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Marghi Y, Gala R, Baftizadeh F, Sümbül U. Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.02.560574. [PMID: 37873271 PMCID: PMC10592946 DOI: 10.1101/2023.10.02.560574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Reproducible definition and identification of cell types is essential to enable investigations into their biological function, and understanding their relevance in the context of development, disease and evolution. Current approaches model variability in data as continuous latent factors, followed by clustering as a separate step, or immediately apply clustering on the data. We show that such approaches can suffer from qualitative mistakes in identifying cell types robustly, particularly when the number of such cell types is in the hundreds or even thousands. Here, we propose an unsupervised method, MMIDAS, which combines a generalized mixture model with a multi-armed deep neural network, to jointly infer the discrete type and continuous type-specific variability. Using four recent datasets of brain cells spanning different technologies, species, and conditions, we demonstrate that MMIDAS can identify reproducible cell types and infer cell type-dependent continuous variability in both uni-modal and multi-modal datasets.
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Affiliation(s)
| | - Rohan Gala
- Allen Institute, 615 Westlake Ave N, Seattle, WA, USA
| | | | - Uygar Sümbül
- Allen Institute, 615 Westlake Ave N, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
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2
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Beau M, Herzfeld DJ, Naveros F, Hemelt ME, D’Agostino F, Oostland M, Sánchez-López A, Chung YY, Michael Maibach, Kyranakis S, Stabb HN, Martínez Lopera MG, Lajko A, Zedler M, Ohmae S, Hall NJ, Clark BA, Cohen D, Lisberger SG, Kostadinov D, Hull C, Häusser M, Medina JF. A deep-learning strategy to identify cell types across species from high-density extracellular recordings. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577845. [PMID: 38352514 PMCID: PMC10862837 DOI: 10.1101/2024.01.30.577845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
High-density probes allow electrophysiological recordings from many neurons simultaneously across entire brain circuits but don't reveal cell type. Here, we develop a strategy to identify cell types from extracellular recordings in awake animals, revealing the computational roles of neurons with distinct functional, molecular, and anatomical properties. We combine optogenetic activation and pharmacology using the cerebellum as a testbed to generate a curated ground-truth library of electrophysiological properties for Purkinje cells, molecular layer interneurons, Golgi cells, and mossy fibers. We train a semi-supervised deep-learning classifier that predicts cell types with greater than 95% accuracy based on waveform, discharge statistics, and layer of the recorded neuron. The classifier's predictions agree with expert classification on recordings using different probes, in different laboratories, from functionally distinct cerebellar regions, and across animal species. Our classifier extends the power of modern dynamical systems analyses by revealing the unique contributions of simultaneously-recorded cell types during behavior.
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Affiliation(s)
- Maxime Beau
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - David J. Herzfeld
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Francisco Naveros
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Engineering, Automation and Robotics, Research Centre for Information and Communication Technologies, University of Granada, Granada, Spain
| | - Marie E. Hemelt
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Federico D’Agostino
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Marlies Oostland
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Young Yoon Chung
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Michael Maibach
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Stephen Kyranakis
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Hannah N. Stabb
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | | | - Agoston Lajko
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Marie Zedler
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Shogo Ohmae
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Nathan J. Hall
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Beverley A. Clark
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Dana Cohen
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Dimitar Kostadinov
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Centre for Developmental Neurobiology, King’s College London, London, UK
| | - Court Hull
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Michael Häusser
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Javier F. Medina
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
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3
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Shen Y, Shao M, Hao ZZ, Huang M, Xu N, Liu S. Multimodal Nature of the Single-cell Primate Brain Atlas: Morphology, Transcriptome, Electrophysiology, and Connectivity. Neurosci Bull 2024; 40:517-532. [PMID: 38194157 PMCID: PMC11003949 DOI: 10.1007/s12264-023-01160-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/23/2023] [Indexed: 01/10/2024] Open
Abstract
Primates exhibit complex brain structures that augment cognitive function. The neocortex fulfills high-cognitive functions through billions of connected neurons. These neurons have distinct transcriptomic, morphological, and electrophysiological properties, and their connectivity principles vary. These features endow the primate brain atlas with a multimodal nature. The recent integration of next-generation sequencing with modified patch-clamp techniques is revolutionizing the way to census the primate neocortex, enabling a multimodal neuronal atlas to be established in great detail: (1) single-cell/single-nucleus RNA-seq technology establishes high-throughput transcriptomic references, covering all major transcriptomic cell types; (2) patch-seq links the morphological and electrophysiological features to the transcriptomic reference; (3) multicell patch-clamp delineates the principles of local connectivity. Here, we review the applications of these technologies in the primate neocortex and discuss the current advances and tentative gaps for a comprehensive understanding of the primate neocortex.
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Affiliation(s)
- Yuhui Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mingting Shao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhao-Zhe Hao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mengyao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Nana Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, 510080, China.
