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Piluso S, Souedet N, Jan C, Hérard AS, Clouchoux C, Delzescaux T. giRAff: an automated atlas segmentation tool adapted to single histological slices. Front Neurosci 2024; 17:1230814. [PMID: 38274499 PMCID: PMC10808556 DOI: 10.3389/fnins.2023.1230814] [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: 05/29/2023] [Accepted: 10/31/2023] [Indexed: 01/27/2024] Open
Abstract
Conventional histology of the brain remains the gold standard in the analysis of animal models. In most biological studies, standard protocols usually involve producing a limited number of histological slices to be analyzed. These slices are often selected into a specific anatomical region of interest or around a specific pathological lesion. Due to the lack of automated solutions to analyze such single slices, neurobiologists perform the segmentation of anatomical regions manually most of the time. Because the task is long, tedious, and operator-dependent, we propose an automated atlas segmentation method called giRAff, which combines rigid and affine registrations and is suitable for conventional histological protocols involving any number of single slices from a given mouse brain. In particular, the method has been tested on several routine experimental protocols involving different anatomical regions of different sizes and for several brains. For a given set of single slices, the method can automatically identify the corresponding slices in the mouse Allen atlas template with good accuracy and segmentations comparable to those of an expert. This versatile and generic method allows the segmentation of any single slice without additional anatomical context in about 1 min. Basically, our proposed giRAff method is an easy-to-use, rapid, and automated atlas segmentation tool compliant with a wide variety of standard histological protocols.
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Affiliation(s)
- Sébastien Piluso
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
- WITSEE, Paris, France
| | - Nicolas Souedet
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Caroline Jan
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Anne-Sophie Hérard
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | | | - Thierry Delzescaux
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
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2
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Kleven H, Bjerke IE, Clascá F, Groenewegen HJ, Bjaalie JG, Leergaard TB. Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration. Nat Methods 2023; 20:1822-1829. [PMID: 37783883 PMCID: PMC10630136 DOI: 10.1038/s41592-023-02034-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023]
Abstract
Volumetric brain atlases are increasingly used to integrate and analyze diverse experimental neuroscience data acquired from animal models, but until recently a publicly available digital atlas with complete coverage of the rat brain has been missing. Here we present an update of the Waxholm Space rat brain atlas, a comprehensive open-access volumetric atlas resource. This brain atlas features annotations of 222 structures, of which 112 are new and 57 revised compared to previous versions. It provides a detailed map of the cerebral cortex, hippocampal region, striatopallidal areas, midbrain dopaminergic system, thalamic cell groups, the auditory system and main fiber tracts. We document the criteria underlying the annotations and demonstrate how the atlas with related tools and workflows can be used to support interpretation, integration, analysis and dissemination of experimental rat brain data.
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Affiliation(s)
- Heidi Kleven
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ingvild E Bjerke
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Francisco Clascá
- Department of Anatomy and Neuroscience, Autónoma de Madrid University, Madrid, Spain
| | - Henk J Groenewegen
- Department of Anatomy and Neurosciences, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
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3
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Bjerke IE, Yates SC, Carey H, Bjaalie JG, Leergaard TB. Scaling up cell-counting efforts in neuroscience through semi-automated methods. iScience 2023; 26:107562. [PMID: 37636060 PMCID: PMC10457595 DOI: 10.1016/j.isci.2023.107562] [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] [Indexed: 08/29/2023] Open
Abstract
Quantifying how the cellular composition of brain regions vary across development, aging, sex, and disease, is crucial in experimental neuroscience, and the accuracy of different counting methods is continuously debated. Due to the tedious nature of most counting procedures, studies are often restricted to one or a few brain regions. Recently, there have been considerable methodological advances in combining semi-automated feature extraction with brain atlases for cell quantification. Such methods hold great promise for scaling up cell-counting efforts. However, little focus has been paid to how these methods should be implemented and reported to support reproducibility. Here, we provide an overview of practices for conducting and reporting cell counting in mouse and rat brains, showing that critical details for interpretation are typically lacking. We go on to discuss how novel methods may increase efficiency and reproducibility of cell counting studies. Lastly, we provide practical recommendations for researchers planning cell counting.
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Affiliation(s)
- Ingvild Elise Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Sharon Christine Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Harry Carey
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan Gunnar Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve Brauns Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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4
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Kleven H, Gillespie TH, Zehl L, Dickscheid T, Bjaalie JG, Martone ME, Leergaard TB. AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures. Sci Data 2023; 10:486. [PMID: 37495585 PMCID: PMC10372146 DOI: 10.1038/s41597-023-02389-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying mapping methodologies differ considerably between atlases and across atlas versions. This lack of standardized description impedes use of atlases in analytic tools and registration of data to different atlases. To establish a machine-readable standard for representing brain atlases, we identified four fundamental atlas elements, defined their relations, and created an ontology model. Here we present our Atlas Ontology Model (AtOM) and exemplify its use by applying it to mouse, rat, and human brain atlases. We discuss how AtOM can facilitate atlas interoperability and data integration, thereby increasing compliance with the FAIR guiding principles. AtOM provides a standardized framework for communication and use of brain atlases to create, use, and refer to specific atlas elements and versions. We argue that AtOM will accelerate analysis, sharing, and reuse of neuroscience data.
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Affiliation(s)
- Heidi Kleven
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Lyuba Zehl
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Timo Dickscheid
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Institute of Computer Science, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maryann E Martone
- Department of Neurosciences, University of California, San Diego, USA
| | - Trygve B Leergaard
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
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5
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Asadi Zarch ME, Afshar A, Rahmanifar F, Jafarzadeh Shirazi MR, Baghban M, Dadpasand M, Mohammad Rezazadeh F, Khoradmehr A, Baharvand H, Tamadon A. Three-dimensional and two-dimensional relationships of gangliogenesis with folliculogenesis in mature mouse ovary: a Golgi-Cox staining approach. Sci Rep 2021; 11:5547. [PMID: 33692376 PMCID: PMC7970916 DOI: 10.1038/s41598-021-84835-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
The present study was set out to investigate two-dimensional (2D) and three-dimensional (3D) evaluations of ovarian nervous network development and the structural relationship between folliculogenesis and gangliogenesis in mouse ovaries. Adult mice ovarian tissue samples were collected from follicular and luteal phases after cardiac perfusion. Ovarian samples were stained by a Golgi-Cox protocol. Following staining, tissues were serially sectioned for imaging. Neural filaments and ganglia were present in the ovaries. In both 2D and 3D studies, an increase in the number and area of ganglia was seen during the follicular growth. The same pattern was also seen in corpora lutea development. However, in some cases such as ratio of ganglia number to follicle area, the ratio of ganglia area to follicular area, 2D findings were different compared with the 3D results. 3D analysis of ovarian gangliogenesis showed the possible direct effect of them on folliculogenesis. Golgi-Cox staining was used in this study for 3D evaluation in non-brain tissue. The results of 3D analysis of the present study showed that, in some cases, the information provided by 2D analysis does not match the reality of ovarian neuronal function. This confirmed the importance of 3D analysis for evaluation of ovarian function.
