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Imenez Silva PH, Pepin M, Figurek A, Gutiérrez-Jiménez E, Bobot M, Iervolino A, Mattace-Raso F, Hoorn EJ, Bailey MA, Hénaut L, Nielsen R, Frische S, Trepiccione F, Hafez G, Altunkaynak HO, Endlich N, Unwin R, Capasso G, Pesic V, Massy Z, Wagner CA. Animal models to study cognitive impairment of chronic kidney disease. Am J Physiol Renal Physiol 2024; 326:F894-F916. [PMID: 38634137 DOI: 10.1152/ajprenal.00338.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/11/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
Mild cognitive impairment (MCI) is common in people with chronic kidney disease (CKD), and its prevalence increases with progressive loss of kidney function. MCI is characterized by a decline in cognitive performance greater than expected for an individual age and education level but with minimal impairment of instrumental activities of daily living. Deterioration can affect one or several cognitive domains (attention, memory, executive functions, language, and perceptual motor or social cognition). Given the increasing prevalence of kidney disease, more and more people with CKD will also develop MCI causing an enormous disease burden for these individuals, their relatives, and society. However, the underlying pathomechanisms are poorly understood, and current therapies mostly aim at supporting patients in their daily lives. This illustrates the urgent need to elucidate the pathogenesis and potential therapeutic targets and test novel therapies in appropriate preclinical models. Here, we will outline the necessary criteria for experimental modeling of cognitive disorders in CKD. We discuss the use of mice, rats, and zebrafish as model systems and present valuable techniques through which kidney function and cognitive impairment can be assessed in this setting. Our objective is to enable researchers to overcome hurdles and accelerate preclinical research aimed at improving the therapy of people with CKD and MCI.
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Affiliation(s)
- Pedro H Imenez Silva
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Marion Pepin
- Institut National de la Santé et de la Recherche Médicale U-1018 Centre de Recherche en Épidémiologie et Santé des Population, Équipe 5, Paris-Saclay University, Versailles Saint-Quentin-en-Yvelines University, Villejuif, France
- Department of Geriatrics, Centre Hospitalier Universitaire Ambroise Paré, Assistance Publique-Hôpitaux de Paris Université Paris-Saclay, Paris, France
| | - Andreja Figurek
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Eugenio Gutiérrez-Jiménez
- Center for Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mickaël Bobot
- Centre de Néphrologie et Transplantation Rénale, Hôpital de la Conception, Assistance Publique-Hopitaux de Marseille, and INSERM 1263, Institut National de la Recherche Agronomique 1260, C2VN, Aix-Marseille Universitaire, Marseille, France
| | - Anna Iervolino
- Department of Translational Medical Sciences, University of Campania 'Luigi Vanvitelli,' Naples, Italy
| | - Francesco Mattace-Raso
- Division of Geriatrics, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ewout J Hoorn
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Matthew A Bailey
- Edinburgh Kidney, Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lucie Hénaut
- UR UPJV 7517, Jules Verne University of Picardie, Amiens, France
| | - Rikke Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Francesco Trepiccione
- Department of Translational Medical Sciences, University of Campania 'Luigi Vanvitelli,' Naples, Italy
| | - Gaye Hafez
- Department of Pharmacology, Faculty of Pharmacy, Altinbas University, Istanbul, Turkey
| | - Hande O Altunkaynak
- Department of Pharmacology, Gulhane Faculty of Pharmacy, University of Health Sciences, Istanbul, Turkey
| | - Nicole Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Robert Unwin
- Department of Renal Medicine, Royal Free Hospital, University College London, London, United Kingdom
| | - Giovambattista Capasso
- Department of Translational Medical Sciences, University of Campania 'Luigi Vanvitelli,' Naples, Italy
- Biogem Research Institute, Ariano Irpino, Italy
| | - Vesna Pesic
- Department of Physiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Ziad Massy
- Centre for Research in Epidemiology and Population Health, INSERM UMRS 1018, Clinical Epidemiology Team, University Paris-Saclay, University Versailles-Saint Quentin, Villejuif, France
- Department of Nephrology, Centre Hospitalier Universitaire Ambroise Paré, Assistance Publique-Hôpitaux de Paris Université Paris-Saclay, Paris, France
| | - Carsten A Wagner