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4
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Hamid A, Gutierrez A, Munroe J, Syed MH. The Drivers of Diversity: Integrated genetic and hormonal cues regulate neural diversity. Semin Cell Dev Biol 2023; 142:23-35. [PMID: 35915026 DOI: 10.1016/j.semcdb.2022.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/06/2022] [Accepted: 07/17/2022] [Indexed: 11/17/2022]
Abstract
Proper functioning of the nervous system relies not only on the generation of a vast repertoire of distinct neural cell types but also on the precise neural circuitry within them. How the generation of highly diverse neural populations is regulated during development remains a topic of interest. Landmark studies in Drosophila have identified the genetic and temporal cues regulating neural diversity and thus have provided valuable insights into our understanding of temporal patterning of the central nervous system. The development of the Drosophila central complex, which is mostly derived from type II neural stem cell (NSC) lineages, showcases how a small pool of NSCs can give rise to vast and distinct progeny. Similar to the human outer subventricular zone (OSVZ) neural progenitors, type II NSCs generate intermediate neural progenitors (INPs) to expand and diversify lineages that populate higher brain centers. Each type II NSC has a distinct spatial identity and timely regulated expression of many transcription factors and mRNA binding proteins. Additionally, INPs derived from them show differential expression of genes depending on their birth order. Together type II NSCs and INPs display a combinatorial temporal patterning that expands neural diversity of the central brain lineages. We cover advances in current understanding of type II NSC temporal patterning and discuss similarities and differences in temporal patterning mechanisms of various NSCs with a focus on how cell-intrinsic and extrinsic hormonal cues regulate temporal transitions in NSCs during larval development. Cell extrinsic ligands activate conserved signaling pathways and extrinsic hormonal cues act as a temporal switch that regulate temporal progression of the NSCs. We conclude by elaborating on how a progenitor's temporal code regulates the fate specification and identity of distinct neural types. At the end, we also discuss open questions in linking developmental cues to neural identity, circuits, and underlying behaviors in the adult fly.
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Affiliation(s)
- Aisha Hamid
- Department of Biology, University of New Mexico, Albuquerque, NM 87113, USA
| | - Andrew Gutierrez
- Department of Biology, University of New Mexico, Albuquerque, NM 87113, USA
| | - Jordan Munroe
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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5
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Fu X, Huang YP, Lindeman S, Mago A, Fukunaga I. Dense and Sparse Labelling of Mitral Cells by Oral and Intraperitoneal Routes of Tamoxifen Administration. Methods Mol Biol 2023; 2710:185-193. [PMID: 37688733 DOI: 10.1007/978-1-0716-3425-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2023]
Abstract
Cell type-specific labelling and manipulation using Cre-driver lines have become integral to analyses of neuronal circuits in the brain. To study how mitral cells of the olfactory bulb process olfactory information and how they contribute to behavior, an inducible Cre-driver line, Lbhd2-CreERT2, can be used. In this chapter, we describe two methods for administering tamoxifen. The first method achieves a dense recombination pattern using tamoxifen-containing food, while the second method involving an intraperitoneal injection is suited for sparse labelling.
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Affiliation(s)
- Xiaochen Fu
- Sensory and Behavioural Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yu-Pei Huang
- Sensory and Behavioural Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sander Lindeman
- Sensory and Behavioural Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Adam Mago
- Sensory and Behavioural Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Izumi Fukunaga
- Sensory and Behavioural Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
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6
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Medina S, Ihrie RA, Irish JM. Learning cell identity in immunology, neuroscience, and cancer. Semin Immunopathol 2023; 45:3-16. [PMID: 36534139 PMCID: PMC9762661 DOI: 10.1007/s00281-022-00976-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022]
Abstract
Suspension and imaging cytometry techniques that simultaneously measure hundreds of cellular features are powering a new era of cell biology and transforming our understanding of human tissues and tumors. However, a central challenge remains in learning the identities of unexpected or novel cell types. Cell identification rubrics that could assist trainees, whether human or machine, are not always rigorously defined, vary greatly by field, and differentially rely on cell intrinsic measurements, cell extrinsic tissue measurements, or external contextual information such as clinical outcomes. This challenge is especially acute in the context of tumors, where cells aberrantly express developmental programs that are normally time, location, or cell-type restricted. Well-established fields have contrasting practices for cell identity that have emerged from convention and convenience as much as design. For example, early immunology focused on identifying minimal sets of protein features that mark individual, functionally distinct cells. In neuroscience, features including morphology, development, and anatomical location were typical starting points for defining cell types. Both immunology and neuroscience now aim to link standardized measurements of protein or RNA to informative cell functions such as electrophysiology, connectivity, lineage potential, phospho-protein signaling, cell suppression, and tumor cell killing ability. The expansion of automated, machine-driven methods for learning cell identity has further created an urgent need for a harmonized framework for distinguishing cell identity across fields and technology platforms. Here, we compare practices in the fields of immunology and neuroscience, highlight concepts from each that might work well in the other, and propose ways to implement these ideas to study neural and immune cell interactions in brain tumors and associated model systems.
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Affiliation(s)
- Stephanie Medina
- grid.152326.10000 0001 2264 7217Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Rebecca A. Ihrie
- grid.152326.10000 0001 2264 7217Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Jonathan M. Irish
- grid.152326.10000 0001 2264 7217Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
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7
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Wang N, Langfelder P, Stricos M, Ramanathan L, Richman JB, Vaca R, Plascencia M, Gu X, Zhang S, Tamai TK, Zhang L, Gao F, Ouk K, Lu X, Ivanov LV, Vogt TF, Lu QR, Morton AJ, Colwell CS, Aaronson JS, Rosinski J, Horvath S, Yang XW. Mapping brain gene coexpression in daytime transcriptomes unveils diurnal molecular networks and deciphers perturbation gene signatures. Neuron 2022; 110:3318-3338.e9. [PMID: 36265442 PMCID: PMC9665885 DOI: 10.1016/j.neuron.2022.09.028] [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: 05/11/2022] [Revised: 08/16/2022] [Accepted: 09/22/2022] [Indexed: 01/07/2023]
Abstract
Brain tissue transcriptomes may be organized into gene coexpression networks, but their underlying biological drivers remain incompletely understood. Here, we undertook a large-scale transcriptomic study using 508 wild-type mouse striatal tissue samples dissected exclusively in the afternoons to define 38 highly reproducible gene coexpression modules. We found that 13 and 11 modules are enriched in cell-type and molecular complex markers, respectively. Importantly, 18 modules are highly enriched in daily rhythmically expressed genes that peak or trough with distinct temporal kinetics, revealing the underlying biology of striatal diurnal gene networks. Moreover, the diurnal coexpression networks are a dominant feature of daytime transcriptomes in the mouse cortex. We next employed the striatal coexpression modules to decipher the striatal transcriptomic signatures from Huntington's disease models and heterozygous null mice for 52 genes, uncovering novel functions for Prkcq and Kdm4b in oligodendrocyte differentiation and bipolar disorder-associated Trank1 in regulating anxiety-like behaviors and nocturnal locomotion.