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Affiliation(s)
| | - Alireza Afshar
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, 75146-33196, Bushehr, Iran
| | - Farhad Rahmanifar
- Department of Basic Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | | | - Mandana Baghban
- Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Dadpasand
- Department of Animal Sciences, College of Agriculture, Shiraz University, 71441-65186, Shiraz, Iran
| | | | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, 75146-33196, Bushehr, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Amin Tamadon
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, 75146-33196, Bushehr, Iran.
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6
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Srivastava A, Hanig JP. Quantitative neurotoxicology: Potential role of artificial intelligence/deep learning approach. J Appl Toxicol 2020; 41:996-1006. [PMID: 33140470 DOI: 10.1002/jat.4098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/17/2020] [Indexed: 12/17/2022]
Abstract
Neurotoxicity studies are important in the preclinical stages of drug development process, because exposure to certain compounds that may enter the brain across a permeable blood brain barrier damages neurons and other supporting cells such as astrocytes. This could, in turn, lead to various neurological disorders such as Parkinson's or Huntington's disease as well as various dementias. Toxicity assessment is often done by pathologists after these exposures by qualitatively or semiquantitatively grading the severity of neurotoxicity in histopathology slides. Quantification of the extent of neurotoxicity supports qualitative histopathological analysis and provides a better understanding of the global extent of brain damage. Stereological techniques such as the utilization of an optical fractionator provide an unbiased quantification of the neuronal damage; however, the process is time-consuming. Advent of whole slide imaging (WSI) introduced digital image analysis which made quantification of neurotoxicity automated, faster and with reduced bias, making statistical comparisons possible. Although automated to a certain level, simple digital image analysis requires manual efforts of experts which is time-consuming and limits analysis of large datasets. Digital image analysis coupled with a deep learning artificial intelligence model provides a good alternative solution to time-consuming stereological and simple digital analysis. Deep learning models could be trained to identify damaged or dead neurons in an automated fashion. This review has focused on and discusses studies demonstrating the role of deep learning in segmentation of brain regions, toxicity detection and quantification of degenerated neurons as well as the estimation of area/volume of degeneration.
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Affiliation(s)
- Anshul Srivastava
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Joseph P Hanig
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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7
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Scarpelli ML, Healey DR, Mehta S, Kodibagkar VD, Quarles CC. A practical method for multimodal registration and assessment of whole-brain disease burden using PET, MRI, and optical imaging. Sci Rep 2020; 10:17324. [PMID: 33057180 PMCID: PMC7560610 DOI: 10.1038/s41598-020-74459-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
Many neurological diseases present with substantial genetic and phenotypic heterogeneity, making assessment of these diseases challenging. This has led to ineffective treatments, significant morbidity, and high mortality rates for patients with neurological diseases, including brain cancers and neurodegenerative disorders. Improved understanding of this heterogeneity is necessary if more effective treatments are to be developed. We describe a new method to measure phenotypic heterogeneity across the whole rodent brain at multiple spatial scales. The method involves co-registration and localized comparison of in vivo radiologic images (e.g. MRI, PET) with ex vivo optical reporter images (e.g. labeled cells, molecular targets, microvasculature) of optically cleared tissue slices. Ex vivo fluorescent images of optically cleared pathology slices are acquired with a preclinical in vivo optical imaging system across the entire rodent brain in under five minutes, making this methodology practical and feasible for most preclinical imaging labs. The methodology is applied in various examples demonstrating how it might be used to cross-validate and compare in vivo radiologic imaging with ex vivo optical imaging techniques for assessing hypoxia, microvasculature, and tumor growth.
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Affiliation(s)
- Matthew L Scarpelli
- Department of Neuroimaging, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | - Debbie R Healey
- Department of Neuroimaging, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | - Shwetal Mehta
- Department of Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | - Vikram D Kodibagkar
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Christopher C Quarles
- Department of Neuroimaging, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA.
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8
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Groeneboom NE, Yates SC, Puchades MA, Bjaalie JG. Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front Neuroinform 2020; 14:37. [PMID: 32973479 PMCID: PMC7472695 DOI: 10.3389/fninf.2020.00037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/17/2020] [Indexed: 02/01/2023] Open
Abstract
With recent technological advances in microscopy and image acquisition of tissue sections, further developments of tools are required for viewing, transforming, and analyzing the ever-increasing amounts of high-resolution data produced. In the field of neuroscience, histological images of whole rodent brain sections are commonly used for investigating brain connections as well as cellular and molecular organization in the normal and diseased brain, but present a problem for the typical neuroscientist with no or limited programming experience in terms of the pre- and post-processing steps needed for analysis. To meet this need we have designed Nutil, an open access and stand-alone executable software that enables automated transformations, post-processing, and analyses of 2D section images using multi-core processing (OpenMP). The software is written in C++ for efficiency, and provides the user with a clean and easy graphical user interface for specifying the input and output parameters. Nutil currently contains four separate tools: (1) A transformation toolchain named “Transform” that allows for rotation, mirroring and scaling, resizing, and renaming of very large tiled tiff images. (2) “TiffCreator” enables the generation of tiled TIFF images from other image formats such as PNG and JPEG. (3) A “Resize” tool completes the preprocessing toolset and allows downscaling of PNG and JPEG images with output in PNG format. (4) The fourth tool is a post-processing method called “Quantifier” that enables the quantification of segmented objects in the context of regions defined by brain atlas maps generated with the QuickNII software based on a 3D reference atlas (mouse or rat). The output consists of a set of report files, point cloud coordinate files for visualization in reference atlas space, and reference atlas images superimposed with color-coded objects. The Nutil software is made available by the Human Brain Project (https://www.humanbrainproject.eu) at https://www.nitrc.org/projects/nutil/.
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Affiliation(s)
- Nicolaas E Groeneboom
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Sharon C Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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9
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Mancini M, Casamitjana A, Peter L, Robinson E, Crampsie S, Thomas DL, Holton JL, Jaunmuktane Z, Iglesias JE. A multimodal computational pipeline for 3D histology of the human brain. Sci Rep 2020; 10:13839. [PMID: 32796937 PMCID: PMC7429828 DOI: 10.1038/s41598-020-69163-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of whole human hemispheres from two donors.
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Affiliation(s)
- Matteo Mancini
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK.
- Department of Neuroscience, Brighton and Sussex Medical School, University of Sussex, Brighton, UK.
