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Damilou A, Cai L, Argunşah AÖ, Han S, Kanatouris G, Karatsoli M, Hanley O, Gesuita L, Kollmorgen S, Helmchen F, Karayannis T. Developmental Cajal-Retzius cell death contributes to the maturation of layer 1 cortical inhibition and somatosensory processing. Nat Commun 2024; 15:6501. [PMID: 39090081 PMCID: PMC11294614 DOI: 10.1038/s41467-024-50658-6] [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: 07/26/2023] [Accepted: 07/11/2024] [Indexed: 08/04/2024] Open
Abstract
The role of developmental cell death in the formation of brain circuits is not well understood. Cajal-Retzius cells constitute a major transient neuronal population in the mammalian neocortex, which largely disappears at the time of postnatal somatosensory maturation. In this study, we used mouse genetics, anatomical, functional, and behavioral approaches to explore the impact of the early postnatal death of Cajal-Retzius cells in the maturation of the cortical circuit. We find that before their death, Cajal-Retzius cells mainly receive inputs from layer 1 neurons, which can only develop their mature connectivity onto layer 2/3 pyramidal cells after Cajal-Retzius cells disappear. This developmental connectivity progression from layer 1 GABAergic to layer 2/3 pyramidal cells regulates sensory-driven inhibition within, and more so, across cortical columns. Here we show that Cajal-Retzius cell death prevention leads to layer 2/3 hyper-excitability, delayed learning and reduced performance in a multi-whisker-dependent texture discrimination task.
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Affiliation(s)
- Angeliki Damilou
- Laboratory of Neural Circuit Assembly, Brain Research Institute (HiFo), University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Adaptive Brain Circuits in Development and Learning (AdaBD), University Research Priority Program (URPP), University of Zürich, Zürich, 8057, Switzerland
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Linbi Cai
- Laboratory of Neural Circuit Assembly, Brain Research Institute (HiFo), University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Ali Özgür Argunşah
- Laboratory of Neural Circuit Assembly, Brain Research Institute (HiFo), University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Shuting Han
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - George Kanatouris
- Laboratory of Neural Circuit Assembly, Brain Research Institute (HiFo), University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Maria Karatsoli
- Laboratory of Neural Circuit Assembly, Brain Research Institute (HiFo), University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Adaptive Brain Circuits in Development and Learning (AdaBD), University Research Priority Program (URPP), University of Zürich, Zürich, 8057, Switzerland
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Olivia Hanley
- Laboratory of Neural Circuit Assembly, Brain Research Institute (HiFo), University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Lorenzo Gesuita
- Laboratory of Neural Circuit Assembly, Brain Research Institute (HiFo), University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Sepp Kollmorgen
- Adaptive Brain Circuits in Development and Learning (AdaBD), University Research Priority Program (URPP), University of Zürich, Zürich, 8057, Switzerland
| | - Fritjof Helmchen
- Adaptive Brain Circuits in Development and Learning (AdaBD), University Research Priority Program (URPP), University of Zürich, Zürich, 8057, Switzerland
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Laboratory of Neural Circuit Dynamics, Brain Research Institute, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Theofanis Karayannis
- Laboratory of Neural Circuit Assembly, Brain Research Institute (HiFo), University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
- Adaptive Brain Circuits in Development and Learning (AdaBD), University Research Priority Program (URPP), University of Zürich, Zürich, 8057, Switzerland.
- Neuroscience Center Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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2
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Glaser A, Chandrashekar J, Vasquez S, Arshadi C, Ouellette N, Jiang X, Baka J, Kovacs G, Woodard M, Seshamani S, Cao K, Clack N, Recknagel A, Grim A, Balaram P, Turschak E, Hooper M, Liddell A, Rohde J, Hellevik A, Takasaki K, Erion Barner L, Logsdon M, Chronopoulos C, de Vries S, Ting J, Perlmutter S, Kalmbach B, Dembrow N, Tasic B, Reid RC, Feng D, Svoboda K. Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.08.544277. [PMID: 37425699 PMCID: PMC10327101 DOI: 10.1101/2023.06.08.544277] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure of cells and tissues at sub-diffraction resolutions and near single molecule sensitivity, driving discoveries in diverse fields of biology, including neuroscience. Biological tissue is organized over scales of nanometers to centimeters. Harnessing molecular imaging across intact, three-dimensional samples on this scale requires new types of microscopes with larger fields of view and working distance, as well as higher throughput. We present a new expansion-assisted selective plane illumination microscope (ExA-SPIM) with aberration-free 1×1×3 μm optical resolution over a large field of view (10.6×8.0 mm 2 ) and working distance (35 mm) at speeds up to 946 megavoxels/sec. Combined with new tissue clearing and expansion methods, the microscope allows imaging centimeter-scale samples with 250×250×750 nm optical resolution (4× expansion), including entire mouse brains, with high contrast and without sectioning. We illustrate ExA-SPIM by reconstructing individual neurons across the mouse brain, imaging cortico-spinal neurons in the macaque motor cortex, and visualizing axons in human white matter.
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3
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Yan C, Mercaldo V, Jacob AD, Kramer E, Mocle A, Ramsaran AI, Tran L, Rashid AJ, Park S, Insel N, Redish AD, Frankland PW, Josselyn SA. Higher-order interactions between hippocampal CA1 neurons are disrupted in amnestic mice. Nat Neurosci 2024:10.1038/s41593-024-01713-4. [PMID: 39030342 DOI: 10.1038/s41593-024-01713-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/18/2024] [Indexed: 07/21/2024]
Abstract
Across systems, higher-order interactions between components govern emergent dynamics. Here we tested whether contextual threat memory retrieval in mice relies on higher-order interactions between dorsal CA1 hippocampal neurons requiring learning-induced dendritic spine plasticity. We compared population-level Ca2+ transients as wild-type mice (with intact learning-induced spine plasticity and memory) and amnestic mice (TgCRND8 mice with high levels of amyloid-β and deficits in learning-induced spine plasticity and memory) were tested for memory. Using machine-learning classifiers with different capacities to use input data with complex interactions, our findings indicate complex neuronal interactions in the memory representation of wild-type, but not amnestic, mice. Moreover, a peptide that partially restored learning-induced spine plasticity also restored the statistical complexity of the memory representation and memory behavior in Tg mice. These findings provide a previously missing bridge between levels of analysis in memory research, linking receptors, spines, higher-order neuronal dynamics and behavior.
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Affiliation(s)
- Chen Yan
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- DeepMind, London, UK
| | - Valentina Mercaldo
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Alexander D Jacob
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Dept. of Psychology, University of Toronto, Toronto, Ontario, Canada
| | - Emily Kramer
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Mocle
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Dept. of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Adam I Ramsaran
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Dept. of Psychology, University of Toronto, Toronto, Ontario, Canada
| | - Lina Tran
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Asim J Rashid
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sungmo Park
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nathan Insel
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Dept. of Psychology, University of Montana, Missoula, MT, USA
- Department of Psychology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - A David Redish
- Dept. of Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Paul W Frankland
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Dept. of Psychology, University of Toronto, Toronto, Ontario, Canada
- Dept. of Physiology, University of Toronto, Toronto, Ontario, Canada
- Child & Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada
| | - Sheena A Josselyn
- Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada.
- Dept. of Psychology, University of Toronto, Toronto, Ontario, Canada.
- Dept. of Physiology, University of Toronto, Toronto, Ontario, Canada.
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4
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Wang Y, Liu X, Zeng Y, Saka SK, Xie W, Goldaracena I, Kohman RE, Yin P, Church GM. Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions. Nucleic Acids Res 2024:gkae592. [PMID: 38966983 DOI: 10.1093/nar/gkae592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Antibodies have long served as vital tools in biological and clinical laboratories for the specific detection of proteins. Conventional methods employ fluorophore or horseradish peroxidase-conjugated antibodies to detect signals. More recently, DNA-conjugated antibodies have emerged as a promising technology, capitalizing on the programmability and amplification capabilities of DNA to enable highly multiplexed and ultrasensitive protein detection. However, the nonspecific binding of DNA-conjugated antibodies has impeded the widespread adoption of this approach. Here, we present a novel DNA-conjugated antibody staining protocol that addresses these challenges and demonstrates superior performance in suppressing nonspecific signals compared to previously published protocols. We further extend the utility of DNA-conjugated antibodies for signal-amplified in situ protein imaging through the hybridization chain reaction (HCR) and design a novel HCR DNA pair to expand the HCR hairpin pool from the previously published 5 pairs to 13, allowing for flexible hairpin selection and higher multiplexing. Finally, we demonstrate highly multiplexed in situ protein imaging using these techniques in both cultured cells and tissue sections.
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Affiliation(s)
- Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Xiaoyu Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Yitian Zeng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wenxin Xie
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Isabel Goldaracena
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richie E Kohman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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5
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Skinnider MA, Gautier M, Teo AYY, Kathe C, Hutson TH, Laskaratos A, de Coucy A, Regazzi N, Aureli V, James ND, Schneider B, Sofroniew MV, Barraud Q, Bloch J, Anderson MA, Squair JW, Courtine G. Single-cell and spatial atlases of spinal cord injury in the Tabulae Paralytica. Nature 2024; 631:150-163. [PMID: 38898272 DOI: 10.1038/s41586-024-07504-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 05/01/2024] [Indexed: 06/21/2024]
Abstract
Here, we introduce the Tabulae Paralytica-a compilation of four atlases of spinal cord injury (SCI) comprising a single-nucleus transcriptome atlas of half a million cells, a multiome atlas pairing transcriptomic and epigenomic measurements within the same nuclei, and two spatial transcriptomic atlases of the injured spinal cord spanning four spatial and temporal dimensions. We integrated these atlases into a common framework to dissect the molecular logic that governs the responses to injury within the spinal cord1. The Tabulae Paralytica uncovered new biological principles that dictate the consequences of SCI, including conserved and divergent neuronal responses to injury; the priming of specific neuronal subpopulations to upregulate circuit-reorganizing programs after injury; an inverse relationship between neuronal stress responses and the activation of circuit reorganization programs; the necessity of re-establishing a tripartite neuroprotective barrier between immune-privileged and extra-neural environments after SCI and a failure to form this barrier in old mice. We leveraged the Tabulae Paralytica to develop a rejuvenative gene therapy that re-established this tripartite barrier, and restored the natural recovery of walking after paralysis in old mice. The Tabulae Paralytica provides a window into the pathobiology of SCI, while establishing a framework for integrating multimodal, genome-scale measurements in four dimensions to study biology and medicine.
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Affiliation(s)
- Michael A Skinnider
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA
| | - Matthieu Gautier
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Alan Yue Yang Teo
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Claudia Kathe
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Thomas H Hutson
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Wyss Center for Bio and Neuroengineering, Geneva, Switzerland
| | - Achilleas Laskaratos
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Alexandra de Coucy
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Nicola Regazzi
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Viviana Aureli
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Nicholas D James
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Bernard Schneider
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Bertarelli Platform for Gene Therapy, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Michael V Sofroniew
- Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Quentin Barraud
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
| | - Jocelyne Bloch
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Mark A Anderson
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland.
- Wyss Center for Bio and Neuroengineering, Geneva, Switzerland.
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Jordan W Squair
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland.
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
| | - Grégoire Courtine
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Defitech Center for Interventional Neurotherapies (.NeuroRestore), CHUV/UNIL/EPFL, Lausanne, Switzerland.
- Department of Neurosurgery, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
- Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
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6
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Oz S, Saar G, Olszakier S, Heinrich R, Kompanets MO, Berlin S. Revealing the MRI-Contrast in Optically Cleared Brains. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400316. [PMID: 38647385 PMCID: PMC11165557 DOI: 10.1002/advs.202400316] [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: 01/09/2024] [Revised: 04/10/2024] [Indexed: 04/25/2024]
Abstract
The current consensus holds that optically-cleared specimens are unsuitable for Magnetic Resonance Imaging (MRI); exhibiting absence of contrast. Prior studies combined MRI with tissue-clearing techniques relying on the latter's ability to eliminate lipids, thereby fostering the assumption that lipids constitute the primary source of ex vivo MRI-contrast. Nevertheless, these findings contradict an extensive body of literature that underscores the contribution of other features to contrast. Furthermore, it remains unknown whether non-delipidating clearing methods can produce MRI-compatible specimens or whether MRI-contrast can be re-established. These limitations hinder the development of multimodal MRI-light-microscopy (LM) imaging approaches. This study assesses the relation between MRI-contrast, and delipidation in optically-cleared whole brains following different tissue-clearing approaches. It is demonstrated that uDISCO and ECi-brains are MRI-compatible upon tissue rehydration, despite both methods' substantial delipidating-nature. It is also demonstrated that, whereas Scale-clearing preserves most lipids, Scale-cleared brain lack MRI-contrast. Furthermore, MRI-contrast is restored to lipid-free CLARITY-brains without introducing lipids. Our results thereby dissociate between the essentiality of lipids to MRI-contrast. A tight association is found between tissue expansion, hyperhydration and loss of MRI-contrast. These findings then enabled us to develop a multimodal MRI-LM-imaging approach, opening new avenues to bridge between the micro- and mesoscale for biomedical research and clinical applications.
