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Singer R, Oganezova I, Hu W, Liu L, Ding Y, de Groot HJM, Spaink HP, Alia A. Ultrahigh field diffusion magnetic resonance imaging uncovers intriguing microstructural changes in the adult zebrafish brain caused by Toll-like receptor 2 genomic deletion. NMR IN BIOMEDICINE 2024; 37:e5170. [PMID: 38742727 DOI: 10.1002/nbm.5170] [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: 12/07/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/16/2024]
Abstract
Toll-like receptor 2 (TLR2) belongs to the TLR protein family that plays an important role in the immune and inflammation response system. While TLR2 is predominantly expressed in immune cells, its expression has also been detected in the brain, specifically in microglia and astrocytes. Recent studies indicate that genomic deletion of TLR2 can result in impaired neurobehavioural function. It is currently not clear if the genomic deletion of TLR2 leads to any alterations in the microstructural features of the brain. In the current study, we noninvasively assess microstructural changes in the brain of TLR2-deficient (tlr2-/-) zebrafish using state-of-the art magnetic resonance imaging (MRI) methods at ultrahigh magnetic field strength (17.6 T). A significant increase in cortical thickness and an overall trend towards increased brain volumes were observed in young tlr2-/- zebrafish. An elevated T2 relaxation time and significantly reduced apparent diffusion coefficient (ADC) unveil brain-wide microstructural alterations, potentially indicative of cytotoxic oedema and astrogliosis in the tlr2-/- zebrafish. Multicomponent analysis of the ADC diffusivity signal by the phasor approach shows an increase in the slow ADC component associated with restricted diffusion. Diffusion tensor imaging and diffusion kurtosis imaging analysis revealed diminished diffusivity and enhanced kurtosis in various white matter tracks in tlr2-/- compared with control zebrafish, identifying the microstructural underpinnings associated with compromised white matter integrity and axonal degeneration. Taken together, our findings demonstrate that the genomic deletion of TLR2 results in severe alterations to the microstructural features of the zebrafish brain. This study also highlights the potential of ultrahigh field diffusion MRI techniques in discerning exceptionally fine microstructural details within the small zebrafish brain, offering potential for investigating microstructural changes in zebrafish models of various brain diseases.
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Affiliation(s)
- Rico Singer
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Ina Oganezova
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Wanbin Hu
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Li Liu
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Yi Ding
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Herman P Spaink
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - A Alia
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Institute of Medical Physics and Biophysics, Leipzig University, Leipzig, Germany
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2
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Casamitjana A, Mancini M, Robinson E, Peter L, Annunziata R, Althonayan J, Crampsie S, Blackburn E, Billot B, Atzeni A, Puonti O, Balbastre Y, Schmidt P, Hughes J, Augustinack JC, Edlow BL, Zöllei L, Thomas DL, Kliemann D, Bocchetta M, Strand C, Holton JL, Jaunmuktane Z, Iglesias JE. A next-generation, histological atlas of the human brain and its application to automated brain MRI segmentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579016. [PMID: 39282320 PMCID: PMC11398399 DOI: 10.1101/2024.02.05.579016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Magnetic resonance imaging (MRI) is the standard tool to image the human brain in vivo. In this domain, digital brain atlases are essential for subject-specific segmentation of anatomical regions of interest (ROIs) and spatial comparison of neuroanatomy from different subjects in a common coordinate frame. High-resolution, digital atlases derived from histology (e.g., Allen atlas [7], BigBrain [13], Julich [15]), are currently the state of the art and provide exquisite 3D cytoarchitectural maps, but lack probabilistic labels throughout the whole brain. Here we present NextBrain, a next-generation probabilistic atlas of human brain anatomy built from serial 3D histology and corresponding highly granular delineations of five whole brain hemispheres. We developed AI techniques to align and reconstruct ~10,000 histological sections into coherent 3D volumes with joint geometric constraints (no overlap or gaps between sections), as well as to semi-automatically trace the boundaries of 333 distinct anatomical ROIs on all these sections. Comprehensive delineation on multiple cases enabled us to build the first probabilistic histological atlas of the whole human brain. Further, we created a companion Bayesian tool for automated segmentation of the 333 ROIs in any in vivo or ex vivo brain MRI scan using the NextBrain atlas. We showcase two applications of the atlas: automated segmentation of ultra-high-resolution ex vivo MRI and volumetric analysis of Alzheimer's disease and healthy brain ageing based on ~4,000 publicly available in vivo MRI scans. We publicly release: the raw and aligned data (including an online visualisation tool); the probabilistic atlas; the segmentation tool; and ground truth delineations for a 100 μm isotropic ex vivo hemisphere (that we use for quantitative evaluation of our segmentation method in this paper). By enabling researchers worldwide to analyse brain MRI scans at a superior level of granularity without manual effort or highly specific neuroanatomical knowledge, NextBrain holds promise to increase the specificity of MRI findings and ultimately accelerate our quest to understand the human brain in health and disease.
