27:277-289.e6. [PMID: 32053791 DOI: 10.1016/j.chom.2020.01.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/15/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022]
Abstract
Hookworms cause a major neglected tropical disease, occurring after larvae penetrate the host skin. Neutrophils are phagocytes that kill large pathogens by releasing neutrophil extracellular traps (NETs), but whether they target hookworms during skin infection is unknown. Using a murine hookworm, Nippostrongylus brasiliensis, we observed neutrophils being rapidly recruited and deploying NETs around skin-penetrating larvae. Neutrophils depletion or NET inhibition altered larvae behavior and enhanced the number of adult worms following murine infection. Nevertheless, larvae were able to mitigate the effect of NETs by secreting a deoxyribonuclease (Nb-DNase II) to degrade the DNA backbone. Critically, neutrophils were able to kill larvae in vitro, which was enhanced by neutralizing Nb-DNase II. Homologs of Nb-DNase II are present in other nematodes, including the human hookworm, Necator americanus, which also evaded NETs in vitro. These findings highlight the importance of neutrophils in hookworm infection and a potential conserved mechanism of immune evasion.
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Affiliation(s)
- Tiffany Bouchery
- Laboratory of Intestinal Immunology, Department of Immunology and Pathology, Monash University, Melbourne, VIC 3004, Australia; Laboratory of Intestinal Immunology, SV, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne CH-1015 Switzerland
| | - Mati Moyat
- Laboratory of Intestinal Immunology, Department of Immunology and Pathology, Monash University, Melbourne, VIC 3004, Australia; Laboratory of Intestinal Immunology, SV, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne CH-1015 Switzerland
| | - Javier Sotillo
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4814, Australia; Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid 28222, Spain
| | - Solomon Silverstein
- Laboratory of Intestinal Immunology, Department of Immunology and Pathology, Monash University, Melbourne, VIC 3004, Australia
| | - Beatrice Volpe
- Laboratory of Intestinal Immunology, SV, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne CH-1015 Switzerland
| | - Gillian Coakley
- Laboratory of Intestinal Immunology, Department of Immunology and Pathology, Monash University, Melbourne, VIC 3004, Australia
| | | | - Luke Becker
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4814, Australia
| | - Kathleen Shah
- Laboratory of Intestinal Immunology, SV, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne CH-1015 Switzerland
| | - Manuel Kulagin
- Laboratory of Intestinal Immunology, SV, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne CH-1015 Switzerland
| | - Romain Guiet
- Bioimaging and Optics Core Facility, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Mali Camberis
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Alfonso Schmidt
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Arne Seitz
- Bioimaging and Optics Core Facility, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Paul Giacomin
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4814, Australia
| | - Graham Le Gros
- Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | | | - Alex Loukas
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4814, Australia
| | - Nicola L Harris
- Laboratory of Intestinal Immunology, Department of Immunology and Pathology, Monash University, Melbourne, VIC 3004, Australia.
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25
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Nietz A, Krook-Magnuson C, Gutierrez H, Klein J, Sauve C, Hoff I, Christenson Wick Z, Krook-Magnuson E. Selective loss of the GABA Aα1 subunit from Purkinje cells is sufficient to induce a tremor phenotype. J Neurophysiol 2020; 124:1183-1197. [PMID: 32902350 DOI: 10.1152/jn.00100.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Previously, an essential tremor-like phenotype has been noted in animals with a global knockout of the GABAAα1 subunit. Given the hypothesized role of the cerebellum in tremor, including essential tremor, we used transgenic mice to selectively knock out the GABAAα1 subunit from cerebellar Purkinje cells. We examined the resulting phenotype regarding impacts on inhibitory postsynaptic currents, survival rates, gross motor abilities, and expression of tremor. Purkinje cell specific knockout of the GABAAα1 subunit abolished all GABAA-mediated inhibition in Purkinje cells, while leaving GABAA-mediated inhibition to cerebellar molecular layer interneurons intact. Selective loss of GABAAα1 from Purkinje cells did not produce deficits on the accelerating rotarod, nor did it result in decreased survival rates. However, a tremor phenotype was apparent, regardless of sex or background strain. This tremor mimicked the tremor seen in animals with a global knockout of the GABAAα1 subunit, and, like essential tremor in patients, was responsive to ethanol. These findings indicate that reduced inhibition to Purkinje cells is sufficient to induce a tremor phenotype, highlighting the importance of the cerebellum, inhibition, and Purkinje cells in tremor.NEW & NOTEWORTHY Animals with a global knockout of the GABAAα1 subunit show a tremor phenotype reminiscent of essential tremor. Here we show that selective knockout of GABAAα1 from Purkinje cells is sufficient to produce a tremor phenotype, although this tremor is less severe than seen in animals with a global knockout. These findings illustrate that the cerebellum can play a key role in the genesis of the observed tremor phenotype.
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Affiliation(s)
- Angela Nietz
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota
| | | | - Haruna Gutierrez
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota
| | - Julia Klein
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota
| | - Clarke Sauve
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota
| | - Isaac Hoff
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota
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26
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Arms L, Robson AL, Woldu A, Martin A, Palmer W, Flynn J, Hua S. Considerations for using optical clearing techniques for 3D imaging of nanoparticle biodistribution. Int J Pharm 2020; 588:119739. [PMID: 32783979 DOI: 10.1016/j.ijpharm.2020.119739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
A key consideration in the clinical translation of nanomedicines is determining their in vivo biodistribution in preclinical studies, which is important for predicting and correlating therapeutic efficacy and safety. There are a number of techniques available for analyzing the in vivo biodistribution of nanoparticles, with each having its own advantages and limitations. However, conventional techniques are limited by their inability to image the three-dimensional (3D) association of nanoparticles with cells, vasculature and other biological structures in whole organs at a subcellular level. Recently, optical clearing techniques have been used to evaluate the biodistribution of nanoparticles by 3D organ imaging. Optical clearing is a procedure that is increasingly being used to improve the imaging of biological tissues, whereby light scattering substances are removed to better match the refractive indices of different tissue layers. The use of optical clearing techniques has the potential to transform the way we evaluate the biodistribution of new and existing nanomedicines, as it allows the visualization of the interaction of nanoparticles with the biological environment in intact tissues. This review will compare the main optical clearing techniques and will address the considerations for the use of these techniques to evaluate nanoparticle biodistribution.
