1
|
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.
Collapse
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
| |
Collapse
|
2
|
Mi X, Chen ABY, Duarte D, Carey E, Taylor CR, Braaker PN, Bright M, Almeida RG, Lim JX, Ruetten VMS, Zheng W, Wang M, Reitman ME, Wang Y, Poskanzer KE, Lyons DA, Nimmerjahn A, Ahrens MB, Yu G. Fast, Accurate, and Versatile Data Analysis Platform for the Quantification of Molecular Spatiotemporal Signals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592259. [PMID: 38766026 PMCID: PMC11100599 DOI: 10.1101/2024.05.02.592259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce Activity Quantification and Analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine learning techniques. It decomposes complex live imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, and imaging modalities. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, and distinct sensorimotor signal propagation patterns in the mouse spinal cord.
Collapse
Affiliation(s)
- Xuelong Mi
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
- These authors contributed equally
| | - Alex Bo-Yuan Chen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Graduate Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
- These authors contributed equally
| | - Daniela Duarte
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Erin Carey
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Charlotte R. Taylor
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, CA, USA
| | - Philipp N. Braaker
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh BioQuarter, Edinburgh EH16 4SB, UK
| | - Mark Bright
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Rafael G. Almeida
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh BioQuarter, Edinburgh EH16 4SB, UK
| | - Jing-Xuan Lim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Virginia M. S. Ruetten
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Gatsby Computational Neuroscience Unit, UCL, London W1T 4JG, USA
| | - Wei Zheng
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Mengfan Wang
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Michael E. Reitman
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, CA, USA
| | - Yizhi Wang
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
| | - Kira E. Poskanzer
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, CA, USA
- Kavli Institute for Fundamental Neuroscience, San Francisco, CA, USA
| | - David A. Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh BioQuarter, Edinburgh EH16 4SB, UK
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Misha B. Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Guoqiang Yu
- Department of Automation, Tsinghua University, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
- Lead contact
| |
Collapse
|
3
|
Yamada H, Makino SI, Okunaga I, Miyake T, Yamamoto-Nonaka K, Oliva Trejo JA, Tominaga T, Empitu MA, Kadariswantiningsih IN, Kerever A, Komiya A, Ichikawa T, Arikawa-Hirasawa E, Yanagita M, Asanuma K. Beyond 2D: A scalable and highly sensitive method for a comprehensive 3D analysis of kidney biopsy tissue. PNAS NEXUS 2024; 3:pgad433. [PMID: 38193136 PMCID: PMC10772983 DOI: 10.1093/pnasnexus/pgad433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 11/06/2023] [Indexed: 01/10/2024]
Abstract
The spatial organization of various cell populations is critical for the major physiological and pathological processes in the kidneys. Most evaluation of these processes typically comes from a conventional 2D tissue cross-section, visualizing a limited amount of cell organization. Therefore, the 2D analysis of kidney biopsy introduces selection bias. The 2D analysis potentially omits key pathological findings outside a 1- to 10-μm thin-sectioned area and lacks information on tissue organization, especially in a particular irregular structure such as crescentic glomeruli. In this study, we introduce an easy-to-use and scalable method for obtaining high-quality images of molecules of interest in a large tissue volume, enabling a comprehensive evaluation of the 3D organization and cellular composition of kidney tissue, especially the glomerular structure. We show that CUBIC and ScaleS clearing protocols could allow a 3D analysis of the kidney tissues in human and animal models of kidney disease. We also demonstrate that the paraffin-embedded human biopsy specimens previously examined via 2D evaluation could be applicable to 3D analysis, showing a potential utilization of this method in kidney biopsy tissue collected in the past. In summary, the 3D analysis of kidney biopsy provides a more comprehensive analysis and a minimized selection bias than 2D tissue analysis. Additionally, this method enables a quantitative evaluation of particular kidney structures and their surrounding tissues, with the potential utilization from basic science investigation to applied diagnostics in nephrology.
Collapse
Affiliation(s)
- Hiroyuki Yamada
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Department of Primary Care and Emergency, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Shin-ichi Makino
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Issei Okunaga
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Takafumi Miyake
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kanae Yamamoto-Nonaka
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Juan Alejandro Oliva Trejo
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
| | - Takahiro Tominaga
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Maulana A Empitu
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | | | - Aurelien Kerever
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Akira Komiya
- Department of Urology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Tomohiko Ichikawa
- Department of Urology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Eri Arikawa-Hirasawa
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Motoko Yanagita
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Katsuhiko Asanuma
- Department of Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
- The Laboratory for Kidney Research (TMK Project), Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto 606-8397, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| |
Collapse
|
4
|
Chourrout M, Rositi H, Ong E, Hubert V, Paccalet A, Foucault L, Autret A, Fayard B, Olivier C, Bolbos R, Peyrin F, Crola-da-Silva C, Meyronet D, Raineteau O, Elleaume H, Brun E, Chauveau F, Wiart M. Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models. BIOMEDICAL OPTICS EXPRESS 2022; 13:1620-1639. [PMID: 35415001 PMCID: PMC8973191 DOI: 10.1364/boe.438832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
White-matter injury leads to severe functional loss in many neurological diseases. Myelin staining on histological samples is the most common technique to investigate white-matter fibers. However, tissue processing and sectioning may affect the reliability of 3D volumetric assessments. The purpose of this study was to propose an approach that enables myelin fibers to be mapped in the whole rodent brain with microscopic resolution and without the need for strenuous staining. With this aim, we coupled in-line (propagation-based) X-ray phase-contrast tomography (XPCT) to ethanol-induced brain sample dehydration. We here provide the proof-of-concept that this approach enhances myelinated axons in rodent and human brain tissue. In addition, we demonstrated that white-matter injuries could be detected and quantified with this approach, using three animal models: ischemic stroke, premature birth and multiple sclerosis. Furthermore, in analogy to diffusion tensor imaging (DTI), we retrieved fiber directions and DTI-like diffusion metrics from our XPCT data to quantitatively characterize white-matter microstructure. Finally, we showed that this non-destructive approach was compatible with subsequent complementary brain sample analysis by conventional histology. In-line XPCT might thus become a novel gold-standard for investigating white-matter injury in the intact brain. This is Part I of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part II shows how in-line XPCT enables the whole-brain 3D morphometric analysis of amyloid- β (A β ) plaques.
