1
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Machold R, Rudy B. Genetic approaches to elucidating cortical and hippocampal GABAergic interneuron diversity. Front Cell Neurosci 2024; 18:1414955. [PMID: 39113758 PMCID: PMC11303334 DOI: 10.3389/fncel.2024.1414955] [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: 04/09/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
GABAergic interneurons (INs) in the mammalian forebrain represent a diverse population of cells that provide specialized forms of local inhibition to regulate neural circuit activity. Over the last few decades, the development of a palette of genetic tools along with the generation of single-cell transcriptomic data has begun to reveal the molecular basis of IN diversity, thereby providing deep insights into how different IN subtypes function in the forebrain. In this review, we outline the emerging picture of cortical and hippocampal IN speciation as defined by transcriptomics and developmental origin and summarize the genetic strategies that have been utilized to target specific IN subtypes, along with the technical considerations inherent to each approach. Collectively, these methods have greatly facilitated our understanding of how IN subtypes regulate forebrain circuitry via cell type and compartment-specific inhibition and thus have illuminated a path toward potential therapeutic interventions for a variety of neurocognitive disorders.
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Affiliation(s)
- Robert Machold
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, United States
| | - Bernardo Rudy
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Anesthesiology, Perioperative Care and Pain Medicine, New York University Grossman School of Medicine, New York, NY, United States
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2
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Chen Y, Wang J, Liu J, Lin J, Lin Y, Nie J, Yue Q, Deng C, Qi X, Li Y, Dai J, Lu Z. A Novel Retrograde AAV Variant for Functional Manipulation of Cortical Projection Neurons in Mice and Monkeys. Neurosci Bull 2024; 40:90-102. [PMID: 37432585 PMCID: PMC10774509 DOI: 10.1007/s12264-023-01091-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/08/2023] [Indexed: 07/12/2023] Open
Abstract
Retrograde adeno-associated viruses (AAVs) are capable of infecting the axons of projection neurons and serve as a powerful tool for the anatomical and functional characterization of neural networks. However, few retrograde AAV capsids have been shown to offer access to cortical projection neurons across different species and enable the manipulation of neural function in non-human primates (NHPs). Here, we report the development of a novel retrograde AAV capsid, AAV-DJ8R, which efficiently labeled cortical projection neurons after local administration into the striatum of mice and macaques. In addition, intrastriatally injected AAV-DJ8R mediated opsin expression in the mouse motor cortex and induced robust behavioral alterations. Moreover, AAV-DJ8R markedly increased motor cortical neuron firing upon optogenetic light stimulation after viral delivery into the macaque putamen. These data demonstrate the usefulness of AAV-DJ8R as an efficient retrograde tracer for cortical projection neurons in rodents and NHPs and indicate its suitability for use in conducting functional interrogations.
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Affiliation(s)
- Yefei Chen
- Department of Anesthesiology, Shenzhen Maternity and Child Healthcare Hospital, The First School of Clinical Medicine, Southern Medical University, Shenzhen, 518027, China
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jingyi Wang
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Liu
- Department of Anesthesiology, Shenzhen Maternity and Child Healthcare Hospital, The First School of Clinical Medicine, Southern Medical University, Shenzhen, 518027, China
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jianbang Lin
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunping Lin
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jinyao Nie
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qi Yue
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chunshan Deng
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaofei Qi
- Department of Anesthesiology, Shenzhen Maternity and Child Healthcare Hospital, The First School of Clinical Medicine, Southern Medical University, Shenzhen, 518027, China.
| | - Yuantao Li
- Department of Anesthesiology, Shenzhen Maternity and Child Healthcare Hospital, The First School of Clinical Medicine, Southern Medical University, Shenzhen, 518027, China
- Biomedical Research Institute, Hubei University of Medicine, Shiyan, 442000, China
| | - Ji Dai
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Zhonghua Lu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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3
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Chen Y, Hong Z, Wang J, Liu K, Liu J, Lin J, Feng S, Zhang T, Shan L, Liu T, Guo P, Lin Y, Li T, Chen Q, Jiang X, Li A, Li X, Li Y, Wilde JJ, Bao J, Dai J, Lu Z. Circuit-specific gene therapy reverses core symptoms in a primate Parkinson's disease model. Cell 2023; 186:5394-5410.e18. [PMID: 37922901 DOI: 10.1016/j.cell.2023.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
Parkinson's disease (PD) is a debilitating neurodegenerative disorder. Its symptoms are typically treated with levodopa or dopamine receptor agonists, but its action lacks specificity due to the wide distribution of dopamine receptors in the central nervous system and periphery. Here, we report the development of a gene therapy strategy to selectively manipulate PD-affected circuitry. Targeting striatal D1 medium spiny neurons (MSNs), whose activity is chronically suppressed in PD, we engineered a therapeutic strategy comprised of a highly efficient retrograde adeno-associated virus (AAV), promoter elements with strong D1-MSN activity, and a chemogenetic effector to enable precise D1-MSN activation after systemic ligand administration. Application of this therapeutic approach rescues locomotion, tremor, and motor skill defects in both mouse and primate models of PD, supporting the feasibility of targeted circuit modulation tools for the treatment of PD in humans.