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Affiliation(s)
- Lauren Arms
- Therapeutic Targeting Research Group, University of Newcastle, Callaghan, NSW, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Annie-Louise Robson
- Therapeutic Targeting Research Group, University of Newcastle, Callaghan, NSW, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Ameha Woldu
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Antony Martin
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - William Palmer
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Jamie Flynn
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Susan Hua
- Therapeutic Targeting Research Group, University of Newcastle, Callaghan, NSW, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.
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27
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Di Bona A, Vita V, Costantini I, Zaglia T. Towards a clearer view of sympathetic innervation of cardiac and skeletal muscles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 154:80-93. [DOI: 10.1016/j.pbiomolbio.2019.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/02/2019] [Accepted: 07/11/2019] [Indexed: 02/07/2023]
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28
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Ueda HR, Dodt HU, Osten P, Economo MN, Chandrashekar J, Keller PJ. Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy. Neuron 2020; 106:369-387. [PMID: 32380050 PMCID: PMC7213014 DOI: 10.1016/j.neuron.2020.03.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/11/2020] [Accepted: 03/04/2020] [Indexed: 01/12/2023]
Abstract
Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.
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Affiliation(s)
- Hiroki R Ueda
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN BDR, Suita, Osaka 565-0871, Japan.
| | - Hans-Ulrich Dodt
- Department of Bioelectronics, FKE, Vienna University of Technology-TU Wien, Vienna, Austria; Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Pavel Osten
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA
| | - Michael N Economo
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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29
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Salamon RJ, Zhang Z, Mahmoud AI. Capturing the Cardiac Injury Response of Targeted Cell Populations via Cleared Heart Three-Dimensional Imaging. J Vis Exp 2020. [PMID: 32250361 DOI: 10.3791/60482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Cardiovascular disease outranks all other causes of death and is responsible for a staggering 31% of mortalities worldwide. This disease manifests in cardiac injury, primarily in the form of an acute myocardial infarction. With little resilience following injury, the once healthy cardiac tissue will be replaced by fibrous, non-contractile scar tissue and often be a prelude to heart failure. To identify novel treatment options in regenerative medicine, research has focused on vertebrates with innate regenerative capabilities. One such model organism is the neonatal mouse, which responds to cardiac injury with robust myocardial regeneration. In order to induce an injury in the neonatal mouse that is clinically relevant, we have developed a surgery to occlude the left anterior descending artery (LAD), mirroring a myocardial infarction triggered by atherosclerosis in the human heart. When matched with the technology to track changes both within cardiomyocytes and non-myocyte populations, this model provides us with a platform to identify the mechanisms that guide heart regeneration. Gaining insight into changes in cardiac cell populations following injury once relied heavily on methods such as tissue sectioning and histological examination, which are limited to two-dimensional analysis and often damage the tissue in the process. Moreover, these methods lack the ability to trace changes in cell lineages, instead providing merely a snapshot of the injury response. Here, we describe how technologically advanced methods in lineage tracing models, whole organ clearing, and three-dimensional (3D) whole-mount microscopy can be used to elucidate mechanisms of cardiac repair. With our protocol for neonatal mouse myocardial infarction surgery, tissue clearing, and 3D whole organ imaging, the complex pathways that induce cardiomyocyte proliferation can be unraveled, revealing novel therapeutic targets for cardiac regeneration.
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Affiliation(s)
- Rebecca J Salamon
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison School of Medicine and Public Health
| | - Ziheng Zhang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison School of Medicine and Public Health
| | - Ahmed I Mahmoud
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison School of Medicine and Public Health;
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30
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Tward D, Brown T, Kageyama Y, Patel J, Hou Z, Mori S, Albert M, Troncoso J, Miller M. Diffeomorphic Registration With Intensity Transformation and Missing Data: Application to 3D Digital Pathology of Alzheimer's Disease. Front Neurosci 2020; 14:52. [PMID: 32116503 PMCID: PMC7027169 DOI: 10.3389/fnins.2020.00052] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 01/14/2020] [Indexed: 12/15/2022] Open
Abstract
This paper examines the problem of diffeomorphic image registration in the presence of differing image intensity profiles and sparsely sampled, missing, or damaged tissue. Our motivation comes from the problem of aligning 3D brain MRI with 100-micron isotropic resolution to histology sections at 1 × 1 × 1,000-micron resolution with multiple varying stains. We pose registration as a penalized Bayesian estimation, exploiting statistical models of image formation where the target images are modeled as sparse and noisy observations of the atlas. In this injective setting, there is no assumption of symmetry between atlas and target. Cross-modality image matching is achieved by jointly estimating polynomial transformations of the atlas intensity. Missing data is accommodated via a multiple atlas selection procedure where several atlas images may be of homogeneous intensity and correspond to "background" or "artifact." The two concepts are combined within an Expectation-Maximization algorithm, where atlas selection posteriors and deformation parameters are updated iteratively and polynomial coefficients are computed in closed form. We validate our method with simulated images, examples from neuropathology, and a standard benchmarking dataset. Finally, we apply it to reconstructing digital pathology and MRI in standard atlas coordinates. By using a standard convolutional neural network to detect tau tangles in histology slices, this registration method enabled us to quantify the 3D density distribution of tauopathy throughout the medial temporal lobe of an Alzheimer's disease postmortem specimen.