Collapse
Affiliation(s)
- Matthieu Chourrout
- Univ-Lyon, Lyon Neuroscience
Research Center, CNRS UMR5292, Inserm U1028,
Université Claude Bernard Lyon 1, Lyon, France
- Co-first authors
| | - Hugo Rositi
- Univ-Clermont Auvergne; CNRS;
SIGMA Clermont; Institut Pascal,
Clermont-Ferrand, France
- Co-first authors
| | - Elodie Ong
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
- Univ-Lyon, Hospices Civils de
Lyon, Lyon, France
| | - Violaine Hubert
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
| | - Alexandre Paccalet
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
| | - Louis Foucault
- Univ-Lyon, Université
Claude Bernard Lyon 1, Inserm, Stem Cell and Brain
Research Institute U1208, 69500 Bron, France
| | | | | | - Cécile Olivier
- Univ-Lyon, INSA-Lyon,
Université Claude Bernard Lyon 1,
CNRS, Inserm, CREATIS UMR5220, U1206, F-69621, France
| | | | - Françoise Peyrin
- Univ-Lyon, INSA-Lyon,
Université Claude Bernard Lyon 1,
CNRS, Inserm, CREATIS UMR5220, U1206, F-69621, France
| | - Claire Crola-da-Silva
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
| | | | - Olivier Raineteau
- Univ-Lyon, Université
Claude Bernard Lyon 1, Inserm, Stem Cell and Brain
Research Institute U1208, 69500 Bron, France
| | - Héléne Elleaume
- Université Grenoble
Alpes, Inserm UA7 Strobe, Grenoble, France
| | - Emmanuel Brun
- Université Grenoble
Alpes, Inserm UA7 Strobe, Grenoble, France
| | - Fabien Chauveau
- Univ-Lyon, Lyon Neuroscience
Research Center, CNRS UMR5292, Inserm U1028,
Université Claude Bernard Lyon 1, Lyon, France
- CNRS, Lyon,
France
- Co-last authors
| | - Marlene Wiart
- Univ-Lyon, CarMeN
laboratory, Inserm U1060, INRA U1397, Université
Claude Bernard Lyon 1, INSA Lyon, Charles Mérieux Medical
School, F-69600, Oullins, France
- CNRS, Lyon,
France
- Co-last authors
| |
Collapse
|
5
|
Son J, Park SJ, Ha T, Lee SN, Cho HY, Choi JW. Electrophysiological Monitoring of Neurochemical-Based Neural Signal Transmission in a Human Brain-Spinal Cord Assembloid. ACS Sens 2022; 7:409-414. [PMID: 35044765 DOI: 10.1021/acssensors.1c02279] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Combining human brain organoids holds great potential in recapitulating the human brain's histological features and modeling neural disorders. However, current combined-brain organoid models focus on the internal interactions between different brain regions. In this study, we develop an engineered brain-spinal cord assembloid (eBSA) by coculturing cerebral organoids (COs) and motor neuron spheroids (MNSs). By connecting COs and MNSs, we generate a terminal for signal transfer from the brain to the whole body by mimicking the brain-spinal cord connection. After the formation of COs from human induced pluripotent stem cells and MNSs from human neural stem cells, MNSs are prepatterned into specific CO regions and assembled to form an eBSA. Caffeine serves as a neurochemical model to demonstrate neural signal transmission. When the MNSs in the eBSA contact the multielectrode array, the eBSA successfully shows an increased neural spiking speed on the motor neuron region by caffeine treatment, which means that neural stimulation signals transfer from the COs to MNSs. The neural stimulation effects of caffeine are tested on the MNSs only to prove the eBSA system's neural signal transmission, and there were no stimulus effects. Our results demonstrate that the eBSA system can monitor a caffeine-mediated excitatory signal as an output signal from the brain to the spinal cord. We believe that the eBSA system can be utilized as a screening platform to validate the stimulus signal transfer by neurochemicals. In addition, the accumulation of understanding of the neural signal transfer from CNS to PNS will provide better knowledge for controlling muscle actuators with the nervous system.