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Affiliation(s)
- Yefei Chen
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zexuan Hong
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Department of Anesthesiology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518027, China
| | - Jingyi Wang
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kunlin Liu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Jing Liu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Department of Anesthesiology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518027, China
| | - Jianbang Lin
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijing Feng
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianhui Zhang
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou 221004, China
| | - Liang Shan
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Taian Liu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Pinyue Guo
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunping Lin
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tian Li
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qian Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Xiaodan Jiang
- Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Anan Li
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou 221004, China
| | - Xiang Li
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuantao Li
- Department of Anesthesiology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518027, China; Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China
| | | | - Jin Bao
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Biomedical Imaging Science and System Key Laboratory, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Ji Dai
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Zhonghua Lu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Biomedical Imaging Science and System Key Laboratory, Chinese Academy of Sciences, Shenzhen 518055, China.
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4
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Qiu L, Zhang B, Gao Z. Lighting Up Neural Circuits by Viral Tracing. Neurosci Bull 2022; 38:1383-1396. [PMID: 35578093 PMCID: PMC9672192 DOI: 10.1007/s12264-022-00860-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/23/2022] [Indexed: 12/03/2022] Open
Abstract
Neurons are highly interwoven to form intricate neural circuits that underlie the diverse functions of the brain. Dissecting the anatomical organization of neural circuits is key to deciphering how the brain processes information, produces thoughts, and instructs behaviors. Over the past decades, recombinant viral vectors have become the most commonly used tracing tools to define circuit architecture. In this review, we introduce the current categories of viral tools and their proper application in circuit tracing. We further discuss some advances in viral tracing strategy and prospective innovations of viral tools for future study.
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Affiliation(s)
- Liyao Qiu
- Department of Neurobiology and Department of Neurology of the Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Bin Zhang
- Department of Neurobiology and Department of Neurology of the Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Zhihua Gao
- Department of Neurobiology and Department of Neurology of the Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310058, China.
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5
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Tsai NY, Wang F, Toma K, Yin C, Takatoh J, Pai EL, Wu K, Matcham AC, Yin L, Dang EJ, Marciano DK, Rubenstein JL, Wang F, Ullian EM, Duan X. Trans-Seq maps a selective mammalian retinotectal synapse instructed by Nephronectin. Nat Neurosci 2022; 25:659-674. [PMID: 35524141 PMCID: PMC9172271 DOI: 10.1038/s41593-022-01068-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 03/30/2022] [Indexed: 12/21/2022]
Abstract
The mouse visual system serves as an accessible model to understand mammalian circuit wiring. Despite rich knowledge in retinal circuits, the long-range connectivity map from distinct retinal ganglion cell (RGC) types to diverse brain neuron types remains unknown. In this study, we developed an integrated approach, called Trans-Seq, to map RGCs to superior collicular (SC) circuits. Trans-Seq combines a fluorescent anterograde trans-synaptic tracer, consisting of codon-optimized wheat germ agglutinin fused to mCherry, with single-cell RNA sequencing. We used Trans-Seq to classify SC neuron types innervated by genetically defined RGC types and predicted a neuronal pair from αRGCs to Nephronectin-positive wide-field neurons (NPWFs). We validated this connection using genetic labeling, electrophysiology and retrograde tracing. We then used transcriptomic data from Trans-Seq to identify Nephronectin as a determinant for selective synaptic choice from αRGC to NPWFs via binding to Integrin α8β1. The Trans-Seq approach can be broadly applied for post-synaptic circuit discovery from genetically defined pre-synaptic neurons.
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Affiliation(s)
- Nicole Y Tsai
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program and Biomedical Science Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Fei Wang
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Kenichi Toma
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Chen Yin
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Jun Takatoh
- McGovern Institute for Brain Research, MIT Brain and Cognitive Sciences, Cambridge, MA, USA
| | - Emily L Pai
- Neuroscience Graduate Program, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Kongyan Wu
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Angela C Matcham
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
- Neuroscience Graduate Program, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Luping Yin
- McGovern Institute for Brain Research, MIT Brain and Cognitive Sciences, Cambridge, MA, USA
| | - Eric J Dang
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Denise K Marciano
- Departments of Cell Biology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John L Rubenstein
- Neuroscience Graduate Program, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Fan Wang
- McGovern Institute for Brain Research, MIT Brain and Cognitive Sciences, Cambridge, MA, USA
| | - Erik M Ullian
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Xin Duan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA.