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Affiliation(s)
- Shimrit Oz
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Galit Saar
- Biomedical Core FacilityFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Shunit Olszakier
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Ronit Heinrich
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Mykhail O. Kompanets
- L.M. Litvinenko Institute of Physico‐Organic Chemistry and Coal ChemistryNational Academy of Sciences of UkraineKyivUkraine
| | - Shai Berlin
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
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7
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Cauzzo S, Bruno E, Boulet D, Nazac P, Basile M, Callara AL, Tozzi F, Ahluwalia A, Magliaro C, Danglot L, Vanello N. A modular framework for multi-scale tissue imaging and neuronal segmentation. Nat Commun 2024; 15:4102. [PMID: 38778027 PMCID: PMC11111705 DOI: 10.1038/s41467-024-48146-y] [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: 04/20/2023] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
The development of robust tools for segmenting cellular and sub-cellular neuronal structures lags behind the massive production of high-resolution 3D images of neurons in brain tissue. The challenges are principally related to high neuronal density and low signal-to-noise characteristics in thick samples, as well as the heterogeneity of data acquired with different imaging methods. To address this issue, we design a framework which includes sample preparation for high resolution imaging and image analysis. Specifically, we set up a method for labeling thick samples and develop SENPAI, a scalable algorithm for segmenting neurons at cellular and sub-cellular scales in conventional and super-resolution STimulated Emission Depletion (STED) microscopy images of brain tissues. Further, we propose a validation paradigm for testing segmentation performance when a manual ground-truth may not exhaustively describe neuronal arborization. We show that SENPAI provides accurate multi-scale segmentation, from entire neurons down to spines, outperforming state-of-the-art tools. The framework will empower image processing of complex neuronal circuitries.
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Affiliation(s)
- Simone Cauzzo
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy.
- Parkinson's Disease and Movement Disorders Unit, Center for Rare Neurological Diseases (ERN-RND), Department of Neurosciences, University of Padova, Padova, Italy.
| | - Ester Bruno
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - David Boulet
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, NeurImag Core Facility, 75014, Paris, France
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane traffic and diseased brain, 75014, Paris, France
| | - Paul Nazac
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane traffic and diseased brain, 75014, Paris, France
| | - Miriam Basile
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Alejandro Luis Callara
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Federico Tozzi
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Arti Ahluwalia
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Chiara Magliaro
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Lydia Danglot
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, NeurImag Core Facility, 75014, Paris, France.
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane traffic and diseased brain, 75014, Paris, France.
| | - Nicola Vanello
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy.
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy.
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8
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Ventura-Antunes L, Nackenoff A, Romero-Fernandez W, Bosworth AM, Prusky A, Wang E, Carvajal-Tapia C, Shostak A, Harmsen H, Mobley B, Maldonado J, Solopova E, Caleb Snider J, David Merryman W, Lippmann ES, Schrag M. Arteriolar degeneration and stiffness in cerebral amyloid angiopathy are linked to β-amyloid deposition and lysyl oxidase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583563. [PMID: 38659767 PMCID: PMC11042178 DOI: 10.1101/2024.03.08.583563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cerebral amyloid angiopathy (CAA) is a vasculopathy characterized by vascular β-amyloid (Aβ) deposition on cerebral blood vessels. CAA is closely linked to Alzheimer's disease (AD) and intracerebral hemorrhage. CAA is associated with the loss of autoregulation in the brain, vascular rupture, and cognitive decline. To assess morphological and molecular changes associated with the degeneration of penetrating arterioles in CAA, we analyzed post-mortem human brain tissue from 26 patients with mild, moderate, and severe CAA end neurological controls. The tissue was optically cleared for three-dimensional light sheet microscopy, and morphological features were quantified using surface volume rendering. We stained Aβ, vascular smooth muscle (VSM), lysyl oxidase (LOX), and vascular markers to visualize the relationship between degenerative morphological features, including vascular dilation, dolichoectasia (variability in lumenal diameter) and tortuosity, and the volumes of VSM, Aβ, and LOX in arterioles. Atomic force microscopy (AFM) was used to assess arteriolar wall stiffness, and we identified a pattern of morphological features associated with degenerating arterioles in the cortex. The volume of VSM associated with the arteriole was reduced by around 80% in arterioles with severe CAA and around 60% in cases with mild/moderate CAA. This loss of VSM correlated with increased arteriolar diameter and variability of diameter, suggesting VSM loss contributes to arteriolar laxity. These vascular morphological features correlated strongly with Aβ deposits. At sites of microhemorrhage, Aβ was consistently present, although the morphology of the deposits changed from the typical organized ring shape to sharply contoured shards with marked dilation of the vessel. AFM showed that arteriolar walls with CAA were more than 400% stiffer than those without CAA. Finally, we characterized the association of vascular degeneration with LOX, finding strong associations with VSM loss and vascular degeneration. These results show an association between vascular Aβ deposition, microvascular degeneration, and increased vascular stiffness, likely due to the combined effects of replacement of VSM by β-amyloid, cross-linking of extracellular matrices (ECM) by LOX, and possibly fibrosis. This advanced microscopic imaging study clarifies the association between Aβ deposition and vascular fragility. Restoration of physiologic ECM properties in penetrating arteries may yield a novel therapeutic strategy for CAA.
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Affiliation(s)
| | - Alex Nackenoff
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Allison M Bosworth
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Alex Prusky
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emmeline Wang
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Alena Shostak
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hannah Harmsen
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bret Mobley
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jose Maldonado
- Vanderbilt Neurovisualization Lab, Vanderbilt University, Nashville, TN, USA
| | - Elena Solopova
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - J. Caleb Snider
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - W. David Merryman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ethan S Lippmann
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Matthew Schrag
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville TN, USA
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
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9
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Refaeli R, Kreisel T, Yaish TR, Groysman M, Goshen I. Astrocytes control recent and remote memory strength by affecting the recruitment of the CA1→ACC projection to engrams. Cell Rep 2024; 43:113943. [PMID: 38483907 PMCID: PMC10995765 DOI: 10.1016/j.celrep.2024.113943] [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: 10/08/2023] [Revised: 01/14/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024] Open
Abstract
The maturation of engrams from recent to remote time points involves the recruitment of CA1 neurons projecting to the anterior cingulate cortex (CA1→ACC). Modifications of G-protein-coupled receptor pathways in CA1 astrocytes affect recent and remote recall in seemingly contradictory ways. To address this inconsistency, we manipulated these pathways in astrocytes during memory acquisition and tagged c-Fos-positive engram cells and CA1→ACC cells during recent and remote recall. The behavioral results were coupled with changes in the recruitment of CA1→ACC projection cells to the engram: Gq pathway activation in astrocytes caused enhancement of recent recall alone and was accompanied by earlier recruitment of CA1→ACC projecting cells to the engram. In contrast, Gi pathway activation in astrocytes resulted in the impairment of only remote recall, and CA1→ACC projecting cells were not recruited during remote memory. Finally, we provide a simple working model, hypothesizing that Gq and Gi pathway activation affect memory differently, by modulating the same mechanism: CA1→ACC projection.
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Affiliation(s)
- Ron Refaeli
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tirzah Kreisel
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | - Maya Groysman
- ELSC Vector Core Facility, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Inbal Goshen
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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10
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Refaeli R, Kreisel T, Goshen I. Analyzing engram reactivation and long-range connectivity. STAR Protoc 2024; 5:102840. [PMID: 38280198 PMCID: PMC10840331 DOI: 10.1016/j.xpro.2024.102840] [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: 09/05/2023] [Revised: 11/07/2023] [Accepted: 01/04/2024] [Indexed: 01/29/2024] Open
Abstract
Here, we present a protocol for marking engram cells to efficiently measure reactivation levels and their projection pathways. We describe steps for genetic manipulation utilizing transgenic mice and viral infections, labeling engram cells, and a modified version of CLARITY, a tissue-clearing technique. This protocol can be adapted to various research inquiries that involve assessing the overlap of cell populations and uncovering novel long-range connectivity pathways. For complete details on the use and execution of this protocol, please refer to Refaeli et al. (2023).1.
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Affiliation(s)
- Ron Refaeli
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Tirzah Kreisel
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Inbal Goshen
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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11
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Alexandrov T, Saez‐Rodriguez J, Saka SK. Enablers and challenges of spatial omics, a melting pot of technologies. Mol Syst Biol 2023; 19:e10571. [PMID: 37842805 PMCID: PMC10632737 DOI: 10.15252/msb.202110571] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 10/17/2023] Open
Abstract
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- BioInnovation InstituteCopenhagenDenmark
| | - Julio Saez‐Rodriguez
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Sinem K Saka
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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12
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Dennis EJ, Bibawi P, Dhanerawala ZM, Lynch LA, Wang SSH, Brody CD. Princeton RAtlas: A Common Coordinate Framework for Fully cleared, Whole Rattus norvegicus Brains. Bio Protoc 2023; 13:e4854. [PMID: 37900100 PMCID: PMC10603261 DOI: 10.21769/bioprotoc.4854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 10/31/2023] Open
Abstract
Whole-brain clearing and imaging methods are becoming more common in mice but have yet to become standard in rats, at least partially due to inadequate clearing from most available protocols. Here, we build on recent mouse-tissue clearing and light-sheet imaging methods and develop and adapt them to rats. We first used cleared rat brains to create an open-source, 3D rat atlas at 25 μm resolution. We then registered and imported other existing labeled volumes and made all of the code and data available for the community (https://github.com/emilyjanedennis/PRA) to further enable modern, whole-brain neuroscience in the rat. Key features • This protocol adapts iDISCO (Renier et al., 2014) and uDISCO (Pan et al., 2016) tissue-clearing techniques to consistently clear rat brains. • This protocol also decreases the number of working hours per day to fit in an 8 h workday. Graphical overview.
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Affiliation(s)
- Emily Jane Dennis
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, USA
| | - Peter Bibawi
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Neurology Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zahra M. Dhanerawala
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Washington University School of Medicine, St. Louis, Missouri, USA
| | - Laura A. Lynch
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
| | - Samuel S.-H. Wang
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
| | - Carlos D. Brody
- Princeton Neuroscience Institute, Princeton University, Princeton, New Jersey, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, USA
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13
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Gungor Aydin A, Conkur ES, Adiguzel E. Compact organ-tissue electrophoresis system (CORES). J Med Eng Technol 2023; 47:339-343. [PMID: 38588474 DOI: 10.1080/03091902.2024.2336497] [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: 03/13/2023] [Accepted: 03/24/2024] [Indexed: 04/10/2024]
Abstract
Electrophoretic tissue clearing has been a commonly used laboratory method since the early twentieth century. Infrastructure for standard procedures has yet to be formed. In particular, control of the heat produced by electrophoresis, the voltage applied to the electrodes, the resistance, and the speed of liquid circulation create difficulty for researchers. We aimed to develop a compact organ electrophoresis system that enables the researcher to have easy, rapid, and inexpensive working opportunities. The system includes an electronic control unit, a liquid tank, a temperature control unit, and an electrophoresis chamber. The control unit software can keep the system stable by using information on temperature and circulation rate received through the sensors using the feedback principle. Corrosion and particle collection are reduced to a minimum as platinum wires are used for electrophoresis electrodes. A temperature control unit can heat and cool via a liquid tank base. The CORES is an all-in-one, easy-to-use solution for electrophoretic tissue clearing. It assures efficient, rapid, and consistent tissue clearing. The system was stable with 72 h of continuous operation. Patent applications and trial version studies for introducing the system to researchers are still in progress.
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Affiliation(s)
- Aysegul Gungor Aydin
- Department of Psychology, Behavioral and Systems Neuroscience, Rutgers University, Piscataway, NJ, USA
| | | | - Esat Adiguzel
- Department of Neuroscience, Graduate School of Health Sciences, Pamukkale University, Denizli, Turkey
- Department of Anatomy, School of Medicine, Pamukkale University, Denizli, Turkey
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14
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Refaeli R, Kreisel T, Groysman M, Adamsky A, Goshen I. Engram stability and maturation during systems consolidation. Curr Biol 2023; 33:3942-3950.e3. [PMID: 37586373 PMCID: PMC10524918 DOI: 10.1016/j.cub.2023.07.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/27/2023] [Accepted: 07/20/2023] [Indexed: 08/18/2023]
Abstract
Remote memories play an important role in how we perceive the world, and they are rooted throughout the brain in "engrams": ensembles of cells that are formed during acquisition. Upon their reactivation, a specific memory can be recalled.1,2,3,4,5,6,7,8,9,10,11,12 Many studies have focused on the ensembles in CA1 of the hippocampus and the anterior cingulate cortex (ACC). However, the evolution of these components during systems' consolidation has not yet been comprehensively addressed.13,14,15,16 By applying transgenic approaches for ensemble identification, CLARITY, retro-AAV, and pseudo-rabies virus for circuit mapping, and chemogenetics for functional interrogation, we addressed the dynamics of recent and remote CA1 ensembles. We expected both stability (as they represent the same memory) and maturation (over time). Indeed, we found that CA1 engrams remain stable between recent and remote recalls, and the inhibition of engrams for recent recall during remote recall functionally impairs memory. We also found that new cells in the remote recall engram in the CA1 are not added randomly during maturation but differ according to their connections. First, we show in two ways that the anterograde CA1 → ACC engram cell projection grows larger. Finally, in the retrograde projections, the ACC reduces input to CA1 engram cells, whereas input from the entorhinal cortex and paraventricular nucleus of the thalamus increases. Our results shine fresh light on systems' consolidation by providing a deeper understanding of engram stability and maturation in the transition from recent to remote memory.
