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Tang Y, Wu Q, Gao M, Ryu E, Pei Z, Kissinger ST, Chen Y, Rao AK, Xiang Z, Wang T, Li W, Chen G, Chubykin AA. Restoration of Visual Function and Cortical Connectivity After Ischemic Injury Through NeuroD1-Mediated Gene Therapy. Front Cell Dev Biol 2021; 9:720078. [PMID: 34490268 PMCID: PMC8416524 DOI: 10.3389/fcell.2021.720078] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Neural circuits underlying brain functions are vulnerable to damage, including ischemic injury, leading to neuronal loss and gliosis. Recent technology of direct conversion of endogenous astrocytes into neurons in situ can simultaneously replenish the neuronal population and reverse the glial scar. However, whether these newly reprogrammed neurons undergo normal development, integrate into the existing neuronal circuit, and acquire functional properties specific for this circuit is not known. We investigated the effect of NeuroD1-mediated in vivo direct reprogramming on visual cortical circuit integration and functional recovery in a mouse model of ischemic injury. After performing electrophysiological extracellular recordings and two-photon calcium imaging of reprogrammed cells in vivo and mapping the synaptic connections formed onto these cells ex vivo, we discovered that NeuroD1 reprogrammed neurons were integrated into the cortical microcircuit and acquired direct visual responses. Furthermore, following visual experience, the reprogrammed neurons demonstrated maturation of orientation selectivity and functional connectivity. Our results show that NeuroD1-reprogrammed neurons can successfully develop and integrate into the visual cortical circuit leading to vision recovery after ischemic injury.
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Affiliation(s)
- Yu Tang
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue Autism Research Center, Purdue University, West Lafayette, IN, United States
| | - Qiuyu Wu
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue Autism Research Center, Purdue University, West Lafayette, IN, United States
| | - Mang Gao
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue Autism Research Center, Purdue University, West Lafayette, IN, United States
| | - Esther Ryu
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue Autism Research Center, Purdue University, West Lafayette, IN, United States
| | - Zifei Pei
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Samuel T. Kissinger
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue Autism Research Center, Purdue University, West Lafayette, IN, United States
| | - Yuchen Chen
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Abhinav K. Rao
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Zongqin Xiang
- Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Tao Wang
- Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Wen Li
- Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Gong Chen
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
- Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Alexander A. Chubykin
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue Autism Research Center, Purdue University, West Lafayette, IN, United States
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High-depth spatial transcriptome analysis by photo-isolation chemistry. Nat Commun 2021; 12:4416. [PMID: 34285220 PMCID: PMC8292322 DOI: 10.1038/s41467-021-24691-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/24/2021] [Indexed: 12/18/2022] Open
Abstract
In multicellular organisms, expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we establish a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. PIC transcriptome analysis detects genes specifically expressed in small distinct areas of the mouse embryo. Photo-irradiation of single cells demonstrated that approximately 8,000 genes were detected with 7 × 104 unique read counts. Furthermore, PIC transcriptome analysis is applicable to the subcellular and subnuclear microstructures (stress granules and nuclear speckles, respectively), where hundreds of genes can be detected as being specifically localised. The spatial density of the read counts is higher than 100 per square micrometre. Thus, PIC enables high-depth transcriptome profiles to be determined from limited regions up to subcellular and subnuclear resolutions. Spatial analysis of RNAseq data is important. Here the authors report a method for transcriptome profiling combined with photo-isolation chemistry to allow determination of expression profiles specifically from photo-irradiated regions of interest which they use in mouse brains and embryonic tissues.
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Kissinger ST, Wu Q, Quinn CJ, Anderson AK, Pak A, Chubykin AA. Visual Experience-Dependent Oscillations and Underlying Circuit Connectivity Changes Are Impaired in Fmr1 KO Mice. Cell Rep 2021; 31:107486. [PMID: 32268079 DOI: 10.1016/j.celrep.2020.03.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 01/30/2020] [Accepted: 03/16/2020] [Indexed: 11/19/2022] Open
Abstract
Fragile X syndrome (FX), the most common inherited form of autism and intellectual disability, is a condition associated with visual perceptual learning deficits. We recently discovered that perceptual experience can encode visual familiarity via persistent low-frequency oscillations in the mouse primary visual cortex (V1). Here, we combine this paradigm with a multifaceted experimental approach to identify neurophysiological impairments of these oscillations in FX mice. Extracellular recordings reveal shorter durations, lower power, and lower frequencies of peak oscillatory activity in FX mice. Directed information analysis of extracellularly recorded spikes reveals differences in functional connectivity from multiple layers in FX mice after the perceptual experience. Channelrhodopsin-2 assisted circuit mapping (CRACM) reveals increased synaptic strength from L5 pyramidal onto L4 fast-spiking cells after experience in wild-type (WT), but not FX, mice. These results suggest differential encoding of visual stimulus familiarity in FX via persistent oscillations and identify circuit connections that may underlie these changes.