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Affiliation(s)
- Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter Langfelder
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Matthew Stricos
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lalini Ramanathan
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeffrey B Richman
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Raymond Vaca
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mary Plascencia
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xiaofeng Gu
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shasha Zhang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - T Katherine Tamai
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Liguo Zhang
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Fuying Gao
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Koliane Ouk
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Xiang Lu
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Thomas F Vogt
- CHDI Management /CHDI Foundation, Princeton, NJ, USA
| | - Qing Richard Lu
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - A Jennifer Morton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Christopher S Colwell
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; UCLA Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Jim Rosinski
- CHDI Management /CHDI Foundation, Princeton, NJ, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - X William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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8
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Zeng H. What is a cell type and how to define it? Cell 2022; 185:2739-2755. [PMID: 35868277 DOI: 10.1016/j.cell.2022.06.031] [Citation(s) in RCA: 138] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/20/2022]
Abstract
Cell types are the basic functional units of an organism. Cell types exhibit diverse phenotypic properties at multiple levels, making them challenging to define, categorize, and understand. This review provides an overview of the basic principles of cell types rooted in evolution and development and discusses approaches to characterize and classify cell types and investigate how they contribute to the organism's function, using the mammalian brain as a primary example. I propose a roadmap toward a conceptual framework and knowledge base of cell types that will enable a deeper understanding of the dynamic changes of cellular function under healthy and diseased conditions.
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Affiliation(s)
- Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
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9
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Smith SJ, von Zastrow M. A Molecular Landscape of Mouse Hippocampal Neuromodulation. Front Neural Circuits 2022; 16:836930. [PMID: 35601530 PMCID: PMC9120848 DOI: 10.3389/fncir.2022.836930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/30/2022] [Indexed: 12/23/2022] Open
Abstract
Adaptive neuronal circuit function requires a continual adjustment of synaptic network parameters known as “neuromodulation.” This process is now understood to be based primarily on the binding of myriad secreted “modulatory” ligands such as dopamine, serotonin and the neuropeptides to G protein-coupled receptors (GPCRs) that, in turn, regulate the function of the ion channels that establish synaptic weights and membrane excitability. Many of the basic molecular mechanisms of neuromodulation are now known, but the organization of neuromodulation at a network level is still an enigma. New single-cell RNA sequencing data and transcriptomic neurotaxonomies now offer bright new lights to shine on this critical “dark matter” of neuroscience. Here we leverage these advances to explore the cell-type-specific expression of genes encoding GPCRs, modulatory ligands, ion channels and intervening signal transduction molecules in mouse hippocampus area CA1, with the goal of revealing broad outlines of this well-studied brain structure’s neuromodulatory network architecture.
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Affiliation(s)
- Stephen J Smith
- Allen Institute for Brain Science, Seattle, WA, United States
- *Correspondence: Stephen J Smith,
| | - Mark von Zastrow
- Departments of Psychiatry and Pharmacology, University of California, San Francisco, San Francisco, CA, United States
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10
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Rapti G. Open Frontiers in Neural Cell Type Investigations; Lessons From Caenorhabditis elegans and Beyond, Toward a Multimodal Integration. Front Neurosci 2022; 15:787753. [PMID: 35321480 PMCID: PMC8934944 DOI: 10.3389/fnins.2021.787753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Nervous system cells, the building blocks of circuits, have been studied with ever-progressing resolution, yet neural circuits appear still resistant to schemes of reductionist classification. Due to their sheer numbers, complexity and diversity, their systematic study requires concrete classifications that can serve reduced dimensionality, reproducibility, and information integration. Conventional hierarchical schemes transformed through the history of neuroscience by prioritizing criteria of morphology, (electro)physiological activity, molecular content, and circuit function, influenced by prevailing methodologies of the time. Since the molecular biology revolution and the recent advents in transcriptomics, molecular profiling gains ground toward the classification of neurons and glial cell types. Yet, transcriptomics entails technical challenges and more importantly uncovers unforeseen spatiotemporal heterogeneity, in complex and simpler nervous systems. Cells change states dynamically in space and time, in response to stimuli or throughout their developmental trajectory. Mapping cell type and state heterogeneity uncovers uncharted terrains in neurons and especially in glial cell biology, that remains understudied in many aspects. Examining neurons and glial cells from the perspectives of molecular neuroscience, physiology, development and evolution highlights the advantage of multifaceted classification schemes. Among the amalgam of models contributing to neuroscience research, Caenorhabditis elegans combines nervous system anatomy, lineage, connectivity and molecular content, all mapped at single-cell resolution, and can provide valuable insights for the workflow and challenges of the multimodal integration of cell type features. This review reflects on concepts and practices of neuron and glial cells classification and how research, in C. elegans and beyond, guides nervous system experimentation through integrated multidimensional schemes. It highlights underlying principles, emerging themes, and open frontiers in the study of nervous system development, regulatory logic and evolution. It proposes unified platforms to allow integrated annotation of large-scale datasets, gene-function studies, published or unpublished findings and community feedback. Neuroscience is moving fast toward interdisciplinary, high-throughput approaches for combined mapping of the morphology, physiology, connectivity, molecular function, and the integration of information in multifaceted schemes. A closer look in mapped neural circuits and understudied terrains offers insights for the best implementation of these approaches.