- CUBRIC, Cardiff University, Cardiff, UK.
- NeuroPoly Lab, Polytechnique Montreal, Montreal, Canada.
| | - Adrià Casamitjana
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Loic Peter
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Eleanor Robinson
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Shauna Crampsie
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - David L Thomas
- Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, University College London, London, UK
- Leonard Wolfson Experimental Neurology Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Zane Jaunmuktane
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Juan Eugenio Iglesias
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK.
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, MA, USA.
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10
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Impairment of Glycolysis-Derived l-Serine Production in Astrocytes Contributes to Cognitive Deficits in Alzheimer's Disease. Cell Metab 2020; 31:503-517.e8. [PMID: 32130882 DOI: 10.1016/j.cmet.2020.02.004] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/25/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
Alteration of brain aerobic glycolysis is often observed early in the course of Alzheimer's disease (AD). Whether and how such metabolic dysregulation contributes to both synaptic plasticity and behavioral deficits in AD is not known. Here, we show that the astrocytic l-serine biosynthesis pathway, which branches from glycolysis, is impaired in young AD mice and in AD patients. l-serine is the precursor of d-serine, a co-agonist of synaptic NMDA receptors (NMDARs) required for synaptic plasticity. Accordingly, AD mice display a lower occupancy of the NMDAR co-agonist site as well as synaptic and behavioral deficits. Similar deficits are observed following inactivation of the l-serine synthetic pathway in hippocampal astrocytes, supporting the key role of astrocytic l-serine. Supplementation with l-serine in the diet prevents both synaptic and behavioral deficits in AD mice. Our findings reveal that astrocytic glycolysis controls cognitive functions and suggest oral l-serine as a ready-to-use therapy for AD.
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11
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Elmer BM, Swanson KA, Bangari DS, Piepenhagen PA, Roberts E, Taksir T, Guo L, Obinu MC, Barneoud P, Ryan S, Zhang B, Pradier L, Yang ZY, Nabel GJ. Gene delivery of a modified antibody to Aβ reduces progression of murine Alzheimer's disease. PLoS One 2019; 14:e0226245. [PMID: 31887144 PMCID: PMC6936806 DOI: 10.1371/journal.pone.0226245] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/24/2019] [Indexed: 12/30/2022] Open
Abstract
Antibody therapies for Alzheimer’s Disease (AD) hold promise but have been limited by the inability of these proteins to migrate efficiently across the blood brain barrier (BBB). Central nervous system (CNS) gene transfer by vectors like adeno-associated virus (AAV) overcome this barrier by allowing the bodies’ own cells to produce the therapeutic protein, but previous studies using this method to target amyloid-β have shown success only with truncated single chain antibodies (Abs) lacking an Fc domain. The Fc region mediates effector function and enhances antigen clearance from the brain by neonatal Fc receptor (FcRn)-mediated reverse transcytosis and is therefore desirable to include for such treatments. Here, we show that single chain Abs fused to an Fc domain retaining FcRn binding, but lacking Fc gamma receptor (FcγR) binding, termed a silent scFv-IgG, can be expressed and released into the CNS following gene transfer with AAV. While expression of canonical IgG in the brain led to signs of neurotoxicity, this modified Ab was efficiently secreted from neuronal cells and retained target specificity. Steady state levels in the brain exceeded peak levels obtained by intravenous injection of IgG. AAV-mediated expression of this scFv-IgG reduced cortical and hippocampal plaque load in a transgenic mouse model of progressive β-amyloid plaque accumulation. These findings suggest that CNS gene delivery of a silent anti-Aβ scFv-IgG was well-tolerated, durably expressed and functional in a relevant disease model, demonstrating the potential of this modality for the treatment of Alzheimer’s disease.
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Affiliation(s)
- Bradford M. Elmer
- Breakthrough Lab, Sanofi, Cambridge, Massachusetts, United States of America
| | - Kurt A. Swanson
- Breakthrough Lab, Sanofi, Cambridge, Massachusetts, United States of America
| | - Dinesh S. Bangari
- Global Discovery Pathology, Sanofi, Framingham, Massachusetts, United States of America
| | - Peter A. Piepenhagen
- Global Discovery Pathology, Sanofi, Framingham, Massachusetts, United States of America
| | - Errin Roberts
- Global Discovery Pathology, Sanofi, Framingham, Massachusetts, United States of America
| | - Tatyana Taksir
- Global Discovery Pathology, Sanofi, Framingham, Massachusetts, United States of America
| | - Lei Guo
- Translational Sciences, Sanofi, Cambridge, Massachusetts, United States of America
| | | | | | - Susan Ryan
- Global Discovery Pathology, Sanofi, Framingham, Massachusetts, United States of America
| | - Bailin Zhang
- Translational Sciences, Sanofi, Cambridge, Massachusetts, United States of America
| | | | - Zhi-Yong Yang
- Breakthrough Lab, Sanofi, Cambridge, Massachusetts, United States of America
| | - Gary J. Nabel
- Breakthrough Lab, Sanofi, Cambridge, Massachusetts, United States of America
- * E-mail:
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12
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You Z, Balbastre Y, Bouvier C, Hérard AS, Gipchtein P, Hantraye P, Jan C, Souedet N, Delzescaux T. Automated Individualization of Size-Varying and Touching Neurons in Macaque Cerebral Microscopic Images. Front Neuroanat 2019; 13:98. [PMID: 31920567 PMCID: PMC6929681 DOI: 10.3389/fnana.2019.00098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022] Open
Abstract
In biomedical research, cell analysis is important to assess physiological and pathophysiological information. Virtual microscopy offers the unique possibility to study the compositions of tissues at a cellular scale. However, images acquired at such high spatial resolution are massive, contain complex information, and are therefore difficult to analyze automatically. In this article, we address the problem of individualization of size-varying and touching neurons in optical microscopy two-dimensional (2-D) images. Our approach is based on a series of processing steps that incorporate increasingly more information. (1) After a step of segmentation of neuron class using a Random Forest classifier, a novel min-max filter is used to enhance neurons' centroids and boundaries, enabling the use of region growing process based on a contour-based model to drive it to neuron boundary and achieve individualization of touching neurons. (2) Taking into account size-varying neurons, an adaptive multiscale procedure aiming at individualizing touching neurons is proposed. This protocol was evaluated in 17 major anatomical regions from three NeuN-stained macaque brain sections presenting diverse and comprehensive neuron densities. Qualitative and quantitative analyses demonstrate that the proposed method provides satisfactory results in most regions (e.g., caudate, cortex, subiculum, and putamen) and outperforms a baseline Watershed algorithm. Neuron counts obtained with our method show high correlation with an adapted stereology technique performed by two experts (respectively, 0.983 and 0.975 for the two experts). Neuron diameters obtained with our method ranged between 2 and 28.6 μm, matching values reported in the literature. Further works will aim to evaluate the impact of staining and interindividual variability on our protocol.