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Affiliation(s)
- Adrià Casamitjana
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
- Research Institute of Computer Vision and Robotics, University of Girona, Girona, Spain
| | - Matteo Mancini
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
- Department of Cardiovascular, Endocrine-Metabolic Diseases and Aging, Italian National Institute of Health, Rome, Italy
- Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, United Kingdom
| | - Eleanor Robinson
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Loïc Peter
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Roberto Annunziata
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Juri Althonayan
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Shauna Crampsie
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Emily Blackburn
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Benjamin Billot
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Alessia Atzeni
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Oula Puonti
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Yaël Balbastre
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Peter Schmidt
- Advanced Research Computing Centre, University College London, London, United Kingdom
| | - James Hughes
- Advanced Research Computing Centre, University College London, London, United Kingdom
| | - Jean C Augustinack
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Brian L Edlow
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Lilla Zöllei
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - David L Thomas
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- Neuroradiological Academic Unit, Department of Brain Repair and Rehabilitation, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Dorit Kliemann
- Department of Psychological and Brain Sciences, University of Iowa, Iowa City, IA, United States
| | - Martina Bocchetta
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- Centre for Cognitive and Clinical Neuroscience, Division of Psychology, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, United Kingdom
| | - Catherine Strand
- Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Zane Jaunmuktane
- Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Juan Eugenio Iglesias
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
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3
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Tsurugizawa T, Kumamoto T, Yoshioka Y. Micro-magnetic resonance imaging of ex vivo mouse embryos with potato starch suspension. STAR Protoc 2023; 4:102483. [PMID: 37516974 PMCID: PMC10407275 DOI: 10.1016/j.xpro.2023.102483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023] Open
Abstract
Potato starch suspension (PSS) holds promise as a solution to issues, such as air bubbles and specimen motion, associated with micro-magnetic resonance imaging (micro-MRI) of ex vivo embryos. Here, we present a protocol for using PSS when scanning specimens with micro-MRI. We describe steps for preparing samples and potato starch with phosphate-buffered saline. We then detail steps for specimen immersion and micro-MRI scanning. This protocol will enable micro-MRI of not only embryos but also other specimens, such as insects. For complete details on the use and execution of this protocol, please refer to Tsurugizawa et al.1.
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Affiliation(s)
- Tomokazu Tsurugizawa
- Human Informatics and Interaction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8568, Japan; Faculty of Engineering, Information and Systems, University of Tsukuba, Tsukuba 305-8573, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Center for Information and Neural Networks (CiNet), Osaka University and National Institute of Information and Communications Technology (NICT), Suita 565-0871, Japan.
| | - Takuma Kumamoto
- Developmental Neuroscience Project, Department of Brain & Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yoshichika Yoshioka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Center for Information and Neural Networks (CiNet), Osaka University and National Institute of Information and Communications Technology (NICT), Suita 565-0871, Japan.
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4
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Martinho RP, Jain MG, Frydman L. High-field ex vivo and in vivo two-dimensional nuclear magnetic resonance spectroscopy in murine brain: Resolving and exploring the molecular environment. NMR IN BIOMEDICINE 2023; 36:e4833. [PMID: 36114827 PMCID: PMC10077987 DOI: 10.1002/nbm.4833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
The structural and chemical complexities within the brain pose a challenge that few noninvasive techniques can tackle with the dexterity of nuclear magnetic resonance (NMR) spectroscopy. Still, even with the advent of ultrahigh fields and of cryogenically cooled coils for in vivo research, the superposition of metabolic resonances arising from the brain remains a challenge. The present study explores the potential to tackle this milieu using a combination of two-dimensional (2D) NMR techniques, implemented on murine brains in vivo at 15.2 T and ex vivo at 14.1 T. While both experiments were affected by substantial inhomogeneous broadenings conveying distinct elongated lineshapes to the cross-peaks, the ability of increased fields to resolve off-diagonal resonances was clear. A comparison between the corresponding conventional and double quantum-filtered correlated spectroscopy traces enabled an improved assignment of in vivo resonances on the basis of more sensitive ex vivo 2D acquisitions, foremost on the basis of homonuclear cross-relaxation-driven correlations for peaks resonating downfield from water, and of heteronuclear correlations at natural abundance for the upfield protons. With the aid of such 2D correlations approximately 29 metabolites could be resolved and identified. This enhanced resolution was used to explore features related to the metabolites' diffusivities, their exposure to water, and their facility to undergo magnetization transfers to amide/amine/hydroxyl resonances. Cross-peaks from main murine brain biomolecules, including choline, creatine, γ-aminobutyric acid, N-acetyl aspartate, glutamine, and glutamate, showed enhancements in several of these various features, opening interesting vistas about metabolite compartmentalization as viewed by these 2D NMR experiments.