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Affiliation(s)
- Daniel Tward
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Center for Imaging Science, Johns Hopkins University, Baltimore, MD, United States
| | - Timothy Brown
- Center for Imaging Science, Johns Hopkins University, Baltimore, MD, United States
| | - Yusuke Kageyama
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jaymin Patel
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Zhipeng Hou
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Susumu Mori
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Juan Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Michael Miller
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Center for Imaging Science, Johns Hopkins University, Baltimore, MD, United States
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31
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Ueda HR, Ertürk A, Chung K, Gradinaru V, Chédotal A, Tomancak P, Keller PJ. Tissue clearing and its applications in neuroscience. Nat Rev Neurosci 2020; 21:61-79. [PMID: 31896771 PMCID: PMC8121164 DOI: 10.1038/s41583-019-0250-1] [Citation(s) in RCA: 273] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2019] [Indexed: 02/06/2023]
Abstract
State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.
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Affiliation(s)
- Hiroki R Ueda
- Department of Systems Pharmacology, University of Tokyo, Tokyo, Japan.
- Laboratory for Synthetic Biology, RIKEN BDR, Suita, Japan.
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University of Munich, Munich, Germany
- Institute of Tissue Engineering and Regenerative Medicine, Helmholtz Zentrum München, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Eli & Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for NanoMedicine, Institute for Basic Science, Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering, Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alain Chédotal
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- IT4Innovations, Technical University of Ostrava, Ostrava, Czech Republic
| | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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Clearing, immunofluorescence, and confocal microscopy for the three-dimensional imaging of murine testes and study of testis biology. J Struct Biol 2020; 209:107449. [PMID: 31931124 DOI: 10.1016/j.jsb.2020.107449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 01/15/2023]
Abstract
Optical clearing techniques provide unprecedented opportunities to study large tissue samples at histological resolution, eliminating the need for physical sectioning while preserving the three-dimensional structure of intact biological systems. There is significant potential for applying optical clearing to reproductive tissues. In testicular biology, for example, the study of spermatogenesis and the use of spermatogonial stem cells offer high-impact applications in fertility medicine and reproductive biotechnology. The objective of our study is to apply optical clearing, immunofluorescence, and confocal microscopy to testicular tissue in order to reconstruct its three-dimensional microstructure in intact samples. We used Triton-X/DMSO clearing in combination with refractive index matching to achieve optical transparency of fixed mouse testes. An antibody against smooth muscle actin was used to label peritubular myoid cells of seminiferous tubules while an antibody against ubiquitin C-terminal hydrolase was used to label Sertoli cells and spermatogonia in the seminiferous epithelium. Specimens were then imaged using confocal fluorescence microscopy. We were able to successfully clear testicular tissue and utilize immunofluorescent probes. Additionally, we successfully visualized the histological compartments of testicular tissue in three-dimensional reconstructions. Optical clearing combined with immunofluorescence and confocal imaging offers a powerful new method to analyze the cytoarchitecture of testicular tissue at histological resolution while maintaining the macro-scale perspective of the intact system. Considering the importance of the murine model, our developed method represents a significant contribution to the field of male reproductive biology, enabling the study of testicular function.
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Touloumes GJ, Ardoña HAM, Casalino EK, Zimmerman JF, Chantre CO, Bitounis D, Demokritou P, Parker KK. Mapping 2D- and 3D-distributions of metal/metal oxide nanoparticles within cleared human ex vivo skin tissues. NANOIMPACT 2020; 17:100208. [PMID: 33251378 PMCID: PMC7687853 DOI: 10.1016/j.impact.2020.100208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
An increasing number of commercial skincare products are being manufactured with engineered nanomaterials (ENMs), prompting a need to fully understand how ENMs interact with the dermal barrier as a major biodistribution entry route. Although animal studies show that certain nanomaterials can cross the skin barrier, physiological differences between human and animal skin, such as the lack of sweat glands, limit the translational validity of these results. Current optical microscopy methods have limited capabilities to visualize ENMs within human skin tissues due to the high amount of background light scattering caused by the dense, ubiquitous extracellular matrix (ECM) of the skin. Here, we hypothesized that organic solvent-based tissue clearing ("immunolabeling-enabled three-dimensional imaging of solvent-cleared organs", or "iDISCO") would reduce background light scattering from the extracellular matrix of the skin to sufficiently improve imaging contrast for both 2D mapping of unlabeled metal oxide ENMs and 3D mapping of fluorescent nanoparticles. We successfully mapped the 2D distribution of label-free TiO2 and ZnO nanoparticles in cleared skin sections using correlated signals from darkfield, brightfield, and confocal microscopy, as well as micro-spectroscopy. Specifically, hyperspectral microscopy and Raman spectroscopy confirmed the identity of label-free ENMs which we mapped within human skin sections. We also measured the 3D distribution of fluorescently labeled Ag nanoparticles in cleared skin biopsies with wounded epidermal layers using light sheet fluorescence microscopy. Overall, this study explores a novel strategy for quantitatively mapping ENM distributions in cleared ex vivo human skin tissue models using multiple imaging modalities. By improving the imaging contrast, we present label-free 2D ENM tracking and 3D ENM mapping as promising capabilities for nanotoxicology investigations.