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11
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Margolin DH, Brice NL, Davidson A, Matthews KL, Carlton MBL. A Phase I, First-In-Human, Healthy Volunteer Study to Investigate the Safety, Tolerability, and Pharmacokinetics of CVN424, a Novel GPR6 Inverse Agonist for Parkinson's Disease. J Pharmacol Exp Ther 2022; 381:33-41. [PMID: 35110393 DOI: 10.1124/jpet.121.000842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/20/2022] [Indexed: 11/22/2022] Open
Abstract
CVN424 is a novel small molecule and first-in-class candidate therapeutic to selectively modulate GPR6, an orphan G-protein coupled receptor. Expression of GPR6 is largely confined to the subset of striatal projection neurons that give rise to the indirect (striatopallidal) pathway, important in the control of movement. CVN424 improves motor function in preclinical animal models of Parkinson's disease. Here we report results of a phase 1, first-in-human study investigating the safety, tolerability, and pharmacokinetics of CVN424 in healthy volunteers. The study (NCT03657030) was randomized, double-blind, and placebo controlled. CVN424 was orally administered in ascending doses to successive cohorts as inpatients in a clinical research unit. Single doses ranged from 1 mg to 225 mg, and repeated (7 day) daily doses were 25 mg, 75 mg, or 150 mg. CVN424 peak plasma concentrations were reached within 2h post-dose in the fasted state and increased with increasing dose. Dosing after a standardized high-fat meal reduced and delayed the peak plasma concentration but total plasma exposure was similar. Mean terminal half-life ranged from 30h to 41h. CVN424 was generally well tolerated: no serious or severe adverse effects were observed, and there were no clinically significant changes in vital signs or laboratory parameters. We conclude that CVN424, a nondopaminergic compound that modulates a novel therapeutic target, was safe and well tolerated. A phase 2 study in patients with Parkinson's disease is underway. Significance Statement This is the first-in-human clinical study of a first-in-class candidate therapeutic. CVN424 modulates a novel drug target, GPR6, which is selectively expressed in a pathway in the brain that has been implicated in the motor dysfunction of patients with Parkinson's disease. This study paves the way for investigating this novel mechanism of action in patients with Parkinson's disease.
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12
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Kölsch Y, Hahn J, Sappington A, Stemmer M, Fernandes AM, Helmbrecht TO, Lele S, Butrus S, Laurell E, Arnold-Ammer I, Shekhar K, Sanes JR, Baier H. Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior. Neuron 2021; 109:645-662.e9. [PMID: 33357413 PMCID: PMC7897282 DOI: 10.1016/j.neuron.2020.12.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/09/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022]
Abstract
Retinal ganglion cells (RGCs) form an array of feature detectors, which convey visual information to central brain regions. Characterizing RGC diversity is required to understand the logic of the underlying functional segregation. Using single-cell transcriptomics, we systematically classified RGCs in adult and larval zebrafish, thereby identifying marker genes for >30 mature types and several developmental intermediates. We used this dataset to engineer transgenic driver lines, enabling specific experimental access to a subset of RGC types. Expression of one or few transcription factors often predicts dendrite morphologies and axonal projections to specific tectal layers and extratectal targets. In vivo calcium imaging revealed that molecularly defined RGCs exhibit specific functional tuning. Finally, chemogenetic ablation of eomesa+ RGCs, which comprise melanopsin-expressing types with projections to a small subset of central targets, selectively impaired phototaxis. Together, our study establishes a framework for systematically studying the functional architecture of the visual system.
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Affiliation(s)
- Yvonne Kölsch
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany; Graduate School of Systemic Neurosciences, Ludwig Maximilian University, 82152 Martinsried, Germany
| | - Joshua Hahn
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, CA 94720, USA
| | - Anna Sappington
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Manuel Stemmer
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - António M Fernandes
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Thomas O Helmbrecht
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Shriya Lele
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, CA 94720, USA
| | - Eva Laurell
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Irene Arnold-Ammer
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, California Institute for Quantitative Biosciences, QB3, Center for Computational Biology, UC Berkeley, Berkeley, CA 94720, USA.
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cell Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Herwig Baier
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany.
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13
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Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, Armañanzas R, Ascoli GA, Bielza C, Bokharaie V, Bergmann TB, Bystron I, Capogna M, Chang Y, Clemens A, de Kock CPJ, DeFelipe J, Dos Santos SE, Dunville K, Feldmeyer D, Fiáth R, Fishell GJ, Foggetti A, Gao X, Ghaderi P, Goriounova NA, Güntürkün O, Hagihara K, Hall VJ, Helmstaedter M, Herculano-Houzel S, Hilscher MM, Hirase H, Hjerling-Leffler J, Hodge R, Huang J, Huda R, Khodosevich K, Kiehn O, Koch H, Kuebler ES, Kühnemund M, Larrañaga P, Lelieveldt B, Louth EL, Lui JH, Mansvelder HD, Marin O, Martinez-Trujillo J, Chameh HM, Mohapatra AN, Munguba H, Nedergaard M, Němec P, Ofer N, Pfisterer UG, Pontes S, Redmond W, Rossier J, Sanes JR, Scheuermann RH, Serrano-Saiz E, Staiger JF, Somogyi P, Tamás G, Tolias AS, Tosches MA, García MT, Wozny C, Wuttke TV, Liu Y, Yuan J, Zeng H, Lein E. A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci 2020; 23:1456-1468. [PMID: 32839617 PMCID: PMC7683348 DOI: 10.1038/s41593-020-0685-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glial cell types, partly due to limited data. Single-cell transcriptomics is enabling, for the first time, systematic high-throughput measurements of cortical cells and generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data reveal clusters that often correspond to cell types previously defined by morphological or physiological criteria and that appear conserved across cortical areas and species. To capitalize on these new methods, we propose the adoption of a transcriptome-based taxonomy of cell types for mammalian neocortex. This classification should be hierarchical and use a standardized nomenclature. It should be based on a probabilistic definition of a cell type and incorporate data from different approaches, developmental stages and species. A community-based classification and data aggregation model, such as a knowledge graph, could provide a common foundation for the study of cortical circuits. This community-based classification, nomenclature and data aggregation could serve as an example for cell type atlases in other parts of the body.