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Affiliation(s)
- Zhenzhen You
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Université Paris-Saclay, Fontenay-aux-Roses, France
- School of Computer Science and Engineering, Xi’an University of Technology, Xi’an, China
| | - Yaël Balbastre
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Clément Bouvier
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Anne-Sophie Hérard
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Pauline Gipchtein
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Caroline Jan
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Nicolas Souedet
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Thierry Delzescaux
- CEA-CNRS-UMR 9199, Laboratoire des Maladies Neurodégénératives, MIRCen, Université Paris-Saclay, Fontenay-aux-Roses, France
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13
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Yates SC, Groeneboom NE, Coello C, Lichtenthaler SF, Kuhn PH, Demuth HU, Hartlage-Rübsamen M, Roßner S, Leergaard T, Kreshuk A, Puchades MA, Bjaalie JG. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front Neuroinform 2019; 13:75. [PMID: 31849633 PMCID: PMC6901597 DOI: 10.3389/fninf.2019.00075] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 11/15/2019] [Indexed: 01/22/2023] Open
Abstract
Transgenic animal models are invaluable research tools for elucidating the pathways and mechanisms involved in the development of neurodegenerative diseases. Mechanistic clues can be revealed by applying labelling techniques such as immunohistochemistry or in situ hybridisation to brain tissue sections. Precision in both assigning anatomical location to the sections and quantifying labelled features is crucial for output validity, with a stereological approach or image-based feature extraction typically used. However, both approaches are restricted by the need to manually delineate anatomical regions. To circumvent this limitation, we present the QUINT workflow for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases. The workflow is semi-automated, combining three open source software that can be operated without scripting knowledge, making it accessible to most researchers. As an example, a brain region-specific quantification of amyloid plaques across whole transgenic Tg2576 mouse brain series, immunohistochemically labelled for three amyloid-related antigens is demonstrated. First, the whole brain image series were registered to the Allen Mouse Brain Atlas to produce customised atlas maps adapted to match the cutting plan and proportions of the sections (QuickNII software). Second, the labelling was segmented from the original images by the Random Forest Algorithm for supervised classification (ilastik software). Finally, the segmented images and atlas maps were used to generate plaque quantifications for each region in the reference atlas (Nutil software). The method yielded comparable results to manual delineations and to the output of a stereological method. While the use case demonstrates the QUINT workflow for quantification of amyloid plaques only, the workflow is suited to all mouse or rat brain series with labelling that is visually distinct from the background, for example for the quantification of cells or labelled proteins.
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Affiliation(s)
- Sharon C Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nicolaas E Groeneboom
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Christopher Coello
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, and Institute for Advanced Study, Technical University of Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Hans-Ulrich Demuth
- Department of Molecular Drug Design and Target Validation Fraunhofer Institute for Cell Therapy and Immunology, Halle (Saale), Leipzig, Germany
| | | | - Steffen Roßner
- Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Trygve Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Anna Kreshuk
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maja A Puchades
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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14
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Levy J, Facchinetti P, Jan C, Achour M, Bouvier C, Brunet JF, Delzescaux T, Giuliano F. Tridimensional mapping of Phox2b expressing neurons in the brainstem of adult Macaca fascicularis and identification of the retrotrapezoid nucleus. J Comp Neurol 2019; 527:2875-2884. [PMID: 31071232 DOI: 10.1002/cne.24713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/29/2019] [Accepted: 04/29/2019] [Indexed: 11/08/2022]
Abstract
Chemosensitivity is a key mechanism for the regulation of breathing in vertebrates. The retrotrapezoid nucleus is a crucial hub for respiratory chemoreception within the brainstem. It integrates chemosensory information that are both peripheral from the carotid bodies (via the nucleus of the solitary tract) and central through the direct sensing of extracellular protons. To date, the location of a genetically defined RTN has only been ascertained in rodents. We first demonstrated that Phox2b, a key determinant for the development of the visceral nervous system and branchiomotor nuclei in the brainstem including the RTN, had a similar distribution in the brainstem of adult macaques compared to adult rats. Second, based on previous description of a specific molecular signature for the RTN in rats, and on an innovative technique for duplex in situ hybridization, we identified parafacial neurons which coexpressed Phox2b and ppGal mRNAs. They were located ventrally to the nucleus of the facial nerve and extended from the caudal part of the nucleus of the superior olive to the rostral tip of the inferior olive. Using the previously described blockface technique, deformations were corrected to allow the proper alignment and stacking of digitized sections, hence providing for the first time a 3D reconstruction of the macaque brainstem, Phox2b distribution and the primate retrotrapezoid nucleus. This description should help bridging the gap between rodents and humans for the description of key respiratory structures in the brainstem.
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Affiliation(s)
- Jonathan Levy
- INSERM UMR1179-Handicap Neuromusculaire, Université de Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France.,Service de Médecine Physique et de Réadaptation-APHP, Hôpital Raymond Poincaré, Garches, France.,Fondation Garches-APHP, Hôpital Raymond Poincaré, Garches, France
| | - Patricia Facchinetti
- INSERM UMR1179-Handicap Neuromusculaire, Université de Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France
| | - Caroline Jan
- Molecular Imaging Research Center (MIRCen)-Commissariat à l'Énergie Atomique (CEA), Fontenay-aux-Roses, France.,CNRS-CEA UMR9199-Neurodegenerative Diseases Laboratory, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Mélyna Achour
- INSERM UMR1179-Handicap Neuromusculaire, Université de Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France
| | - Clément Bouvier
- Molecular Imaging Research Center (MIRCen)-Commissariat à l'Énergie Atomique (CEA), Fontenay-aux-Roses, France.,NEOXIA, Paris, France
| | - Jean-François Brunet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université, Paris, France
| | - Thierry Delzescaux
- Molecular Imaging Research Center (MIRCen)-Commissariat à l'Énergie Atomique (CEA), Fontenay-aux-Roses, France.,CNRS-CEA UMR9199-Neurodegenerative Diseases Laboratory, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - François Giuliano
- INSERM UMR1179-Handicap Neuromusculaire, Université de Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France.,Service de Médecine Physique et de Réadaptation-APHP, Hôpital Raymond Poincaré, Garches, France
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15
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Nguyen D, Uhlmann V, Planchette AL, Marchand PJ, Van De Ville D, Lasser T, Radenovic A. Supervised learning to quantify amyloidosis in whole brains of an Alzheimer's disease mouse model acquired with optical projection tomography. BIOMEDICAL OPTICS EXPRESS 2019; 10:3041-3060. [PMID: 31259073 PMCID: PMC6583328 DOI: 10.1364/boe.10.003041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/19/2019] [Accepted: 05/19/2019] [Indexed: 05/14/2023]
Abstract
Alzheimer's disease (AD) is characterized by amyloidosis of brain tissues. This phenomenon is studied with genetically-modified mouse models. We propose a method to quantify amyloidosis in whole 5xFAD mouse brains, a model of AD. We use optical projection tomography (OPT) and a random forest voxel classifier to segment and measure amyloid plaques. We validate our method in a preliminary cross-sectional study, where we measure 6136 ± 1637, 8477 ± 3438, and 17267 ± 4241 plaques (AVG ± SD) at 11, 17, and 31 weeks. Overall, this method can be used in the evaluation of new treatments against AD.