Collapse
Affiliation(s)
- Joohyung Son
- Department of Chemical & Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Soo Jeong Park
- Department of Chemical & Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Taehyeong Ha
- Department of Chemical & Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Sang-Nam Lee
- Uniance Gene Inc., 1107 Teilhard Hall, 35 Baekbeom-Ro, Mapo-Gu, Seoul, 04107, Republic of Korea
| | - Hyeon-Yeol Cho
- Department of Bio & Fermentation Convergence Technology, Kookmin University, Seoul, 02707, Republic of Korea
| | - Jeong-Woo Choi
- Department of Chemical & Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| |
Collapse
|
6
|
Lu W, Pei Z, Hu W, Tan C, Tong X, Feng Y, Sun X. Recent progress in optical clearing of eye tissues. Exp Eye Res 2021; 212:108796. [PMID: 34662543 DOI: 10.1016/j.exer.2021.108796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/20/2021] [Accepted: 10/13/2021] [Indexed: 12/21/2022]
Abstract
The growing need for viewing the detailed 3D structures of various tissues and organs requires advanced tissue processing and imaging techniques. However, light scattering by tissues hinders detailed structural observations. To overcome this, the emerging technique of "tissue optical clearing" has been flourishing in recent decades, providing excellent opportunities for imaging deep, micro-scale structures of various organs, or even of the whole body. In recent years, advanced tissue clearing techniques have been optimized for specific tissues and organs. Among these tissues, the eye is unique owing to its delicate structure and pigmented retinal epithelial cells, calling for more work on making these tissues "transparent". In this review, we searched Medline and Embase for studies published between January 2006 and August 2021 using the terms "tissue optical clearing", "ophthalmology", "eye", and "optical clearing agents", and we reviewed the publications on the optical clearing techniques of eye tissue from 2006 to the present, including both the clearing procedures and the subsequent analytical processes, thus gaining more insight into the application of tissue optical clearing in basic eye research. Furthermore, we discuss the future potential of optical clearing applications in clinical ophthalmology.
Collapse
Affiliation(s)
- Wenhan Lu
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, 200031, China; Department of Integrative Medicine and Neurobiology, State Key Lab of Medical Neurobiology, Institute of Integrative Medicine of Fudan University, Institute of Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhenle Pei
- Department of Integrative Medicine and Neurobiology, State Key Lab of Medical Neurobiology, Institute of Integrative Medicine of Fudan University, Institute of Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wei Hu
- Department of Integrative Medicine and Neurobiology, State Key Lab of Medical Neurobiology, Institute of Integrative Medicine of Fudan University, Institute of Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Chen Tan
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, 200031, China
| | - Xiaoyu Tong
- Department of Integrative Medicine and Neurobiology, State Key Lab of Medical Neurobiology, Institute of Integrative Medicine of Fudan University, Institute of Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yi Feng
- Department of Integrative Medicine and Neurobiology, State Key Lab of Medical Neurobiology, Institute of Integrative Medicine of Fudan University, Institute of Brain Science, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Xinghuai Sun
- Department of Ophthalmology & Visual Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, 200031, China; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China; NHC Key Laboratory of Myopia, Chinese Academy of Medical Sciences, And Shanghai Key Laboratory of Visual Impairment and Restoration (Fudan University), Shanghai, 200031, China.
| |
Collapse
|
7
|
Localizing Microemboli within the Rodent Brain through Block-Face Imaging and Atlas Registration. eNeuro 2021; 8:ENEURO.0216-21.2021. [PMID: 34272259 PMCID: PMC8342264 DOI: 10.1523/eneuro.0216-21.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 12/01/2022] Open
Abstract
Brain microinfarcts are prevalent in humans, however because of the inherent difficulty of identifying and localizing individual microinfarcts, brain-wide quantification is impractical. In mice, microinfarcts have been created by surgically introducing microemboli into the brain, but a major limitation of this model is the absence of automated methods to identify and localize individual occlusions. We present a novel and semi-automated workflow to identify the anatomic location of fluorescent emboli (microspheres) within the mouse brain through histologic processing and atlas registration. By incorporating vibratome block-face imaging with the QuickNII brain registration tool, we show that the anatomic location of microspheres can be accurately registered to brain structures within the Allen mouse brain (AMB) atlas (e.g., somatomotor areas, hippocampal region, visual areas, etc.). Compared with registering images of slide mounted sections to the AMB atlas, microsphere location was more accurately determined when block-face images were used. As a proof of principle, using this workflow we compared the distribution of microspheres within the brains of mice that were either perfused or immersion fixed. No significant effect of perfusion on total microsphere number or location was detected. In general, microspheres were distributed brain-wide, with the largest density found in the thalamus. In sum, our block-face imaging workflow enables efficient characterization of the widespread distribution of fluorescent microemboli, facilitating future investigation into the impact of microinfarct load and location on brain health.
Collapse
|
8
|
Czéh B, Simon M. Benefits of animal models to understand the pathophysiology of depressive disorders. Prog Neuropsychopharmacol Biol Psychiatry 2021; 106:110049. [PMID: 32735913 DOI: 10.1016/j.pnpbp.2020.110049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/13/2020] [Accepted: 07/21/2020] [Indexed: 12/14/2022]
Abstract
Major depressive disorder (MDD) is a potentially life-threatening mental disorder imposing severe social and economic burden worldwide. Despite the existence of effective antidepressant treatment strategies the exact pathophysiology of the disease is still unknown. Large number of animal models of MDD have been developed over the years, but all of them suffer from significant shortcomings. Despite their limitations these models have been extensively used in academic research and drug development. The aim of this review is to highlight the benefits of animal models of MDD. We focus here on recent experimental data where animal models were used to examine current theories of this complex disease. We argue, that despite their evident imperfections, these models provide invaluable help to understand cellular and molecular mechanisms contributing to the development of MDD. Furthermore, animal models are utilized in research to find clinically useful biomarkers. We discuss recent neuroimaging and microRNA studies since these investigations yielded promising candidates for biomarkers. Finally, we briefly summarize recent progresses in drug development, i.e. the FDA approval of two novel antidepressant drugs: S-ketamine and brexanolone (allopregnanolone). Deeper understanding of the exact molecular and cellular mechanisms of action responsible for the antidepressant efficacy of these rapid acting drugs could aid us to design further compounds with similar effectiveness, but less side effects. Animal studies are likely to provide valuable help in this endeavor.
