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Gao P, Rivera M, Lin X, Holmes TC, Zhao H, Xu X. Immunolabeling-compatible PEGASOS tissue clearing for high-resolution whole mouse brain imaging. Front Neural Circuits 2024; 18:1345692. [PMID: 38694272 PMCID: PMC11061518 DOI: 10.3389/fncir.2024.1345692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 05/04/2024] Open
Abstract
Novel brain clearing methods revolutionize imaging by increasing visualization throughout the brain at high resolution. However, combining the standard tool of immunostaining targets of interest with clearing methods has lagged behind. We integrate whole-mount immunostaining with PEGASOS tissue clearing, referred to as iPEGASOS (immunostaining-compatible PEGASOS), to address the challenge of signal quenching during clearing processes. iPEGASOS effectively enhances molecular-genetically targeted fluorescent signals that are otherwise compromised during conventional clearing procedures. Additionally, we demonstrate the utility of iPEGASOS for visualizing neurochemical markers or viral labels to augment visualization that transgenic mouse lines cannot provide. Our study encompasses three distinct applications, each showcasing the versatility and efficacy of this approach. We employ whole-mount immunostaining to enhance molecular signals in transgenic reporter mouse lines to visualize the whole-brain spatial distribution of specific cellular populations. We also significantly improve the visualization of neural circuit connections by enhancing signals from viral tracers injected into the brain. Last, we show immunostaining without genetic markers to selectively label beta-amyloid deposits in a mouse model of Alzheimer's disease, facilitating the comprehensive whole-brain study of pathological features.
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Affiliation(s)
- Pan Gao
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Matthew Rivera
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Xiaoxiao Lin
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Todd C. Holmes
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, United States
- Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
| | - Hu Zhao
- Chinese Institute for Brain Research, Beijing, China
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, United States
- Center for Neural Circuit Mapping, University of California, Irvine, Irvine, CA, United States
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2
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Schroeder A, Pardi MB, Keijser J, Dalmay T, Groisman AI, Schuman EM, Sprekeler H, Letzkus JJ. Inhibitory top-down projections from zona incerta mediate neocortical memory. Neuron 2023; 111:727-738.e8. [PMID: 36610397 DOI: 10.1016/j.neuron.2022.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 10/19/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023]
Abstract
Top-down projections convey a family of signals encoding previous experiences and current aims to the sensory neocortex, where they converge with external bottom-up information to enable perception and memory. Whereas top-down control has been attributed to excitatory pathways, the existence, connectivity, and information content of inhibitory top-down projections remain elusive. Here, we combine synaptic two-photon calcium imaging, circuit mapping, cortex-dependent learning, and chemogenetics in mice to identify GABAergic afferents from the subthalamic zona incerta as a major source of top-down input to the neocortex. Incertocortical transmission undergoes robust plasticity during learning that improves information transfer and mediates behavioral memory. Unlike excitatory pathways, incertocortical afferents form a disinhibitory circuit that encodes learned top-down relevance in a bidirectional manner where the rapid appearance of negative responses serves as the main driver of changes in stimulus representation. Our results therefore reveal the distinctive contribution of long-range (dis)inhibitory afferents to the computational flexibility of neocortical circuits.
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Affiliation(s)
- Anna Schroeder
- Institute for Physiology, Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany; Max Planck Institute for Brain Research, 60438 Frankfurt, Germany.
| | - M Belén Pardi
- Institute for Physiology, Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany; Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, 75014 Paris, France
| | - Joram Keijser
- Modelling of Cognitive Processes, Institute of Software Engineering and Theoretical Computer Science, Technische Universität Berlin, 10587 Berlin, Germany; Charité - Universitätsmedizin Berlin, Einstein Center for Neurosciences Berlin, 10117 Berlin, Germany
| | - Tamas Dalmay
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Ayelén I Groisman
- Institute for Physiology, Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany
| | - Henning Sprekeler
- Modelling of Cognitive Processes, Institute of Software Engineering and Theoretical Computer Science, Technische Universität Berlin, 10587 Berlin, Germany; Bernstein Center for Computational Neuroscience Berlin, 10115 Berlin, Germany; Science of Intelligence, Research Cluster of Excellence, 10587 Berlin, Germany
| | - Johannes J Letzkus
- Institute for Physiology, Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany; Center for Basics in NeuroModulation (NeuroModul Basics), University of Freiburg, 79106 Freiburg, Germany; IMBIT//BrainLinks-BrainTools, University of Freiburg, 79110 Freiburg, Germany.
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3
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Patiño M, Lagos WN, Patne NS, Tasic B, Zeng H, Callaway EM. Single-cell transcriptomic classification of rabies-infected cortical neurons. Proc Natl Acad Sci U S A 2022; 119:e2203677119. [PMID: 35609197 DOI: 10.1073/pnas.2203677119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Cortical circuit tracing using modified rabies virus can identify input neurons making direct monosynaptic connections onto neurons of interest. However, challenges remain in our ability to establish the cell type identity of rabies-labeled input neurons. While transcriptomics may offer an avenue to characterize inputs, the extent of rabies-induced transcriptional changes in distinct neuronal cell types remains unclear, and whether these changes preclude characterization of rabies-infected neurons according to established transcriptomic cell types is unknown. We used single-nucleus RNA sequencing to survey the gene expression profiles of rabies-infected neurons and assessed their correspondence with established transcriptomic cell types. We demonstrated that when using transcriptome-wide RNA profiles, rabies-infected cortical neurons can be transcriptomically characterized despite global and cell-type-specific rabies-induced transcriptional changes. Notably, we found differential modulation of neuronal marker gene expression, suggesting that caution should be taken when attempting to characterize rabies-infected cells with single genes or small gene sets.