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Affiliation(s)
- David Nguyen
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
- Medical Image Processing Lab, École Polytechnique Fédérale de Lausanne, Genève, Genève,
Switzerland
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Virginie Uhlmann
- Biomedical Imaging Group, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
- European Bioinformatics Institute, EMBL-EBI, Cambridge,
United Kingdom
| | - Arielle L. Planchette
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Paul J. Marchand
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Dimitri Van De Ville
- Medical Image Processing Lab, École Polytechnique Fédérale de Lausanne, Genève, Genève,
Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Genève, Genève,
Switzerland
| | - Theo Lasser
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
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16
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Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLoS One 2019; 14:e0216796. [PMID: 31141518 PMCID: PMC6541252 DOI: 10.1371/journal.pone.0216796] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/29/2019] [Indexed: 12/28/2022] Open
Abstract
Modern high throughput brain wide profiling techniques for cells and their morphology, connectivity, and other properties, make the use of reference atlases with 3D coordinate frameworks essential. However, anatomical location of observations made in microscopic sectional images from rodent brains is typically determined by comparison with 2D anatomical reference atlases. A major challenge in this regard is that microscopic sections often are cut with orientations deviating from the standard planes used in the reference atlases, resulting in inaccuracies and a need for tedious correction steps. Overall, efficient tools for registration of large series of section images to reference atlases are currently not widely available. Here we present QuickNII, a stand-alone software tool for semi-automated affine spatial registration of sectional image data to a 3D reference atlas coordinate framework. A key feature in the tool is the capability to generate user defined cut planes through the reference atlas, matching the orientation of the cut plane of the sectional image data. The reference atlas is transformed to match anatomical landmarks in the corresponding experimental images. In this way, the spatial relationship between experimental image and atlas is defined, without introducing distortions in the original experimental images. Following anchoring of a limited number of sections containing key landmarks, transformations are propagated across the entire series of sectional images to reduce the amount of manual steps required. By having coordinates assigned to the experimental images, further analysis of the distribution of features extracted from the images is greatly facilitated.
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17
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Sato C, Sawada K, Wright D, Higashi T, Aoki I. Isotropic 25-Micron 3D Neuroimaging Using ex vivo Microstructural Manganese-Enhanced MRI (MEMRI). Front Neural Circuits 2018; 12:110. [PMID: 30574072 PMCID: PMC6291442 DOI: 10.3389/fncir.2018.00110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/23/2018] [Indexed: 12/27/2022] Open
Abstract
MRI observations following in vivo administration of Mn2+ [manganese (Mn)-enhanced MRI, MEMRI] have been used as an excellent morphological and functional MRI tool for in vivo preclinical studies. To detect brain three-dimensional (3D) microstructures, we improved the ex vivo MEMRI method for mouse brains after in vivo Mn administration and obtained high-resolution MRIs using a cryogenic radiofrequency (RF) coil. Male C57BL/6 mice (n = 8) were injected with 50 mM MnCl2 intravenously and MEMRIs of the brain were acquired in vivo after 24 h, followed by perfusion fixation with a 4% paraformaldehyde (PFA) solution. High-resolution 25-μm isotropic MRIs were successfully acquired from the extracted brain tissue and could identify the brain microstructures, especially in the hippocampus [the pyramidal cell layer through CA1–3 and the dentate gyrus (DG) granular layers (GLs)], cell layers of cerebellum, three sub-regions of the deep cerebellar nucleus, and white matter (WM) structures [e.g., the fasciculus retroflexus (fr) and optic tract in the thalamus]. The following technical conditions were also examined: (i) the longitudinal stability of Mn-enhanced ex vivo tissue after in vivo administration; and (ii) the effects of mixing glutaraldehyde (GA) with the fixative solution for the preservation of in vivo MEMRI contrast. Our results indicate that ex vivo MEMRI observations made shortly after fixation maintain the contrast observed in vivo. This research will be useful for non-destructive whole-brain pathological analysis.
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Affiliation(s)
- Chika Sato
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology (QST), Chiba, Japan.,Group of Quantum-State Controlled MRI, QST, Chiba, Japan
| | - Kazuhiko Sawada
- Department of Nutrition, Faculty of Medical and Health Sciences, Tsukuba International University, Ibaraki, Japan
| | - David Wright
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia.,Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
| | - Tatsuya Higashi
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology (QST), Chiba, Japan.,Group of Quantum-State Controlled MRI, QST, Chiba, Japan
| | - Ichio Aoki
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology (QST), Chiba, Japan.,Group of Quantum-State Controlled MRI, QST, Chiba, Japan
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18
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Vandenberghe ME, Souedet N, Hérard AS, Ayral AM, Letronne F, Balbastre Y, Sadouni E, Hantraye P, Dhenain M, Frouin F, Lambert JC, Delzescaux T. Voxel-Based Statistical Analysis of 3D Immunostained Tissue Imaging. Front Neurosci 2018; 12:754. [PMID: 30498427 PMCID: PMC6250035 DOI: 10.3389/fnins.2018.00754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 10/01/2018] [Indexed: 12/23/2022] Open
Abstract
Recently developed techniques to visualize immunostained tissues in 3D and in large samples have expanded the scope of microscopic investigations at the level of the whole brain. Here, we propose to adapt voxel-based statistical analysis to 3D high-resolution images of the immunostained rodent brain. The proposed approach was first validated with a simulation dataset with known cluster locations. Then, it was applied to characterize the effect of ADAM30, a gene involved in the metabolism of the amyloid precursor protein, in a mouse model of Alzheimer's disease. This work introduces voxel-based analysis of 3D immunostained microscopic brain images and, therefore, opens the door to localized whole-brain exploratory investigation of pathological markers and cellular alterations.