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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Chang S, Yang J, Novoseltseva A, Abdelhakeem A, Hyman M, Fu X, Li C, Chen S, Augustinack JC, Magnain C, Fischl B, Mckee AC, Boas DA, Chen IA, Wang H. Multi-Scale Label-Free Human Brain Imaging with Integrated Serial Sectioning Polarization Sensitive Optical Coherence Tomography and Two-Photon Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303381. [PMID: 37882348 PMCID: PMC10724383 DOI: 10.1002/advs.202303381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/29/2023] [Indexed: 10/27/2023]
Abstract
The study of aging and neurodegenerative processes in the human brain requires a comprehensive understanding of cytoarchitectonic, myeloarchitectonic, and vascular structures. Recent computational advances have enabled volumetric reconstruction of the human brain using thousands of stained slices, however, tissue distortions and loss resulting from standard histological processing have hindered deformation-free reconstruction. Here, the authors describe an integrated serial sectioning polarization-sensitive optical coherence tomography (PSOCT) and two photon microscopy (2PM) system to provide label-free multi-contrast imaging of intact brain structures, including scattering, birefringence, and autofluorescence of human brain tissue. The authors demonstrate high-throughput reconstruction of 4 × 4 × 2cm3 sample blocks and simple registration between PSOCT and 2PM images that enable comprehensive analysis of myelin content, vascular structure, and cellular information. The high-resolution 2PM images provide microscopic validation and enrichment of the cellular information provided by the PSOCT optical properties on the same sample, revealing the densely packed fibers, capillaries, and lipofuscin-filled cell bodies in the cortex and white matter. It is shown that the imaging system enables quantitative characterization of various pathological features in aging process, including myelin degradation, lipofuscin accumulation, and microvascular changes, which opens up numerous opportunities in the study of neurodegenerative diseases in the future.
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Affiliation(s)
- Shuaibin Chang
- Department of Electrical and Computer EngineeringBoston University8 St Mary's StBoston02215USA
| | - Jiarui Yang
- Department of Biomedical EngineeringBoston University44 Cummington MallBoston02215USA
| | - Anna Novoseltseva
- Department of Biomedical EngineeringBoston University44 Cummington MallBoston02215USA
| | - Ayman Abdelhakeem
- Department of Electrical and Computer EngineeringBoston University8 St Mary's StBoston02215USA
| | - Mackenzie Hyman
- Department of Biomedical EngineeringBoston University44 Cummington MallBoston02215USA
| | - Xinlei Fu
- Department of Mechanical EngineeringThe Chinese University of Hong KongHong Kong999077China
| | - Chenglin Li
- Department of Mechanical EngineeringThe Chinese University of Hong KongHong Kong999077China
| | - Shih‐Chi Chen
- Department of Mechanical EngineeringThe Chinese University of Hong KongHong Kong999077China
| | - Jean C. Augustinack
- Department of RadiologyMassachusetts General HospitalA.A. Martinos Center for Biomedical Imaging13th StreetBoston02129USA
| | - Caroline Magnain
- Department of RadiologyMassachusetts General HospitalA.A. Martinos Center for Biomedical Imaging13th StreetBoston02129USA
| | - Bruce Fischl
- Department of RadiologyMassachusetts General HospitalA.A. Martinos Center for Biomedical Imaging13th StreetBoston02129USA
| | - Ann C. Mckee
- VA Boston Healthcare SystemU.S. Department of Veteran AffairsBoston02132USA
- Boston University Chobanian and Avedisian School of MedicineBoston University Alzheimer's Disease Research Center and CTE CenterBoston02118USA
- Department of NeurologyBoston University Chobanian and Avedisian School of MedicineBoston02118USA
- Department of Pathology and Laboratory MedicineBoston University Chobanian and Avedisian School of MedicineBoston02118USA
- VA Bedford Healthcare SystemU.S. Department of Veteran AffairsBedfordMA01730‐1114USA
| | - David A. Boas
- Department of Electrical and Computer EngineeringBoston University8 St Mary's StBoston02215USA
- Department of Biomedical EngineeringBoston University44 Cummington MallBoston02215USA
| | - Ichun Anderson Chen
- Department of Biomedical EngineeringBoston University44 Cummington MallBoston02215USA
| | - Hui Wang
- Department of RadiologyMassachusetts General HospitalA.A. Martinos Center for Biomedical Imaging13th StreetBoston02129USA