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Affiliation(s)
| | | | | | | | - Detlev Arendt
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ruben Armañanzas
- George Mason University, Fairfax, VA, USA
- BrainScope Company Inc., Bethesda, MD, USA
| | | | | | - Vahid Bokharaie
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | | | | | - Marco Capogna
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - YoonJeung Chang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | - Richárd Fiáth
- Research Centre for Natural Sciences, Budapest, Hungary
| | | | | | - Xuefan Gao
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Parviz Ghaderi
- École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | | | - Kenta Hagihara
- Friedrich Miescher Institute for Biological Research, Basel, Switzerland
| | | | | | | | - Markus M Hilscher
- Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | | | | | | | - Josh Huang
- Cold Spring Harbor Laboratory, Laurel Hollow, NY, USA
| | - Rafiq Huda
- WM Keck Center for Collaborative Neuroscience, Department of Cell Biology and Neuroscience, Rutgers University - New Brunswick, Piscataway, NJ, USA
| | | | - Ole Kiehn
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | | | - Eric S Kuebler
- Robarts Research Institute, Western University, London, Ontario, Canada
| | | | | | | | | | - Jan H Lui
- Stanford University, Stanford, CA, USA
| | | | | | - Julio Martinez-Trujillo
- Schulich School of Medicine and Dentistry, Departments of Physiology, Pharmacology and Psychiatry, University of Western Ontario, London, Ontario, Canada
| | | | | | | | | | | | | | | | | | | | | | | | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, CA, USA
| | | | - Jochen F Staiger
- Institute for Neuroanatomy, University of Göttingen, Göttingen, Germany
| | | | | | | | | | | | - Christian Wozny
- University of Strathclyde, Glasgow, UK
- MSH Medical School, Hamburg, Germany
| | - Thomas V Wuttke
- Departments of Neurosurgery and of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Yong Liu
- University of Copenhagen, Copenhagen, Denmark
| | - Juan Yuan
- Karolinska Institutet, Stockholm, Sweden
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
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14
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Roussarie JP, Rodriguez-Rodriguez P. Deciphering cell-type specific signal transduction in the brain: Challenges and promises. ADVANCES IN PHARMACOLOGY 2020; 90:145-171. [PMID: 33706931 DOI: 10.1016/bs.apha.2020.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Signal transduction designates the set of molecular events that take place within a cell upon extracellular stimulation to mediate a functional outcome. Decades after the discovery that dopamine triggers opposing signaling pathways in D1- and D2-expressing medium spiny neurons, it is now clear that there are as many different flavors of signaling pathways in the brain as there are neuron types. One of the biggest challenges in molecular neuroscience is to elucidate cell-type specific signaling, in order to understand neurological diseases with regional vulnerability, but also to identify targets for precision drugs devoid of off-target effects. Here, we make a case for the importance of the study of neuron-type specific molecular characteristics. We then review the technologies that exist to study neurons in their full diversity and highlight their disease-relevant idiosyncrasies.
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Affiliation(s)
- Jean-Pierre Roussarie
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, United States.
| | - Patricia Rodriguez-Rodriguez
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, United States; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
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15
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Ozdemir AT, Lagler M, Lagoun S, Malagon-Vina H, Lasztóczi B, Klausberger T. Unexpected Rule-Changes in a Working Memory Task Shape the Firing of Histologically Identified Delay-Tuned Neurons in the Prefrontal Cortex. Cell Rep 2020; 30:1613-1626.e4. [DOI: 10.1016/j.celrep.2019.12.102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/28/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022] Open
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16
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Scammell TE, Jackson AC, Franks NP, Wisden W, Dauvilliers Y. Histamine: neural circuits and new medications. Sleep 2019; 42:5099478. [PMID: 30239935 PMCID: PMC6335869 DOI: 10.1093/sleep/zsy183] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Indexed: 12/12/2022] Open
Abstract
Histamine was first identified in the brain about 50 years ago, but only in the last few years have researchers gained an understanding of how it regulates sleep/wake behavior. We provide a translational overview of the histamine system, from basic research to new clinical trials demonstrating the usefulness of drugs that enhance histamine signaling. The tuberomammillary nucleus is the sole neuronal source of histamine in the brain, and like many of the arousal systems, histamine neurons diffusely innervate the cortex, thalamus, and other wake-promoting brain regions. Histamine has generally excitatory effects on target neurons, but paradoxically, histamine neurons may also release the inhibitory neurotransmitter GABA. New research demonstrates that activity in histamine neurons is essential for normal wakefulness, especially at specific circadian phases, and reducing activity in these neurons can produce sedation. The number of histamine neurons is increased in narcolepsy, but whether this affects brain levels of histamine is controversial. Of clinical importance, new compounds are becoming available that enhance histamine signaling, and clinical trials show that these medications reduce sleepiness and cataplexy in narcolepsy.