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Affiliation(s)
- Ricardo P. Martinho
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Mukul G. Jain
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Lucio Frydman
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
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5
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Huszar IN, Pallebage-Gamarallage M, Bangerter-Christensen S, Brooks H, Fitzgibbon S, Foxley S, Hiemstra M, Howard AFD, Jbabdi S, Kor DZL, Leonte A, Mollink J, Smart A, Tendler BC, Turner MR, Ansorge O, Miller KL, Jenkinson M. Tensor image registration library: Deformable registration of stand-alone histology images to whole-brain post-mortem MRI data. Neuroimage 2023; 265:119792. [PMID: 36509214 PMCID: PMC10933796 DOI: 10.1016/j.neuroimage.2022.119792] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/26/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Accurate registration between microscopy and MRI data is necessary for validating imaging biomarkers against neuropathology, and to disentangle complex signal dependencies in microstructural MRI. Existing registration methods often rely on serial histological sampling or significant manual input, providing limited scope to work with a large number of stand-alone histology sections. Here we present a customisable pipeline to assist the registration of stand-alone histology sections to whole-brain MRI data. METHODS Our pipeline registers stained histology sections to whole-brain post-mortem MRI in 4 stages, with the help of two photographic intermediaries: a block face image (to undistort histology sections) and coronal brain slab photographs (to insert them into MRI space). Each registration stage is implemented as a configurable stand-alone Python script using our novel platform, Tensor Image Registration Library (TIRL), which provides flexibility for wider adaptation. We report our experience of registering 87 PLP-stained histology sections from 14 subjects and perform various experiments to assess the accuracy and robustness of each stage of the pipeline. RESULTS All 87 histology sections were successfully registered to MRI. Histology-to-block registration (Stage 1) achieved 0.2-0.4 mm accuracy, better than commonly used existing methods. Block-to-slice matching (Stage 2) showed great robustness in automatically identifying and inserting small tissue blocks into whole brain slices with 0.2 mm accuracy. Simulations demonstrated sub-voxel level accuracy (0.13 mm) of the slice-to-volume registration (Stage 3) algorithm, which was observed in over 200 actual brain slice registrations, compensating 3D slice deformations up to 6.5 mm. Stage 4 combined the previous stages and generated refined pixelwise aligned multi-modal histology-MRI stacks. CONCLUSIONS Our open-source pipeline provides robust automation tools for registering stand-alone histology sections to MRI data with sub-voxel level precision, and the underlying framework makes it readily adaptable to a diverse range of microscopy-MRI studies.
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Affiliation(s)
- Istvan N Huszar
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
| | | | - Sarah Bangerter-Christensen
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Brigham Young University, Provo, UT, USA
| | - Hannah Brooks
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sean Fitzgibbon
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Sean Foxley
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Department of Radiology, University of Chicago, Chicago, IL, USA
| | - Marlies Hiemstra
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Department of Anatomy, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Amy F D Howard
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Saad Jbabdi
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Daniel Z L Kor
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Anna Leonte
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Department of Neuroscience, University of Groningen, Groningen, the Netherlands
| | - Jeroen Mollink
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Department of Anatomy, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Adele Smart
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Benjamin C Tendler
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Martin R Turner
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Karla L Miller
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Mark Jenkinson
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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6
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Tsurugizawa T, Kumamoto T, Yoshioka Y. Utilization of potato starch suspension for MR-microimaging in ex vivo mouse embryos. iScience 2022; 25:105694. [PMID: 36567713 PMCID: PMC9768372 DOI: 10.1016/j.isci.2022.105694] [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: 05/25/2022] [Revised: 07/31/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Magnetic resonance (MR) microimaging of the mouse embryo is a promising tool to noninvasively investigate the microstructure of the brain of a developing mouse. The proton-free fluid is used for the liquid surrounding the specimen in MR microimaging, but the potential issue of image quality remains due to the air bubbles on the specimen and the retained water proton in the curvature of the embryo. Furthermore, the specimen may move during the scanning, resulting in motion artifact. Here, we developed the new concept of the ex vivo microimaging protocol with the robust method using the potato starch-containing biological polymers. Potato starch suspension with PBS significantly reduced T1 and T2 signal intensity of the suspension and strongly suppressed the motion of the embryo. Furthermore, potato starch-PBS suspension is stable for long-time scanning at room temperature. These results indicate the utility of potato starch suspension for MR microimaging in mouse embryos.