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Wang Y, LeDue JM, Murphy TH. Multiscale imaging informs translational mouse modeling of neurological disease. Neuron 2022; 110:3688-3710. [PMID: 36198319 DOI: 10.1016/j.neuron.2022.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/26/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Multiscale neurophysiology reveals that simple motor actions are associated with changes in neuronal firing in virtually every brain region studied. Accordingly, the assessment of focal pathology such as stroke or progressive neurodegenerative diseases must also extend widely across brain areas. To derive mechanistic information through imaging, multiple resolution scales and multimodal factors must be included, such as the structure and function of specific neurons and glial cells and the dynamics of specific neurotransmitters. Emerging multiscale methods in preclinical animal studies that span micro- to macroscale examinations fill this gap, allowing a circuit-based understanding of pathophysiological mechanisms. Combined with high-performance computation and open-source data repositories, these emerging multiscale and large field-of-view techniques include live functional ultrasound, multi- and single-photon wide-scale light microscopy, video-based miniscopes, and tissue-penetrating fiber photometry, as well as variants of post-mortem expansion microscopy. We present these technologies and outline use cases and data pipelines to uncover new knowledge within animal models of stroke, Alzheimer's disease, and movement disorders.
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Affiliation(s)
- Yundi Wang
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological Research, Detwiller Pavilion, 2255 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jeffrey M LeDue
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological Research, Detwiller Pavilion, 2255 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Timothy H Murphy
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological Research, Detwiller Pavilion, 2255 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada.
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Pierre WC, Zhang E, Londono I, De Leener B, Lesage F, Lodygensky GA. Non-invasive in vivo MRI detects long-term microstructural brain alterations related to learning and memory impairments in a model of inflammation-induced white matter injury. Behav Brain Res 2022; 428:113884. [DOI: 10.1016/j.bbr.2022.113884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/18/2022] [Accepted: 04/03/2022] [Indexed: 11/28/2022]
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Yin X, Zhang X, Zhang J, Yang W, Sun X, Zhang H, Gao Z, Jiang H. High-Resolution Digital Panorama of Multiple Structures in Whole Brain of Alzheimer's Disease Mice. Front Neurosci 2022; 16:870520. [PMID: 35516801 PMCID: PMC9067162 DOI: 10.3389/fnins.2022.870520] [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: 02/06/2022] [Accepted: 03/11/2022] [Indexed: 11/24/2022] Open
Abstract
Simultaneously visualizing Amyloid-β (Aβ) plaque with its surrounding brain structures at the subcellular level in the intact brain is essential for understanding the complex pathology of Alzheimer's disease, but is still rarely achieved due to the technical limitations. Combining the micro-optical sectioning tomography (MOST) system, whole-brain Nissl staining, and customized image processing workflow, we generated a whole-brain panorama of Alzheimer's disease mice without specific labeling. The workflow employed the steps that include virtual channel splitting, feature enhancement, iso-surface rendering, direct volume rendering, and feature fusion to extract and reconstruct the different signals with distinct gray values and morphologies. Taking advantage of this workflow, we found that the denser-distribution areas of Aβ plaques appeared with relatively more somata and smaller vessels, but show a dissimilar distributing pattern with nerve tracts. In addition, the entorhinal cortex and adjacent subiculum regions present the highest density and biggest diameter of plaques. The neuronal processes in the vicinity of these Aβ plaques showed significant structural alternation such as bending or abrupt branch ending. The capillaries inside or adjacent to the plaques were observed with abundant distorted micro-vessels and abrupt ending. Depicting Aβ plaques, somata, nerve processes and tracts, and blood vessels simultaneously, this panorama enables us for the first time, to analyze how the Aβ plaques interact with capillaries, somata, and processes at a submicron resolution of 3D whole-brain scale, which reveals potential pathological effects of Aβ plaques from a new cross-scale view. Our approach opens a door to routine systematic studies of complex interactions among brain components in mouse models of Alzheimer's disease.