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Affiliation(s)
- Ron Refaeli
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tirzah Kreisel
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Maya Groysman
- ELSC Vector Core Facility, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Adar Adamsky
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Inbal Goshen
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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15
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Zhang Y, Liu G, Li X, Gong H, Luo Q, Yang X. On-line clearing and staining method for the efficient optical imaging of large volume samples at the cellular resolution. BIOMEDICAL OPTICS EXPRESS 2023; 14:4800-4813. [PMID: 37791250 PMCID: PMC10545182 DOI: 10.1364/boe.499115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023]
Abstract
Optical microscopy is a powerful tool for exploring the structure and function of organisms. However, the three-dimensional (3D) imaging of large volume samples is time-consuming and difficult. In this manuscript, we described an on-line clearing and staining method for efficient imaging of large volume samples at the cellular resolution. The optimized cocktail can increase staining and imaging depth to reduce the sectioning and scanning time, more than doubling the operational efficiency of the system. Using this method, we demonstrated the rapid acquisition of Aβ plaques in whole mouse brain and obtained a complete set of cytoarchitecture images of an adult porcine hemisphere at 1.625 × 1.625 × 10 µm3 voxel resolution for about 49 hours.
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Affiliation(s)
- Yunfei Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guangcai Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215123, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215123, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215123, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan 430074, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, 215123, China
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16
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Yuan PQ, Li T, Million M, Larauche M, Atmani K, Bellier JP, Taché Y. New insight on the enteric cholinergic innervation of the pig colon by central and peripheral nervous systems: reduction by repeated loperamide administration. Front Neurosci 2023; 17:1204233. [PMID: 37650102 PMCID: PMC10463754 DOI: 10.3389/fnins.2023.1204233] [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: 04/11/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Introduction The central and peripheral nervous systems provide cholinergic innervation in the colon. The ability to assess their neuroanatomical distinctions is still a challenge. The pig is regarded as a relevant translational model due to the close similarity of its enteric nervous system (ENS) with that of human. Opioid-induced constipation is one of the most common side effects of opioid therapy. Methods We developed an approach to differentiate the central and peripheral cholinergic innervation of the pig colon using double immunolabeling with a novel mouse anti-human peripheral type of choline acetyltransferase (hpChAT) antibody combined with a rabbit anti-common type of ChAT (cChAT) antibody, a reliable marker of cholinergic neurons in the central nervous system. We examined their spatial configurations in 3D images of the ENS generated from CLARITY-cleared colonic segments. The density was quantitated computationally using Imaris 9.7. We assessed changes in the distal colon induced by daily oral treatment for 4 weeks with the μ opioid receptor agonist, loperamide (0.4 or 3 mg/kg). Results The double labeling showed strong cChAT immunoreactive (ir) fibers in the cervical vagus nerve and neuronal somata and fibers in the ventral horn of the sacral (S2) cord while hpChAT immunoreactivity was visualized only in the ENS but not in the vagus or sacral neural structures indicating the selectivity of these two antibodies. In the colonic myenteric plexus, dense hpChAT-ir neurons and fibers and varicose cChAT-ir fibers surrounding hpChAT-ir neurons were simultaneously visualized in 3D. The density of cChAT-ir varicose fibers in the outer submucosal plexus of both males and females were higher in the transverse and distal colon than in the proximal colon and in the myenteric plexus compared to the outer submucosal plexus and there was no cChAT innervation in the inner submucosal plexus. The density of hpChAT in the ENS showed no segmental or plexus differences in both sexes. Loperamide at the highest dose significantly decreased the density hpChAT-ir fibers + somata in the myenteric plexus of the distal colon. Discussion These data showed the distinct density of central cholinergic innervation between myenteric and submucosal plexuses among colonic segments and the localization of cChAT-ir fibers around peripheral hpChAT neurons in 3D. The reduction of cholinergic myenteric innervation by chronic opiate treatment points to target altered prokinetic cholinergic pathway to counteract opiate constipation.
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Affiliation(s)
- Pu-Qing Yuan
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
- VA GLAHS, Los Angeles, CA, United States
| | - Tao Li
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Mulugeta Million
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Muriel Larauche
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Karim Atmani
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Jean-Pierre Bellier
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Yvette Taché
- CURE/Digestive Diseases Research Center, Vatche and Tamar Manoukian Digestive Diseases Division, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
- VA GLAHS, Los Angeles, CA, United States
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17
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Wang J, Zhang T, Liao Y, Chen W, Liang S, Xu S, Fang H, Wang M, Zheng L, Gu Z, Zhang Z, Wang B, Bi Y, Feng W. 3D-imaging and quantitative assessment for size-related penetration of HfO 2 nanoparticles in breast cancer tumor by synchrotron radiation microcomputed tomography. Anal Chim Acta 2023; 1266:341352. [PMID: 37244662 DOI: 10.1016/j.aca.2023.341352] [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: 02/16/2023] [Revised: 04/22/2023] [Accepted: 05/09/2023] [Indexed: 05/29/2023]
Abstract
The development of quantitative analytical methods to assess the heterogeneous distribution and penetration of nanodrugs in solid tumors is of great importance for anticancer nanomedicine. Herein, Expectation-Maximization (EM) iterate algorithm and threshold segmentation methods were used to visualize and quantify the spatial distribution patterns, penetration depth and diffusion features of two-sized hafnium oxide nanoparticles (s-HfO2 NPs in 2 nm and l-HfO2 NPs in 50 nm sizes) in mouse models of breast cancer using synchrotron radiation micro-computed tomography (SR-μCT) imaging technique. The three-dimensional (3D) SR-μCT images were reconstructed based on the EM iterate algorithm thus clearly displayed the size-related penetration and distribution within the tumors after intra-tumoral injection of HfO2 NPs and X-ray irradiation treatment. The obtained 3D animations clearly show that a considerable amount of s-HfO2 and l-HfO2 NPs diffused into tumor tissues at 2 h post-injection and displayed the obvious increase in the tumor penetration and distribution area within the tumors at day 7 after combination with low-dose X-ray irradiation treatment. A thresholding segmentation for 3D SR-μCT image was developed to assess the penetration depth and quantity of HfO2 NPs along the injection sites in tumors. The developed 3D-imaging techniques revealed that the s-HfO2 NPs presented more homogeneous distribution pattern, diffused more quickly and penetrated more deeply within tumor tissues than the l-HfO2 NPs did. Whereas, the low-dose X-ray irradiation treatment greatly enhanced the wide distribution and deep penetration of both s-HfO2 and l-HfO2 NPs. This developed method may provide quantitative distribution and penetration information for the X-ray sensitive high-Z metal nanodrugs in the cancer imaging and therapy.
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Affiliation(s)
- Jiali Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, China; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Tingfeng Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - You Liao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shanshan Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Si Xu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, China; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingna Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhanjun Gu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiyong Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yi Bi
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, China.
| | - Weiyue Feng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
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18
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Rosen G, Kirsch D, Horowitz S, Cherry JD, Nicks R, Kelley H, Uretsky M, Dell'Aquila K, Mathias R, Cormier KA, Kubilus CA, Mez J, Tripodis Y, Stein TD, Alvarez VE, Alosco ML, McKee AC, Huber BR. Three dimensional evaluation of cerebrovascular density and branching in chronic traumatic encephalopathy. Acta Neuropathol Commun 2023; 11:123. [PMID: 37491342 PMCID: PMC10369801 DOI: 10.1186/s40478-023-01612-y] [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: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/27/2023] Open
Abstract
Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with exposure to repetitive head impacts (RHI) and characterized by perivascular accumulations of hyperphosphorylated tau protein (p-tau) at the depths of the cortical sulci. Studies of living athletes exposed to RHI, including concussive and nonconcussive impacts, have shown increased blood-brain barrier permeability, reduced cerebral blood flow, and alterations in vasoreactivity. Blood-brain barrier abnormalities have also been reported in individuals neuropathologically diagnosed with CTE. To further investigate the three-dimensional microvascular changes in individuals diagnosed with CTE and controls, we used SHIELD tissue processing and passive delipidation to optically clear and label blocks of postmortem human dorsolateral frontal cortex. We used fluorescent confocal microscopy to quantitate vascular branch density and fraction volume. We compared the findings in 41 male brain donors, age at death 31-89 years, mean age 64 years, including 12 donors with low CTE (McKee stage I-II), 13 with high CTE (McKee stage III-IV) to 16 age- and sex-matched non-CTE controls (7 with RHI exposure and 9 with no RHI exposure). The density of vessel branches in the gray matter sulcus was significantly greater in CTE cases than in controls. The ratios of sulcus versus gyrus vessel branch density and fraction volume were also greater in CTE than in controls and significantly above one for the CTE group. Hyperphosphorylated tau pathology density correlated with gray matter sulcus fraction volume. These findings point towards increased vascular coverage and branching in the dorsolateral frontal cortex (DLF) sulci in CTE, that correlates with p-tau pathology.
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Affiliation(s)
- Grace Rosen
- VA Boston Healthcare System, US Department of Veterans Affairs, 150 S Huntington Avenue, Boston, MA, 02130, USA
- National Center for PTSD, US Department of Veterans Affairs, Boston, MA, USA
| | - Daniel Kirsch
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Sarah Horowitz
- VA Boston Healthcare System, US Department of Veterans Affairs, 150 S Huntington Avenue, Boston, MA, 02130, USA
- National Center for PTSD, US Department of Veterans Affairs, Boston, MA, USA
| | - Jonathan D Cherry
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
| | - Raymond Nicks
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
| | - Hunter Kelley
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
| | - Madeline Uretsky
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
| | - Kevin Dell'Aquila
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
| | - Rebecca Mathias
- VA Boston Healthcare System, US Department of Veterans Affairs, 150 S Huntington Avenue, Boston, MA, 02130, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Kerry A Cormier
- VA Boston Healthcare System, US Department of Veterans Affairs, 150 S Huntington Avenue, Boston, MA, 02130, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
- VA Bedford Healthcare System, US Department of Veterans Affairs, Bedford, MA, USA
| | - Caroline A Kubilus
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
- VA Bedford Healthcare System, US Department of Veterans Affairs, Bedford, MA, USA
| | - Jesse Mez
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
| | - Yorghos Tripodis
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, USA
| | - Thor D Stein
- VA Boston Healthcare System, US Department of Veterans Affairs, 150 S Huntington Avenue, Boston, MA, 02130, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
| | - Victor E Alvarez
- VA Boston Healthcare System, US Department of Veterans Affairs, 150 S Huntington Avenue, Boston, MA, 02130, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
| | - Michael L Alosco
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
| | - Ann C McKee
- VA Boston Healthcare System, US Department of Veterans Affairs, 150 S Huntington Avenue, Boston, MA, 02130, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA
- VA Bedford Healthcare System, US Department of Veterans Affairs, Bedford, MA, USA
| | - Bertrand R Huber
- VA Boston Healthcare System, US Department of Veterans Affairs, 150 S Huntington Avenue, Boston, MA, 02130, USA.
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, USA.
- Boston University Alzheimer's Disease Research Center and Boston University CTE Center, Boston, USA.
- National Center for PTSD, US Department of Veterans Affairs, Boston, MA, USA.
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19
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Edlow BL, Olchanyi M, Freeman HJ, Li J, Maffei C, Snider SB, Zöllei L, Iglesias JE, Augustinack J, Bodien YG, Haynes RL, Greve DN, Diamond BR, Stevens A, Giacino JT, Destrieux C, van der Kouwe A, Brown EN, Folkerth RD, Fischl B, Kinney HC. Sustaining wakefulness: Brainstem connectivity in human consciousness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548265. [PMID: 37502983 PMCID: PMC10369992 DOI: 10.1101/2023.07.13.548265] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Consciousness is comprised of arousal (i.e., wakefulness) and awareness. Substantial progress has been made in mapping the cortical networks that modulate awareness in the human brain, but knowledge about the subcortical networks that sustain arousal is lacking. We integrated data from ex vivo diffusion MRI, immunohistochemistry, and in vivo 7 Tesla functional MRI to map the connectivity of a subcortical arousal network that we postulate sustains wakefulness in the resting, conscious human brain, analogous to the cortical default mode network (DMN) that is believed to sustain self-awareness. We identified nodes of the proposed default ascending arousal network (dAAN) in the brainstem, hypothalamus, thalamus, and basal forebrain by correlating ex vivo diffusion MRI with immunohistochemistry in three human brain specimens from neurologically normal individuals scanned at 600-750 μm resolution. We performed deterministic and probabilistic tractography analyses of the diffusion MRI data to map dAAN intra-network connections and dAAN-DMN internetwork connections. Using a newly developed network-based autopsy of the human brain that integrates ex vivo MRI and histopathology, we identified projection, association, and commissural pathways linking dAAN nodes with one another and with cortical DMN nodes, providing a structural architecture for the integration of arousal and awareness in human consciousness. We release the ex vivo diffusion MRI data, corresponding immunohistochemistry data, network-based autopsy methods, and a new brainstem dAAN atlas to support efforts to map the connectivity of human consciousness.