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA.
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA.
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6
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Attili SM, Moradi K, Wheeler DW, Ascoli GA. Quantification of neuron types in the rodent hippocampal formation by data mining and numerical optimization. Eur J Neurosci 2022; 55:1724-1741. [PMID: 35301768 PMCID: PMC10026515 DOI: 10.1111/ejn.15639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/25/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022]
Abstract
Quantifying the population sizes of distinct neuron types in different anatomical regions is an essential step towards establishing a brain cell census. Although estimates exist for the total neuronal populations in different species, the number and definition of each specific neuron type are still intensively investigated. Hippocampome.org is an open-source knowledge base with morphological, physiological and molecular information for 122 neuron types in the rodent hippocampal formation. While such framework identifies all known neuron types in this system, their relative abundances remain largely unknown. This work quantitatively estimates the counts of all Hippocampome.org neuron types by literature mining and numerical optimization. We report the number of neurons in each type identified by main neurotransmitter (glutamate or GABA) and axonal-dendritic patterns throughout 26 subregions and layers of the dentate gyrus, Ammon's horn, subiculum and entorhinal cortex. We produce by sensitivity analysis reliable numerical ranges for each type and summarize the amounts across broad neuronal families defined by biomarkers expression and firing dynamics. Study of density distributions indicates that the number of dendritic-targeting interneurons, but not of other neuronal classes, is independent of anatomical volumes. All extracted values, experimental evidence and related software code are released on Hippocampome.org.
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Affiliation(s)
- Sarojini M Attili
- Center for Neural Informatics, Structures, and Plasticity, Interdisciplinary Neuroscience Program, Krasnow Institute for Advanced Study, Fairfax, Virginia, USA
| | - Keivan Moradi
- Center for Neural Informatics, Structures, and Plasticity, Interdisciplinary Neuroscience Program, Krasnow Institute for Advanced Study, Fairfax, Virginia, USA
| | - Diek W Wheeler
- Bioengineering Department and Volgenau School of Engineering, George Mason University, Fairfax, Virginia, USA
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures, and Plasticity, Interdisciplinary Neuroscience Program, Krasnow Institute for Advanced Study, Fairfax, Virginia, USA
- Bioengineering Department and Volgenau School of Engineering, George Mason University, Fairfax, Virginia, USA
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7
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Emerging strategies for the genetic dissection of gene functions, cell types, and neural circuits in the mammalian brain. Mol Psychiatry 2022; 27:422-435. [PMID: 34561609 DOI: 10.1038/s41380-021-01292-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
The mammalian brain is composed of a large number of highly diverse cell types with different molecular, anatomical, and functional features. Distinct cellular identities are generated during development under the regulation of intricate genetic programs and manifested through unique combinations of gene expression. Recent advancements in our understanding of the molecular and cellular mechanisms underlying the assembly, function, and pathology of the brain circuitry depend on the invention and application of genetic strategies that engage intrinsic gene regulatory mechanisms. Here we review the strategies for gene regulation on DNA, RNA, and protein levels and their applications in cell type targeting and neural circuit dissection. We highlight newly emerged strategies and emphasize the importance of combinatorial approaches. We also discuss the potential caveats and pitfalls in current methods and suggest future prospects to improve their comprehensiveness and versatility.
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8
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Abstract
Visual images can be described in terms of the illuminants and objects that are causal to the light reaching the eye, the retinal image, its neural representation, or how the image is perceived. Respecting the differences among these distinct levels of description can be challenging but is crucial for a clear understanding of color vision. This article approaches color by reviewing what is known about its neural representation in the early visual cortex, with a brief description of signals in the eye and the thalamus for context. The review focuses on the properties of single neurons and advances the general theme that experimental approaches based on knowledge of feedforward signals have promoted greater understanding of the neural code for color than approaches based on correlating single-unit responses with color perception. New data from area V1 illustrate the strength of the feedforward approach. Future directions for progress in color neurophysiology are discussed: techniques for improved single-neuron characterization, for investigations of neural populations and small circuits, and for the analysis of natural image statistics.