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Affiliation(s)
- George J. Touloumes
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
| | - Herdeline Ann M. Ardoña
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
| | - Evan K. Casalino
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
| | - John F. Zimmerman
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
| | - Christophe O. Chantre
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
| | - Dimitrios Bitounis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115 USA
| | - Kevin Kit Parker
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
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Abstract
Neuroinflammation has become a key hallmark of neurological complications including perioperative pathologies such as postoperative delirium and longer-lasting postoperative cognitive dysfunction. Dysregulated inflammation and neuronal injury are emerging from clinical studies as key features of perioperative neurocognitive disorders. These findings are paralleled by a growing body of preclinical investigations aimed at better understanding how surgery and anesthesia affect the central nervous system and possibly contribute to cognitive decline. Herein, we review the role of postoperative neuroinflammation and underlying mechanisms in immune-to-brain signaling after peripheral surgery.
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Affiliation(s)
- Saraswathi Subramaniyan
- From the Center for Translational Pain Medicine, Department of Anesthe siology, Duke University Medical Center, Durham, North Carolina
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Goubran M, Leuze C, Hsueh B, Aswendt M, Ye L, Tian Q, Cheng MY, Crow A, Steinberg GK, McNab JA, Deisseroth K, Zeineh M. Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Nat Commun 2019; 10:5504. [PMID: 31796741 PMCID: PMC6890789 DOI: 10.1038/s41467-019-13374-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 11/04/2019] [Indexed: 01/21/2023] Open
Abstract
3D histology, slice-based connectivity atlases, and diffusion MRI are common techniques to map brain wiring. While there are many modality-specific tools to process these data, there is a lack of integration across modalities. We develop an automated resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling the analysis of histological features across multiple fiber tracts and networks, and their correlation with in-vivo biomarkers. We apply our pipeline in a murine stroke model, demonstrating not only strong correspondence between MRI abnormalities and CLARITY-tissue staining, but also uncovering acute cellular effects in areas connected to the ischemic core. We provide improved maps of connectivity by quantifying projection terminals from CLARITY viral injections, and integrate diffusion MRI with CLARITY viral tracing to compare connectivity maps across scales. Finally, we demonstrate tract-level histological changes of stroke through this multimodal integration. This resource can propel investigations of network alterations underlying neurological disorders.
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Affiliation(s)
- Maged Goubran
- Department of Radiology, Stanford University, Stanford, CA, 94035, USA.
| | - Christoph Leuze
- Department of Radiology, Stanford University, Stanford, CA, 94035, USA
| | - Brian Hsueh
- Department of Bioengineering, Stanford University, Stanford, CA, 94035, USA
- CNC Program, Stanford University, Stanford, CA, 94035, USA
| | - Markus Aswendt
- Department of Neurosurgery and Stanford Stroke Center, Stanford University, Stanford, CA, 94035, USA
| | - Li Ye
- Department of Bioengineering, Stanford University, Stanford, CA, 94035, USA
- CNC Program, Stanford University, Stanford, CA, 94035, USA
| | - Qiyuan Tian
- Department of Radiology, Stanford University, Stanford, CA, 94035, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94035, USA
| | - Michelle Y Cheng
- Department of Neurosurgery and Stanford Stroke Center, Stanford University, Stanford, CA, 94035, USA
| | - Ailey Crow
- CNC Program, Stanford University, Stanford, CA, 94035, USA
| | - Gary K Steinberg
- Department of Neurosurgery and Stanford Stroke Center, Stanford University, Stanford, CA, 94035, USA
| | - Jennifer A McNab
- Department of Radiology, Stanford University, Stanford, CA, 94035, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, 94035, USA
- CNC Program, Stanford University, Stanford, CA, 94035, USA
- Department of Psychiatry, Stanford University, Stanford, CA, 94035, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94035, USA
| | - Michael Zeineh
- Department of Radiology, Stanford University, Stanford, CA, 94035, USA.
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Roostalu U, Salinas CBG, Thorbek DD, Skytte JL, Fabricius K, Barkholt P, John LM, Jurtz VI, Knudsen LB, Jelsing J, Vrang N, Hansen HH, Hecksher-Sørensen J. Quantitative whole-brain 3D imaging of tyrosine hydroxylase-labeled neuron architecture in the mouse MPTP model of Parkinson's disease. Dis Model Mech 2019; 12:dmm.042200. [PMID: 31704726 PMCID: PMC6899010 DOI: 10.1242/dmm.042200] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023] Open
Abstract
Parkinson's disease (PD) is a basal ganglia movement disorder characterized by progressive degeneration of the nigrostriatal dopaminergic system. Immunohistochemical methods have been widely used for characterization of dopaminergic neuronal injury in animal models of PD, including the MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) mouse model. However, conventional immunohistochemical techniques applied to tissue sections have inherent limitations with respect to loss of 3D resolution, yielding insufficient information on the architecture of the dopaminergic system. To provide a more comprehensive and non-biased map of MPTP-induced changes in central dopaminergic pathways, we used iDISCO immunolabeling, light-sheet fluorescence microscopy (LSFM) and deep-learning computational methods for whole-brain three-dimensional visualization and automated quantitation of tyrosine hydroxylase (TH)-positive neurons in the adult mouse brain. Mice terminated 7 days after acute MPTP administration demonstrated widespread alterations in TH expression. Compared to vehicle controls, MPTP-dosed mice showed a significant loss of TH-positive neurons in the substantia nigra pars compacta and ventral tegmental area. Also, MPTP dosing reduced overall TH signal intensity in basal ganglia nuclei, i.e. the substantia nigra, caudate-putamen, globus pallidus and subthalamic nucleus. In contrast, increased TH signal intensity was predominantly observed in limbic regions, including several subdivisions of the amygdala and hypothalamus. In conclusion, mouse whole-brain 3D imaging is ideal for unbiased automated counting and densitometric analysis of TH-positive cells. The LSFM–deep learning pipeline tracked brain-wide changes in catecholaminergic pathways in the MPTP mouse model of PD, and may be applied for preclinical characterization of compounds targeting dopaminergic neurotransmission. Summary: Whole-brain immunolabeling, mapping and absolute quantification of tyrosine hydroxylase neurons in the adult mouse brain provides a useful tool for studying changes in dopaminergic signaling in a mouse model of PD.