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Affiliation(s)
- Xianzhen Yin
- Center for MOST and Image Fusion Analysis, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Lingang Laboratory, Shanghai, China
- *Correspondence: Xianzhen Yin
| | - Xiaochuan Zhang
- Center for MOST and Image Fusion Analysis, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jingjing Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Weicheng Yang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xian Sun
- Center for MOST and Image Fusion Analysis, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Haiyan Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Haiyan Zhang
| | - Zhaobing Gao
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute of Drug Discovery, Institution for Drug Discovery Innovation, Chinese Academy of Science, Zhongshan, China
- Zhaobing Gao
| | - Hualiang Jiang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Lingang Laboratory, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- Hualiang Jiang
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Bennett HC, Kim Y. Advances in studying whole mouse brain vasculature using high-resolution 3D light microscopy imaging. NEUROPHOTONICS 2022; 9:021902. [PMID: 35402638 PMCID: PMC8983067 DOI: 10.1117/1.nph.9.2.021902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Significance: The cerebrovasculature has become increasingly recognized as a major player in overall brain health and many brain disorders. Although there have been several landmark studies to understand details of these crucially important structures in an anatomically defined area, brain-wide examination of the whole cerebrovasculature, including microvessels, has been challenging. However, emerging techniques, including tissue processing and three-dimensional (3D) microscopy imaging, enable neuroscientists to examine the total vasculature in the entire mouse brain. Aim: Here, we aim to highlight advances in these high-resolution 3D mapping methods including block-face imaging and light sheet fluorescent microscopy. Approach: We summarize latest mapping tools to understand detailed anatomical arrangement of the cerebrovascular network and the organizing principles of the neurovascular unit (NVU) as a whole. Results: We discuss biological insights gained from studies using these imaging methods and how these tools can be used to advance our understanding of the cerebrovascular network and related cell types in the entire brain. Conclusions: This review article will help to understand recent advance in high-resolution NVU mapping in mice and provide perspective on future studies.