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Affiliation(s)
- Gregory D Horwitz
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA; .,Washington National Primate Research Center, University of Washington, Seattle, Washington 98121, USA
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9
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Zhong H, Ceballos CC, Massengill CI, Muniak MA, Ma L, Qin M, Petrie SK, Mao T. High-fidelity, efficient, and reversible labeling of endogenous proteins using CRISPR-based designer exon insertion. eLife 2021; 10:64911. [PMID: 34100715 PMCID: PMC8211447 DOI: 10.7554/elife.64911] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/07/2021] [Indexed: 12/26/2022] Open
Abstract
Precise and efficient insertion of large DNA fragments into somatic cells using gene editing technologies to label or modify endogenous proteins remains challenging. Non-specific insertions/deletions (INDELs) resulting from the non-homologous end joining pathway make the process error-prone. Further, the insert is not readily removable. Here, we describe a method called CRISPR-mediated insertion of exon (CRISPIE) that can precisely and reversibly label endogenous proteins using CRISPR/Cas9-based editing. CRISPIE inserts a designer donor module, which consists of an exon encoding the protein sequence flanked by intron sequences, into an intronic location in the target gene. INDELs at the insertion junction will be spliced out, leaving mRNAs nearly error-free. We used CRISPIE to fluorescently label endogenous proteins in mammalian neurons in vivo with previously unachieved efficiency. We demonstrate that this method is broadly applicable, and that the insert can be readily removed later. CRISPIE permits protein sequence insertion with high fidelity, efficiency, and flexibility.
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Affiliation(s)
- Haining Zhong
- Vollum Institute, Oregon Health & Science University, Portland, United States
| | - Cesar C Ceballos
- Vollum Institute, Oregon Health & Science University, Portland, United States
| | | | - Michael A Muniak
- Vollum Institute, Oregon Health & Science University, Portland, United States
| | - Lei Ma
- Vollum Institute, Oregon Health & Science University, Portland, United States
| | - Maozhen Qin
- Vollum Institute, Oregon Health & Science University, Portland, United States
| | - Stefanie Kaech Petrie
- Department of Neurology, Oregon Health & Science University, Portland, United States
| | - Tianyi Mao
- Vollum Institute, Oregon Health & Science University, Portland, United States
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10
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Hou Y, Zhang Q, Liu H, Wu J, Shi Y, Qi Y, Shao M, Yang Z, Lu J, Wu Z, Gong L, He M. Topographical organization of mammillary neurogenesis and efferent projections in the mouse brain. Cell Rep 2021; 34:108712. [PMID: 33567285 DOI: 10.1016/j.celrep.2021.108712] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/01/2020] [Accepted: 01/12/2021] [Indexed: 01/23/2023] Open
Abstract
The mammillary body is a hypothalamic nucleus that has important functions in memory and spatial navigation, but its developmental principles remain not well understood. Here, we identify progenitor-specific Fezf2 expression in the developing mammillary body and develop an intersectional fate-mapping approach to demonstrate that Fezf2+ mammillary progenitors generate mammillary neurons in a rostral-dorsal-lateral to caudal-ventral-medial fashion. Axonal tracing from different temporal cohorts of labeled mammillary neurons reveal their topographical organization. Unsupervised hierarchical clustering based on intrinsic properties further identify two distinct neuronal clusters independent of birthdates in the medial nuclei. In addition, we generate Fezf2 knockout mice and observe the smaller mammillary body with largely normal anatomy and mildly affected cellular electrophysiology, in contrast to more severe deficits in neuronal differentiation and projection in many other brain regions. These results indicate that Fezf2 may function differently in the mammillary body. Our results provide important insights for mammillary development and connectivity.
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Affiliation(s)
- Yongjie Hou
- Institutes of Brain Science, Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qi Zhang
- Institutes of Brain Science, Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hongzhi Liu
- Institutes of Brain Science, Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jinyun Wu
- Institutes of Brain Science, Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Shi
- Institutes of Brain Science, Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanqing Qi
- Institutes of Brain Science, Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengmeng Shao
- Department of Anatomy and Physiology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhengang Yang
- Institutes of Brain Science, Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiangteng Lu
- Department of Anatomy and Physiology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhuhao Wu
- Department of Cell, Developmental and Regenerative Biology, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ling Gong
- Institutes of Brain Science, Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Miao He
- Institutes of Brain Science, Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China.