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Affiliation(s)
- Brian L. Edlow
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Mark Olchanyi
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Holly J. Freeman
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Jian Li
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Chiara Maffei
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Samuel B. Snider
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lilla Zöllei
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - J. Eugenio Iglesias
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Jean Augustinack
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Yelena G. Bodien
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital and Harvard Medical School, Charlestown, MA 02129 USA
| | - Robin L. Haynes
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Douglas N. Greve
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Bram R. Diamond
- Center for Neurotechnology and Neurorecovery, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Allison Stevens
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Joseph T. Giacino
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital and Harvard Medical School, Charlestown, MA 02129 USA
| | - Christophe Destrieux
- UMR 1253, iBrain, Université de Tours, Inserm, 10 Boulevard Tonnellé, 37032, Tours, France
- CHRU de Tours, 2 Boulevard Tonnellé, Tours, France
| | - Andre van der Kouwe
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
| | - Emery N. Brown
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Bruce Fischl
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown MA 02129, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannah C. Kinney
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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20
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Georgiadis M, Menzel M, Reuter JA, Born DE, Kovacevich SR, Alvarez D, Taghavi HM, Schroeter A, Rudin M, Gao Z, Guizar-Sicairos M, Weiss TM, Axer M, Rajkovic I, Zeineh MM. Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering. Acta Biomater 2023; 164:317-331. [PMID: 37098400 PMCID: PMC10811447 DOI: 10.1016/j.actbio.2023.04.029] [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: 11/28/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/27/2023]
Abstract
Myelinated axons (nerve fibers) efficiently transmit signals throughout the brain via action potentials. Multiple methods that are sensitive to axon orientations, from microscopy to magnetic resonance imaging, aim to reconstruct the brain's structural connectome. As billions of nerve fibers traverse the brain with various possible geometries at each point, resolving fiber crossings is necessary to generate accurate structural connectivity maps. However, doing so with specificity is a challenging task because signals originating from oriented fibers can be influenced by brain (micro)structures unrelated to myelinated axons. X-ray scattering can specifically probe myelinated axons due to the periodicity of the myelin sheath, which yields distinct peaks in the scattering pattern. Here, we show that small-angle X-ray scattering (SAXS) can be used to detect myelinated, axon-specific fiber crossings. We first demonstrate the capability using strips of human corpus callosum to create artificial double- and triple-crossing fiber geometries, and we then apply the method in mouse, pig, vervet monkey, and human brains. We compare results to polarized light imaging (3D-PLI), tracer experiments, and to outputs from diffusion MRI that sometimes fails to detect crossings. Given its specificity, capability of 3-dimensional sampling and high resolution, SAXS could serve as a ground truth for validating fiber orientations derived using diffusion MRI as well as microscopy-based methods. STATEMENT OF SIGNIFICANCE: To study how the nerve fibers in our brain are interconnected, scientists need to visualize their trajectories, which often cross one another. Here, we show the unique capacity of small-angle X-ray scattering (SAXS) to study these fiber crossings without use of labeling, taking advantage of SAXS's specificity to myelin - the insulating sheath that is wrapped around nerve fibers. We use SAXS to detect double and triple crossing fibers and unveil intricate crossings in mouse, pig, vervet monkey, and human brains. This non-destructive method can uncover complex fiber trajectories and validate other less specific imaging methods (e.g., MRI or microscopy), towards accurate mapping of neuronal connectivity in the animal and human brain.
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Affiliation(s)
- Marios Georgiadis
- Department of Radiology, Stanford School of Medicine, Stanford, CA, USA; Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland.
| | - Miriam Menzel
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich 52425, Germany; Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
| | - Jan A Reuter
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Donald E Born
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | | | - Dario Alvarez
- Department of Radiology, Stanford School of Medicine, Stanford, CA, USA
| | | | - Aileen Schroeter
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Markus Rudin
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Zirui Gao
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | | | - Thomas M Weiss
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, USA
| | - Markus Axer
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Ivan Rajkovic
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, USA
| | - Michael M Zeineh
- Department of Radiology, Stanford School of Medicine, Stanford, CA, USA
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21
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Hsiao FT, Chien HJ, Chou YH, Peng SJ, Chung MH, Huang TH, Lo LW, Shen CN, Chang HP, Lee CY, Chen CC, Jeng YM, Tien YW, Tang SC. Transparent tissue in solid state for solvent-free and antifade 3D imaging. Nat Commun 2023; 14:3395. [PMID: 37296117 PMCID: PMC10256715 DOI: 10.1038/s41467-023-39082-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Optical clearing with high-refractive-index (high-n) reagents is essential for 3D tissue imaging. However, the current liquid-based clearing condition and dye environment suffer from solvent evaporation and photobleaching, causing difficulties in maintaining the tissue optical and fluorescent features. Here, using the Gladstone-Dale equation [(n-1)/density=constant] as a design concept, we develop a solid (solvent-free) high-n acrylamide-based copolymer to embed mouse and human tissues for clearing and imaging. In the solid state, the fluorescent dye-labeled tissue matrices are filled and packed with the high-n copolymer, minimizing scattering in in-depth imaging and dye fading. This transparent, liquid-free condition provides a friendly tissue and cellular environment to facilitate high/super-resolution 3D imaging, preservation, transfer, and sharing among laboratories to investigate the morphologies of interest in experimental and clinical conditions.
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Affiliation(s)
- Fu-Ting Hsiao
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Hung-Jen Chien
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ya-Hsien Chou
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Shih-Jung Peng
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Mei-Hsin Chung
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Pathology, National Taiwan University Hospital-Hsinchu Branch, Hsinchu, Taiwan
| | - Tzu-Hui Huang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
| | - Li-Wen Lo
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Ning Shen
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Pi Chang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Yuan Lee
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Chia Chen
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yung-Ming Jeng
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Wen Tien
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Shiue-Cheng Tang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan.
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan.
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
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22
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Manubens-Gil L, Zhou Z, Chen H, Ramanathan A, Liu X, Liu Y, Bria A, Gillette T, Ruan Z, Yang J, Radojević M, Zhao T, Cheng L, Qu L, Liu S, Bouchard KE, Gu L, Cai W, Ji S, Roysam B, Wang CW, Yu H, Sironi A, Iascone DM, Zhou J, Bas E, Conde-Sousa E, Aguiar P, Li X, Li Y, Nanda S, Wang Y, Muresan L, Fua P, Ye B, He HY, Staiger JF, Peter M, Cox DN, Simonneau M, Oberlaender M, Jefferis G, Ito K, Gonzalez-Bellido P, Kim J, Rubel E, Cline HT, Zeng H, Nern A, Chiang AS, Yao J, Roskams J, Livesey R, Stevens J, Liu T, Dang C, Guo Y, Zhong N, Tourassi G, Hill S, Hawrylycz M, Koch C, Meijering E, Ascoli GA, Peng H. BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets. Nat Methods 2023; 20:824-835. [PMID: 37069271 DOI: 10.1038/s41592-023-01848-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 03/14/2023] [Indexed: 04/19/2023]
Abstract
BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.
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Affiliation(s)
- Linus Manubens-Gil
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Zhi Zhou
- Microsoft Corporation, Redmond, WA, USA
| | | | - Arvind Ramanathan
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, IL, USA
| | | | - Yufeng Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | | | - Todd Gillette
- Center for Neural Informatics, Structures and Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Zongcai Ruan
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Jian Yang
- Faculty of Information Technology, Beijing University of Technology, Beijing, China
- Beijing International Collaboration Base on Brain Informatics and Wisdom Services, Beijing, China
| | | | - Ting Zhao
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Li Cheng
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Lei Qu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing, Anhui University, Hefei, China
| | | | - Kristofer E Bouchard
- Scientific Data Division and Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
- Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience, UC Berkeley, Berkeley, CA, USA
| | - Lin Gu
- RIKEN AIP, Tokyo, Japan
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo, Japan
| | - Weidong Cai
- School of Computer Science, University of Sydney, Sydney, New South Wales, Australia
| | - Shuiwang Ji
- Texas A&M University, College Station, TX, USA
| | - Badrinath Roysam
- Cullen College of Engineering, University of Houston, Houston, TX, USA
| | - Ching-Wei Wang
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Hongchuan Yu
- National Centre for Computer Animation, Bournemouth University, Poole, UK
| | | | - Daniel Maxim Iascone
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Jie Zhou
- Department of Computer Science, Northern Illinois University, DeKalb, IL, USA
| | | | - Eduardo Conde-Sousa
- i3S, Instituto de Investigação E Inovação Em Saúde, Universidade Do Porto, Porto, Portugal
- INEB, Instituto de Engenharia Biomédica, Universidade Do Porto, Porto, Portugal
| | - Paulo Aguiar
- i3S, Instituto de Investigação E Inovação Em Saúde, Universidade Do Porto, Porto, Portugal
| | - Xiang Li
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yujie Li
- Allen Institute for Brain Science, Seattle, WA, USA
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA
| | - Sumit Nanda
- Center for Neural Informatics, Structures and Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Yuan Wang
- Program in Neuroscience, Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA
| | - Leila Muresan
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, UK
| | - Pascal Fua
- Computer Vision Laboratory, EPFL, Lausanne, Switzerland
| | - Bing Ye
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Hai-Yan He
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center Göttingen, Georg-August- University Göttingen, Goettingen, Germany
| | - Manuel Peter
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Daniel N Cox
- Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - Michel Simonneau
- 42 ENS Paris-Saclay, CNRS, CentraleSupélec, LuMIn, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Marcel Oberlaender
- Max Planck Group: In Silico Brain Sciences, Max Planck Institute for Neurobiology of Behavior - caesar, Bonn, Germany
| | - Gregory Jefferis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Kei Ito
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Institute for Quantitative Biosciences, University of Tokyo, Tokyo, Japan
- Institute of Zoology, Biocenter Cologne, University of Cologne, Cologne, Germany
| | | | - Jinhyun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea
| | - Edwin Rubel
- Virginia Merrill Bloedel Hearing Research Center, University of Washington, Seattle, WA, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Aljoscha Nern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Ann-Shyn Chiang
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Jane Roskams
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Zoology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rick Livesey
- Zayed Centre for Rare Disease Research, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Janine Stevens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Tianming Liu
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA
| | - Chinh Dang
- Virginia Merrill Bloedel Hearing Research Center, University of Washington, Seattle, WA, USA
| | - Yike Guo
- Data Science Institute, Imperial College London, London, UK
| | - Ning Zhong
- Faculty of Information Technology, Beijing University of Technology, Beijing, China
- Beijing International Collaboration Base on Brain Informatics and Wisdom Services, Beijing, China
- Department of Life Science and Informatics, Maebashi Institute of Technology, Maebashi, Japan
| | | | - Sean Hill
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Erik Meijering
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia.
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures and Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA.
| | - Hanchuan Peng
- Institute for Brain and Intelligence, Southeast University, Nanjing, China.
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23
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Wang K, Yu Y, Xu Y, Yue Y, Zhao F, Feng W, Duan Y, Duan W, Yue J, Liao Z, Fei P, Sun H, Xiong B. TSA-PACT: a method for tissue clearing and immunofluorescence staining on zebrafish brain with improved sensitivity, specificity and stability. Cell Biosci 2023; 13:97. [PMID: 37237300 DOI: 10.1186/s13578-023-01043-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
For comprehensive studies of the brain structure and function, fluorescence imaging of the whole brain is essential. It requires large-scale volumetric imaging in cellular or molecular resolution, which could be quite challenging. Recent advances in tissue clearing technology (e.g. CLARITY, PACT) provide new solutions by homogenizing the refractive index of the samples to create transparency. However, it has been difficult to acquire high quality results through immunofluorescence (IF) staining on the cleared samples. To address this issue, we developed TSA-PACT, a method combining tyramide signal amplification (TSA) and PACT, to transform samples into hydrogel polymerization frameworks with covalent fluorescent biomarkers assembled. We show that TSA-PACT is able to reduce the opacity of the zebrafish brain by more than 90% with well-preserved structure. Compared to traditional method, TSA-PACT achieves approximately tenfold signal amplification and twofold improvement in signal-to-noise ratio (SNR). Moreover, both the structure and the fluorescent signal persist for at least 16 months with excellent signal retention ratio. Overall, this method improves immunofluorescence signal sensitivity, specificity and stability in the whole brain of juvenile and adult zebrafish, which is applicable for fine structural analysis, neural circuit mapping and three-dimensional cell counting.