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Affiliation(s)
- Michel E. Vandenberghe
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Nicolas Souedet
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Anne-Sophie Hérard
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Anne-Marie Ayral
- INSERM U1167, Institut Pasteur de LilleUniversité Lille-Nord de France, Lille, France
| | - Florent Letronne
- INSERM U1167, Institut Pasteur de LilleUniversité Lille-Nord de France, Lille, France
| | - Yaël Balbastre
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Elmahdi Sadouni
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Marc Dhenain
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Frédérique Frouin
- Laboratoire Imagerie Moléculaire in vivo (IMIV UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS)Orsay, France
| | - Jean-Charles Lambert
- INSERM U1167, Institut Pasteur de LilleUniversité Lille-Nord de France, Lille, France
| | - Thierry Delzescaux
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
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19
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Lefebvre J, Delafontaine-Martel P, Pouliot P, Girouard H, Descoteaux M, Lesage F. Fully automated dual-resolution serial optical coherence tomography aimed at diffusion MRI validation in whole mouse brains. NEUROPHOTONICS 2018; 5:045004. [PMID: 30681668 PMCID: PMC6215086 DOI: 10.1117/1.nph.5.4.045004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
An automated dual-resolution serial optical coherence tomography (2R-SOCT) scanner is developed. The serial histology system combines a low-resolution ( 25 μ m / voxel ) 3 × OCT with a high-resolution ( 1.5 μ m / voxel ) 40 × OCT to acquire whole mouse brains at low resolution and to target specific regions of interest (ROIs) at high resolution. The 40 × ROIs positions are selected either manually by the microscope operator or using an automated ROI positioning selection algorithm. Additionally, a multimodal and multiresolution registration pipeline is developed in order to align the 2R-SOCT data onto diffusion MRI (dMRI) data acquired in the same ex vivo mouse brains prior to automated histology. Using this imaging system, 3 whole mouse brains are imaged, and 250 high-resolution 40 × three-dimensional ROIs are acquired. The capability of this system to perform multimodal imaging studies is demonstrated by labeling the ROIs using a mouse brain atlas and by categorizing the ROIs based on their associated dMRI measures. This reveals a good correspondence of the tissue microstructure imaged by the high-resolution OCT with various dMRI measures such as fractional anisotropy, number of fiber orientations, apparent fiber density, orientation dispersion, and intracellular volume fraction.
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Affiliation(s)
- Joël Lefebvre
- École Polytechnique de Montréal, Laboratoire d’imagerie optique et moléculaire, Montreal, Canada
| | | | - Philippe Pouliot
- École Polytechnique de Montréal, Laboratoire d’imagerie optique et moléculaire, Montreal, Canada
- Université de Montréal, Research Centre, Montréal Heart Institute, Montreal, Canada
| | - Hélène Girouard
- Université de Montréal, Institut universitaire de gériatrie de Montréal, Montreal, Canada
| | - Maxime Descoteaux
- Université de Sherbrooke, Sherbrooke Connectivity Imaging Laboratory, Sherbrooke, Canada
| | - Frédéric Lesage
- École Polytechnique de Montréal, Laboratoire d’imagerie optique et moléculaire, Montreal, Canada
- Université de Montréal, Research Centre, Montréal Heart Institute, Montreal, Canada
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20
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Shiffman S, Basak S, Kozlowski C, Fuji RN. An automated mapping method for Nissl-stained mouse brain histologic sections. J Neurosci Methods 2018; 308:219-227. [PMID: 30096343 DOI: 10.1016/j.jneumeth.2018.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 02/09/2023]
Abstract
BACKGROUND Histologic evaluation of the central nervous system is often a critical endpoint in in vivo efficacy studies, and is considered the essential component of neurotoxicity assessment in safety studies. Automated image analysis is a powerful tool that can radically reduce the workload associated with evaluating brain histologic sections. NEW METHOD We developed an automated brain mapping method that identifies neuroanatomic structures in mouse histologic coronal brain sections. The method utilizes the publicly available Allen Brain Atlas to map brain regions on digitized Nissl-stained sections. RESULTS The method's accuracy was first assessed by comparing the mapping results to structure delineations from the Franklin and Paxinos (FP) mouse brain atlas. Brain regions mapped from FP Nissl-stained sections and calculated volumes were similar to structure delineations and volumes derived from corresponding FP illustrations. We subsequently applied our method to mouse brain sections from an in vivo study where the hippocampus was the structure of interest. Nissl-stained sections were mapped and hippocampal boundaries transferred to adjacent immunohistochemically stained sections. Optical density quantification results were comparable to those from time-consuming, manually drawn hippocampal delineations on the IHC-stained sections. COMPARISON WITH EXISTING METHODS Compared to other published methods, our method requires less manual input, and has been validated comprehensively using a secondary atlas, as well as manually annotated brain IHC sections from 68 study mice. CONCLUSIONS We propose that our automated brain mapping method enables greater efficiency and consistency in mouse neuropathologic assessments.
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Affiliation(s)
- Smadar Shiffman
- Safety Assessment Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA94080, USA
| | - Sayantani Basak
- Safety Assessment Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA94080, USA
| | - Cleopatra Kozlowski
- Safety Assessment Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA94080, USA.
| | - Reina N Fuji
- Safety Assessment Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA94080, USA.
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21
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Zhang B, Zhou Z, Tao Y, Lin H. A novel robust color gradient estimator for photographic volume visualization. J Vis (Tokyo) 2018. [DOI: 10.1007/s12650-018-0477-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Non-imaged based method for matching brains in a common anatomical space for cellular imagery. J Neurosci Methods 2018; 304:136-145. [DOI: 10.1016/j.jneumeth.2018.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 11/18/2022]
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23
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Pichat J, Iglesias JE, Yousry T, Ourselin S, Modat M. A Survey of Methods for 3D Histology Reconstruction. Med Image Anal 2018; 46:73-105. [DOI: 10.1016/j.media.2018.02.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 02/08/2023]
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24
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Ogunleke A, Recur B, Balacey H, Chen HH, Delugin M, Hwu Y, Javerzat S, Petibois C. 3D chemical imaging of the brain using quantitative IR spectro-microscopy. Chem Sci 2018; 9:189-198. [PMID: 29629087 PMCID: PMC5869290 DOI: 10.1039/c7sc03306k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/13/2017] [Indexed: 01/14/2023] Open
Abstract
Three-dimensional (3D) histology is the next frontier for modern anatomo-pathology. Characterizing abnormal parameters in a tissue is essential to understand the rationale of pathology development. However, there is no analytical technique, in vivo or histological, that is able to discover such abnormal features and provide a 3D distribution at microscopic resolution. Here, we introduce a unique high-throughput infrared (IR) microscopy method that combines automated image correction and subsequent spectral data analysis for 3D-IR image reconstruction. We performed spectral analysis of a complete organ for a small animal model, a mouse brain with an implanted glioma tumor. The 3D-IR image is reconstructed from 370 consecutive tissue sections and corrected using the X-ray tomogram of the organ for an accurate quantitative analysis of the chemical content. A 3D matrix of 89 × 106 IR spectra is generated, allowing us to separate the tumor mass from healthy brain tissues based on various anatomical, chemical, and metabolic parameters. We demonstrate that quantitative metabolic parameters can be extracted from the IR spectra for the characterization of the brain vs. tumor metabolism (assessing the Warburg effect in tumors). Our method can be further exploited by searching for the whole spectral profile, discriminating tumor vs. healthy tissue in a non-supervised manner, which we call 'spectromics'.