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Affiliation(s)
- Samuel T Kissinger
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Qiuyu Wu
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Christopher J Quinn
- Department of Industrial Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Adam K Anderson
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Alexandr Pak
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Alexander A Chubykin
- Department of Biological Sciences, Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA.
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Cai L, Gutruf P. Soft, Wireless and subdermally implantable recording and neuromodulation tools. J Neural Eng 2021; 18. [PMID: 33607646 DOI: 10.1088/1741-2552/abe805] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 02/19/2021] [Indexed: 12/14/2022]
Abstract
Progress in understanding neuronal interaction and circuit behavior of the central and peripheral nervous system strongly relies on the advancement of tools that record and stimulate with high fidelity and specificity. Currently, devices used in exploratory research predominantly utilize cables or tethers to provide pathways for power supply, data communication, stimulus delivery and recording, which constrains the scope and use of such devices. In particular, the tethered connection, mechanical mismatch to surrounding soft tissues and bones frustrate the interface leading to irritation and limitation of motion of the subject, which in the case of fundamental and preclinical studies, impacts naturalistic behaviors of animals and precludes the use in experiments involving social interaction and ethologically relevant three-dimensional environments, limiting the use of current tools to mostly rodents and exclude species such as birds and fish. This review explores the current state-of-the-art in wireless, subdermally implantable tools that quantitively expand capabilities in analysis and perturbation of the central and peripheral nervous system by removing tethers and externalized features of implantable neuromodulation and recording tools. Specifically, the review explores power harvesting strategies, wireless communication schemes, and soft materials and mechanics that enable the creation of such devices and discuss their capabilities in the context of freely-behaving subjects. Highlights of this class of devices includes wireless battery-free and fully implantable operation with capabilities in cell specific recording, multimodal neural stimulation and electrical, optogenetic and pharmacological neuromodulation capabilities. We conclude with discussion on translation of such technologies which promises routes towards broad dissemination.
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Affiliation(s)
- Le Cai
- Biomedical Engineering, University of Arizona, 1230 N Cherry Ave., Tucson, Arizona, 85719, UNITED STATES
| | - Philipp Gutruf
- Biomedical Engineering, University of Arizona, 1230 N Cherry Ave., Tucson, Arizona, 85719, UNITED STATES
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Harris JM, Wang AYD, Boulanger-Weill J, Santoriello C, Foianini S, Lichtman JW, Zon LI, Arlotta P. Long-Range Optogenetic Control of Axon Guidance Overcomes Developmental Boundaries and Defects. Dev Cell 2020; 53:577-588.e7. [PMID: 32516597 PMCID: PMC7375170 DOI: 10.1016/j.devcel.2020.05.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 03/12/2020] [Accepted: 05/11/2020] [Indexed: 01/12/2023]
Abstract
Axons connect neurons together, establishing the wiring architecture of neuronal networks. Axonal connectivity is largely built during embryonic development through highly constrained processes of axon guidance, which have been extensively studied. However, the inability to control axon guidance, and thus neuronal network architecture, has limited investigation of how axonal connections influence subsequent development and function of neuronal networks. Here, we use zebrafish motor neurons expressing a photoactivatable Rac1 to co-opt endogenous growth cone guidance machinery to precisely and non-invasively direct axon growth using light. Axons can be guided over large distances, within complex environments of living organisms, overriding competing endogenous signals and redirecting axons across potent repulsive barriers to construct novel circuitry. Notably, genetic axon guidance defects can be rescued, restoring functional connectivity. These data demonstrate that intrinsic growth cone guidance machinery can be co-opted to non-invasively build new connectivity, allowing investigation of neural network dynamics in intact living organisms.