Collapse
Affiliation(s)
- Boldizsár Czéh
- Neurobiology of Stress Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary; Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary.
| | - Maria Simon
- Neurobiology of Stress Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary; Department of Psychiatry and Psychotherapy, Medical School, University of Pécs, Hungary
| |
Collapse
|
9
|
Leuze C, Goubran M, Barakovic M, Aswendt M, Tian Q, Hsueh B, Crow A, Weber EMM, Steinberg GK, Zeineh M, Plowey ED, Daducci A, Innocenti G, Thiran JP, Deisseroth K, McNab JA. Comparison of diffusion MRI and CLARITY fiber orientation estimates in both gray and white matter regions of human and primate brain. Neuroimage 2021; 228:117692. [PMID: 33385546 PMCID: PMC7953593 DOI: 10.1016/j.neuroimage.2020.117692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 11/30/2022] Open
Abstract
Diffusion MRI (dMRI) represents one of the few methods for mapping brain fiber orientations non-invasively. Unfortunately, dMRI fiber mapping is an indirect method that relies on inference from measured diffusion patterns. Comparing dMRI results with other modalities is a way to improve the interpretation of dMRI data and help advance dMRI technologies. Here, we present methods for comparing dMRI fiber orientation estimates with optical imaging of fluorescently labeled neurofilaments and vasculature in 3D human and primate brain tissue cuboids cleared using CLARITY. The recent advancements in tissue clearing provide a new opportunity to histologically map fibers projecting in 3D, which represents a captivating complement to dMRI measurements. In this work, we demonstrate the capability to directly compare dMRI and CLARITY in the same human brain tissue and assess multiple approaches for extracting fiber orientation estimates from CLARITY data. We estimate the three-dimensional neuronal fiber and vasculature orientations from neurofilament and vasculature stained CLARITY images by calculating the tertiary eigenvector of structure tensors. We then extend CLARITY orientation estimates to an orientation distribution function (ODF) formalism by summing multiple sub-voxel structure tensor orientation estimates. In a sample containing part of the human thalamus, there is a mean angular difference of 19o±15o between the primary eigenvectors of the dMRI tensors and the tertiary eigenvectors from the CLARITY neurofilament stain. We also demonstrate evidence that vascular compartments do not affect the dMRI orientation estimates by showing an apparent lack of correspondence (mean angular difference = 49o±23o) between the orientation of the dMRI tensors and the structure tensors in the vasculature stained CLARITY images. In a macaque brain dataset, we examine how the CLARITY feature extraction depends on the chosen feature extraction parameters. By varying the volume of tissue over which the structure tensor estimates are derived, we show that orientation estimates are noisier with more spurious ODF peaks for sub-voxels below 30 µm3 and that, for our data, the optimal gray matter sub-voxel size is between 62.5 µm3 and 125 µm3. The example experiments presented here represent an important advancement towards robust multi-modal MRI-CLARITY comparisons.
Collapse
Affiliation(s)
- C Leuze
- Department of Radiology, Stanford University, Stanford, CA, USA.
| | - M Goubran
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - M Barakovic
- Department of Radiology, Stanford University, Stanford, CA, USA; Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - M Aswendt
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Q Tian
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - B Hsueh
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - A Crow
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - E M M Weber
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - G K Steinberg
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - M Zeineh
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - E D Plowey
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - A Daducci
- Department of Computer Science, University of Verona, Verona, Italy
| | - G Innocenti
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden; Brain and Mind Institute, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - J-P Thiran
- Signal Processing Lab (LTS5), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - K Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - J A McNab
- Department of Radiology, Stanford University, Stanford, CA, USA
| |
Collapse
|
10
|
Martínez-Lorenzana G, Gamal-Eltrabily M, Tello-García IA, Martínez-Torres A, Becerra-González M, González-Hernández A, Condés-Lara M. CLARITY with neuronal tracing and immunofluorescence to study the somatosensory system in rats. J Neurosci Methods 2020; 350:109048. [PMID: 33359224 DOI: 10.1016/j.jneumeth.2020.109048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND The CLARITY technique enables researchers to visualize different neuronal connections along the nervous system including the somatosensory system. NEW METHOD The present work describes the antero-lateral and dorsal column pathways until the thalamic and cortical stations, as well as descending oxytocinergic and vasopressinergic innervations by means of combined CLARITY, neuronal tracing, and immunofluorescence techniques. We used male Sprague-Dawley rats of 13, 30, and 60 days. RESULTS The main results are as follows: A) CLARITY is a reliable technique that can be combined with fluorescent neuronal tracers and immunofluorescence techniques without major procedure modifications; B) at spinal level, some primary afferent fibers were labeled by CGRP, as well as the presence of neuronal populations that simultaneously project to the gracile and ventral posterolateral thalamic nuclei; C) corticothalamic connections were visible when retrograde tracers were injected at thalamic level; D) oxytocin receptors were expressed in the spinal dorsal horn by GABAergic-positive neurons, reinforcing previous outcomes about the possible mechanism for oxytocin blocking the primary afferent sensory input. COMPARISON WITH EXISTING METHODS AND CONCLUSIONS The CLARITY technique lets us observe in a transparent way the entire processed tissue compared with classical histological methods. CLARITY is a potentially useful tool to describe neuroanatomical structures and their neurochemical stratus.