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11
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Kim B, Kim J, Chun M, Park I, Kwak D, Choi M, Kim K, Choe HK. Multiplexed CRISPR-Cas9 system in a single adeno-associated virus to simultaneously knock out redundant clock genes. Sci Rep 2021; 11:2575. [PMID: 33510438 PMCID: PMC7844015 DOI: 10.1038/s41598-021-82287-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
The mammalian molecular clock is based on a transcription-translation feedback loop (TTFL) comprising the Period1, 2 (Per1, 2), Cryptochrome1, 2 (Cry1, 2), and Brain and Muscle ARNT-Like 1 (Bmal1) genes. The robustness of the TTFL is attributed to genetic redundancy among some essential clock genes, deterring genetic studies on molecular clocks using genome editing targeting single genes. To manipulate multiple clock genes in a streamlined and efficient manner, we developed a CRISPR-Cas9-based single adeno-associated viral (AAV) system targeting the circadian clock (CSAC) for essential clock genes including Pers, Crys, or Bmal1. First, we tested several single guide RNAs (sgRNAs) targeting individual clock genes in silico and validated their efficiency in Neuro2a cells. To target multiple genes, multiplex sgRNA plasmids were constructed using Golden Gate assembly and packaged into AAVs. CSAC efficiency was evident through protein downregulation in vitro and ablated molecular oscillation ex vivo. We also measured the efficiency of CSAC in vivo by assessing circadian rhythms after injecting CSAC into the suprachiasmatic nuclei of Cas9-expressing knock-in mice. Circadian locomotor activity and body temperature rhythms were severely disrupted in these mice, indicating that our CSAC is a simple yet powerful tool for investigating the molecular clock in vivo.
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Affiliation(s)
- Boil Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), E4-311, 333 Technojoongang-daero, Dalseong-gun, Daegu, 42988, South Korea
| | - Jihoon Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), E4-311, 333 Technojoongang-daero, Dalseong-gun, Daegu, 42988, South Korea
| | - Minjeong Chun
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), E4-311, 333 Technojoongang-daero, Dalseong-gun, Daegu, 42988, South Korea
| | - Inah Park
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), E4-311, 333 Technojoongang-daero, Dalseong-gun, Daegu, 42988, South Korea
| | - Damhyeon Kwak
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), E4-311, 333 Technojoongang-daero, Dalseong-gun, Daegu, 42988, South Korea
| | - Mijung Choi
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), E4-311, 333 Technojoongang-daero, Dalseong-gun, Daegu, 42988, South Korea
| | - Kyungjin Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), E4-311, 333 Technojoongang-daero, Dalseong-gun, Daegu, 42988, South Korea
| | - Han Kyoung Choe
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), E4-311, 333 Technojoongang-daero, Dalseong-gun, Daegu, 42988, South Korea.
- Convergence Research Advanced Centre for Olfaction, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea.
- Korean Brain Research Institute (KBRI), Daegu, South Korea.
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12
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Zhao J, Lai HM, Qi Y, He D, Sun H. Current Status of Tissue Clearing and the Path Forward in Neuroscience. ACS Chem Neurosci 2021; 12:5-29. [PMID: 33326739 DOI: 10.1021/acschemneuro.0c00563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Due to the complexity and limited availability of human brain tissues, for decades, pathologists have sought to maximize information gained from individual samples, based on which (patho)physiological processes could be inferred. Recently, new understandings of chemical and physical properties of biological tissues and multiple chemical profiling have given rise to the development of scalable tissue clearing methods allowing superior optical clearing of across-the-scale samples. In the past decade, tissue clearing techniques, molecular labeling methods, advanced laser scanning microscopes, and data visualization and analysis have become commonplace. Combined, they have made 3D visualization of brain tissues with unprecedented resolution and depth widely accessible. To facilitate further advancements and applications, here we provide a critical appraisal of these techniques. We propose a classification system of current tissue clearing and expansion methods that allows users to judge the applicability of individual ones to their questions, followed by a review of the current progress in molecular labeling, optical imaging, and data processing to demonstrate the whole 3D imaging pipeline based on tissue clearing and downstream techniques for visualizing the brain. We also raise the path forward of tissue-clearing-based imaging technology, that is, integrating with state-of-the-art techniques, such as multiplexing protein imaging, in situ signal amplification, RNA detection and sequencing, super-resolution imaging techniques, multiomics studies, and deep learning, for drawing the complete atlas of the human brain and building a 3D pathology platform for central nervous system disorders.
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Affiliation(s)
- Jiajia Zhao
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Hei Ming Lai
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yuwei Qi
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Dian He
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
| | - Haitao Sun
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Clinical Medical College, Southern Medical University, Guangzhou 510515, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Clinical Biobank Center, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
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13
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Roth RH, Ding JB. From Neurons to Cognition: Technologies for Precise Recording of Neural Activity Underlying Behavior. BME FRONTIERS 2020; 2020:7190517. [PMID: 37849967 PMCID: PMC10521756 DOI: 10.34133/2020/7190517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 10/19/2023] Open
Abstract
Understanding how brain activity encodes information and controls behavior is a long-standing question in neuroscience. This complex problem requires converging efforts from neuroscience and engineering, including technological solutions to perform high-precision and large-scale recordings of neuronal activity in vivo as well as unbiased methods to reliably measure and quantify behavior. Thanks to advances in genetics, molecular biology, engineering, and neuroscience, in recent decades, a variety of optical imaging and electrophysiological approaches for recording neuronal activity in awake animals have been developed and widely applied in the field. Moreover, sophisticated computer vision and machine learning algorithms have been developed to analyze animal behavior. In this review, we provide an overview of the current state of technology for neuronal recordings with a focus on optical and electrophysiological methods in rodents. In addition, we discuss areas that future technological development will need to cover in order to further our understanding of the neural activity underlying behavior.