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Affiliation(s)
- Kang Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yuxin Yu
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yinhui Xu
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yingzi Yue
- Key Laboratory of Environment and Health (HUST), Ministry of Education, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fang Zhao
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wenyang Feng
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yijie Duan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Weicheng Duan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jingjing Yue
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhiyun Liao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Peng Fei
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
- MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hui Sun
- Department of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Bo Xiong
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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24
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Ma G, Worthy KH, Liu C, Rosa MG, Atapour N. Parvalbumin as a neurochemical marker of the primate optic radiation. iScience 2023; 26:106608. [PMID: 37168578 PMCID: PMC10165026 DOI: 10.1016/j.isci.2023.106608] [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: 12/23/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 05/13/2023] Open
Abstract
Parvalbumin (PV) is a calcium-binding protein that labels neuronal cell bodies in the magno and parvocellular layers of the primate lateral geniculate nucleus (LGN). Here we demonstrate that PV immunohistochemistry can also be used to trace the optic radiation (OR) of the marmoset monkey (Callithrix jacchus) from its LGN origin to its destinations in the primary visual cortex (V1), thus providing a high-resolution method for identification of the OR with single axon resolution. The emergence of fibers from LGN, their entire course and even the entry points to V1 were clearly defined in coronal, parasagittal, and horizontal sections of marmoset brain. In all cases, the trajectory revealed by PV staining paralleled that defined by high-resolution diffusion tensor imaging (DTI). We found that V1 was the exclusive target for the PV-containing fibers, with abrupt transitions in staining observed in the white matter at the border with area V2, and no evidence of PV-labeled axons feeding into other visual areas. Changes in the pattern of PV staining in the OR were detected following V1 lesions, demonstrating that this method can be used to assess the progress of retrograde degeneration of geniculocortical projections. These results suggest a technically simple approach to advance our understanding of a major white matter structure, which provides a cellular resolution suitable for the detection of microstructural variations during development, health and disease. Understanding the relationship between PV staining and DTI in non-human primates may also offer clues for improving the specificity and sensitivity of OR tractography for clinical purposes.
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Affiliation(s)
- Gaoyuan Ma
- Neuroscience Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Katrina H. Worthy
- Neuroscience Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Cirong Liu
- Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, Chinese Academy of Sciences, Shanghai, China
| | - Marcello G.P. Rosa
- Neuroscience Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Nafiseh Atapour
- Neuroscience Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, VIC 3800, Australia
- Corresponding author
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25
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Guo J, Chen L, Xiong F, Zhang Y, Wang R, Zhang X, Wen Q, Gao S, Zhang Y. Bidirectional near-infrared regulation of motor behavior using orthogonal emissive upconversion nanoparticles. NANOSCALE 2023; 15:7845-7853. [PMID: 37057392 DOI: 10.1039/d3nr00009e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bidirectional optogenetic manipulation enables specific neural function dissection and animal behaviour regulation with high spatial-temporal resolution. It relies on the respective activation of two or more visible-light responsive optogenetic sensors, which inevitably induce signal crosstalk due to their spectral overlap, low photoactivation efficiency and potentially high biotoxicity. Herein, a strategy that combines dual-NIR-excited orthogonal emissive upconversion nanoparticles (OUCNPs) with a single dual-colour sensor, BiPOLES, is demonstrated to achieve bidirectional, crosstalk-free NIR manipulation of motor behaviour in vivo. Core@shell-structured OUCNPs with Tm3+ and Er3+ dopants in isolated layers exhibit orthogonal blue and red emissions in response to excitation at 808 and 980 nm, respectively. The OUCNPs subsequently activate BiPOLES-expressing excitatory cholinergic motor neurons in C. elegans, leading to significant inhibition and excitation of motor neurons and body bends, respectively. Importantly, these OUCNPs exhibit negligible toxicity toward neural development, motor function and reproduction. Such an OUCNP-BiPOLES system not only greatly facilitates independent, bidirectional NIR activation of a specific neuronal population and functional dissection, but also greatly simplifies the bidirectional NIR optogenetics toolset, thus endowing it with great potential for flexible upconversion optogenetic manipulation.
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Affiliation(s)
- Jingxuan Guo
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lili Chen
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Feihong Xiong
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yongning Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Ruipeng Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Xuefei Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Quan Wen
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shangbang Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Yan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
- National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China
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26
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Von Roemeling CA, Doonan BP, Klippel K, Schultz D, Hoang-Minh L, Trivedi V, Li C, Russell RA, Kanumuri RS, Sharma A, Tun HW, Mitchell DA. Oral IRAK-4 Inhibitor CA-4948 Is Blood-Brain Barrier Penetrant and Has Single-Agent Activity against CNS Lymphoma and Melanoma Brain Metastases. Clin Cancer Res 2023; 29:1751-1762. [PMID: 36749885 PMCID: PMC10150246 DOI: 10.1158/1078-0432.ccr-22-1682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/19/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
PURPOSE An ongoing challenge in cancer is the management of primary and metastatic brain malignancies. This is partly due to restrictions of the blood-brain barrier and their unique microenvironment. These challenges are most evident in cancers such as lymphoma and melanoma, which are typically responsive to treatment in systemic locations but resistant when established in the brain. We propose interleukin-1 receptor-associated kinase-4 (IRAK-4) as a potential target across these diseases and describe the activity and mechanism of oral IRAK-4 inhibitor CA-4948. EXPERIMENTAL DESIGN Human primary central nervous system lymphoma (PCNSL) and melanoma brain metastases (MBM) samples were analyzed for expression of IRAK-4 and downstream transcription pathways. We next determined the central nervous system (CNS) applicability of CA-4948 in naïve and tumor-bearing mice using models of PCNSL and MBM. The mechanistic effect on tumors and the tumor microenvironment was then analyzed. RESULTS Human PCNSL and MBM have high expression of IRAK-4, IRAK-1, and nuclear factor kappa B (NF-κB). This increase in inflammation results in reflexive inhibitory signaling. Similar profiles are observed in immunocompetent murine models. Treatment of tumor-bearing animals with CA-4948 results in the downregulation of mitogen-activated protein kinase (MAPK) signaling in addition to decreased NF-κB. These intracellular changes are associated with a survival advantage. CONCLUSIONS IRAK-4 is an attractive target in PCNSL and MBM. The inhibition of IRAK-4 with CA-4948 downregulates the expression of important transcription factors involved in tumor growth and proliferation. CA-4948 is currently being investigated in clinical trials for relapsed and refractory lymphoma and warrants further translation into PCNSL and MBM.
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Affiliation(s)
- Christina A. Von Roemeling
- Lillian S. Wells Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, Florida
| | - Bently P. Doonan
- Lillian S. Wells Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, Florida
- Department of Medicine, Hematology and Oncology, University of Florida, Gainesville, Florida
| | - Kelena Klippel
- Lillian S. Wells Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, Florida
| | - Daniel Schultz
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida
| | - Lan Hoang-Minh
- Lillian S. Wells Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, Florida
| | - Vrunda Trivedi
- Lillian S. Wells Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, Florida
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida
| | - Rylynn A. Russell
- Lillian S. Wells Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, Florida
| | - Raju S. Kanumuri
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida
- Translational Drug Development Core, Clinical and Translational Science Institute, University of Florida, Gainesville, Florida
| | - Abhisheak Sharma
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida
- Translational Drug Development Core, Clinical and Translational Science Institute, University of Florida, Gainesville, Florida
| | - Han W. Tun
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, Florida
| | - Duane A. Mitchell
- Lillian S. Wells Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, Florida
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27
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Cai Y, Zhang X, Li C, Ghashghaei HT, Greenbaum A. COMBINe enables automated detection and classification of neurons and astrocytes in tissue-cleared mouse brains. CELL REPORTS METHODS 2023; 3:100454. [PMID: 37159668 PMCID: PMC10163164 DOI: 10.1016/j.crmeth.2023.100454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/28/2023] [Accepted: 03/23/2023] [Indexed: 05/11/2023]
Abstract
Tissue clearing renders entire organs transparent to accelerate whole-tissue imaging; for example, with light-sheet fluorescence microscopy. Yet, challenges remain in analyzing the large resulting 3D datasets that consist of terabytes of images and information on millions of labeled cells. Previous work has established pipelines for automated analysis of tissue-cleared mouse brains, but the focus there was on single-color channels and/or detection of nuclear localized signals in relatively low-resolution images. Here, we present an automated workflow (COMBINe, Cell detectiOn in Mouse BraIN) to map sparsely labeled neurons and astrocytes in genetically distinct mouse forebrains using mosaic analysis with double markers (MADM). COMBINe blends modules from multiple pipelines with RetinaNet at its core. We quantitatively analyzed the regional and subregional effects of MADM-based deletion of the epidermal growth factor receptor (EGFR) on neuronal and astrocyte populations in the mouse forebrain.
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Affiliation(s)
- Yuheng Cai
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - Xuying Zhang
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Chen Li
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - H. Troy Ghashghaei
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Alon Greenbaum
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
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28
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Xu Y, Zhang J, Lee HW, Zhang G, Bai Y, Simons M. High-resolution visualization of pial surface vessels by flattened whole mount staining. iScience 2023; 26:106467. [PMID: 37020957 PMCID: PMC10067958 DOI: 10.1016/j.isci.2023.106467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 12/06/2022] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
Understanding development of the cerebral vasculature is essential for the central nervous system (CNS) research and therapeutic developments. Here, we developed a simple, convenient, and fast method-the flattened cortex whole mount (FCWM) technique-for imaging of pial cerebral vessels. FCWM involves dissection of the whole cerebral cortex followed by flattening, sectioning and application of CLARITY technology. Compared to conventional methods, FCWM offers several advantages including (1) high-resolution visualization of the whole cortex pial surface vessel structures and distributions; (2) precise localization of a particular blood vessel, allowing observations of a desired blood vessel during normal development or in disease settings; (3) compatibility with confocal imaging. Application of FCWM for examination of cerebral vasculature during postnatal development or in stroke settings allowed us to demonstrate that cerebral blood vessels manifest type-specific maturation and remodeling which are linked to the rate of endothelial proliferation.
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Affiliation(s)
- Yanying Xu
- Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Jiasheng Zhang
- Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
| | - Heon-Woo Lee
- Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
| | - Guogang Zhang
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yongping Bai
- Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Michael Simons
- Yale Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
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29
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Laurino A, Franceschini A, Pesce L, Cinci L, Montalbano A, Mazzamuto G, Sancataldo G, Nesi G, Costantini I, Silvestri L, Pavone FS. A Guide to Perform 3D Histology of Biological Tissues with Fluorescence Microscopy. Int J Mol Sci 2023; 24:ijms24076747. [PMID: 37047724 PMCID: PMC10094801 DOI: 10.3390/ijms24076747] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2023] Open
Abstract
The analysis of histological alterations in all types of tissue is of primary importance in pathology for highly accurate and robust diagnosis. Recent advances in tissue clearing and fluorescence microscopy made the study of the anatomy of biological tissue possible in three dimensions. The combination of these techniques with classical hematoxylin and eosin (H&E) staining has led to the birth of three-dimensional (3D) histology. Here, we present an overview of the state-of-the-art methods, highlighting the optimal combinations of different clearing methods and advanced fluorescence microscopy techniques for the investigation of all types of biological tissues. We employed fluorescence nuclear and eosin Y staining that enabled us to obtain hematoxylin and eosin pseudo-coloring comparable with the gold standard H&E analysis. The computational reconstructions obtained with 3D optical imaging can be analyzed by a pathologist without any specific training in volumetric microscopy, paving the way for new biomedical applications in clinical pathology.
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Affiliation(s)
- Annunziatina Laurino
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
| | - Alessandra Franceschini
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
| | - Luca Pesce
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
| | - Lorenzo Cinci
- Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit n. 2, Careggi University Hospital, 50134 Florence, Italy
| | - Alberto Montalbano
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Neurofarba Section of Pharmacology and Toxicology, University of Florence, 50139 Florence, Italy
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
- National Research Council—National Institute of Optics (CNR-INO), 50125 Sesto Fiorentino, Italy
| | - Giuseppe Sancataldo
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
| | - Gabriella Nesi
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
| | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- National Research Council—National Institute of Optics (CNR-INO), 50125 Sesto Fiorentino, Italy
- Department of Biology, University of Florence, 50019 Florence, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
- National Research Council—National Institute of Optics (CNR-INO), 50125 Sesto Fiorentino, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, 50019 Florence, Italy
- National Research Council—National Institute of Optics (CNR-INO), 50125 Sesto Fiorentino, Italy
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30
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Liu Z, He B, Wang X, Peng J, Sun Q, Luo C. Deep cortical microinfarction induced by femtosecond laser in mice: Long-term secondary pathological changes in corresponding superficial cortex. Neurosci Lett 2023; 802:137170. [PMID: 36898650 DOI: 10.1016/j.neulet.2023.137170] [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: 01/08/2023] [Revised: 02/19/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND AND PURPOSE Previous studies have explored the clinical consequences of cortical microinfarction, mainly age-related cognitive decline. However, functional impairment of deep cortical microinfarction remains poorly understood. Based on anatomical knowledge and previous research, we infer that damage to the deep cortex may lead to cognitive deficits and communication impairment between the superficial cortex and thalamus. This study aimed to develop a new model of deep cortical microinfarction based on femtosecond laser ablation of a perforating artery. METHODS Twenty-eight mice were anesthetized with isoflurane, and a cranial window was thinned using a microdrill. Intensively focused femtosecond laser pulses were used to produce perforating arteriolar occlusions and ischemic brain damage was examined using histological analysis. RESULTS Occlusion of different perforating arteries induced different types of cortical microinfarctions. Blocking the perforating artery, which enters the cerebral cortex vertically and has no branches within 300 μm below, can result in deep cortical microinfarction. Moreover, this model showed neuronal loss and microglial activation in the lesions as well as dysplasia of nerve fibers and β-amyloid deposition in the corresponding superficial cortex. CONCLUSIONS We present here a new model of deep cortical microinfarction in mice, in which specific perforating arteries are selectively occluded by a femtosecond laser, and we preliminarily observe several long-term effects related to cognition. This animal model is helpful in investigating the pathophysiology of deep cerebral microinfarction. However, further clinical and experimental studies are required to explore deep cortical microinfarctions in greater molecular and physiological detail.