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Affiliation(s)
- Thomas E Scammell
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Alexander C Jackson
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT
| | - Nicholas P Franks
- Department of Life Sciences and UK Dementia Research Institute, Imperial College London, UK
| | - William Wisden
- Department of Life Sciences and UK Dementia Research Institute, Imperial College London, UK
| | - Yves Dauvilliers
- Centre National de Référence Narcolepsie Hypersomnies, Unité des Troubles du Sommeil, Service de Neurologie, Hôpital Gui-de-Chauliac, Université Montpellier, INSERM, Montpellier, France
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17
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Bhattacherjee A, Djekidel MN, Chen R, Chen W, Tuesta LM, Zhang Y. Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction. Nat Commun 2019; 10:4169. [PMID: 31519873 PMCID: PMC6744514 DOI: 10.1038/s41467-019-12054-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/12/2019] [Indexed: 11/15/2022] Open
Abstract
Coordinated activity-induced transcriptional changes across multiple neuron subtypes of the prefrontal cortex (PFC) play a pivotal role in encoding and regulating major cognitive behaviors. Yet, the specific transcriptional programs in each neuron subtype remain unknown. Using single-cell RNA sequencing (scRNA-seq), here we comprehensively classify all unique cell subtypes in the PFC. We analyze transcriptional dynamics of each cell subtype under a naturally adaptive and an induced condition. Adaptive changes during adolescence (between P21 and P60), a highly dynamic phase of postnatal neuroplasticity, profoundly impacted transcription in each neuron subtype, including cell type-specific regulation of genes implicated in major neuropsychiatric disorders. On the other hand, an induced plasticity evoked by chronic cocaine addiction resulted in progressive transcriptional changes in multiple neuron subtypes and became most pronounced upon prolonged drug withdrawal. Our findings lay a foundation for understanding cell type-specific postnatal transcriptional dynamics under normal PFC function and in neuropsychiatric disease states.
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Affiliation(s)
- Aritra Bhattacherjee
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Mohamed Nadhir Djekidel
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Renchao Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Wenqiang Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Luis M Tuesta
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA.
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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18
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Ahmed NY, Knowles R, Dehorter N. New Insights Into Cholinergic Neuron Diversity. Front Mol Neurosci 2019; 12:204. [PMID: 31551706 PMCID: PMC6736589 DOI: 10.3389/fnmol.2019.00204] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022] Open
Abstract
Cholinergic neurons comprise a small population of cells in the striatum but have fundamental roles in fine tuning brain function, and in the etiology of neurological and psychiatric disorders such as Parkinson’s disease (PD) or schizophrenia. The process of developmental cell specification underlying neuronal identity and function is an area of great current interest. There has been significant progress in identifying the developmental origins, commonalities in molecular markers, and physiological properties of the cholinergic neurons. Currently, we are aware of a number of key factors that promote cholinergic fate during development. However, the extent of cholinergic cell diversity is still largely underestimated. New insights into the biological basis of their specification indicate that cholinergic neurons may be far more diverse than previously thought. This review article, highlights the physiological features and the synaptic properties that segregate cholinergic cell subtypes. It provides an accurate picture of cholinergic cell diversity underlying their organization and function in neuronal networks. This review article, also discusses current challenges in deciphering the logic of the cholinergic cell heterogeneity that plays a fundamental role in the control of neural processes in health and disease.
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Affiliation(s)
- Noorya Yasmin Ahmed
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Rhys Knowles
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Nathalie Dehorter
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
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19
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Li S, Quan T, Zhou H, Huang Q, Guan T, Chen Y, Xu C, Kang H, Li A, Fu L, Luo Q, Gong H, Zeng S. Brain-Wide Shape Reconstruction of a Traced Neuron Using the Convex Image Segmentation Method. Neuroinformatics 2019; 18:199-218. [PMID: 31396858 DOI: 10.1007/s12021-019-09434-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Neuronal shape reconstruction is a helpful technique for establishing neuron identity, inferring neuronal connections, mapping neuronal circuits, and so on. Advances in optical imaging techniques have enabled data collection that includes the shape of a neuron across the whole brain, considerably extending the scope of neuronal anatomy. However, such datasets often include many fuzzy neurites and many crossover regions that neurites are closely attached, which make neuronal shape reconstruction more challenging. In this study, we proposed a convex image segmentation model for neuronal shape reconstruction that segments a neurite into cross sections along its traced skeleton. Both the sparse nature of gradient images and the rule that fuzzy neurites usually have a small radius are utilized to improve neuronal shape reconstruction in regions with fuzzy neurites. Because the model is closely related to the traced skeleton point, we can use this relationship for identifying neurite with crossover regions. We demonstrated the performance of our model on various datasets, including those with fuzzy neurites and neurites with crossover regions, and we verified that our model could robustly reconstruct the neuron shape on a brain-wide scale.