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Affiliation(s)
- Hannah C. Bennett
- The Pennsylvania State University, Department of Neural and Behavioral Sciences, Hershey, Pennsylvania, United States
| | - Yongsoo Kim
- The Pennsylvania State University, Department of Neural and Behavioral Sciences, Hershey, Pennsylvania, United States
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7
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Ni R. Magnetic Resonance Imaging in Animal Models of Alzheimer's Disease Amyloidosis. Int J Mol Sci 2021; 22:12768. [PMID: 34884573 PMCID: PMC8657987 DOI: 10.3390/ijms222312768] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
Amyloid-beta (Aβ) plays an important role in the pathogenesis of Alzheimer's disease. Aberrant Aβ accumulation induces neuroinflammation, cerebrovascular alterations, and synaptic deficits, leading to cognitive impairment. Animal models recapitulating the Aβ pathology, such as transgenic, knock-in mouse and rat models, have facilitated the understanding of disease mechanisms and the development of therapeutics targeting Aβ. There is a rapid advance in high-field MRI in small animals. Versatile high-field magnetic resonance imaging (MRI) sequences, such as diffusion tensor imaging, arterial spin labeling, resting-state functional MRI, anatomical MRI, and MR spectroscopy, as well as contrast agents, have been developed for preclinical imaging in animal models. These tools have enabled high-resolution in vivo structural, functional, and molecular readouts with a whole-brain field of view. MRI has been used to visualize non-invasively the Aβ deposits, synaptic deficits, regional brain atrophy, impairment in white matter integrity, functional connectivity, and cerebrovascular and glymphatic system in animal models of Alzheimer's disease amyloidosis. Many of the readouts are translational toward clinical MRI applications in patients with Alzheimer's disease. In this review, we summarize the recent advances in MRI for visualizing the pathophysiology in amyloidosis animal models. We discuss the outstanding challenges in brain imaging using MRI in small animals and propose future outlook in visualizing Aβ-related alterations in the brains of animal models.
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Affiliation(s)
- Ruiqing Ni
- Institute for Biomedical Engineering, ETH Zurich & University of Zurich, 8093 Zurich, Switzerland;
- Institute for Regenerative Medicine, University of Zurich, 8952 Zurich, Switzerland
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Milecki L, Poree J, Belgharbi H, Bourquin C, Damseh R, Delafontaine-Martel P, Lesage F, Gasse M, Provost J. A Deep Learning Framework for Spatiotemporal Ultrasound Localization Microscopy. IEEE TRANSACTIONS ON MEDICAL IMAGING 2021; 40:1428-1437. [PMID: 33534705 DOI: 10.1109/tmi.2021.3056951] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ultrasound Localization Microscopy (ULM) can resolve the microvascular bed down to a few micrometers. To achieve such performance, microbubble contrast agents must perfuse the entire microvascular network. Microbubbles are then located individually and tracked over time to sample individual vessels, typically over hundreds of thousands of images. To overcome the fundamental limit of diffraction and achieve a dense reconstruction of the network, low microbubble concentrations must be used, which leads to acquisitions lasting several minutes. Conventional processing pipelines are currently unable to deal with interference from multiple nearby microbubbles, further reducing achievable concentrations. This work overcomes this problem by proposing a Deep Learning approach to recover dense vascular networks from ultrasound acquisitions with high microbubble concentrations. A realistic mouse brain microvascular network, segmented from 2-photon microscopy, was used to train a three-dimensional convolutional neural network (CNN) based on a V-net architecture. Ultrasound data sets from multiple microbubbles flowing through the microvascular network were simulated and used as ground truth to train the 3D CNN to track microbubbles. The 3D-CNN approach was validated in silico using a subset of the data and in vivo in a rat brain. In silico, the CNN reconstructed vascular networks with higher precision (81%) than a conventional ULM framework (70%). In vivo, the CNN could resolve micro vessels as small as 10 μ m with an improvement in resolution when compared against a conventional approach.