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Affiliation(s)
- Zhoujing Liu
- Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, No. 628 Zhenyuan Road, Shenzhen 518017, China
| | - Baixuan He
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, No. 107 Yan Jiang West Road, Guangzhou 510120, China
| | - Xuemin Wang
- Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, No. 628 Zhenyuan Road, Shenzhen 518017, China
| | - Jiamin Peng
- Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, No. 628 Zhenyuan Road, Shenzhen 518017, China
| | - Qiaosong Sun
- Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, No. 628 Zhenyuan Road, Shenzhen 518017, China.
| | - Chuanming Luo
- Department of Neurology, The Seventh Affiliated Hospital, Sun Yat-Sen University, No. 628 Zhenyuan Road, Shenzhen 518017, China.
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31
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Lu Y, Zhu Y, Zhao X, Pan M, He H. An optical system for noninvasive microscopy of psoriatic mice in vivo. JOURNAL OF BIOPHOTONICS 2023; 16:e202200310. [PMID: 36519190 DOI: 10.1002/jbio.202200310] [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: 10/11/2022] [Revised: 11/10/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Psoriasis is a chronic inflammatory skin disease involved with both complex morphological changes of skin and immune processes. The clinical diagnostics and research of psoriasis often require invasive biopsy which lacks their real-time dynamics in vivo. Here we report a noninvasive microscopic system developed by combining in vivo fluorescent microscopy, optical clearing, and immunolabeling to enable real-time imaging of immune cells and cytokines in blood flow in psoriatic animal models. The vascular morphology and time-lapse kinetics of interleukin (IL)-23, IL-17, tumor necrosis factor-α, and CD4+ cells in blood are captured at submicron resolution through the thickening epidermis and opaque scales during the development of psoriasis in vivo. Our data suggest IL-23 recruits CD4+ cells to release IL-17 in blood that further leaks out in the psoriatic skin area. This optical system enables noninvasive and real-time assessment of immune molecules and cells in vivo, providing good potential for medical researches on psoriasis.
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Affiliation(s)
- Yiting Lu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yujie Zhu
- Department of Dermatology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Dermatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaohui Zhao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Pan
- Department of Dermatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao He
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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32
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Sorelli M, Costantini I, Bocchi L, Axer M, Pavone FS, Mazzamuto G. Fiber enhancement and 3D orientation analysis in label-free two-photon fluorescence microscopy. Sci Rep 2023; 13:4160. [PMID: 36914673 PMCID: PMC10011555 DOI: 10.1038/s41598-023-30953-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/03/2023] [Indexed: 03/16/2023] Open
Abstract
Fluorescence microscopy can be exploited for evaluating the brain's fiber architecture with unsurpassed spatial resolution in combination with different tissue preparation and staining protocols. Differently from state-of-the-art polarimetry-based neuroimaging modalities, the quantification of fiber tract orientations from fluorescence microscopy volume images entails the application of specific image processing techniques, such as Fourier or structure tensor analysis. These, however, may lead to unreliable outcomes as they do not isolate myelinated fibers from the surrounding tissue. In this work, we describe a novel image processing pipeline that enables the computation of accurate 3D fiber orientation maps from both grey and white matter regions, exploiting the selective multiscale enhancement of tubular structures of varying diameters provided by a 3D implementation of the Frangi filter. The developed software tool can efficiently generate orientation distribution function maps at arbitrary spatial scales which may support the histological validation of modern diffusion-weighted magnetic resonance imaging tractography. Despite being tested here on two-photon scanning fluorescence microscopy images, acquired from tissue samples treated with a label-free technique enhancing the autofluorescence of myelinated fibers, the presented pipeline was developed to be employed on all types of 3D fluorescence images and fiber staining.
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Affiliation(s)
- Michele Sorelli
- Department of Physics and Astronomy, University of Florence, 50019, Sesto Fiorentino, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, Italy
| | - Irene Costantini
- European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, Italy. .,Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy. .,National Research Council, National Institute of Optics (CNR-INO), 50019, Sesto Fiorentino, Italy.
| | - Leonardo Bocchi
- Department of Information Engineering, University of Florence, 50039, Florence, Italy
| | - Markus Axer
- Research Centre Jülich, Institute of Neuroscience and Medicine, 52428, Jülich, Germany
| | - Francesco Saverio Pavone
- Department of Physics and Astronomy, University of Florence, 50019, Sesto Fiorentino, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, Italy.,National Research Council, National Institute of Optics (CNR-INO), 50019, Sesto Fiorentino, Italy
| | - Giacomo Mazzamuto
- Department of Physics and Astronomy, University of Florence, 50019, Sesto Fiorentino, Italy.,European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, Italy.,National Research Council, National Institute of Optics (CNR-INO), 50019, Sesto Fiorentino, Italy
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33
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Directionality quantification of in vitro grown dorsal root ganglion neurites using Fast Fourier Transform. J Neurosci Methods 2023; 386:109796. [PMID: 36652975 DOI: 10.1016/j.jneumeth.2023.109796] [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: 09/21/2022] [Revised: 12/22/2022] [Accepted: 01/13/2023] [Indexed: 01/16/2023]
Abstract
BACKGROUND The directionality analysis of the neurite outgrowths is an important methodology in neuroscience, especially in determining the behavior of neurons grown on silicon substrates. NEW METHOD Here we aimed to describe the methodology for quantification of the directionality of neurites based on the Fast Fourier Transform (FFT). We performed an image analysis case study that incorporates several software solutions and provides a rapid and precise technique to determine the directionality of neurites. In order to elicit aligned or unaligned neurite growth patterns, we used adult and newborn dorsal root ganglion (DRG) neurons grown on silicon micro-pillar substrates (MPS) with different pillar widths and spacing. RESULTS Compared to the control glass surfaces the neonatal and adult N52 and IB4 DRG neurites exhibited regular growth patterns more pronounced in the MPS regions with s narrow pillar spacing range. The neurites were preferentially oriented along three directional axes at 30°, 90°, and 150°. CONCLUSION The proposed methodology showed that FFT analysis is a reliable and easily reproducible method that can be successfully used to test growth patterns of DRG neurites grown on different substrates by considering the direction and angle of the neurites as well as the size of the soma.
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34
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Urata S, Okabe S. Three-dimensional mouse cochlea imaging based on the modified Sca/eS using confocal microscopy. Anat Sci Int 2023:10.1007/s12565-023-00703-z. [PMID: 36773194 DOI: 10.1007/s12565-023-00703-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/13/2023] [Indexed: 02/12/2023]
Abstract
The three-dimensional stria vascularis (SV) and cochlear blood vessel structure is essential for inner ear function. Here, modified Sca/eS, a sorbitol-based optical-clearing method, was reported to visualize SV and vascular structure in the intact mouse cochlea. Cochlear macrophages as well as perivascular-resident macrophage-like melanocytes were detected as GFP-positive cells of the CX3CR1+/GFP mice. This study's method was effective in elucidating inner ear function under both physiological and pathological conditions.
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Affiliation(s)
- Shinji Urata
- Department of Otolaryngology, Graduate School of Medicine, University of Tokyo, Tokyo, 113-0033, Japan.
| | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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35
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Rakhilin N, Yang B, Spilker ME, Manzuk LK, Montgomery MK, Shin E, Prashad N, Hwang J, Song Y, Loganzo F, Giddabasappa A, Ram S. Volumetric imaging of optically cleared and fluorescently labeled animal tissue (VIOLA) for quantifying the 3D biodistribution of nanoparticles at cellular resolution in tumor tissue. J Control Release 2023; 354:244-259. [PMID: 36596340 DOI: 10.1016/j.jconrel.2022.12.060] [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: 09/23/2022] [Revised: 12/17/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Nanoparticle (NP) technology holds significant promise to mediate targeted drug delivery to specific organs in the body. Understanding the 3D biodistribution of NPs in heterogeneous environments such as the tumor tissue can provide crucial information on efficacy, safety and potential clinical outcomes. Here we present a novel end-to-end workflow, VIOLA, which makes use of tissue clearing methodology in conjunction with high resolution imaging and advanced 3D image processing to quantify the spatiotemporal 3D biodistribution of fluorescently labeled ACCURIN® NPs. Specifically, we investigate the spatiotemporal biodistribution of NPs in three different murine tumor models (CT26, EMT6, and KPC-GEM) of increasing complexity and translational relevance. We have developed new endpoints to characterize NP biodistribution at multiple length scales. Our observations reveal that the macroscale NP biodistribution is spatially heterogeneous and exhibits a gradient with relatively high accumulation at the tumor periphery that progressively decreases towards the tumor core in all the tumor models. Microscale analysis revealed that NP extravasation from blood vessels increases in a time dependent manner and plateaus at 72 h post injection. Volumetric analysis and pharmacokinetic modeling of NP biodistribution in the vicinity of the blood vessels revealed that the local NP density exhibits a distance dependent spatiotemporal biodistribution which provide insights into the dynamics of NP extravasation in the tumor tissue. Our data represents a comprehensive analysis of NP biodistribution at multiple length scales in different tumor models providing unique insights into their spatiotemporal dynamics. Specifically, our results show that NPs exhibit a dynamic equilibrium with macroscale heterogeneity combined with microscale homogeneity.
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Affiliation(s)
| | - Bing Yang
- Comparative Medicine, Pfizer Inc., United States
| | - Mary E Spilker
- Medicine Design - Translational Modeling and Simulation, Pfizer Inc., United States
| | | | | | - Eyoung Shin
- Oncology Research Unit, Pfizer Inc., United States
| | | | | | - Youngho Song
- Oncology Research Unit, Pfizer Inc., United States
| | | | | | - Sripad Ram
- Drug Safety R&D, Pfizer Inc., United States.
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36
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Zhan YJ, Zhang SW, Zhu S, Jiang N. Tissue Clearing and Its Application in the Musculoskeletal System. ACS OMEGA 2023; 8:1739-1758. [PMID: 36687066 PMCID: PMC9850472 DOI: 10.1021/acsomega.2c05180] [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: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The musculoskeletal system is an integral part of the human body. Currently, most skeletal muscle research is conducted through conventional histological sections due to technological limitations and the structure of skeletal muscles. For studying and observing bones and muscles, there is an urgent need for three-dimensional, objective imaging technologies. Optical tissue-clearing technologies seem to offer a novel and accessible approach to research of the musculoskeletal system. Using this approach, the components which cause refraction or prevent light from penetrating into the tissue are physically and chemically eliminated; then the liquid in the tissue is replaced with high-refractive-index chemicals. This innovative method, which allows three-dimensional reconstruction at the cellular and subcellular scale, significantly improves imaging depth and resolution. Nonetheless, this technology was not originally developed to image bones or muscles. When compared with brain and nerve organs which have attracted considerable attention in this field, the musculoskeletal system contains fewer lipids and has high levels of hemoglobin, collagen fibers, and inorganic hydroxyapatite crystals. Currently, three-dimensional imaging methods are widely used in the diagnosis and treatment of skeletal and muscular illnesses. In this regard, it is vitally important to review and evaluate the optical tissue-clearing technologies currently employed in the musculoskeletal system, so that researchers may make an informed decision. In the meantime, this study offers guidelines and recommendations for expanding the use of this technology in the musculoskeletal system.
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Affiliation(s)
- Yan-Jing Zhan
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Shi-Wen Zhang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - SongSong Zhu
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Nan Jiang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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37
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Shi J, Hu Y, Shao G, Zhu Y, Zhao Z, Xu Y, Zhang Z, Wu H. Quantifying Podocyte Number in a Small Sample Size of Glomeruli with CUBIC to Evaluate Podocyte Depletion of db/db Mice. J Diabetes Res 2023; 2023:1901105. [PMID: 36776229 PMCID: PMC9908347 DOI: 10.1155/2023/1901105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023] Open
Abstract
The loss of podocyte is crucial for diagnosis and prognosis of diabetic kidney disease, whereas commonly two-dimensional methods for quantifying podocyte number existed with issues of low fidelity and accuracy. In this study, clear, unobstructed brain imaging cocktails and computational analysis (CUBIC), one of three-dimensional optical clearing approaches, was used which combines tissue clearing, immunolabeling, and a light-sheet microscope to image and evaluate podocytes in C57BL/6 (C57) and db/db mice. We discovered that 77 podocytes per glomerulus were in C57 mice. On the subject of db/db mice, there were 74 podocytes by the age of 8 w, 72 podocytes by the age of 12 w, and 66 podocytes by the age of 16 w, compared with 76 podocytes in the control group, suggesting that there was a significant decrease in podocyte number in db/db mice with the age of 16 w, showing a trend which positively correlated to the deterioration of kidney function. Sample size estimation using the PASS software revealed that taking 5%, 7.5%, and 10% of the mean podocyte number per glomerulus as the statistical allowable error and 95% as total confidence interval, 33, 15, and 9 glomeruli were independently needed to be sampled in C57 mice to represent the overall glomeruli to calculate podocyte number. Furthermore, in the control group of db/db mice, 36, 18, and 11 glomeruli were needed, compared with 46, 24, and 14 glomeruli in db/db mice by the age of 8 w, 43, 21, and 12 glomeruli by the age of 12 w, and 52, 27, and 16 by the age of 16 w. These findings indicated that precise quantification of podocyte number could judge the progression of diabetic kidney disease. In addition, a small number of glomeruli could be actually representative of the whole sample size, which indicated apparent practicability of CUBIC for clinical use.