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Affiliation(s)
- James M. Harris
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
| | - Andy Yu-Der Wang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Current Address: Tufts University School of Medicine, Boston, MA 02115, USA
| | - Jonathan Boulanger-Weill
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Cristina Santoriello
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stem Cell Program and Division of Hematology/Oncology, Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA 02115, USA
| | - Stephan Foianini
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jeff W. Lichtman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Leonard I. Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stem Cell Program and Division of Hematology/Oncology, Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA 02115, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA.,Lead contact. Correspondence:
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Rogers KW, Müller P. Optogenetic approaches to investigate spatiotemporal signaling during development. Curr Top Dev Biol 2019; 137:37-77. [PMID: 32143750 DOI: 10.1016/bs.ctdb.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Embryogenesis is coordinated by signaling pathways that pattern the developing organism. Many aspects of this process are not fully understood, including how signaling molecules spread through embryonic tissues, how signaling amplitude and dynamics are decoded, and how multiple signaling pathways cooperate to pattern the body plan. Optogenetic approaches can be used to address these questions by providing precise experimental control over a variety of biological processes. Here, we review how these strategies have provided new insights into developmental signaling and discuss how they could contribute to future investigations.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany; Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.
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Mahmoudi P, Veladi H, Pakdel FG. Optogenetics, Tools and Applications in Neurobiology. JOURNAL OF MEDICAL SIGNALS & SENSORS 2017; 7:71-79. [PMID: 28553579 PMCID: PMC5437765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Comprehension of the brain function can be helpful for therapy of neurodegenerative diseases. The brain consists of various types of neuron sets, which organize in three-dimensional complex networks and form neural circuits underlying different behaviors. The circuits act based on the patterns that encode the brain functions. Recognition of the neural patterns requires methods to manipulate the neurons. Electrical stimulation may be the most common method. However, it has significant drawbacks including failure to identify specific neurons in experiments. As an alternative, optical stimulation is a new method that acts in combination with genetic approaches. The novel, optogenetic technology makes it feasible to manipulate either the specific cell types or the neural circuits. This is associated with minimum tissue damages as well as side effects. In this study, a new technology has been introduced, and then its optical and genetical tools have been investigated.
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Affiliation(s)
- Parisa Mahmoudi
- Department of Electrical Engineering, Payame Noor University, Tehran, Iran
| | - Hadi Veladi
- Microsystem Fabrication Lab, Faculty of Electrical Engineering, University of Tabriz, Tabriz, Iran
| | - Firooz G. Pakdel
- Department of Physiology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
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Evans BD, Jarvis S, Schultz SR, Nikolic K. PyRhO: A Multiscale Optogenetics Simulation Platform. Front Neuroinform 2016; 10:8. [PMID: 27148037 PMCID: PMC4834562 DOI: 10.3389/fninf.2016.00008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/19/2016] [Indexed: 01/07/2023] Open
Abstract
Optogenetics has become a key tool for understanding the function of neural circuits and controlling their behavior. An array of directly light driven opsins have been genetically isolated from several families of organisms, with a wide range of temporal and spectral properties. In order to characterize, understand and apply these opsins, we present an integrated suite of open-source, multi-scale computational tools called PyRhO. The purpose of developing PyRhO is three-fold: (i) to characterize new (and existing) opsins by automatically fitting a minimal set of experimental data to three-, four-, or six-state kinetic models, (ii) to simulate these models at the channel, neuron and network levels, and (iii) provide functional insights through model selection and virtual experiments in silico. The module is written in Python with an additional IPython/Jupyter notebook based GUI, allowing models to be fit, simulations to be run and results to be shared through simply interacting with a webpage. The seamless integration of model fitting algorithms with simulation environments (including NEURON and Brian2) for these virtual opsins will enable neuroscientists to gain a comprehensive understanding of their behavior and rapidly identify the most suitable variant for application in a particular biological system. This process may thereby guide not only experimental design and opsin choice but also alterations of the opsin genetic code in a neuro-engineering feed-back loop. In this way, we expect PyRhO will help to significantly advance optogenetics as a tool for transforming biological sciences.
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Affiliation(s)
- Benjamin D Evans
- Centre for Bio-Inspired Technology, Institute of Biomedical Engineering, Department of Electrical and Electronic Engineering, Imperial College London London, UK
| | - Sarah Jarvis
- Centre for Neurotechnology, Institute of Biomedical Engineering, Department of Bioengineering, Imperial College London London, UK
| | - Simon R Schultz
- Centre for Neurotechnology, Institute of Biomedical Engineering, Department of Bioengineering, Imperial College London London, UK
| | - Konstantin Nikolic
- Centre for Bio-Inspired Technology, Institute of Biomedical Engineering, Department of Electrical and Electronic Engineering, Imperial College London London, UK
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