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Affiliation(s)
| | | | | | | | | | | | - Linu M John
- Department of Obesity Research, Global Drug Discovery, Novo Nordisk A/S, 2760 Måløv, Denmark
| | | | - Lotte Bjerre Knudsen
- Department of Diabetes Research, Global Drug Discovery, Novo Nordisk A/S, 2760 Måløv, Denmark
| | | | - Niels Vrang
- Gubra, Hørsholm Kongevej 11B, 2970 Hørholm, Denmark
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Velagapudi R, Subramaniyan S, Xiong C, Porkka F, Rodriguiz RM, Wetsel WC, Terrando N. Orthopedic Surgery Triggers Attention Deficits in a Delirium-Like Mouse Model. Front Immunol 2019; 10:2675. [PMID: 31911786 PMCID: PMC6918861 DOI: 10.3389/fimmu.2019.02675] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/30/2019] [Indexed: 01/15/2023] Open
Abstract
Postoperative delirium is a frequent and debilitating complication, especially amongst high risk procedures such as orthopedic surgery, and its pathogenesis remains unclear. Inattention is often reported in the clinical diagnosis of delirium, however limited attempts have been made to study this cognitive domain in preclinical models. Here we implemented the 5-choice serial reaction time task (5-CSRTT) to evaluate attention in a clinically relevant mouse model following orthopedic surgery. The 5-CSRTT showed a time-dependent impairment in the number of responses made by the mice acutely after orthopedic surgery, with maximum impairment at 24 h and returning to pre-surgical performance by day 5. Similarly, the latency to the response was also delayed during this time period but returned to pre-surgical levels within several days. While correct responses decreased following surgery, the accuracy of the response (e.g., selection of the correct nose-poke) remained relatively unchanged. In a separate cohort we evaluated neuroinflammation and blood-brain barrier (BBB) dysfunction using clarified brain tissue with light-sheet microscopy. CLARITY revealed significant changes in microglial morphology and impaired astrocytic-tight junction interactions using high-resolution 3D reconstructions of the neurovascular unit. Deposition of IgG, fibrinogen, and autophagy markers (TFEB and LAMP1) were also altered in the hippocampus 24 h after surgery. Together, these results provide translational evidence for the role of peripheral surgery contributing to delirium-like behavior and disrupted neuroimmunity in adult mice.
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Affiliation(s)
- Ravikanth Velagapudi
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University Medical Center, Durham, NC, United States
| | - Saraswathi Subramaniyan
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University Medical Center, Durham, NC, United States
| | - Chao Xiong
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University Medical Center, Durham, NC, United States
| | - Fiona Porkka
- Department of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC, United States
| | - Ramona M. Rodriguiz
- Department of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC, United States
| | - William C. Wetsel
- Department of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC, United States
- Departments of Neurobiology and Cell Biology, Duke University Medical Center, Durham, NC, United States
| | - Niccolò Terrando
- Department of Anesthesiology, Center for Translational Pain Medicine, Duke University Medical Center, Durham, NC, United States
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Sauvage M, Kitsukawa T, Atucha E. Single-cell memory trace imaging with immediate-early genes. J Neurosci Methods 2019; 326:108368. [DOI: 10.1016/j.jneumeth.2019.108368] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 11/29/2022]
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Zach P, Mrzílková J, Pala J, Uttl L, Kútna V, Musil V, Sommerová B, Tůma P. New Design of the Electrophoretic Part of CLARITY Technology for Confocal Light Microscopy of Rat and Human Brains. Brain Sci 2019; 9:brainsci9090218. [PMID: 31470513 PMCID: PMC6770398 DOI: 10.3390/brainsci9090218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/15/2019] [Accepted: 08/28/2019] [Indexed: 12/17/2022] Open
Abstract
Background: CLARITY is a method of rendering postmortem brain tissue transparent using acrylamide-based hydrogels so that this tissue could be further used for immunohistochemistry, molecular biology, or gross anatomical studies. Published papers using the CLARITY method have included studies on human brains suffering from Alzheimer’s disease using mouse spinal cords as animal models for multiple sclerosis. Methods: We modified the original design of the Chung CLARITY system by altering the electrophoretic flow-through cell, the shape of the platinum electrophoresis electrodes and their positions, as well as the cooling and recirculation system, so that it provided a greater effect and can be used in any laboratory. Results: The adapted CLARITY system is assembled from basic laboratory components, in contrast to the original design. The modified CLARITY system was tested both on rat brain stained with a rabbit polyclonal anti-Iba-1 for microglial cells and on human nucleus accumbens stained with parvalbumin and tyrosine hydroxylase for visualization of specific neurons by confocal laser scanning microscopy. Conclusions: Our design has the advantage of simplicity, functional robustness, and minimal requirement for specialized additional items for the construction of the CLARITY apparatus.
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Affiliation(s)
- Petr Zach
- Department of Anatomy, Third Faculty of Medicine, Charles University, Ruská 87, 100 00 Prague 10, Czech Republic
- National Institute of Mental Health, Topolová 748, 250 67 Klecany, Czech Republic
| | - Jana Mrzílková
- Department of Anatomy, Third Faculty of Medicine, Charles University, Ruská 87, 100 00 Prague 10, Czech Republic
| | - Jan Pala
- National Institute of Mental Health, Topolová 748, 250 67 Klecany, Czech Republic
- Department of Pathophysiology, Third Faculty of Medicine, Charles University, Ruská 87, 100 00 Prague 10, Czech Republic
| | - Libor Uttl
- National Institute of Mental Health, Topolová 748, 250 67 Klecany, Czech Republic
| | - Viera Kútna
- National Institute of Mental Health, Topolová 748, 250 67 Klecany, Czech Republic
| | - Vladimír Musil
- Centre of Scientific Information, Third Faculty of Medicine, Charles University, Ruská 87, 100 00 Prague 10, Czech Republic
| | - Blanka Sommerová
- Department of Hygiene, Third Faculty of Medicine, Charles University, Ruská 87, 100 00 Prague 10, Czech Republic
| | - Petr Tůma
- Department of Hygiene, Third Faculty of Medicine, Charles University, Ruská 87, 100 00 Prague 10, Czech Republic.