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Affiliation(s)
- Abiodun Ogunleke
- University of Bordeaux , Inserm U1029 LAMC , Allée Geoffroy Saint-Hilaire Bat. B2, F33600 Pessac , France . ;
| | - Benoit Recur
- University of Bordeaux , Inserm U1029 LAMC , Allée Geoffroy Saint-Hilaire Bat. B2, F33600 Pessac , France . ;
| | - Hugo Balacey
- University of Bordeaux , Inserm U1029 LAMC , Allée Geoffroy Saint-Hilaire Bat. B2, F33600 Pessac , France . ;
| | - Hsiang-Hsin Chen
- Academia Sinica , Institute of Physics , 128 Sec. 2, Academia Rd., Nankang , Taipei 11529 , Taiwan , Republic of China
| | - Maylis Delugin
- University of Bordeaux , Inserm U1029 LAMC , Allée Geoffroy Saint-Hilaire Bat. B2, F33600 Pessac , France . ;
| | - Yeukuang Hwu
- Academia Sinica , Institute of Physics , 128 Sec. 2, Academia Rd., Nankang , Taipei 11529 , Taiwan , Republic of China
| | - Sophie Javerzat
- University of Bordeaux , Inserm U1029 LAMC , Allée Geoffroy Saint-Hilaire Bat. B2, F33600 Pessac , France . ;
| | - Cyril Petibois
- University of Bordeaux , Inserm U1029 LAMC , Allée Geoffroy Saint-Hilaire Bat. B2, F33600 Pessac , France . ;
- Academia Sinica , Institute of Physics , 128 Sec. 2, Academia Rd., Nankang , Taipei 11529 , Taiwan , Republic of China
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25
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Abstract
Magnetic resonance imaging, positron emission tomography, and optical imaging have emerged as key tools to understand brain function and neurological disorders in preclinical mouse models. They offer the unique advantage of monitoring individual structural and functional changes over time. What remained unsolved until recently was to generate whole-brain microscopy data which can be correlated to the 3D in vivo neuroimaging data. Conventional histological sections are inappropriate especially for neuronal tracing or the unbiased screening for molecular targets through the whole brain. As part of the European Society for Molecular Imaging (ESMI) meeting 2016 in Utrecht, the Netherlands, we addressed this issue in the Molecular Neuroimaging study group meeting. Presentations covered new brain clearing methods, light sheet microscopes for large samples, and automatic registration of microscopy to in vivo imaging data. In this article, we summarize the discussion; give an overview of the novel techniques; and discuss the practical needs, benefits, and limitations.
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Lefebvre J, Castonguay A, Pouliot P, Descoteaux M, Lesage F. Whole mouse brain imaging using optical coherence tomography: reconstruction, normalization, segmentation, and comparison with diffusion MRI. NEUROPHOTONICS 2017; 4:041501. [PMID: 28721357 PMCID: PMC5506292 DOI: 10.1117/1.nph.4.4.041501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/19/2017] [Indexed: 05/10/2023]
Abstract
An automated massive histology setup combined with an optical coherence tomography (OCT) microscope was used to image a total of [Formula: see text] whole mouse brains. Each acquisition generated a dataset of thousands of OCT volumetric tiles at a sampling resolution of [Formula: see text]. This paper describes techniques for reconstruction and segmentation of the sliced brains. In addition to the measured OCT optical reflectivity, a single scattering photon model was used to compute the attenuation coefficients within each tissue slice. Average mouse brain templates were generated for both the OCT reflectivity and attenuation contrasts and were used with an [Formula: see text]-tissue segmentation algorithm. To better understand the brain tissue OCT contrast origin, one of the mouse brains was acquired using dMRI and coregistered to its corresponding assembled brain. Our results indicate that the optical reflectivity in a fiber bundle varies with its orientation, its fiber density, and the number of fiber orientations it contains. The OCT mouse brain template generation and coregistration to dMRI data demonstrate the potential of this massive histology technique to pursue cross-sectional, multimodal, and multisubject investigations of small animal brains.
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Affiliation(s)
- Joël Lefebvre
- École Polytechnique de Montréal, Montréal, Québec, Canada
- Address all correspondence to: Joël Lefebvre, E-mail:
| | | | - Philippe Pouliot
- École Polytechnique de Montréal, Montréal, Québec, Canada
- Institut de Cardiologie de Montréal, Montréal, Québec, Canada
| | - Maxime Descoteaux
- Université de Sherbrooke, Sherbrooke Connectivity Imaging Laboratory, Sherbrooke, Québec, Canada
| | - Frédéric Lesage
- École Polytechnique de Montréal, Montréal, Québec, Canada
- Institut de Cardiologie de Montréal, Montréal, Québec, Canada
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27
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Lin YC, Hwu Y, Huang GS, Hsiao M, Lee TT, Yang SM, Lee TK, Chen NY, Yang SS, Chen A, Ka SM. Differential synchrotron X-ray imaging markers based on the renal microvasculature for tubulointerstitial lesions and glomerulopathy. Sci Rep 2017; 7:3488. [PMID: 28615647 PMCID: PMC5471266 DOI: 10.1038/s41598-017-03677-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/03/2017] [Indexed: 12/13/2022] Open
Abstract
High resolution synchrotron microtomography capable of revealing microvessels in three dimensional (3D) establishes distinct imaging markers of mouse kidney disease strongly associated to renal tubulointerstitial (TI) lesions and glomerulopathy. Two complementary mouse models of chronic kidney disease (CKD), unilateral ureteral obstruction (UUO) and focal segmental glomerulosclerosis (FSGS), were used and five candidates of unique 3D imaging markers were identified. Our characterization to differentially reflect the altered microvasculature of renal TI lesions and/or glomerulopathy demonstrated these image features can be used to differentiate the disease status and the possible cause therefore qualified as image markers. These 3D imaging markers were further correlated with the histopathology and renal microvessel-based molecular study using antibodies against vascular endothelial cells (CD31), the connective tissue growth factor or the vascular endothelial growth factor. We also found that these 3D imaging markers individually characterize the development of renal TI lesions or glomerulopathy, quantitative and integrated use of all of them provide more information for differentiating the two renal conditions. Our findings thus establish a practical strategy to characterize the CKD-associated renal injuries by the microangiography-based 3D imaging and highlight the impact of dysfunctional microvasculature as a whole on the pathogenesis of the renal lesions.