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Affiliation(s)
- Tomokazu Tsurugizawa
- Human Informatics and Interaction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8568, Japan,Faculty of Engineering, Information and Systems, University of Tsukuba, Tsukuba 305-8573, Japan,Jikei University School of Medicine, 3-25-8 Nishishinbashi, Tokyo 105-8461, Japan,Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan,Center for Information and Neural Networks (CiNet), Osaka University and National Institute of Information and Communications Technology (NICT), Suita 565-0871, Japan,Corresponding author
| | - Takuma Kumamoto
- Developmental Neuroscience Project, Department of Brain & Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yoshichika Yoshioka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan,Center for Information and Neural Networks (CiNet), Osaka University and National Institute of Information and Communications Technology (NICT), Suita 565-0871, Japan,Corresponding author
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7
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Haider L, Hametner S, Endmayr V, Mangesius S, Eppensteiner A, Frischer JM, Iglesias JE, Barkhof F, Kasprian G. Post-mortem correlates of Virchow-Robin spaces detected on in vivo MRI. J Cereb Blood Flow Metab 2022; 42:1224-1235. [PMID: 35581687 PMCID: PMC9207491 DOI: 10.1177/0271678x211067455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The purpose of our study is to quantify the extent to which Virchow-Robin spaces (VRS) detected on in vivo MRI are reproducible by post-mortem MRI.Double Echo Steady State 3T MRIs were acquired post-mortem in 49 double- and 32 single-hemispheric formalin-fixed brain sections from 12 patients, who underwent conventional diagnostic 1.5 or 3T MRI in median 22 days prior to death (25% to 75%: 12 to 134 days). The overlap of in vivo and post-mortem VRS segmentations was determined accounting for potential confounding factors.The reproducibility of VRS found on in vivo MRI by post-mortem MRI, in the supratentorial white matter was in median 80% (25% to 75%: 60 to 100). A lower reproducibility was present in the basal ganglia, with a median of 47% (25% to 75%: 30 to 50).VRS segmentations were histologically confirmed in one double hemispheric section.Overall, the majority of VRS found on in vivo MRI was stable throughout death and formalin fixation, emphasizing the translational potential of post-mortem VRS studies.
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Affiliation(s)
- Lukas Haider
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Institute of Neurology, London, UK.,Department of Biomedical Imaging and Image Guided Therapy, Medical University of Vienna, Wien, Austria
| | - Simon Hametner
- Clinical Institute of Neurology, Centre for Brain Research, Medical University of Vienna, Wien, Austria
| | - Verena Endmayr
- Clinical Institute of Neurology, Centre for Brain Research, Medical University of Vienna, Wien, Austria
| | - Stephanie Mangesius
- Department of Neuroradiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Eppensteiner
- Department of Neuroradiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Josa M Frischer
- Department of Neurosurgery, Medical University Vienna, Wien, Austria
| | - Juan Eugenio Iglesias
- Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Frederik Barkhof
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Institute of Neurology, London, UK.,Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London, UK.,National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London, UK.,Department of Radiology and Nuclear Medicine, VU University Medical Centre, Amsterdam, Netherlands
| | - Gregor Kasprian
- Department of Biomedical Imaging and Image Guided Therapy, Medical University of Vienna, Wien, Austria
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8