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Schwanke S, Jenssen J, Eipert P, Schmitt O. Towards Differential Connectomics with NeuroVIISAS. Neuroinformatics 2019; 17:163-179. [PMID: 30014279 DOI: 10.1007/s12021-018-9389-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The comparison of connectomes is an essential step to identify changes in structural and functional neuronal networks. However, the connectomes themselves as well as the comparisons of connectomes could be manifold. In most applications, comparisons of connectomes are applied to specific sets of data. In many studies collections of scripts are applied optimized for certain species (non-generic approaches) or diseases (control versus disease group connectomes). These collections of scripts have a limited functionality which do not support functional and topographic mappings of connectomes (hemispherical asymmetries, peripheral nervous system). The platform-independent and generic neuroVIISAS framework is built to circumvent limitations that come with variants of nomenclatures, connectivity lists and connectional hierarchies as well as restrictions to structural connectome analyses. A new analytical module is introduced into the framework to compare different types of connectomes and different representations of the same connectome within a unique software environment. As an example a differential analysis of the partial connectome of the laboratory rat that is based on virus tract tracing with the same regions of non-virus tract tracing has been performed. A relatively large connectional coherence between the two different techniques was found. However, some detected connections are described by virus tract-tracing only.
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Affiliation(s)
- Sebastian Schwanke
- Department of Anatomy, University of Rostock, Gertrudenstr. 9, 18057, Rostock, Germany
| | - Jörg Jenssen
- Department of Anatomy, University of Rostock, Gertrudenstr. 9, 18057, Rostock, Germany
| | - Peter Eipert
- Department of Anatomy, University of Rostock, Gertrudenstr. 9, 18057, Rostock, Germany
| | - Oliver Schmitt
- Department of Anatomy, University of Rostock, Gertrudenstr. 9, 18057, Rostock, Germany.
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Optimisation and validation of hydrogel-based brain tissue clearing shows uniform expansion across anatomical regions and spatial scales. Sci Rep 2019; 9:12084. [PMID: 31427619 PMCID: PMC6700094 DOI: 10.1038/s41598-019-48460-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 08/01/2019] [Indexed: 11/25/2022] Open
Abstract
Imaging of fixed tissue is routine in experimental neuroscience, but is limited by the depth of tissue that can be imaged using conventional methods. Optical clearing of brain tissue using hydrogel-based methods (e.g. CLARITY) allows imaging of large volumes of tissue and is rapidly becoming commonplace in the field. However, these methods suffer from a lack of standardized protocols and validation of the effect they have upon tissue morphology. We present a simple and reliable protocol for tissue clearing along with a quantitative assessment of the effect of tissue clearing upon morphology. Tissue clearing caused tissue swelling (compared to conventional methods), but this swelling was shown to be similar across spatial scales and the variation was within limits acceptable to the field. The results of many studies rely upon an assumption of uniformity in tissue swelling, and by demonstrating this quantitatively, research using these methods can be interpreted more reliably.
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3D-Imaging of Whole Neuronal and Vascular Networks of the Human Dental Pulp via CLARITY and Light Sheet Microscopy. Sci Rep 2019; 9:10860. [PMID: 31350423 PMCID: PMC6659648 DOI: 10.1038/s41598-019-47221-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/12/2019] [Indexed: 01/10/2023] Open
Abstract
Direct visualization of the spatial relationships of the dental pulp tissue at the whole-organ has remained challenging. CLARITY (Clear Lipid-exchanged Acrylamide Tissue hYdrogel) is a tissue clearing method that has enabled successful 3-dimensional (3D) imaging of intact tissues with high-resolution and preserved anatomic structures. We used CLARITY to study the whole human dental pulp with emphasis on the neurovascular components. Dental pulps from sound teeth were CLARITY-cleared, immunostained for PGP9.5 and CD31, as markers for peripheral neurons and blood vessels, respectively, and imaged with light sheet microscopy. Visualization of the whole dental pulp innervation and vasculature was achieved. Innervation comprised 40% of the dental pulp volume and the vasculature another 40%. Marked innervation morphological differences between uni- and multiradicular teeth were found, also distinct neurovascular interplays. Quantification of the neural and vascular structures distribution, diameter and area showed that blood vessels in the capillary size range was twice as high as that of nerve fibers. In conclusion whole CLARITY-cleared dental pulp samples revealed 3D-morphological neurovascular interactions that could not be visualized with standard microscopy. This represents an outstanding tool to study the molecular and structural intricacies of whole dental tissues in the context of disease and treatment methods.