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Affiliation(s)
- Jiaoyu Shi
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yuan Hu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guangze Shao
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yixiang Zhu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education, NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Zhonghua Zhao
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yanyong Xu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Pathology of School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Frontier Innovation Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zhigang Zhang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Huijuan Wu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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38
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Karthikeyan S, Kim K, Asakura Y, Verma M, Asakura A. Three-Dimensional Imaging Analysis for Skeletal Muscle. Methods Mol Biol 2023; 2640:463-477. [PMID: 36995614 DOI: 10.1007/978-1-0716-3036-5_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Skeletal muscle is a highly ordered tissue composed of a complex network of a diverse variety of cells. The dynamic spatial and temporal interaction between these cells during homeostasis and during times of injury gives the skeletal muscle its regenerative capacity. In order to properly understand the process of regeneration, a three-dimensional (3-D) imaging process must be conducted. While there have been several protocols studying 3-D imaging, it has primarily been focused on the nervous system. This protocol aims to outline the workflow for rendering a 3-D image of the skeletal muscle using spatial data from confocal microscope images. This protocol uses the ImageJ, Ilastik, and Imaris software for 3-D rendering and computational image analysis as both are relatively easy to use and have powerful segmentation capabilities.
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Affiliation(s)
- Smrithi Karthikeyan
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Kyutae Kim
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Yoko Asakura
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mayank Verma
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Atsushi Asakura
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA.
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39
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Lovely AM, Duerr TJ, Stein DF, Mun ET, Monaghan JR. Hybridization Chain Reaction Fluorescence In Situ Hybridization (HCR-FISH) in Ambystoma mexicanum Tissue. Methods Mol Biol 2023; 2562:109-122. [PMID: 36272070 PMCID: PMC10949069 DOI: 10.1007/978-1-0716-2659-7_6] [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] [Indexed: 02/12/2023]
Abstract
In situ hybridization is a standard procedure for visualizing mRNA transcripts in tissues. The recent adoption of fluorescent probes and new signal amplification methods have facilitated multiplexed RNA imaging in tissue sections and whole tissues. Here we present protocols for multiplexed hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) staining, imaging, cell segmentation, and mRNA quantification in regenerating axolotl tissue sections. We also present a protocol for whole-mount staining and imaging of developing axolotl limbs.
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Affiliation(s)
- Alex M Lovely
- Department of Biology, Northeastern University, Boston, MA, USA
- Northeastern University, Institute for Chemical Imaging of Living Systems, Boston, MA, USA
| | - Timothy J Duerr
- Department of Biology, Northeastern University, Boston, MA, USA
| | - David F Stein
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Evan T Mun
- Department of Biology, Northeastern University, Boston, MA, USA
| | - James R Monaghan
- Department of Biology, Northeastern University, Boston, MA, USA.
- Northeastern University, Institute for Chemical Imaging of Living Systems, Boston, MA, USA.
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40
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Karthikeyan S, Asakura Y, Verma M, Asakura A. Tissue Clearing and Confocal Microscopic Imaging for Skeletal Muscle. Methods Mol Biol 2023; 2640:453-462. [PMID: 36995613 DOI: 10.1007/978-1-0716-3036-5_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Skeletal muscle is a highly ordered tissue composed of a complex network of a diverse variety of cells. The dynamic spatial and temporal interaction between these cells during homeostasis and during times of injury gives the skeletal muscle its regenerative capacity. To properly understand the process of regeneration, a three-dimensional (3-D) imaging process must be conducted. With the advancement of imaging and computing technology, it has become powerful to analyze spatial data from confocal microscope images. In order to prepare whole tissue skeletal muscle samples for confocal imaging, the muscle must be subjected to tissue clearing. With the use of an ideal optical clearing protocol - one that minimizes light scattering via refractive index mismatching - a more accurate 3-D image of the muscle can be produced as it does not involve the physical sectioning of the muscle. While there have been several protocols relating to the study of 3-D biology in whole tissue, these protocols have primarily been focused on the nervous system. In this chapter, we present a new method for skeletal muscle tissue clearing. In addition, this protocol aims to outline the specific parameters required for taking 3-D images of immunofluorescence-stained skeletal muscle samples using a confocal microscope.
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Affiliation(s)
- Smrithi Karthikeyan
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Yoko Asakura
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mayank Verma
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Atsushi Asakura
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA.
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41
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Terstege DJ, Epp JR. Network Neuroscience Untethered: Brain-Wide Immediate Early Gene Expression for the Analysis of Functional Connectivity in Freely Behaving Animals. BIOLOGY 2022; 12:biology12010034. [PMID: 36671727 PMCID: PMC9855808 DOI: 10.3390/biology12010034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
Abstract
Studying how spatially discrete neuroanatomical regions across the brain interact is critical to advancing our understanding of the brain. Traditional neuroimaging techniques have led to many important discoveries about the nature of these interactions, termed functional connectivity. However, in animal models these traditional neuroimaging techniques have generally been limited to anesthetized or head-fixed setups or examination of small subsets of neuroanatomical regions. Using the brain-wide expression density of immediate early genes (IEG), we can assess brain-wide functional connectivity underlying a wide variety of behavioural tasks in freely behaving animal models. Here, we provide an overview of the necessary steps required to perform IEG-based analyses of functional connectivity. We also outline important considerations when designing such experiments and demonstrate the implications of these considerations using an IEG-based network dataset generated for the purpose of this review.
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42
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Macrophage NFATC2 mediates angiogenic signaling during mycobacterial infection. Cell Rep 2022; 41:111817. [PMID: 36516756 PMCID: PMC9880963 DOI: 10.1016/j.celrep.2022.111817] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/05/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
During mycobacterial infections, pathogenic mycobacteria manipulate both host immune and stromal cells to establish and maintain a productive infection. In humans, non-human primates, and zebrafish models of infection, pathogenic mycobacteria produce and modify the specialized lipid trehalose 6,6'-dimycolate (TDM) in the bacterial cell envelope to drive host angiogenesis toward the site of forming granulomas, leading to enhanced bacterial growth. Here, we use the zebrafish-Mycobacterium marinum infection model to define the signaling basis of the host angiogenic response. Through intravital imaging and cell-restricted peptide-mediated inhibition, we identify macrophage-specific activation of NFAT signaling as essential to TDM-mediated angiogenesis in vivo. Exposure of cultured human cells to Mycobacterium tuberculosis results in robust induction of VEGFA, which is dependent on a signaling pathway downstream of host TDM detection and culminates in NFATC2 activation. As granuloma-associated angiogenesis is known to serve bacterial-beneficial roles, these findings identify potential host targets to improve tuberculosis disease outcomes.
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43
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Anderson MA, Squair JW, Gautier M, Hutson TH, Kathe C, Barraud Q, Bloch J, Courtine G. Natural and targeted circuit reorganization after spinal cord injury. Nat Neurosci 2022; 25:1584-1596. [PMID: 36396975 DOI: 10.1038/s41593-022-01196-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/05/2022] [Indexed: 11/18/2022]
Abstract
A spinal cord injury disrupts communication between the brain and the circuits in the spinal cord that regulate neurological functions. The consequences are permanent paralysis, loss of sensation and debilitating dysautonomia. However, the majority of circuits located above and below the injury remain anatomically intact, and these circuits can reorganize naturally to improve function. In addition, various neuromodulation therapies have tapped into these processes to further augment recovery. Emerging research is illuminating the requirements to reconstitute damaged circuits. Here, we summarize these natural and targeted reorganizations of circuits after a spinal cord injury. We also advocate for new concepts of reorganizing circuits informed by multi-omic single-cell atlases of recovery from injury. These atlases will uncover the molecular logic that governs the selection of 'recovery-organizing' neuronal subpopulations, and are poised to herald a new era in spinal cord medicine.
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Affiliation(s)
- Mark A Anderson
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.,Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.,Defitech Center for Interventional Neurotherapies (NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland.,Wyss Center for Bio and Neuroengineering, Geneva, Switzerland
| | - Jordan W Squair
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.,Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.,Defitech Center for Interventional Neurotherapies (NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland
| | - Matthieu Gautier
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.,Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.,Defitech Center for Interventional Neurotherapies (NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland
| | - Thomas H Hutson
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.,Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.,Defitech Center for Interventional Neurotherapies (NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland.,Wyss Center for Bio and Neuroengineering, Geneva, Switzerland
| | - Claudia Kathe
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.,Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.,Defitech Center for Interventional Neurotherapies (NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland
| | - Quentin Barraud
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.,Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.,Defitech Center for Interventional Neurotherapies (NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland
| | - Jocelyne Bloch
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.,Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.,Defitech Center for Interventional Neurotherapies (NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland
| | - Grégoire Courtine
- NeuroX Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland. .,Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland. .,Defitech Center for Interventional Neurotherapies (NeuroRestore), EPFL/CHUV/UNIL, Lausanne, Switzerland.
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44
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Abdellah M, Cantero JJG, Guerrero NR, Foni A, Coggan JS, Calì C, Agus M, Zisis E, Keller D, Hadwiger M, Magistretti PJ, Markram H, Schürmann F. Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience. Brief Bioinform 2022; 24:6847753. [PMID: 36434788 PMCID: PMC9851302 DOI: 10.1093/bib/bbac491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/27/2022] [Accepted: 10/14/2022] [Indexed: 11/27/2022] Open
Abstract
Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) and even multicellular scales of resolution (e.g. cerebral vasculature and minicolumns). Resulting models are exported as triangulated surface meshes and annotated volumes for multiple applications in in silico neuroscience, allowing scalable supercomputer simulations that can unravel intricate cellular structure-function relationships. Ultraliser implements a high-performance and unconditionally robust voxelization engine adapted to create optimized watertight surface meshes and annotated voxel grids from arbitrary non-watertight triangular soups, digitized morphological skeletons or binary volumetric masks. The framework represents a major leap forward in simulation-based neuroscience, making it possible to employ high-resolution 3D structural models for quantification of surface areas and volumes, which are of the utmost importance for cellular and system simulations. The power of Ultraliser is demonstrated with several use cases in which hundreds of models are created for potential application in diverse types of simulations. Ultraliser is publicly released under the GNU GPL3 license on GitHub (BlueBrain/Ultraliser). SIGNIFICANCE There is crystal clear evidence on the impact of cell shape on its signaling mechanisms. Structural models can therefore be insightful to realize the function; the more realistic the structure can be, the further we get insights into the function. Creating realistic structural models from existing ones is challenging, particularly when needed for detailed subcellular simulations. We present Ultraliser, a neuroscience-dedicated framework capable of building these structural models with realistic and detailed cellular geometries that can be used for simulations.
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Affiliation(s)
- Marwan Abdellah
- Corresponding authors. Marwan Abdellah, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail: ; Felix Schürmann, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail:
| | | | - Nadir Román Guerrero
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Alessandro Foni
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Jay S Coggan
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Corrado Calì
- Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia,Neuroscience Institute Cavalieri Ottolenghi (NICO) Orbassano, Italy,Department of Neuroscience, University of Torino Torino, Italy
| | - Marco Agus
- Visual Computing Center King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia,College of Science and Engineering Hamad Bin Khalifa University Doha, Qatar
| | - Eleftherios Zisis
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Daniel Keller
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Markus Hadwiger
- Visual Computing Center King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia
| | - Pierre J Magistretti
- Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal, Saudi Arabia
| | - Henry Markram
- Blue Brain Project (BBP) École Polytecnique Fédérale de Lausanne (EPFL) Geneva, Switzerland
| | - Felix Schürmann
- Corresponding authors. Marwan Abdellah, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail: ; Felix Schürmann, Blue Brain Project (BBP), École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland. E-mail:
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45
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Kathe C, Skinnider MA, Hutson TH, Regazzi N, Gautier M, Demesmaeker R, Komi S, Ceto S, James ND, Cho N, Baud L, Galan K, Matson KJE, Rowald A, Kim K, Wang R, Minassian K, Prior JO, Asboth L, Barraud Q, Lacour SP, Levine AJ, Wagner F, Bloch J, Squair JW, Courtine G. The neurons that restore walking after paralysis. Nature 2022; 611:540-547. [DOI: 10.1038/s41586-022-05385-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 09/23/2022] [Indexed: 11/10/2022]
Abstract
AbstractA spinal cord injury interrupts pathways from the brain and brainstem that project to the lumbar spinal cord, leading to paralysis. Here we show that spatiotemporal epidural electrical stimulation (EES) of the lumbar spinal cord1–3 applied during neurorehabilitation4,5 (EESREHAB) restored walking in nine individuals with chronic spinal cord injury. This recovery involved a reduction in neuronal activity in the lumbar spinal cord of humans during walking. We hypothesized that this unexpected reduction reflects activity-dependent selection of specific neuronal subpopulations that become essential for a patient to walk after spinal cord injury. To identify these putative neurons, we modelled the technological and therapeutic features underlying EESREHAB in mice. We applied single-nucleus RNA sequencing6–9 and spatial transcriptomics10,11 to the spinal cords of these mice to chart a spatially resolved molecular atlas of recovery from paralysis. We then employed cell type12,13 and spatial prioritization to identify the neurons involved in the recovery of walking. A single population of excitatory interneurons nested within intermediate laminae emerged. Although these neurons are not required for walking before spinal cord injury, we demonstrate that they are essential for the recovery of walking with EES following spinal cord injury. Augmenting the activity of these neurons phenocopied the recovery of walking enabled by EESREHAB, whereas ablating them prevented the recovery of walking that occurs spontaneously after moderate spinal cord injury. We thus identified a recovery-organizing neuronal subpopulation that is necessary and sufficient to regain walking after paralysis. Moreover, our methodology establishes a framework for using molecular cartography to identify the neurons that produce complex behaviours.