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Affiliation(s)
- Richard H Roth
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Jun B Ding
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
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14
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Identification and quantification of neuronal ensembles in optical imaging experiments. J Neurosci Methods 2020; 351:109046. [PMID: 33359231 DOI: 10.1016/j.jneumeth.2020.109046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/30/2022]
Abstract
Recent technical advances in molecular biology and optical imaging have made it possible to record from up to thousands of densely packed neurons in superficial and deep brain regions in vivo, with cellular subtype specificity and high spatiotemporal fidelity. Such optical neurotechnologies are enabling increasingly fine-scaled studies of neuronal circuits and reliably co-active groups of neurons, so-called ensembles. Neuronal ensembles are thought to constitute the basic functional building blocks of brain systems, potentially exhibiting collective computational properties. While the technical framework of in vivo optical imaging and quantification of neuronal activity follows certain widely held standards, analytical methods for study of neuronal co-activity and ensembles lack consensus and are highly varied across the field. Here we provide a comprehensive step-by-step overview of theoretical, experimental, and analytical considerations for the identification and quantification of neuronal ensemble dynamics in high-resolution in vivo optical imaging studies.
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15
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Ca 2+ imaging of neurons in freely moving rats with automatic post hoc histological identification. J Neurosci Methods 2020; 341:108765. [PMID: 32407804 DOI: 10.1016/j.jneumeth.2020.108765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Cognitive neuroscientists aim to understand behavior often based on the underlying activity of individual neurons. Recently developed miniaturized epifluorescence microscopes allow recording of cellular calcium transients, resembling neuronal activity, of individual neurons even in deep brain areas in freely behaving animals. At the same time, molecular markers allow the characterization of diverse neuronal subtypes by post hoc immunohistochemical labeling. Combining both methods would allow researchers to increase insights into how individual neuronal activity and entities contribute to behavior. NEW METHOD Here, we present a novel method for identifying the same neurons, recorded with calcium imaging using a miniaturized epifluorescence microscope, post hoc in fixed histological sections. This allows immunohistochemical investigations to detect the molecular signature of in vivo recorded neurons. Our method utilizes the structure of blood vessels for aligning in vivo acquired 2D images with a reconstructed 3D histological model. RESULTS We automatically matched, 60 % of all in vivo recorded cells post hoc in histology. Across all animals, we successfully matched 43 % to 89 % of the recorded neurons. We provide a measure for the confidence of matched cells and validated our method by multiple simulation studies. COMPARISON WITH EXISTING METHODS To our knowledge, we present the first method for matching cells, recorded with a miniaturized epifluorescence microscope in freely moving animals, post hoc in histological sections. CONCLUSIONS Our method allows a comprehensive analysis of how cortical circuits relate to freely moving animal behavior by combining functional activity of individual neurons with their underlying histological profiles.
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16
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Cong W, Shi Y, Qi Y, Wu J, Gong L, He M. Viral approaches to study the mammalian brain: Lineage tracing, circuit dissection and therapeutic applications. J Neurosci Methods 2020; 335:108629. [PMID: 32045571 DOI: 10.1016/j.jneumeth.2020.108629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 02/09/2023]
Abstract
Viral vectors are widely used to study the development, function and pathology of neural circuits in the mammalian brain. Their flexible payloads with customizable choices of tool genes allow versatile applications ranging from lineage tracing, circuit mapping and functional interrogation, to translational and therapeutic applications. Different applications have distinct technological requirements, therefore, often utilize different types of virus. This review introduces the most commonly used viruses for these applications and some recent advances in improving the resolution and throughput of lineage tracing, the efficacy and selectivity of circuit tracing and the specificity of cell type targeting.
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Affiliation(s)
- Wei Cong
- Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Shi
- Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanqing Qi
- Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jinyun Wu
- Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ling Gong
- Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miao He
- Department of Neurology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China.