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Du H, Hou P, Wang L, Wang Z, Li Q. Modified CLARITY Achieving Faster and Better Intact Mouse Brain Clearing and Immunostaining. Sci Rep 2019; 9:10571. [PMID: 31332235 PMCID: PMC6646319 DOI: 10.1038/s41598-019-46814-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/29/2019] [Indexed: 01/10/2023] Open
Abstract
CLARITY is a hydrogel embedding clearing method that has the advantages of transparency, different tissue compatibility and immunostaining compatibility. However, there are also some limitations to CLARITY as it requires a long time to achieve transparency, and the electrophoresis clearing is complex. Therefore, we aimed to simplify the electrophoresis system and shorten the processing time of CLARITY. In our study, we developed a non-circulation electrophoresis system to achieve easier manipulation of electrophoresis clearing. We modified the original CLARITY protocol in hydrogel embedding methods, clearing buffer and immunostaining. When comparing brains processed by our modified method or the original protocol, we found our modifications permit faster and more efficient clearing and labeling. Moreover, we developed a new clearing method named Passive pRe-Electrophroresis CLARITY (PRE-CLARITY) and a new immunostaining method named Centrifugation-Expansion staining (CEx staining). PRE-CLARITY achieved faster clearing and higher transparency, and CEx staining accomplished intact mouse brain labeling faster. With our modifications to CLARITY, we accomplished intact mouse brain clearing and immunostaining within one week, while this requires weeks to months with the original CLARITY. Our studies would allow high-content tracing and analysis of intact brain or other large-scale samples in a short time.
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Affiliation(s)
- Hao Du
- Department of Anatomy, Third Military Medical University, Chongqing, 400038, China
| | - Peihong Hou
- Department of Anatomy, Third Military Medical University, Chongqing, 400038, China
| | - Liting Wang
- Biomedical Analysis Center, Third Military Medical University, Chongqing, 400038, China
| | - Zhongke Wang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Qiyu Li
- Department of Anatomy, Third Military Medical University, Chongqing, 400038, China.
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44
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Pavlova IP, Shipley SC, Lanio M, Hen R, Denny CA. Optimization of immunolabeling and clearing techniques for indelibly labeled memory traces. Hippocampus 2019; 28:523-535. [PMID: 29663578 DOI: 10.1002/hipo.22951] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 03/20/2018] [Accepted: 04/04/2018] [Indexed: 12/31/2022]
Abstract
Recent genetic tools have allowed researchers to visualize and manipulate memory traces (i.e., engrams) in small brain regions. However, the ultimate goal is to visualize memory traces across the entire brain in order to better understand how memories are stored in neural networks and how multiple memories may coexist. Intact tissue clearing and imaging is a new and rapidly growing area of focus that could accomplish this task. Here, we utilized the leading protocols for whole-brain clearing and applied them to the ArcCreERT2 mice, a murine line that allows for the indelible labeling of memory traces. We found that CLARITY and PACT greatly distorted the tissue, and iDISCO quenched enhanced yellow fluorescent protein (EYFP) fluorescence and hindered immunolabeling. Alternative clearing solutions, such as tert-Butanol, circumvented these harmful effects, but still did not permit whole-brain immunolabeling. CUBIC and CUBIC with Reagent-1A produced improved antibody penetration and preserved EYFP fluorescence, but also did not allow for whole-brain memory trace visualization. Modification of CUBIC with Reagent-1A resulted in EYFP fluorescence preservation and immunolabeling of the immediate early gene (IEG) Arc in deep brain areas; however, optimized memory trace labeling still required tissue slicing into mm-thick tissue sections. In summary, our data show that CUBIC with Reagent-1A* is the ideal method for reproducible clearing and immunolabeling for the visualization of memory traces in mm-thick tissue sections from ArcCreERT2 mice.
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Affiliation(s)
- Ina P Pavlova
- Division of Integrative Neuroscience, Research Foundation for Mental Hygiene, Inc. (RFMH)/New York State Psychiatric Institute (NYSPI), New York, New York, 10032
| | - Shannon C Shipley
- Division of Integrative Neuroscience, Research Foundation for Mental Hygiene, Inc. (RFMH)/New York State Psychiatric Institute (NYSPI), New York, New York, 10032
| | - Marcos Lanio
- Department of Neuroscience, MD-PhD Program, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, 10032
| | - René Hen
- Division of Integrative Neuroscience, Research Foundation for Mental Hygiene, Inc. (RFMH)/New York State Psychiatric Institute (NYSPI), New York, New York, 10032.,Department of Psychiatry, Columbia University, New York, New York, 10032
| | - Christine A Denny
- Division of Integrative Neuroscience, Research Foundation for Mental Hygiene, Inc. (RFMH)/New York State Psychiatric Institute (NYSPI), New York, New York, 10032.,Department of Psychiatry, Columbia University, New York, New York, 10032
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Gradinaru V, Treweek J, Overton K, Deisseroth K. Hydrogel-Tissue Chemistry: Principles and Applications. Annu Rev Biophys 2019; 47:355-376. [PMID: 29792820 PMCID: PMC6359929 DOI: 10.1146/annurev-biophys-070317-032905] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.
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Affiliation(s)
- Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Jennifer Treweek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Kristin Overton
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA;
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA; .,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, USA.,H oward Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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46
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Three-dimensional imaging and quantitative analysis in CLARITY processed breast cancer tissues. Sci Rep 2019; 9:5624. [PMID: 30948791 PMCID: PMC6449377 DOI: 10.1038/s41598-019-41957-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/18/2019] [Indexed: 02/07/2023] Open
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47
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Wang H, Khoradmehr A, Tamadon A. FACT or PACT: A Comparison between Free-Acrylamide and Acrylamide-Based Passive Sodium Dodecyl Sulfate Tissue Clearing for whole Tissue Imaging. CELL JOURNAL 2019; 21:103-114. [PMID: 30825283 PMCID: PMC6397597 DOI: 10.22074/cellj.2019.5989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/26/2018] [Indexed: 01/13/2023]
Abstract
Major biological processes rely on the spatial organization of cells in complex, highly orchestrated three-dimensional (3D)
tissues. Until the recent decade, most of information on spatial neural representation primarily came from microscopic imaging
of “2D” (5-50 μm) tissue using traditional immunohistochemical techniques. However, serially sectioned and imaged tissue
sections for tissue visualization can lead to unique non-linear deformations, which dramatically hinders scientists’ insight into
the structural organization of intact organs. An emerging technique known as CLARITY renders large-scale biological tissues
transparent for 3D phenotype mapping and thereby, greatly facilitates structure-function relationships analyses. Since then,
numerous modifications and improvements have been reported to push the boundaries of knowledge on tissue clearing
techniques in research on assembled biological systems. This review aims to outline our current knowledge on next-generation
protocols of fast free-of-acrylamide clearing tissue (FACT) and passive CLARITY (PACT). The most important question is what
method we should select for tissue clearing, FACT or PACT. This review also highlights how FACT differs from PACT on
spanning multiple dimensions of the workflow. We systematically compared a number of factors including hydrogel formation,
clearing solution, and clearing temperatures between free-acrylamide and acrylamide-based passive sodium dodecyl sulfate
(SDS) tissue clearing and discussed negative effects of polyacrylamide on clearing, staining, and imaging in detail. Such
information may help to gain a perspective for interrogating neural circuits spatial interactions between molecules and cells
and provide guidance for developing novel tissue clearing strategies to probe deeply into intact organ.