Collapse
Affiliation(s)
- Guadalupe Martínez-Lorenzana
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla, No. 3001, C.P. 76230, Querétaro, Mexico
| | - Mohammed Gamal-Eltrabily
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla, No. 3001, C.P. 76230, Querétaro, Mexico
| | - Irma Alejandra Tello-García
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla, No. 3001, C.P. 76230, Querétaro, Mexico
| | - Ataulfo Martínez-Torres
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla, No. 3001, C.P. 76230, Querétaro, Mexico
| | - Marymar Becerra-González
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla, No. 3001, C.P. 76230, Querétaro, Mexico
| | - Abimael González-Hernández
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla, No. 3001, C.P. 76230, Querétaro, Mexico
| | - Miguel Condés-Lara
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla, No. 3001, C.P. 76230, Querétaro, Mexico.
| |
Collapse
|
11
|
Carbó-Carreté M, Cañete-Massé C, Peró-Cebollero M, Guàrdia-Olmos J. Using fMRI to Assess Brain Activity in People With Down Syndrome: A Systematic Review. Front Hum Neurosci 2020; 14:147. [PMID: 32395104 PMCID: PMC7197628 DOI: 10.3389/fnhum.2020.00147] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background: In the last few years, many investigations have focused on brain activity in general and in populations with different pathologies using non-invasive techniques such as electroencefalography (EEG), positron emission tomography (PET), functional magnetic resonance imaging (fMRI) and magnetic resonance imaging (MRI). However, the use of non-invasive techniques to detect brain signals to evaluate the cognitive activity of people with Down syndrome (DS) has not been sufficiently addressed. The objective of this study is to describe the state-of-the-art in fMRI techniques for recording brain signals in people with DS. Method: A systematic review was performed based on PRISMA recommendations; only nine papers on this topic have been published. Three independent researchers selected all relevant information from each paper. Analyses of information concordance showed a high value of agreement between researchers. Results: Although few relevant works have been published, the use of fMRI in people with DS is becoming an appropriate option to study brain function in this population. Of the nine identified papers, five used task designs, and four used resting-state paradigms. Conclusion: Thus, we emphasize the need to incorporate rigorous cognitive activity procedures in evaluations of the DS population. We suggest several factors (such as head correction movements and paired sample techniques) that must be considered when designing an fMRI study with a task or a resting-state paradigm in a DS population.
Collapse
Affiliation(s)
- Maria Carbó-Carreté
- Department of Cognition, Development and Educational Psychology, Faculty of Psychology, University of Barcelona, Barcelona, Spain.,Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Cristina Cañete-Massé
- Department of Social Psychology and Quantitative Psychology, Faculty of Psychology, University of Barcelona, Barcelona, Spain.,UB Institute of Complex Systems, University of Barcelona, Barcelona, Spain.,Quantitative Psychology Research Group (SGR 266), Generalitat de Catalunya, Barcelona, Spain
| | - Maribel Peró-Cebollero
- Institute of Neuroscience, University of Barcelona, Barcelona, Spain.,Department of Social Psychology and Quantitative Psychology, Faculty of Psychology, University of Barcelona, Barcelona, Spain.,UB Institute of Complex Systems, University of Barcelona, Barcelona, Spain.,Quantitative Psychology Research Group (SGR 266), Generalitat de Catalunya, Barcelona, Spain
| | - Joan Guàrdia-Olmos
- Institute of Neuroscience, University of Barcelona, Barcelona, Spain.,Department of Social Psychology and Quantitative Psychology, Faculty of Psychology, University of Barcelona, Barcelona, Spain.,UB Institute of Complex Systems, University of Barcelona, Barcelona, Spain.,Quantitative Psychology Research Group (SGR 266), Generalitat de Catalunya, Barcelona, Spain
| |
Collapse
|
12
|
Porter DDL, Morton PD. Clearing techniques for visualizing the nervous system in development, injury, and disease. J Neurosci Methods 2020; 334:108594. [PMID: 31945400 PMCID: PMC10674098 DOI: 10.1016/j.jneumeth.2020.108594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 01/05/2023]
Abstract
Modern clearing techniques enable high resolution visualization and 3D reconstruction of cell populations and their structural details throughout large biological samples, including intact organs and even entire organisms. In the past decade, these methods have become more tractable and are now being utilized to provide unforeseen insights into the complexities of the nervous system. While several iterations of optical clearing techniques have been developed, some are more suitable for specific applications than others depending on the type of specimen under study. Here we review findings from select studies utilizing clearing methods to visualize the developing, injured, and diseased nervous system within numerous model systems and species. We note trends and imbalances in the types of research questions being addressed with clearing methods across these fields in neuroscience. In addition, we discuss restrictions in applying optical clearing methods for postmortem tissue from humans and large animals and emphasize the lack in continuity between studies of these species. We aim for this review to serve as a key outline of available tissue clearing methods used successfully to address issues across neuronal development, injury/repair, and aging/disease.