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Stram MN, Seifert AC, Cortes E, Akyatan A, Woodoff-Leith E, Borukhov V, Tetlow A, Alyemni D, Greenberg M, Gupta A, Krausert A, Mecca L, Rodriguez S, Stahl-Herz J, Guzman MA, Delman B, Crary JF, Dams-O'Connor K, Folkerth RD. Neuropathology of Pediatric SARS-CoV-2 Infection in the Forensic Setting: Novel Application of Ex Vivo Imaging in Analysis of Brain Microvasculature. Front Neurol 2022; 13:894565. [PMID: 35685741 PMCID: PMC9170881 DOI: 10.3389/fneur.2022.894565] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Two years into the COVID-19 pandemic, there are few published accounts of postmortem SARS-CoV-2 pathology in children. We report 8 such cases (4 infants aged 7–36 weeks, 4 children aged 5–15 years). Four underwent ex vivo magnetic resonance neuroimaging, to assist in identification of subtle lesions related to vascular compromise. All infants were found unresponsive (3 in unsafe sleeping conditions); all but 1 had recent rhinitis and/or influenza-like illness (ILI) in the family; 1 had history of sickle cell disease. Ex vivo neuroimaging in 1 case revealed white matter (WM) signal hyperintensity and diffuse exaggeration of perivascular spaces, corresponding microscopically to WM mineralization. Neurohistology in the remaining 3 infants variably encompassed WM gliosis and mineralization; brainstem gliosis; perivascular vacuolization; perivascular lymphocytes and brainstem microglia. One had ectopic hippocampal neurons (with pathogenic variant in DEPDC5). Among the children, 3 had underlying conditions (e.g., obesity, metabolic disease, autism) and all presented with ILI. Three had laboratory testing suggesting multisystem inflammatory syndrome (MIS-C). Two were hospitalized for critical care including mechanical ventilation and extracorporeal membrane oxygenation (ECMO); one (co-infected with adenovirus) developed right carotid stroke ipsilateral to the ECMO cannula and the other required surgery for an ingested foreign body. Autopsy findings included: acute lung injury in 3 (1 with microthrombi); and one each with diabetic ketoacidosis and cardiac hypertrophy; coronary and cerebral arteritis and aortitis, resembling Kawasaki disease; and neuronal storage and enlarged fatty liver. All 4 children had subtle meningoencephalitis, focally involving the brainstem. On ex vivo neuroimaging, 1 had focal pontine susceptibility with corresponding perivascular inflammation/expanded perivascular spaces on histopathology. Results suggest SARS-CoV-2 in infants may present as sudden unexpected infant death, while in older children, signs and symptoms point to severe disease. Underlying conditions may predispose to fatal outcomes. As in adults, the neuropathologic changes may be subtle, with vascular changes such as perivascular vacuolization and gliosis alongside sparse perivascular lymphocytes. Detection of subtle vascular pathology is enhanced by ex vivo neuroimaging. Additional analysis of the peripheral/autonomic nervous system and investigation of co-infection in children with COVID-19 is necessary to understand risk for cardiovascular collapse/sudden death.
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Affiliation(s)
- Michelle N. Stram
- Office of Chief Medical Examiner, New York, NY, United States
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Alan C. Seifert
- Department of Diagnostic, Molecular and Interventional Radiology, Biomedical Engineering and Imaging Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Etty Cortes
- Department of Pathology, Molecular and Cell Based Medicine, Mount Sinai Hospital, New York, NY, United States
- Neuropathology Brain Bank & Research Center of Research Excellence (CoRE), Mount Sinai Hospital, New York, NY, United States
| | - Alara Akyatan
- University of New England College of Medicine, Biddeford, ME, United States
| | - Emma Woodoff-Leith
- Department of Pathology, Molecular and Cell Based Medicine, Mount Sinai Hospital, New York, NY, United States
- Neuropathology Brain Bank & Research Center of Research Excellence (CoRE), Mount Sinai Hospital, New York, NY, United States
| | - Valeriy Borukhov
- Department of Pathology, Molecular and Cell Based Medicine, Mount Sinai Hospital, New York, NY, United States
- Neuropathology Brain Bank & Research Center of Research Excellence (CoRE), Mount Sinai Hospital, New York, NY, United States
| | - Amber Tetlow
- Department of Pathology, Molecular and Cell Based Medicine, Mount Sinai Hospital, New York, NY, United States
- Neuropathology Brain Bank & Research Center of Research Excellence (CoRE), Mount Sinai Hospital, New York, NY, United States
| | - Dimath Alyemni
- Office of Chief Medical Examiner, New York, NY, United States
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Michael Greenberg
- Office of Chief Medical Examiner, New York, NY, United States