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Affiliation(s)
- Huimei Wang
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Institute of Acupuncture and Moxibustion, Fudan Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Arezoo Khoradmehr
- Research and Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Amin Tamadon
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran. Electronic Address:
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Iida T, Tanaka S, Okabe S. Spatial impact of microglial distribution on dynamics of dendritic spines. Eur J Neurosci 2019; 49:1400-1417. [DOI: 10.1111/ejn.14325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/10/2018] [Accepted: 12/20/2018] [Indexed: 01/31/2023]
Affiliation(s)
- Tadatsune Iida
- Department of Cellular Neurobiology Graduate School of Medicine The University of Tokyo Tokyo Japan
| | - Shinji Tanaka
- Department of Cellular Neurobiology Graduate School of Medicine The University of Tokyo Tokyo Japan
| | - Shigeo Okabe
- Department of Cellular Neurobiology Graduate School of Medicine The University of Tokyo Tokyo Japan
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49
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Mesenchymal Precursor Cells in Adult Nerves Contribute to Mammalian Tissue Repair and Regeneration. Cell Stem Cell 2018; 24:240-256.e9. [PMID: 30503141 DOI: 10.1016/j.stem.2018.10.024] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/11/2018] [Accepted: 10/29/2018] [Indexed: 12/18/2022]
Abstract
Peripheral innervation plays an important role in regulating tissue repair and regeneration. Here we provide evidence that injured peripheral nerves provide a reservoir of mesenchymal precursor cells that can directly contribute to murine digit tip regeneration and skin repair. In particular, using single-cell RNA sequencing and lineage tracing, we identify transcriptionally distinct mesenchymal cell populations within the control and injured adult nerve, including neural crest-derived cells in the endoneurium with characteristics of mesenchymal precursor cells. Culture and transplantation studies show that these nerve-derived mesenchymal cells have the potential to differentiate into non-nerve lineages. Moreover, following digit tip amputation, neural crest-derived nerve mesenchymal cells contribute to the regenerative blastema and, ultimately, to the regenerated bone. Similarly, neural crest-derived nerve mesenchymal cells contribute to the dermis during skin wound healing. These findings support a model where peripheral nerves directly contribute mesenchymal precursor cells to promote repair and regeneration of injured mammalian tissues.
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Khoradmehr A, Mazaheri F, Anvari M, Tamadon A. A Simple Technique for Three-Dimensional Imaging and Segmentation of Brain Vasculature U sing Fast Free-of-Acrylamide Clearing Tissue in Murine. CELL JOURNAL 2018; 21:49-56. [PMID: 30507088 PMCID: PMC6275429 DOI: 10.22074/cellj.2019.5684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/30/2018] [Indexed: 12/26/2022]
Abstract
Objective Fast Free-of-Acrylamide Clearing Tissue (FACT) is a recently developed protocol for the whole tissue
three-dimensional (3D) imaging. The FACT protocol clears lipids using sodium dodecyl sulfate (SDS) to increase the
penetration of light and reflection of fluorescent signals from the depth of cleared tissue. The aim of the present study
was using FACT protocol in combination with imaging of auto-fluorescency of red blood cells in vessels to image the
vasculature of a translucent mouse tissues.
Materials and Methods In this experimental study, brain and other tissues of adult female mice or rats were dissected
out without the perfusion. Mice brains were sliced for vasculature imaging before the clearing. Brain slices and other
whole tissues of rodent were cleared by the FACT protocol and their clearing times were measured. After 1 mm of the
brain slice clearing, the blood vessels containing auto-fluorescent red blood cells were imaged by a z-stack motorized
epifluorescent microscope. The 3D structures of the brain vessels were reconstructed by Imaris software.
Results Auto-fluorescent blood vessels were 3D imaged by the FACT in mouse brain cortex. Clearing tissues of
mice and rats were carried out by the FACT on the brain slices, spinal cord, heart, lung, adrenal gland, pancreas, liver,
esophagus, duodenum, jejunum, ileum, skeletal muscle, bladder, ovary, and uterus.
Conclusion The FACT protocol can be used for the murine whole tissue clearing. We highlighted that the 3D imaging
of cortex vasculature can be done without antibody staining of non-perfused brain tissue, rather by a simple auto-
fluorescence.
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Affiliation(s)
- Arezoo Khoradmehr
- Research and Clinical Center for Infertility, Yazd Reproduction Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Fahime Mazaheri
- Research and Clinical Center for Infertility, Yazd Reproduction Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Morteza Anvari
- Research and Clinical Center for Infertility, Yazd Reproduction Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Biology and Anatomical Sciences, Shahid Sadoughi University of Medical Sciences, Yazd, Iran. Electronic Address:
| | - Amin Tamadon
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran. Electronic Address:
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