Collapse
Affiliation(s)
- Demisha D L Porter
- Virginia Tech Graduate Program in Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Paul D Morton
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
| |
Collapse
|
13
|
Carneiro I, Carvalho S, Henrique R, Oliveira L, Tuchin V. Moving tissue spectral window to the deep-ultraviolet via optical clearing. JOURNAL OF BIOPHOTONICS 2019; 12:e201900181. [PMID: 31465137 DOI: 10.1002/jbio.201900181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/25/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
The optical immersion clearing technique has been successfully applied through the last 30 years in the visible to near infrared spectral range, and has proven to be a promising method to promote the application of optical technologies in clinical practice. To investigate its potential in the ultraviolet range, collimated transmittance spectra from 200 to 1000 nm were measured from colorectal muscle samples under treatment with glycerol-water solutions. The treatments created two new optical windows with transmittance efficiency peaks at 230 and 300 nm, with magnitude increasing with glycerol concentration in the treating solution. Such discovery opens the opportunity to develop clinical procedures to perform diagnosis or treatments in the ultraviolet.
Collapse
Affiliation(s)
- Isa Carneiro
- Department of Pathology and Cancer Biology, and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Sónia Carvalho
- Department of Pathology and Cancer Biology, and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rui Henrique
- Department of Pathology and Cancer Biology, and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar - University of Porto (ICBAS-UP), Porto, Portugal
| | - Luís Oliveira
- Physics Department - Polytechnic Institute of Porto, School of Engineering, Porto, Portugal
- Centre of Innovation in Engineering and Industrial Technology (CIETI), School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Valery Tuchin
- Research-Educational Institute of Optics and Biophotonics, Saratov State University, Saratov, Russian Federation
- Interdisciplinary Laboratory of Biophotonics, Tomsk State University, Tomsk, Russian Federation
- Laboratory of Laser Diagnostics of Technical and Living Systems, Institute of Precision Mechanics and Control of the Russian Academy of Sciences, Saratov, Russian Federation
- Laboratory of Molecular Imaging, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| |
Collapse
|
14
|
Foster DS, Nguyen AT, Chinta M, Salhotra A, Jones RE, Mascharak S, Titan AL, Ransom RC, da Silva OL, Foley E, Briger E, Longaker MT. A Clearing Technique to Enhance Endogenous Fluorophores in Skin and Soft Tissue. Sci Rep 2019; 9:15791. [PMID: 31673001 PMCID: PMC6823366 DOI: 10.1038/s41598-019-50359-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/06/2019] [Indexed: 12/26/2022] Open
Abstract
Fluorescent proteins are used extensively in transgenic animal models to label and study specific cell and tissue types. Expression of these proteins can be imaged and analyzed using fluorescent and confocal microscopy. Conventional confocal microscopes cannot penetrate through tissue more than 4–6 μm thick. Tissue clearing procedures overcome this challenge by rendering thick specimens into translucent tissue. However, most tissue clearing techniques do not satisfactorily preserve expression of endogenous fluorophores. Using simple adjustments to the BABB (Benzoic Acid Benzyl Benzoate) clearing methodology, preservation of fluorophore expression can be maintained. Modified BABB tissue clearing is a reliable technique to clear skin and soft tissue specimens for the study of dermal biology, wound healing and fibrotic pathologies.
Collapse
Affiliation(s)
- Deshka S Foster
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alan T Nguyen
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Malini Chinta
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ankit Salhotra
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - R Ellen Jones
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shamik Mascharak
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ashley L Titan
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - R Chase Ransom
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Oscar L da Silva
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Eliza Foley
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Emma Briger
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| |
Collapse
|
15
|
Fogli B, Corthout N, Kerstens A, Bosse F, Klimaschewski L, Munck S, Schweigreiter R. Imaging axon regeneration within synthetic nerve conduits. Sci Rep 2019; 9:10095. [PMID: 31300753 PMCID: PMC6626049 DOI: 10.1038/s41598-019-46579-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/28/2019] [Indexed: 11/23/2022] Open
Abstract
While axons within the central nervous system (CNS) do not regenerate following injury, those in the peripheral nervous system (PNS) do, although not in a clinically satisfactory manner as only a small proportion of axons exhibit long-distance regeneration. Moreover, functional recovery is hampered by excessive axonal sprouting and aberrant reinnervation of target tissue. In order to investigate the mechanisms governing the regrowth of axons following injury, previous studies have used lesion paradigms of peripheral nerves in rat or mouse models, and reagents or cells have been administered to the lesion site through nerve conduits, aiming to improve early-stage regeneration. Morphological analysis of such in vivo experiments has however been limited by the incompatibility of synthetic nerve conduits with existing tissue-clearing and imaging techniques. We present herein a novel experimental approach that allows high-resolution imaging of individual axons within nerve conduits, together with quantitative assessment of fiber growth. We used a GFP-expressing mouse strain in a lesion model of the sciatic nerve to describe a strategy that combines nerve clearing, chemical treatment of chitosan nerve conduits, and long working distance confocal microscopy with image processing and analysis. This novel experimental setup provides a means of documenting axon growth within the actual conduit during the critical initial stage of regeneration. This will greatly facilitate the development and evaluation of treatment regimens to improve axonal regeneration following nerve damage.