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Avneesh Gupta
- Office of Chief Medical Examiner, New York, NY, United States
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Amanda Krausert
- Department of Pathology, Molecular and Cell Based Medicine, Mount Sinai Hospital, New York, NY, United States
| | - Lauren Mecca
- Office of Chief Medical Examiner, New York, NY, United States
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Sophia Rodriguez
- Office of the Medical Investigator, Albuquerque, NM, United States
| | - Jay Stahl-Herz
- Office of Chief Medical Examiner, New York, NY, United States
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Miguel A. Guzman
- Department of Pathology at Saint Louis University School of Medicine, SSM Cardinal Glennon Hospital, St. Louis, MO, United States
| | - Bradley Delman
- Department of Diagnostic, Molecular and Interventional Radiology, Biomedical Engineering and Imaging Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - John F. Crary
- Department of Pathology, Molecular and Cell Based Medicine, Mount Sinai Hospital, New York, NY, United States
- Neuropathology Brain Bank & Research Center of Research Excellence (CoRE), Mount Sinai Hospital, New York, NY, United States
| | - Kristen Dams-O'Connor
- Department of Rehabilitation and Human Performance, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Rebecca D. Folkerth
- Office of Chief Medical Examiner, New York, NY, United States
- Department of Forensic Medicine, New York University Grossman School of Medicine, New York, NY, United States
- *Correspondence: Rebecca D. Folkerth
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9
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Extended Ischemic Recovery After Implantation of Human Mesenchymal Stem Cell Aggregates Indicated by Sodium MRI at 21.1 T. Transl Stroke Res 2022; 13:543-555. [DOI: 10.1007/s12975-021-00976-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/17/2021] [Accepted: 12/12/2021] [Indexed: 12/19/2022]
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10
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Müller-Axt C, Eichner C, Rusch H, Kauffmann L, Bazin PL, Anwander A, Morawski M, von Kriegstein K. Mapping the human lateral geniculate nucleus and its cytoarchitectonic subdivisions using quantitative MRI. Neuroimage 2021; 244:118559. [PMID: 34562697 DOI: 10.1016/j.neuroimage.2021.118559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 11/17/2022] Open
Abstract
The human lateral geniculate nucleus (LGN) of the visual thalamus is a key subcortical processing site for visual information analysis. Due to its small size and deep location within the brain, a non-invasive characterization of the LGN and its microstructurally distinct magnocellular (M) and parvocellular (P) subdivisions in humans is challenging. Here, we investigated whether structural quantitative MRI (qMRI) methods that are sensitive to underlying microstructural tissue features enable MR-based mapping of human LGN M and P subdivisions. We employed high-resolution 7 Tesla in-vivo qMRI in N = 27 participants and ultra-high resolution 7 Tesla qMRI of a post-mortem human LGN specimen. We found that a quantitative assessment of the LGN and its subdivisions is possible based on microstructure-informed qMRI contrast alone. In both the in-vivo and post-mortem qMRI data, we identified two components of shorter and longer longitudinal relaxation time (T1) within the LGN that coincided with the known anatomical locations of a dorsal P and a ventral M subdivision, respectively. Through ground-truth histological validation, we further showed that the microstructural MRI contrast within the LGN pertains to cyto- and myeloarchitectonic tissue differences between its subdivisions. These differences were based on cell and myelin density, but not on iron content. Our qMRI-based mapping strategy paves the way for an in-depth understanding of LGN function and microstructure in humans. It further enables investigations into the selective contributions of LGN subdivisions to human behavior in health and disease.
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Affiliation(s)
- Christa Müller-Axt
- Faculty of Psychology, Technical University of Dresden, Dresden 01069, Germany; Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig 04103, Germany.