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Düring DN, Dittrich F, Rocha MD, Tachibana RO, Mori C, Okanoya K, Boehringer R, Ehret B, Grewe BF, Gerber S, Ma S, Rauch M, Paterna JC, Kasper R, Gahr M, Hahnloser RHR. Fast Retrograde Access to Projection Neuron Circuits Underlying Vocal Learning in Songbirds. Cell Rep 2020; 33:108364. [PMID: 33176132 PMCID: PMC8236207 DOI: 10.1016/j.celrep.2020.108364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/29/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
Understanding the structure and function of neural circuits underlying speech and language is a vital step toward better treatments for diseases of these systems. Songbirds, among the few animal orders that share with humans the ability to learn vocalizations from a conspecific, have provided many insights into the neural mechanisms of vocal development. However, research into vocal learning circuits has been hindered by a lack of tools for rapid genetic targeting of specific neuron populations to meet the quick pace of developmental learning. Here, we present a viral tool that enables fast and efficient retrograde access to projection neuron populations. In zebra finches, Bengalese finches, canaries, and mice, we demonstrate fast retrograde labeling of cortical or dopaminergic neurons. We further demonstrate the suitability of our construct for detailed morphological analysis, for in vivo imaging of calcium activity, and for multi-color brainbow labeling. Düring et al. describe a fast and efficient viral vector to dissect structure and function of neural circuits underlying learned vocalizations in songbirds. The AAV variant provides retrograde access to projection neuron circuits, including dopaminergic pathways in songbirds and additionally in mice, and allows for retrograde calcium imaging and multispectral brainbow labeling.
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Affiliation(s)
- Daniel N Düring
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland; Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.
| | - Falk Dittrich
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Mariana D Rocha
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | | | - Chihiro Mori
- Department of Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuo Okanoya
- Department of Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Roman Boehringer
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland
| | - Benjamin Ehret
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland
| | - Benjamin F Grewe
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland
| | - Stefan Gerber
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Shouwen Ma
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Melanie Rauch
- Viral Vector Facility, Neuroscience Center Zurich, Zurich, Switzerland
| | | | - Robert Kasper
- Imaging Facility at the Max Planck Institute of Neurobiology, Munich, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Richard H R Hahnloser
- Institute of Neuroinformatics, University of Zurich/ETH Zurich, Zurich, Switzerland; Neuroscience Center Zurich, Zurich, Switzerland
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Abstract
Canine adenovirus-2 (CAV) is a canine pathogen that has been used in a variety of applications, from vaccines against more infectious strains of CAV to treatments for neurological disorders. With recent engineering, CAV has become a natural choice for neuroscientists dissecting the connectivity and function of brain circuits. Specifically, as a reliable genetic vector with minimal immunogenic and cytotoxic reactivity, CAV has been used for the retrograde transduction of various types of projection neurons. Consequently, CAV is particularly useful when studying the anatomy and functions of long-range projections. Moreover, combining CAV with conditional expression and transsynaptic tracing results in the ability to study circuits with cell- and/or projection-type specificity. Lastly, with the well-documented knowledge of viral transduction, new innovations have been developed to increase the transduction efficiency of CAV and circumvent its tropism, expanding the potential of CAV for circuit analysis.
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Affiliation(s)
- Andréanne Lavoie
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Bao-Hua Liu
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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Lavin TK, Jin L, Lea NE, Wickersham IR. Monosynaptic Tracing Success Depends Critically on Helper Virus Concentrations. Front Synaptic Neurosci 2020; 12:6. [PMID: 32116642 PMCID: PMC7033752 DOI: 10.3389/fnsyn.2020.00006] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/23/2020] [Indexed: 11/13/2022] Open
Abstract
Monosynaptically-restricted transsynaptic tracing using deletion-mutant rabies virus (RV) has become a widely used technique in neuroscience, allowing identification, imaging, and manipulation of neurons directly presynaptic to a starting neuronal population. Its most common implementation is to use Cre mouse lines in combination with Cre-dependent "helper" adeno-associated viral vectors (AAVs) to supply the required genes to the targeted population before subsequent injection of a first-generation (ΔG) rabies viral vector. Here we show that the efficiency of transsynaptic spread and the degree of nonspecific labeling in wild-type control animals depend strongly on the concentrations of these helper AAVs. Our results suggest practical guidelines for achieving good results.
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Affiliation(s)
| | | | | | - Ian R. Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States
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7
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Abstract
Anatomical labeling approaches are essential for understanding brain organization. Among these approaches are various methods of performing tract tracing. However, a major hurdle to overcome when marking neurons in vivo is visibility. Poor visibility makes it challenging to image a desired neuronal pathway so that it can be easily differentiated from a closely neighboring pathway. As a result, it becomes impossible to analyze individual projections or their connections. The tracer that is chosen for a given purpose has a major influence on the quality of the tracing. Here, we describe the wheat germ agglutinin (WGA) tracer conjugated to Alexa fluorophores for reliable high-resolution tracing of central nervous system projections. Using the mouse cerebellum as a model system, we implement WGA-Alexa tracing for marking and mapping neural circuits that control motor function. We also show its utility for marking localized regions of the cerebellum after performing single-unit extracellular recordings in vivo. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sabrina L Levy
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, Houston, Texas
| | - Joshua J White
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, Houston, Texas.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas
| | - Elizabeth P Lackey
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, Houston, Texas.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas
| | - Lindsey Schwartz
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, Houston, Texas
| | - Roy V Sillitoe
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, Houston, Texas.,Department of Neuroscience, Baylor College of Medicine, Houston, Texas.,Program in Developmental Biology, Baylor College of Medicine, Houston, Texas
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