Collapse
Affiliation(s)
- Barbara Fogli
- Innsbruck Medical University, Department of Anatomy, Histology and Embryology, Division of Neuroanatomy, 6020, Innsbruck, Austria
| | - Nikky Corthout
- VIB-KU Leuven Center for Brain & Disease Research O&N 4, Campus Gasthuisberg, 3000, Leuven, Belgium.,KU Leuven, Department for Neuroscience, Campus Gasthuisberg, 3000, Leuven, Belgium.,VIB Bio Imaging Core, Campus Gasthuisberg, 3000, Leuven, Belgium
| | - Axelle Kerstens
- VIB-KU Leuven Center for Brain & Disease Research O&N 4, Campus Gasthuisberg, 3000, Leuven, Belgium.,KU Leuven, Department for Neuroscience, Campus Gasthuisberg, 3000, Leuven, Belgium.,VIB Bio Imaging Core, Campus Gasthuisberg, 3000, Leuven, Belgium
| | - Frank Bosse
- Heinrich-Heine-University Düsseldorf, Department of Neurology, Molecular Neurobiology Laboratory, 40225, Düsseldorf, Germany
| | - Lars Klimaschewski
- Innsbruck Medical University, Department of Anatomy, Histology and Embryology, Division of Neuroanatomy, 6020, Innsbruck, Austria
| | - Sebastian Munck
- VIB-KU Leuven Center for Brain & Disease Research O&N 4, Campus Gasthuisberg, 3000, Leuven, Belgium. .,KU Leuven, Department for Neuroscience, Campus Gasthuisberg, 3000, Leuven, Belgium. .,VIB Bio Imaging Core, Campus Gasthuisberg, 3000, Leuven, Belgium.
| | - Rüdiger Schweigreiter
- Innsbruck Medical University, Biocenter, Division of Neurobiochemistry, 6020, Innsbruck, Austria.
| |
Collapse
|
16
|
Wykes RC, Khoo HM, Caciagli L, Blumenfeld H, Golshani P, Kapur J, Stern JM, Bernasconi A, Dedeurwaerdere S, Bernasconi N. WONOEP appraisal: Network concept from an imaging perspective. Epilepsia 2019; 60:1293-1305. [PMID: 31179547 DOI: 10.1111/epi.16067] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 02/01/2023]
Abstract
Neuroimaging techniques applied to a variety of organisms-from zebrafish, to rodents to humans-can offer valuable insights into neuronal network properties and their dysfunction in epilepsy. A wide range of imaging methods used to monitor neuronal circuits and networks during evoked seizures in animal models and advances in functional magnetic resonance imaging (fMRI) applied to patients with epilepsy were discussed during the XIV Workshop on Neurobiology of Epilepsy (XIV WONOEP) organized in 2017 by the Neurobiology Commission of the International League Against Epilepsy (ILAE). We review the growing number of technological approaches developed, as well as the current state of knowledge gained from studies applying these advanced imaging approaches to epilepsy research.
Collapse
Affiliation(s)
- Robert C Wykes
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Hui Ming Khoo
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.,Department of Neurosurgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Lorenzo Caciagli
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.,Neuroimaging of Epilepsy Laboratory, Department of Neurosciences and McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Hal Blumenfeld
- Department of Neurology, Neuroscience and Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Peyman Golshani
- Department of Neurology, Geffen School of Medicine, UCLA, Los Angeles, California
| | - Jaideep Kapur
- School of Medicine, University of Virginia, Charlottesville, Virginia
| | - John M Stern
- Department of Neurology, Geffen School of Medicine, UCLA, Los Angeles, California
| | - Andrea Bernasconi
- Neuroimaging of Epilepsy Laboratory, Department of Neurosciences and McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Neda Bernasconi
- Neuroimaging of Epilepsy Laboratory, Department of Neurosciences and McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
17
|
Lindsey BW, Douek AM, Loosli F, Kaslin J. A Whole Brain Staining, Embedding, and Clearing Pipeline for Adult Zebrafish to Visualize Cell Proliferation and Morphology in 3-Dimensions. Front Neurosci 2018; 11:750. [PMID: 29386991 PMCID: PMC5776138 DOI: 10.3389/fnins.2017.00750] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/22/2017] [Indexed: 01/08/2023] Open
Abstract
The field of macro-imaging has grown considerably with the appearance of innovative clearing methods and confocal microscopes with lasers capable of penetrating increasing tissue depths. The ability to visualize and model the growth of whole organs as they develop from birth, or with manipulation, disease or injury, provides new ways of thinking about development, tissue-wide signaling, and cell-to-cell interactions. The zebrafish (Danio rerio) has ascended from a predominantly developmental model to a leading adult model of tissue regeneration. The unmatched neurogenic and regenerative capacity of the mature central nervous system, in particular, has received much attention, however tools to interrogate the adult brain are sparse. At present there exists no straightforward methods of visualizing changes in the whole adult brain in 3-dimensions (3-D) to examine systemic patterns of cell proliferation or cell populations of interest under physiological, injury, or diseased conditions. The method presented here is the first of its kind to offer an efficient step-by-step pipeline from intraperitoneal injections of the proliferative marker, 5-ethynyl-2′-deoxyuridine (EdU), to whole brain labeling, to a final embedded and cleared brain sample suitable for 3-D imaging using optical projection tomography (OPT). Moreover, this method allows potential for imaging GFP-reporter lines and cell-specific antibodies in the presence or absence of EdU. The small size of the adult zebrafish brain, the highly consistent degree of EdU labeling, and the use of basic clearing agents, benzyl benzoate, and benzyl alcohol, makes this method highly tractable for most laboratories interested in understanding the vertebrate central nervous system in health and disease. Post-processing of OPT-imaged adult zebrafish brains injected with EdU illustrate that proliferative patterns in EdU can readily be observed and analyzed using IMARIS and/or FIJI/IMAGEJ software. This protocol will be a valuable tool to unlock new ways of understanding systemic patterns in cell proliferation in the healthy and injured brain, brain-wide cellular interactions, stem cell niche development, and changes in brain morphology.