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Young DM, Fazel Darbandi S, Schwartz G, Bonzell Z, Yuruk D, Nojima M, Gole LC, Rubenstein JL, Yu W, Sanders SJ. Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain. eLife 2021; 10:61408. [PMID: 33570495 PMCID: PMC7994002 DOI: 10.7554/elife.61408] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/10/2021] [Indexed: 12/17/2022] Open
Abstract
3D imaging data necessitate 3D reference atlases for accurate quantitative interpretation. Existing computational methods to generate 3D atlases from 2D-derived atlases result in extensive artifacts, while manual curation approaches are labor-intensive. We present a computational approach for 3D atlas construction that substantially reduces artifacts by identifying anatomical boundaries in the underlying imaging data and using these to guide 3D transformation. Anatomical boundaries also allow extension of atlases to complete edge regions. Applying these methods to the eight developmental stages in the Allen Developing Mouse Brain Atlas (ADMBA) led to more comprehensive and accurate atlases. We generated imaging data from 15 whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries). We provide the pipeline as the MagellanMapper software and the eight 3D reconstructed ADMBA atlases. These resources facilitate whole-organ quantitative analysis between samples and across development. The research community needs precise, reliable 3D atlases of organs to pinpoint where biological structures and processes are located. For instance, these maps are essential to understand where specific genes are turned on or off, or the spatial organization of various groups of cells over time. For centuries, atlases have been built by thinly ‘slicing up’ an organ, and then precisely representing each 2D layer. Yet this approach is imperfect: each layer may be accurate on its own, but inevitable mismatches appear between the slices when viewed in 3D or from another angle. Advances in microscopy now allow entire organs to be imaged in 3D. Comparing these images with atlases could help to detect subtle differences that indicate or underlie disease. However, this is only possible if 3D maps are accurate and do not feature mismatches between layers. To create an atlas without such artifacts, one approach consists in starting from scratch and manually redrawing the maps in 3D, a labor-intensive method that discards a large body of well-established atlases. Instead, Young et al. set out to create an automated method which could help to refine existing ‘layer-based’ atlases, releasing software that anyone can use to improve current maps. The package was created by harnessing eight atlases in the Allen Developing Mouse Brain Atlas, and then using the underlying anatomical images to resolve discrepancies between layers or fill out any missing areas. Known as MagellanMapper, the software was extensively tested to demonstrate the accuracy of the maps it creates, including comparison to whole-brain imaging data from 15 mouse brains. Armed with this new software, researchers can improve the accuracy of their atlases, helping them to understand the structure of organs at the level of the cell and giving them insight into a broad range of human disorders.
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Affiliation(s)
- David M Young
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, United States.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Siavash Fazel Darbandi
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, United States
| | - Grace Schwartz
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, United States
| | - Zachary Bonzell
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, United States
| | - Deniz Yuruk
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, United States
| | - Mai Nojima
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, United States
| | - Laurent C Gole
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - John Lr Rubenstein
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, United States
| | - Weimiao Yu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, United States
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Lu X, Moeini M, Li B, Lu Y, Damseh R, Pouliot P, Thorin É, Lesage F. A Pilot Study Investigating Changes in Capillary Hemodynamics and Its Modulation by Exercise in the APP-PS1 Alzheimer Mouse Model. Front Neurosci 2019; 13:1261. [PMID: 31920472 PMCID: PMC6915102 DOI: 10.3389/fnins.2019.01261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/06/2019] [Indexed: 12/11/2022] Open
Abstract
Dysfunction in neurovascular coupling that results in a mismatch between cerebral blood flow and neuronal activity has been suggested to play a key role in the pathogenesis of Alzheimer's disease (AD). Meanwhile, physical exercise is a powerful approach for maintaining cognitive health and could play a preventive role against the progression of AD. Given the fundamental role of capillaries in oxygen transport to tissue, our pilot study aimed to characterize changes in capillary hemodynamics with AD and AD supplemented by exercise. Exploiting two-photon microscopy, intrinsic signal optical imaging, and magnetic resonance imaging, we found hemodynamic alterations and lower vascular density with AD that were reversed by exercise. We further observed that capillary properties were branch order-dependent and that stimulation-evoked changes were attenuated with AD but increased by exercise. Our study provides novel indications into cerebral microcirculatory disturbances with AD and the modulating role of voluntary exercise on these alterations.
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Affiliation(s)
- Xuecong Lu
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Mohammad Moeini
- Department of Biomedical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Baoqiang Li
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States
| | - Yuankang Lu
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Rafat Damseh
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Philippe Pouliot
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Éric Thorin
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
- Department of Surgery, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Frédéric Lesage
- Biomedical Engineering Institute, École Polytechnique de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
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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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