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Affiliation(s)
- Shiwei Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Tingwei Quan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China. .,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China. .,School of Mathematics and Economics, Hubei University of Education, Wuhan, 430205, Hubei, China.
| | - Hang Zhou
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qing Huang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Tao Guan
- School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yijun Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Cheng Xu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Hongtao Kang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Ling Fu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Shaoqun Zeng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
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20
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Sestan N, State MW. Lost in Translation: Traversing the Complex Path from Genomics to Therapeutics in Autism Spectrum Disorder. Neuron 2019; 100:406-423. [PMID: 30359605 DOI: 10.1016/j.neuron.2018.10.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/29/2018] [Accepted: 10/08/2018] [Indexed: 12/24/2022]
Abstract
Recent progress in the genomics of non-syndromic autism spectrum disorder (nsASD) highlights rare, large-effect, germline, heterozygous de novo coding mutations. This distinguishes nsASD from later-onset psychiatric disorders where gene discovery efforts have predominantly yielded common alleles of small effect. These differences point to distinctive opportunities for clarifying the neurobiology of nsASD and developing novel treatments. We argue that the path ahead also presents key challenges, including distinguishing human pathophysiology from the potentially pleiotropic neurobiology mediated by established risk genes. We present our view of some of the conceptual limitations of traditional studies of model organisms, suggest a strategy focused on investigating the convergence of multiple nsASD genes, and propose that the detailed characterization of the molecular and cellular landscapes of developing human brain is essential to illuminate disease mechanisms. Finally, we address how recent advances are leading to novel strategies for therapeutics that target various points along the path from genes to behavior.
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Affiliation(s)
- Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Departments of Genetics, of Psychiatry, and of Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Matthew W State
- Department of Psychiatry, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, Institute for Human Genetics, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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21
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Lagerman CE, López Acevedo SN, Fahad AS, Hailemariam AT, Madan B, DeKosky BJ. Ultrasonically-guided flow focusing generates precise emulsion droplets for high-throughput single cell analyses. J Biosci Bioeng 2019; 128:226-233. [PMID: 30904454 PMCID: PMC6688500 DOI: 10.1016/j.jbiosc.2019.01.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 12/27/2022]
Abstract
Emulsion-based techniques have dramatically advanced our understanding of single-cell biology and complex single-cell features over the past two decades. Most approaches for precise single cell isolation rely on microfluidics, which has proven highly effective but requires substantial investment in equipment and expertise that can be difficult to access for researchers that specialize in other areas of bioengineering and molecular biotechnology. Inspired by the robust droplet generation technologies in modern flow cytometry instrumentation, here we established a new platform for high-throughput isolation of single cells within droplets of tunable sizes by combining flow focusing with ultrasonic vibration for rapid and effective droplet formation. Application of ultrasonic pressure waves to the flowing jet provided enhanced control of emulsion droplet size, permitting capture of 25,000 to 50,000 single cells per minute. As an example application, we applied this new droplet generation platform to sequence the antibody variable region heavy and light chain pairings (VH:VL) from large repertoires of single B cells. We demonstrated the recovery of > 40,000 paired CDRH3:CDRL3 antibody clusters from a single individual, validating that these droplet systems can enable the genetic analysis of very large single-cell populations. These accessible new technologies will allow rapid, large-scale, and precise single-cell analyses for a broad range of bioengineering and molecular biotechnology applications.
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Affiliation(s)
- Colton E Lagerman
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS 66044, USA
| | - Sheila N López Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Amen T Hailemariam
- Department of Biochemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Brandon J DeKosky
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS 66044, USA; Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA; Kansas Vaccine Institute, The University of Kansas, Lawrence, KS 66044, USA.
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22
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Lamonica JM, Zhou Z. Disentangling chromatin architecture to gain insights into the etiology of brain disorders. Curr Opin Genet Dev 2019; 55:76-81. [PMID: 31323465 DOI: 10.1016/j.gde.2019.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/09/2019] [Accepted: 06/15/2019] [Indexed: 11/25/2022]
Abstract
Chromatin organization, together with DNA and histone modifications, is directly linked to the spatiotemporal control of gene expression that specifies and maintains cell type-specific functions. This is particularly important in the brain where hundreds of cell types with distinct functions reside. Recent advances in molecular and computational technologies have enabled the query of chromatin architecture at unprecedented resolution and detail. Here, we review recent studies on the emerging importance of chromatin architecture in the pathogenesis of brain disorders, with emphasis on schizophrenia, autism spectrum disorders (ASD), and unstable repeat expansion disorders. These studies provide molecular insights into how these brain disorders arise at the level of chromatin architecture and implicate new therapeutic directions.
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Affiliation(s)
- Janine M Lamonica
- Department of Genetics and Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Zhaolan Zhou
- Department of Genetics and Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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23
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Mukamel EA, Ngai J. Perspectives on defining cell types in the brain. Curr Opin Neurobiol 2019; 56:61-68. [PMID: 30530112 PMCID: PMC6551297 DOI: 10.1016/j.conb.2018.11.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/10/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022]
Abstract
The diversity of brain cell types was one of the earliest observations in modern neuroscience and continues to be one of the central concerns of current neuroscience research. Despite impressive recent progress, including single cell transcriptome and epigenome profiling as well as anatomical methods, we still lack a complete census or taxonomy of brain cell types. We argue this is due partly to the conceptual difficulty in defining a cell type. By considering the biological drivers of cell identity, such as networks of genes and gene regulatory elements, we propose a definition of cell type that emphasizes self-stabilizing regulation. We explore the predictions and hypotheses that arise from this definition. Integration of data from multiple modalities, including molecular profiling of genes and gene products, epigenetic landscape, cellular morphology, connectivity, and physiology, will be essential for a meaningful and broadly useful definition of brain cell types.
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Affiliation(s)
- Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, CA 92037, United States.
| | - John Ngai
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, CA 94720, United States.