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17
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Qiu F, Mao X, Liu P, Wu J, Zhang Y, Sun D, Zhu Y, Gong L, Shao M, Fan K, Chen J, Lu J, Jiang Y, Zhang Y, Curia G, Li A, He M. microRNA Deficiency in VIP+ Interneurons Leads to Cortical Circuit Dysfunction. Cereb Cortex 2019; 30:2229-2249. [PMID: 33676371 DOI: 10.1093/cercor/bhz236] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 01/01/2019] [Accepted: 01/01/2019] [Indexed: 12/13/2022] Open
Abstract
Genetically distinct GABAergic interneuron subtypes play diverse roles in cortical circuits. Previous studies revealed that microRNAs (miRNAs) are differentially expressed in cortical interneuron subtypes, and are essential for the normal migration, maturation, and survival of medial ganglionic eminence-derived interneuron subtypes. How miRNAs function in vasoactive intestinal peptide expressing (VIP+) interneurons derived from the caudal ganglionic eminence remains elusive. Here, we conditionally removed Dicer in postmitotic VIP+ interneurons to block miRNA biogenesis. We found that the intrinsic and synaptic properties of VIP+ interneurons and pyramidal neurons were concordantly affected prior to a progressive loss of VIP+ interneurons. In vivo recording further revealed elevated cortical local field potential power. Mutant mice had a shorter life span but exhibited better spatial working memory and motor coordination. Our results demonstrate that miRNAs are indispensable for the function and survival of VIP+ interneurons, and highlight a key role of VIP+ interneurons in cortical circuits.
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Affiliation(s)
- Fang Qiu
- Department of Neurology, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xingfeng Mao
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou 221004, China
| | - Penglai Liu
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou 221004, China
| | - Jinyun Wu
- Department of Neurology, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yuan Zhang
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Daijing Sun
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Yueyan Zhu
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Ling Gong
- Department of Neurology, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Mengmeng Shao
- Department of Anatomy and Physiology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Keyang Fan
- Department of Neurology, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Junjie Chen
- Department of Neurology, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiangteng Lu
- Department of Anatomy and Physiology, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yan Jiang
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Yubin Zhang
- Department of Toxicology, School of Public Health, Fudan University, Shanghai 200032, China
| | - Giulia Curia
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy.,Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena 41121, Italy
| | - Anan Li
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou 221004, China
| | - Miao He
- Department of Neurology, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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18
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Macknik SL, Alexander RG, Caballero O, Chanovas J, Nielsen KJ, Nishimura N, Schaffer CB, Slovin H, Babayoff A, Barak R, Tang S, Ju N, Yazdan-Shahmorad A, Alonso JM, Malinskiy E, Martinez-Conde S. Advanced Circuit and Cellular Imaging Methods in Nonhuman Primates. J Neurosci 2019; 39:8267-8274. [PMID: 31619496 PMCID: PMC6794937 DOI: 10.1523/jneurosci.1168-19.2019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/15/2022] Open
Abstract
Novel genetically encoded tools and advanced microscopy methods have revolutionized neural circuit analyses in insects and rodents over the last two decades. Whereas numerous technical hurdles originally barred these methodologies from success in nonhuman primates (NHPs), current research has started to overcome those barriers. In some cases, methodological advances developed with NHPs have even surpassed their precursors. One such advance includes new ultra-large imaging windows on NHP cortex, which are larger than the entire rodent brain and allow analysis unprecedented ultra-large-scale circuits. NHP imaging chambers now remain patent for periods longer than a mouse's lifespan, allowing for long-term all-optical interrogation of identified circuits and neurons over timeframes that are relevant to human cognitive development. Here we present some recent imaging advances brought forth by research teams using macaques and marmosets. These include technical developments in optogenetics; voltage-, calcium- and glutamate-sensitive dye imaging; two-photon and wide-field optical imaging; viral delivery; and genetic expression of indicators and light-activated proteins that result in the visualization of tens of thousands of identified cortical neurons in NHPs. We describe a subset of the many recent advances in circuit and cellular imaging tools in NHPs focusing here primarily on the research presented during the corresponding mini-symposium at the 2019 Society for Neuroscience annual meeting.