Collapse
Affiliation(s)
- Benjamin W Lindsey
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - Alon M Douek
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - Felix Loosli
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| |
Collapse
|
18
|
Jones EE, Quiason C, Dale S, Shahidi-Latham SK. Feasibility Assessment of a MALDI FTICR Imaging Approach for the 3D Reconstruction of a Mouse Lung. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1709-1715. [PMID: 28401432 DOI: 10.1007/s13361-017-1658-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 05/13/2023]
Abstract
Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has proven to be a quick, robust, and label-free tool to produce two-dimensional (2D) ion-density maps representing the distribution of a variety of analytes across a tissue section of interest. In addition, three-dimensional (3D) imaging mass spectrometry workflows have been developed that are capable of visualizing these same analytes throughout an entire volume of a tissue rather than a single cross-section. Until recently, the use of Fourier transform ion cyclotron resonance (FTICR) mass spectrometers for 3D volume reconstruction has been impractical due to software limitations, such as inadequate capacity to manipulate the extremely large data files produced during an imaging experiment. Fortunately with recent software and hardware advancements, 3D reconstruction from MALDI FTICR IMS datasets is now feasible. Here we describe the first proof of principle study for a 3D volume reconstruction of an entire mouse lung using data collected on a FTICR mass spectrometer. Each lung tissue section was analyzed with high mass resolution and mass accuracy, and considered as an independent dataset. Each subsequent lung section image, or lung dataset, was then co-registered to its adjacent section to reconstruct a 3D volume. Volumes representing various endogenous lipid species were constructed, including sphingolipids and phosphatidylcholines (PC), and species confirmation was performed with on-tissue collision induced dissociation (CID). Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- E Ellen Jones
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way MS 41-2a, South San Francisco, CA, 94080, USA
| | - Cristine Quiason
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way MS 41-2a, South San Francisco, CA, 94080, USA
| | - Stephanie Dale
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way MS 41-2a, South San Francisco, CA, 94080, USA
| | - Sheerin K Shahidi-Latham
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way MS 41-2a, South San Francisco, CA, 94080, USA.
| |
Collapse
|
19
|
Leuze C, Aswendt M, Ferenczi E, Liu CW, Hsueh B, Goubran M, Tian Q, Steinberg G, Zeineh MM, Deisseroth K, McNab JA. The separate effects of lipids and proteins on brain MRI contrast revealed through tissue clearing. Neuroimage 2017; 156:412-422. [PMID: 28411157 DOI: 10.1016/j.neuroimage.2017.04.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/20/2017] [Accepted: 04/08/2017] [Indexed: 01/01/2023] Open
Abstract
Despite the widespread use of magnetic resonance imaging (MRI) of the brain, the relative contribution of different biological components (e.g. lipids and proteins) to structural MRI contrasts (e.g., T1, T2, T2*, proton density, diffusion) remains incompletely understood. This limitation can undermine the interpretation of clinical MRI and hinder the development of new contrast mechanisms. Here, we determine the respective contribution of lipids and proteins to MRI contrast by removing lipids and preserving proteins in mouse brains using CLARITY. We monitor the temporal dynamics of tissue clearance via NMR spectroscopy, protein assays and optical emission spectroscopy. MRI of cleared brain tissue showed: 1) minimal contrast on standard MRI sequences; 2) increased relaxation times; and 3) diffusion rates close to free water. We conclude that lipids, present in myelin and membranes, are a dominant source of MRI contrast in brain tissue.
Collapse
Affiliation(s)
- Christoph Leuze
- Department of Radiology, Stanford University, Stanford, CA, USA.
| | - Markus Aswendt
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Emily Ferenczi
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Corey W Liu
- Stanford Magnetic Resonance Laboratory, Stanford University, Stanford, CA, USA
| | - Brian Hsueh
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Maged Goubran
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Qiyuan Tian
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Gary Steinberg
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | | | - Karl Deisseroth
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | | |
Collapse
|
20
|
Laviña B. Brain Vascular Imaging Techniques. Int J Mol Sci 2016; 18:ijms18010070. [PMID: 28042833 PMCID: PMC5297705 DOI: 10.3390/ijms18010070] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/13/2016] [Accepted: 12/26/2016] [Indexed: 12/13/2022] Open
Abstract
Recent major improvements in a number of imaging techniques now allow for the study of the brain in ways that could not be considered previously. Researchers today have well-developed tools to specifically examine the dynamic nature of the blood vessels in the brain during development and adulthood; as well as to observe the vascular responses in disease situations in vivo. This review offers a concise summary and brief historical reference of different imaging techniques and how these tools can be applied to study the brain vasculature and the blood-brain barrier integrity in both healthy and disease states. Moreover, it offers an overview on available transgenic animal models to study vascular biology and a description of useful online brain atlases.
Collapse
Affiliation(s)
- Bàrbara Laviña
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden.
| |
Collapse
|