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46
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Wells G, Glasgow JN, Nargan K, Lumamba K, Madansein R, Maharaj K, Perumal LY, Matthew M, Hunter RL, Pacl H, Peabody Lever JE, Stanford DD, Singh SP, Bajpai P, Manne U, Benson PV, Rowe SM, le Roux S, Sigal A, Tshibalanganda M, Wells C, du Plessis A, Msimang M, Naidoo T, Steyn AJC. A high-resolution 3D atlas of the spectrum of tuberculous and COVID-19 lung lesions. EMBO Mol Med 2022; 14:e16283. [PMID: 36285507 PMCID: PMC9641421 DOI: 10.15252/emmm.202216283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 02/01/2023] Open
Abstract
Our current understanding of the spectrum of TB and COVID-19 lesions in the human lung is limited by a reliance on low-resolution imaging platforms that cannot provide accurate 3D representations of lesion types within the context of the whole lung. To characterize TB and COVID-19 lesions in 3D, we applied micro/nanocomputed tomography to surgically resected, postmortem, and paraffin-embedded human lung tissue. We define a spectrum of TB pathologies, including cavitary lesions, calcium deposits outside and inside necrotic granulomas and mycetomas, and vascular rearrangement. We identified an unusual spatial arrangement of vasculature within an entire COVID-19 lobe, and 3D segmentation of blood vessels revealed microangiopathy associated with hemorrhage. Notably, segmentation of pathological anomalies reveals hidden pathological structures that might otherwise be disregarded, demonstrating a powerful method to visualize pathologies in 3D in TB lung tissue and whole COVID-19 lobes. These findings provide unexpected new insight into the spatial organization of the spectrum of TB and COVID-19 lesions within the framework of the entire lung.
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Affiliation(s)
- Gordon Wells
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Joel N Glasgow
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Kievershen Nargan
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Kapongo Lumamba
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Rajhmun Madansein
- Inkosi Albert Luthuli Central Hospital and University of KwaZulu‐NatalDurbanSouth Africa
| | - Kameel Maharaj
- Inkosi Albert Luthuli Central Hospital and University of KwaZulu‐NatalDurbanSouth Africa
| | - Leon Y Perumal
- Perumal & Partners RadiologistsAhmed Al‐Kadi Private HospitalDurbanSouth Africa
| | - Malcolm Matthew
- Perumal & Partners RadiologistsAhmed Al‐Kadi Private HospitalDurbanSouth Africa
| | - Robert L Hunter
- Department of Pathology and Laboratory MedicineUniversity of Texas Health Sciences Center at HoustonHoustonTXUSA
| | - Hayden Pacl
- Medical Scientist Training ProgramUniversity of Alabama at BirminghamBirminghamALUSA
| | | | - Denise D Stanford
- Department of MedicineUniversity of Alabama at BirminghamBirminghamALUSA
- Cystic Fibrosis Research CenterUniversity of Alabama at BirminghamBirminghamALUSA
| | - Satinder P Singh
- Department of MedicineUniversity of Alabama at BirminghamBirminghamALUSA
- Department of RadiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Prachi Bajpai
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Upender Manne
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Paul V Benson
- Department of PathologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Steven M Rowe
- Department of MedicineUniversity of Alabama at BirminghamBirminghamALUSA
- Cystic Fibrosis Research CenterUniversity of Alabama at BirminghamBirminghamALUSA
| | | | - Alex Sigal
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Muofhe Tshibalanganda
- Research Group 3D Innovation, Physics DepartmentStellenbosch UniversityStellenboschSouth Africa
| | - Carlyn Wells
- CT Scanner Facility, Central Analytical FacilitiesStellenbosch UniversityStellenboschSouth Africa
| | - Anton du Plessis
- Research Group 3D Innovation, Physics DepartmentStellenbosch UniversityStellenboschSouth Africa
- Object Research SystemsMontrealQCCanada
| | - Mpumelelo Msimang
- Department of Anatomical Pathology, National Health Laboratory ServiceInkosi Albert Luthuli Central HospitalDurbanSouth Africa
| | - Threnesan Naidoo
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
- Department of Anatomical Pathology, National Health Laboratory ServiceInkosi Albert Luthuli Central HospitalDurbanSouth Africa
- Department of Laboratory Medicine & PathologyWalter Sisulu UniversityEastern CapeSouth Africa
| | - Adrie J C Steyn
- Africa Health Research InstituteUniversity of KwaZulu‐NatalDurbanSouth Africa
- Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamALUSA
- Centers for AIDS Research and Free Radical BiologyUniversity of Alabama at BirminghamBirminghamALUSA
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47
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Lee JH, Liu Q, Dadgar-Kiani E. Solving brain circuit function and dysfunction with computational modeling and optogenetic fMRI. Science 2022; 378:493-499. [PMID: 36327349 PMCID: PMC10543742 DOI: 10.1126/science.abq3868] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Can we construct a model of brain function that enables an understanding of whole-brain circuit mechanisms underlying neurological disease and use it to predict the outcome of therapeutic interventions? How are pathologies in neurological disease, some of which are observed to have spatial spreading mechanisms, associated with circuits and brain function? In this review, we discuss approaches that have been used to date and future directions that can be explored to answer these questions. By combining optogenetic functional magnetic resonance imaging (fMRI) with computational modeling, cell type-specific, large-scale brain circuit function and dysfunction are beginning to be quantitatively parameterized. We envision that these developments will pave the path for future therapeutics developments based on a systems engineering approach aimed at directly restoring brain function.
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Affiliation(s)
- Jin Hyung Lee
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
- Department of Electrical Engineering, Stanford University, CA 94305, USA
| | - Qin Liu
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Ehsan Dadgar-Kiani
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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48
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Hsu CW, Cerda J, Kirk JM, Turner WD, Rasmussen TL, Flores Suarez CP, Dickinson ME, Wythe JD. EZ Clear for simple, rapid, and robust mouse whole organ clearing. eLife 2022; 11:e77419. [PMID: 36218247 PMCID: PMC9555867 DOI: 10.7554/elife.77419] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Tissue clearing for whole organ cell profiling has revolutionized biology and imaging for exploration of organs in three-dimensional space without compromising tissue architecture. But complicated, laborious procedures, or expensive equipment, as well as the use of hazardous, organic solvents prevent the widespread adoption of these methods. Here, we report a simple and rapid tissue clearing method, EZ Clear, that can clear whole adult mouse organs in 48 hr in just three simple steps. Samples stay at room temperature and remain hydrated throughout the clearing process, preserving endogenous and synthetic fluorescence, without altering sample size. After wholemount clearing and imaging, samples processed with EZ Clear can be subjected to downstream applications, such as tissue embedding and cryosectioning followed by standard histology or immunofluorescent staining without loss of fluorescence signal from endogenous or synthetic reporters. Furthermore, we demonstrate that wholemount adult mouse brains processed with EZ Clear can be successfully immunolabeled for fluorescent imaging while still retaining signal from endogenous fluorescent reporters. Overall, the simplicity, speed, and flexibility of EZ Clear make it easy to adapt and implement in diverse imaging modalities in biomedical research.
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Affiliation(s)
- Chih-Wei Hsu
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
- Optical Imaging and Vital Microscopy Core, Advance Technology Cores, Baylor College of MedicineHoustonUnited States
- Department of Education, Innovation and Technology, Baylor College of MedicineHoustonUnited States
- Cardiovascular Research Institute, Baylor College of MedicineHoustonUnited States
| | - Juan Cerda
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
| | - Jason M Kirk
- Optical Imaging and Vital Microscopy Core, Advance Technology Cores, Baylor College of MedicineHoustonUnited States
| | - Williamson D Turner
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
| | - Tara L Rasmussen
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
- Cardiovascular Research Institute, Baylor College of MedicineHoustonUnited States
| | | | - Mary E Dickinson
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
- Optical Imaging and Vital Microscopy Core, Advance Technology Cores, Baylor College of MedicineHoustonUnited States
- Cardiovascular Research Institute, Baylor College of MedicineHoustonUnited States
| | - Joshua D Wythe
- Department of Integrative Physiology, Baylor College of MedicineHoustonUnited States
- Cardiovascular Research Institute, Baylor College of MedicineHoustonUnited States
- Department of Neurosurgery, Baylor College of MedicineHoustonUnited States
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49
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Bissardon C, Mermet X, Quintard C, Sanjuan F, Fouillet Y, Bottausci F, Carriere M, Rivera F, Blandin P. Selective plane illumination microscope dedicated to volumetric imaging in microfluidic chambers. BIOMEDICAL OPTICS EXPRESS 2022; 13:5261-5274. [PMID: 36425641 PMCID: PMC9664896 DOI: 10.1364/boe.455377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 05/31/2023]
Abstract
In this article, we are presenting an original selective plane illumination fluorescence microscope dedicated to image "Organ-on-chip"-like biostructures in microfluidic chips. In order to be able to morphologically analyze volumetric samples in development at the cellular scale inside microfluidic chambers, the setup presents a compromise between relatively large field of view (∼ 200 µm) and moderate resolution (∼ 5 µm). The microscope is based on a simple design, built around the chip and its microfluidic environment to allow 3D imaging inside the chip. In particular, the sample remains horizontally avoiding to disturb the fluidics phenomena. The experimental setup, its optical characterization and the first volumetric images are reported.
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Affiliation(s)
| | - Xavier Mermet
- Univ. Grenoble Alpes, CEA, LETI, DTBS, F-38000 Grenoble, France
| | | | - Federico Sanjuan
- Univ. de Pau et des Pays de l'Adour, E2S UPPA, CNRS, Total, LFCR, Pau, France
| | - Yves Fouillet
- Univ. Grenoble Alpes, CEA, LETI, DTBS, F-38000 Grenoble, France
| | | | - Marie Carriere
- Univ. Grenoble-Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France
| | - Florence Rivera
- Univ. Grenoble Alpes, CEA, LETI, DTBS, F-38000 Grenoble, France
| | - Pierre Blandin
- Univ. Grenoble Alpes, CEA, LETI, DTBS, F-38000 Grenoble, France
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50
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Himthani N, Brunn M, Kim JY, Schulte M, Mang A, Biros G. CLAIRE-Parallelized Diffeomorphic Image Registration for Large-Scale Biomedical Imaging Applications. J Imaging 2022; 8:jimaging8090251. [PMID: 36135416 PMCID: PMC9501197 DOI: 10.3390/jimaging8090251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
We study the performance of CLAIRE—a diffeomorphic multi-node, multi-GPU image-registration algorithm and software—in large-scale biomedical imaging applications with billions of voxels. At such resolutions, most existing software packages for diffeomorphic image registration are prohibitively expensive. As a result, practitioners first significantly downsample the original images and then register them using existing tools. Our main contribution is an extensive analysis of the impact of downsampling on registration performance. We study this impact by comparing full-resolution registrations obtained with CLAIRE to lower resolution registrations for synthetic and real-world imaging datasets. Our results suggest that registration at full resolution can yield a superior registration quality—but not always. For example, downsampling a synthetic image from 10243 to 2563 decreases the Dice coefficient from 92% to 79%. However, the differences are less pronounced for noisy or low contrast high resolution images. CLAIRE allows us not only to register images of clinically relevant size in a few seconds but also to register images at unprecedented resolution in reasonable time. The highest resolution considered are CLARITY images of size 2816×3016×1162. To the best of our knowledge, this is the first study on image registration quality at such resolutions.
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Affiliation(s)
- Naveen Himthani
- Oden Institute, The University of Texas at Austin, Austin, TX 78712, USA
- Correspondence:
| | - Malte Brunn
- Institute for Parallel and Distributed Systems, University of Stuttgart, 70569 Stuttgart, Germany
| | - Jae-Youn Kim
- Department of Mathematics, University of Houston, Houston, TX 77004, USA
| | - Miriam Schulte
- Institute for Parallel and Distributed Systems, University of Stuttgart, 70569 Stuttgart, Germany
| | - Andreas Mang
- Department of Mathematics, University of Houston, Houston, TX 77004, USA
| | - George Biros
- Oden Institute, The University of Texas at Austin, Austin, TX 78712, USA
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