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Affiliation(s)
- Yu-Chuan Lin
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Yeukuang Hwu
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Guo-Shu Huang
- Department of Radiology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Tsung-Tse Lee
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Shun-Min Yang
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Ting-Kuo Lee
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Nan-Yow Chen
- National Center for High-Performance Computing, Hsinchu, Taiwan
| | - Sung-Sen Yang
- Division of Nephrology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ann Chen
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.
| | - Shuk-Man Ka
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.
- Graduate Institute of Aerospace and Undersea Medicine, Academy of Medicine, National Defense Medical Center, Taipei, Taiwan.
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28
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Letronne F, Laumet G, Ayral AM, Chapuis J, Demiautte F, Laga M, Vandenberghe ME, Malmanche N, Leroux F, Eysert F, Sottejeau Y, Chami L, Flaig A, Bauer C, Dourlen P, Lesaffre M, Delay C, Huot L, Dumont J, Werkmeister E, Lafont F, Mendes T, Hansmannel F, Dermaut B, Deprez B, Hérard AS, Dhenain M, Souedet N, Pasquier F, Tulasne D, Berr C, Hauw JJ, Lemoine Y, Amouyel P, Mann D, Déprez R, Checler F, Hot D, Delzescaux T, Gevaert K, Lambert JC. ADAM30 Downregulates APP-Linked Defects Through Cathepsin D Activation in Alzheimer's Disease. EBioMedicine 2016; 9:278-292. [PMID: 27333034 PMCID: PMC4972530 DOI: 10.1016/j.ebiom.2016.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 01/12/2023] Open
Abstract
Although several ADAMs (A disintegrin-like and metalloproteases) have been shown to contribute to the amyloid precursor protein (APP) metabolism, the full spectrum of metalloproteases involved in this metabolism remains to be established. Transcriptomic analyses centred on metalloprotease genes unraveled a 50% decrease in ADAM30 expression that inversely correlates with amyloid load in Alzheimer's disease brains. Accordingly, in vitro down- or up-regulation of ADAM30 expression triggered an increase/decrease in Aβ peptides levels whereas expression of a biologically inactive ADAM30 (ADAM30(mut)) did not affect Aβ secretion. Proteomics/cell-based experiments showed that ADAM30-dependent regulation of APP metabolism required both cathepsin D (CTSD) activation and APP sorting to lysosomes. Accordingly, in Alzheimer-like transgenic mice, neuronal ADAM30 over-expression lowered Aβ42 secretion in neuron primary cultures, soluble Aβ42 and amyloid plaque load levels in the brain and concomitantly enhanced CTSD activity and finally rescued long term potentiation alterations. Our data thus indicate that lowering ADAM30 expression may favor Aβ production, thereby contributing to Alzheimer's disease development.
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Affiliation(s)
- Florent Letronne
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Geoffroy Laumet
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Anne-Marie Ayral
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Julien Chapuis
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Florie Demiautte
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Mathias Laga
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Michel E Vandenberghe
- CEA, DSV, I2BM, MIRCen, Fontenay aux Roses, France; CNRS, UMR 9199, Fontenay aux Roses, France
| | - Nicolas Malmanche
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Florence Leroux
- Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France; INSERM U1177, Drugs and Molecules for Living Systems, F5900 Lille, France
| | - Fanny Eysert
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Yoann Sottejeau
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Linda Chami
- Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275 CNRS, Laboratoire d'Excellence Distalz, Nice, France; Université de Nice-Sophia-Antipolis, Valbonne, France
| | - Amandine Flaig
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Charlotte Bauer
- Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275 CNRS, Laboratoire d'Excellence Distalz, Nice, France; Université de Nice-Sophia-Antipolis, Valbonne, France
| | - Pierre Dourlen
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Marie Lesaffre
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Charlotte Delay
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Ludovic Huot
- Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France; Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM 1019, Lille, France
| | - Julie Dumont
- Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France; INSERM U1177, Drugs and Molecules for Living Systems, F5900 Lille, France
| | | | | | - Tiago Mendes
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Franck Hansmannel
- INSERM, U954, Vandoeuvre-lès-Nancy, France; Department of Hepato-Gastroenterology, University Hospital of Nancy, Université Henri Poincaré 1, Vandoeuvre-lès-Nancy, France
| | - Bart Dermaut
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France
| | - Benoit Deprez
- Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France; INSERM U1177, Drugs and Molecules for Living Systems, F5900 Lille, France
| | - Anne-Sophie Hérard
- CEA, DSV, I2BM, MIRCen, Fontenay aux Roses, France; CNRS, UMR 9199, Fontenay aux Roses, France
| | - Marc Dhenain
- CEA, DSV, I2BM, MIRCen, Fontenay aux Roses, France; CNRS, UMR 9199, Fontenay aux Roses, France
| | - Nicolas Souedet
- CEA, DSV, I2BM, MIRCen, Fontenay aux Roses, France; CNRS, UMR 9199, Fontenay aux Roses, France
| | - Florence Pasquier
- Univ. Lille, Inserm, U1171, - Degenerative & Vascular Cognitive Disorders, Laboratoire d'Excellence Distalz, F-59000 Lille, France; CHR&U, Lille, France
| | - David Tulasne
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T - Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Claudine Berr
- INSERM, U1061, Université de Montpellier I, Hôpital La Colombière, Montpellier, France
| | - Jean-Jacques Hauw
- APHP-Raymond Escourolle Neuropathology Laboratory, la salpétrière Hospital, Paris, France
| | - Yves Lemoine
- Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France; Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM 1019, Lille, France
| | - Philippe Amouyel
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France; CHR&U, Lille, France
| | - David Mann
- Institute of Brain, Behaviour and Mental Health, University of Manchester, Salford Royal Hospital, Salford, UK
| | - Rebecca Déprez
- Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France; INSERM U1177, Drugs and Molecules for Living Systems, F5900 Lille, France
| | - Frédéric Checler
- Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275 CNRS, Laboratoire d'Excellence Distalz, Nice, France; Université de Nice-Sophia-Antipolis, Valbonne, France
| | - David Hot
- Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France; Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM 1019, Lille, France
| | - Thierry Delzescaux
- CEA, DSV, I2BM, MIRCen, Fontenay aux Roses, France; CNRS, UMR 9199, Fontenay aux Roses, France
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jean-Charles Lambert
- INSERM, U1167, Laboratoire d'Excellence Distalz, F59000 Lille, France; Institut Pasteur de Lille, F59000 Lille, France; Univ. Lille, F59000 Lille, France.
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