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Affiliation(s)
- Stephen L Macknik
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203,
| | - Robert G Alexander
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203
| | - Olivya Caballero
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203
| | - Jordi Chanovas
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203
| | - Kristina J Nielsen
- Zanvyl Krieger Mind/Brain Institute, Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland 21218
| | - Nozomi Nishimura
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853
| | - Chris B Schaffer
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853
| | - Hamutal Slovin
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Amit Babayoff
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Ravid Barak
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Shiming Tang
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, and Peking University-International Data Group-McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Niansheng Ju
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, and Peking University-International Data Group-McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Azadeh Yazdan-Shahmorad
- Department of Bioengineering, University of Washington, Seattle, Washington 98195
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195
| | - Jose-Manuel Alonso
- State University of New York, College of Optometry, New York, New York 10036, and
| | | | - Susana Martinez-Conde
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203
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19
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Engel TA, Steinmetz NA. New perspectives on dimensionality and variability from large-scale cortical dynamics. Curr Opin Neurobiol 2019; 58:181-190. [PMID: 31585331 PMCID: PMC6859189 DOI: 10.1016/j.conb.2019.09.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/27/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022]
Abstract
The neocortex is a multi-scale network, with intricate local circuitry interwoven into a global mesh of long-range connections. Neural activity propagates within this network on a wide range of temporal and spatial scales. At the micro scale, neurophysiological recordings reveal coordinated dynamics in local neural populations, which support behaviorally relevant computations. At the macro scale, neuroimaging modalities measure global activity fluctuations organized into spatiotemporal patterns across the entire brain. Here we review recent advances linking the local and global scales of cortical dynamics and their relationship to behavior. We argue that diverse experimental observations on the dimensionality and variability of neural activity can be reconciled by considering how activity propagates in space and time on multiple spatial scales.
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Affiliation(s)
- Tatiana A Engel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, United States.
| | - Nicholas A Steinmetz
- Department of Biological Structure, University of Washington, Seattle, WA 98195, United States.
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20
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Huang ZJ, Paul A. The diversity of GABAergic neurons and neural communication elements. Nat Rev Neurosci 2019; 20:563-572. [PMID: 31222186 PMCID: PMC8796706 DOI: 10.1038/s41583-019-0195-4] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2019] [Indexed: 12/18/2022]
Abstract
The phenotypic diversity of cortical GABAergic neurons is probably necessary for their functional versatility in shaping the spatiotemporal dynamics of neural circuit operations underlying cognition. Deciphering the logic of this diversity requires comprehensive analysis of multi-modal cell features and a framework of neuronal identity that reflects biological mechanisms and principles. Recent high-throughput single-cell analyses have generated unprecedented data sets characterizing the transcriptomes, morphology and electrophysiology of interneurons. We posit that cardinal interneuron types can be defined by their synaptic communication properties, which are encoded in key transcriptional signatures. This conceptual framework integrates multi-modal cell features, captures neuronal input-output properties fundamental to circuit operation and may advance understanding of the appropriate granularity of neuron types, towards a biologically grounded and operationally useful interneuron taxonomy.
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Affiliation(s)
- Z Josh Huang
- Cold Spring Harbor Laboratory, New York, NY, USA.
| | - Anirban Paul
- Cold Spring Harbor Laboratory, New York, NY, USA
- Department of Neural & Behavioral Sciences, Penn State University College of Medicine, Hershey, PA, USA
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Katz PS, Quinlan PD. The importance of identified neurons in gastropod molluscs to neuroscience. Curr Opin Neurobiol 2019; 56:1-7. [PMID: 30390485 DOI: 10.1016/j.conb.2018.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/08/2018] [Indexed: 01/10/2023]
Abstract
Gastropod molluscs have large neurons that are uniquely identifiable across individuals and across species based on neuroanatomical and neurochemical criteria, facilitating research into neural signaling and neural circuits. Novel neuropeptides have been identified through RNA sequencing and mass spectroscopic analysis of single neurons. The roles of peptides and other signaling molecules including second messengers have been placed in the context of small circuits that control simple behaviors. Despite the stereotypy, neurons vary over time in their activity in large ensembles. Furthermore, there is both intra-species and inter-species variation in synaptic properties and gene expression. Research on gastropod identified neurons highlights the features that might be expected to be stable in more complex systems when trying to identify cell types.
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Affiliation(s)
- Paul S Katz
- Neuroscience and Behavior Graduate Program, Department of Biology, University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill Science Center 3, Amherst, MA 01003, United States.
| | - Phoenix D Quinlan
- Neuroscience and Behavior Graduate Program, Department of Biology, University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill Science Center 3, Amherst, MA 01003, United States
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Abstract
Anticipatory defensive responses to an aversive or harmful event depend on memories linking the event with the predictive environmental cues. Extensive evidence indicates that the central amygdala is essential for the acquisition and recall of such memories. The evidence came initially from studies that relied on traditional lesion and pharmacological techniques, and recently from studies in which new methodologies were used to target, record and manipulate neuronal activities with improved precision and specificity. In this review, I will discuss the current understanding of the roles of central amygdala neurons in the learning and expression of defensive behaviors, with a focus on the major neuronal populations identified on the basis of their genetic markers.
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