| | - Cornelius Eichner
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig 04103, Germany
| | - Henriette Rusch
- Paul Flechsig Institute of Brain Research, University of Leipzig, Leipzig 04103, Germany
| | - Louise Kauffmann
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig 04103, Germany; LPNC, Grenoble Alpes University, Grenoble 38000, France
| | - Pierre-Louis Bazin
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig 04103, Germany; Integrative Model-Based Cognitive Neuroscience Research Unit, Department of Psychology, University of Amsterdam, Amsterdam 1001 NK, The Netherlands
| | - Alfred Anwander
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig 04103, Germany
| | - Markus Morawski
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig 04103, Germany; Paul Flechsig Institute of Brain Research, University of Leipzig, Leipzig 04103, Germany
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11
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Boonstra JT, Michielse S, Roebroeck A, Temel Y, Jahanshahi A. Dedicated container for postmortem human brain ultra-high field magnetic resonance imaging. Neuroimage 2021; 235:118010. [PMID: 33819610 DOI: 10.1016/j.neuroimage.2021.118010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/14/2021] [Accepted: 03/23/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The emerging field of ultra-high field MRI (UHF-MRI, 7 Tesla and higher) provides the opportunity to image human brains at a higher resolution and with higher signal-to-noise ratios compared to the more widely available 1.5 and 3T scanners. Scanning postmortem tissue additionally allows for greatly increased scan times and fewer movement issues leading to improvements in image quality. However, typical postmortem neuroimaging routines involve placing the tissue within plastic bags that leave room for susceptibility artifacts from tissue-air interfaces, inadequate submersion, and leakage issues. To address these challenges in postmortem imaging, a custom-built nonferromagnetic container was developed that allows whole brain hemispheres to be scanned at sub-millimeter resolution within typical head-coils. METHOD The custom-built polymethylmethacrylaat container consists of a cylinder with a hemispheric side and a lid with valves on the adjacent side. This shape fits within common MR head-coils and allows whole hemispheres to be submerged and vacuum sealed within it reducing imaging artifacts that would otherwise arise at air-tissue boundaries. Two hemisphere samples were scanned on a Siemens 9.4T Magnetom MRI scanner. High resolution T2* weighted data was obtained with a custom 3D gradient echo (GRE) sequence and diffusion-weighted imaging (DWI) scans were obtained with a 3D kT-dSTEAM sequence along 48 directions. RESULTS The custom-built container proved to submerge and contain tissue samples effectively and showed no interferences with MR scanning acquisition. The 3D GRE sequence provided high resolution isotropic T2* weighted data at 250 μm which showed a clear visualization of gray and white matter structures. DWI scans allowed for dense reconstruction of structural white matter connections via tractography. CONCLUSION Using this custom-built container worked towards achieving high quality MR images of postmortem brain material. This procedure can have advantages over traditional schemes including utilization of a standardized protocol and the reduced likelihood of leakage. This methodology could be adjusted and used to improve typical postmortem imaging routines.
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Affiliation(s)
- Jackson Tyler Boonstra
- Department of Neurosurgery, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, 6202 AZ, the Netherlands; School for Mental Health and Neuroscience (MHeNS), Maastricht University Medical Center, P. Debyelaan 25, Maastricht, 6200 MD, the Netherlands.
| | - Stijn Michielse
- Department of Neurosurgery, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, 6202 AZ, the Netherlands; School for Mental Health and Neuroscience (MHeNS), Maastricht University Medical Center, P. Debyelaan 25, Maastricht, 6200 MD, the Netherlands
| | - Alard Roebroeck
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, the Netherlands
| | - Yasin Temel
- Department of Neurosurgery, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, 6202 AZ, the Netherlands; School for Mental Health and Neuroscience (MHeNS), Maastricht University Medical Center, P. Debyelaan 25, Maastricht, 6200 MD, the Netherlands
| | - Ali Jahanshahi
- Department of Neurosurgery, Maastricht University Medical Center, P. Debyelaan 25, Maastricht, 6202 AZ, the Netherlands; School for Mental Health and Neuroscience (MHeNS), Maastricht University Medical Center, P. Debyelaan 25, Maastricht, 6200 MD, the Netherlands
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12
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Mancini M, Casamitjana A, Peter L, Robinson E, Crampsie S, Thomas DL, Holton JL, Jaunmuktane Z, Iglesias JE. A multimodal computational pipeline for 3D histology of the human brain. Sci Rep 2020; 10:13839. [PMID: 32796937 PMCID: PMC7429828 DOI: 10.1038/s41598-020-69163-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/30/2020] [Indexed: 12/14/2022] Open
Abstract
Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of whole human hemispheres from two donors.
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Affiliation(s)
- Matteo Mancini
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK.
- Department of Neuroscience, Brighton and Sussex Medical School, University of Sussex, Brighton, UK.
- CUBRIC, Cardiff University, Cardiff, UK.
- NeuroPoly Lab, Polytechnique Montreal, Montreal, Canada.
| | - Adrià Casamitjana
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Loic Peter
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Eleanor Robinson
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Shauna Crampsie
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - David L Thomas
- Neuroradiological Academic Unit, UCL Queen Square Institute of Neurology, University College London, London, UK
- Leonard Wolfson Experimental Neurology Centre, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Zane Jaunmuktane
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Juan Eugenio Iglesias
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK.
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, MA, USA.
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13
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Mariager CØ, Hansen ESS, Bech SK, Munk A, Kjaergaard U, Lyhne MD, Søberg K, Nielsen PF, Ringgaard S, Laustsen C. Graft assessment of the ex vivo perfused porcine kidney using hyperpolarized [1- 13 C]pyruvate. Magn Reson Med 2020; 84:2645-2655. [PMID: 32557782 DOI: 10.1002/mrm.28363] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/07/2020] [Accepted: 05/21/2020] [Indexed: 01/06/2023]
Abstract
PURPOSE Normothermic perfusion is an emerging strategy for donor organ preservation and therapy, incited by the high worldwide demand for organs for transplantation. Hyperpolarized MRI and MRS using [1-13 C]pyruvate and other 13 C-labeled molecules pose a novel way to acquire highly detailed information about metabolism and function in a noninvasive manner. This study investigates the use of this methodology as a means to study and monitor the state of ex vivo perfused porcine kidneys, in the context of kidney graft preservation research. METHODS Kidneys from four 40-kg Danish domestic pigs were perfused ex vivo with whole blood under normothermic conditions, using an MR-compatible perfusion system. Kidneys were investigated using 1 H MRI as well as hyperpolarized [1-13 C]pyruvate MRI and MRS. Using the acquired anatomical, functional and metabolic data, the state of the ex vivo perfused porcine kidney could be quantified. RESULTS Four kidneys were successfully perfused for 120 minutes and verified using a DCE perfusion experiment. Renal metabolism was examined using hyperpolarized [1-13 C]pyruvate MRI and MRS, and displayed an apparent reduction in pyruvate turnover compared with the usual case in vivo. Perfusion and blood gas parameters were in the normal ex vivo range. CONCLUSION This study demonstrates the ability to monitor ex vivo graft metabolism and function in a large animal model, resembling human renal physiology. The ability of hyperpolarized MRI and MRS to directly compare the metabolic state of an organ in vivo and ex vivo, in combination with the simple MR implementation of normothermic perfusion, renders this methodology a powerful future tool for graft preservation research.
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Affiliation(s)
| | | | - Sabrina Kahina Bech
- Department of Clinical Medicine, The MR Research Centre, Aarhus University, Aarhus, Denmark
| | - Anders Munk
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Uffe Kjaergaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mads Dam Lyhne
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karsten Søberg
- Department of Anesthesia and Intensive Care, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Fast Nielsen
- Department of Anesthesia and Intensive Care, Aarhus University Hospital, Aarhus, Denmark
| | - Steffen Ringgaard
- Department of Clinical Medicine, The MR Research Centre, Aarhus University, Aarhus, Denmark
| | - Christoffer Laustsen
- Department of Clinical Medicine, The MR Research Centre, Aarhus University, Aarhus, Denmark
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14
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Scher Y, Reuveni S, Cohen Y. Constant gradient FEXSY: A time-efficient method for measuring exchange. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 311:106667. [PMID: 31865183 DOI: 10.1016/j.jmr.2019.106667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/01/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Filter-Exchange NMR Spectroscopy (FEXSY) is a method for measurement of apparent transmembranal water exchange rates. The experiment is comprised of two co-linear sequential pulsed-field gradient (PFG) blocks, separated by a mixing period in which exchange takes place. The first block remains constant and serves as a diffusion-based filter that removes signal coming from fast-diffusing water. The mixing time and the gradient area (q-value) of the second block are varied on repeated iterations to produce a 2D data set that is analyzed using a bi-compartmental model which assumes that intra- and extra-cellular water are slow and fast diffusing, respectively. Here we suggest a variant of the FEXSY method in which measurements for different mixing times are taken at a constant gradient. This Constant Gradient FEXSY (CG-FEXSY) allows for the determination of the exchange rate by using a smaller 1D data set, so that the same information can be gathered during a considerably shorter scan time. Furthermore, in the limit of high diffusion weighting, such that the extra-cellular water signal is removed while the intra-cellular signal is retained, CG-FEXSY also allows for determination of the intra-cellular mean residence time (MRT). The theoretical results are validated on a living yeast cells sample and on a fixed porcine optic nerve, where the values obtained from the two methods are shown to be in agreement.
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Affiliation(s)
- Yuval Scher
- School of Chemistry, The Center for Physics and Chemistry of Living Systems, The Raymond and Beverly Sackler Center for Computational Molecular and Materials Science, The Mark Ratner Institute for Single Molecule Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Shlomi Reuveni
- School of Chemistry, The Center for Physics and Chemistry of Living Systems, The Raymond and Beverly Sackler Center for Computational Molecular and Materials Science, The Mark Ratner Institute for Single Molecule Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yoram Cohen
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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