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24
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Fan X, Markram H. A Brief History of Simulation Neuroscience. Front Neuroinform 2019; 13:32. [PMID: 31133838 PMCID: PMC6513977 DOI: 10.3389/fninf.2019.00032] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/12/2019] [Indexed: 12/19/2022] Open
Abstract
Our knowledge of the brain has evolved over millennia in philosophical, experimental and theoretical phases. We suggest that the next phase is simulation neuroscience. The main drivers of simulation neuroscience are big data generated at multiple levels of brain organization and the need to integrate these data to trace the causal chain of interactions within and across all these levels. Simulation neuroscience is currently the only methodology for systematically approaching the multiscale brain. In this review, we attempt to reconstruct the deep historical paths leading to simulation neuroscience, from the first observations of the nerve cell to modern efforts to digitally reconstruct and simulate the brain. Neuroscience began with the identification of the neuron as the fundamental unit of brain structure and function and has evolved towards understanding the role of each cell type in the brain, how brain cells are connected to each other, and how the seemingly infinite networks they form give rise to the vast diversity of brain functions. Neuronal mapping is evolving from subjective descriptions of cell types towards objective classes, subclasses and types. Connectivity mapping is evolving from loose topographic maps between brain regions towards dense anatomical and physiological maps of connections between individual genetically distinct neurons. Functional mapping is evolving from psychological and behavioral stereotypes towards a map of behaviors emerging from structural and functional connectomes. We show how industrialization of neuroscience and the resulting large disconnected datasets are generating demand for integrative neuroscience, how the scale of neuronal and connectivity maps is driving digital atlasing and digital reconstruction to piece together the multiple levels of brain organization, and how the complexity of the interactions between molecules, neurons, microcircuits and brain regions is driving brain simulation to understand the interactions in the multiscale brain.
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Affiliation(s)
- Xue Fan
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
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25
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Majolo F, Marinowic DR, Machado DC, Da Costa JC. Important advances in Alzheimer's disease from the use of induced pluripotent stem cells. J Biomed Sci 2019; 26:15. [PMID: 30728025 PMCID: PMC6366077 DOI: 10.1186/s12929-019-0501-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/09/2019] [Indexed: 12/14/2022] Open
Abstract
Among the various types of dementia, Alzheimer’s disease (AD) is the most prevalent and is clinically defined as the appearance of progressive deficits in cognition and memory. Considering that AD is a central nervous system disease, getting tissue from the patient to study the disease before death is challenging. The discovery of the technique called induced pluripotent stem cells (iPSCs) allows to reprogram the patient’s somatic cells to a pluripotent state by the forced expression of a defined set of transcription factors. Many studies have shown promising results and made important conclusions beyond AD using iPSCs approach. Due to the accumulating knowledge related to this topic and the important advances obtained until now, we review, using PubMed, and present an update of all publications related to AD from the use of iPSCs. The first iPSCs generated for AD were carried out in 2011 by Yahata et al. (PLoS One 6:e25788, 2011) and Yaqi et al. (Hum Mol Genet 20:4530–9, 2011). Like other authors, both authors used iPSCs as a pre-clinical tool for screening therapeutic compounds. This approach is also essential to model AD, testing early toxicity and efficacy, and developing a platform for drug development. Considering that the iPSCs technique is relatively recent, we can consider that the AD field received valuable contributions from iPSCs models, contributing to our understanding and the treatment of this devastating disorder.
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Affiliation(s)
- Fernanda Majolo
- Brain Institute of Rio Grande do Sul (BraIns), Postgraduate Program in Medicine and Health Sciences (PUCRS), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, 90610000, Brazil.
| | - Daniel Rodrigo Marinowic
- Brain Institute of Rio Grande do Sul (BraIns), Postgraduate Program in Medicine and Health Sciences (PUCRS), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, 90610000, Brazil
| | - Denise Cantarelli Machado
- Brain Institute of Rio Grande do Sul (BraIns), Postgraduate Program in Medicine and Health Sciences (PUCRS), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, 90610000, Brazil
| | - Jaderson Costa Da Costa
- Brain Institute of Rio Grande do Sul (BraIns), Postgraduate Program in Medicine and Health Sciences (PUCRS), Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, 90610000, Brazil
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26
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Lee JH, Kim JH, Kim S, Cho KS, Lee SB. Chromatin Changes Associated with Neuronal Maintenance and Their Pharmacological Application. Curr Neuropharmacol 2018; 16:118-125. [PMID: 28571546 PMCID: PMC5883374 DOI: 10.2174/1570159x15666170601124220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/03/2017] [Accepted: 05/31/2017] [Indexed: 01/07/2023] Open
Abstract
Background: The transcriptional control of neuronal specification and early development has been intensively stud-ied over the past few decades. However, relatively little is known about transcriptional programs associated with the mainte-nance of terminally differentiated neuronal cells with respect to their functions, structures, and cell type-specific identity features. Methods: Notably, largely because of the recent advances in related techniques such as next generation sequencing and chromatin immunoprecipitation sequencing, the physiological implications of system-wide regulation of gene expression through changes in chromatin states have begun to be extensively studied in various contexts and systems, including the nervous system. Results: Here, we attempt to review our current understanding of the link between chromatin changes and neuronal mainte-nance in the period of life after the completion of neuronal development. Perturbations involving chromatin changes in the system-wide transcriptional control are believed to be closely associated with diverse aspects of neuronal aging and neuro-degenerative conditions. Conclusion: In this review, we focused on heterochromatin and epigenetic dysregulation in neurodegenerative conditions as well as neuronal aging, the most important risk factor leading to neuronal degeneration, in order to highlight the close association between chromatin changes and neuronal maintenance. Lastly, we reviewed the cur-rently available and potential future applications of pharmacological control of the chromatin states associated with neuronal maintenance.
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Affiliation(s)
- Jang Ho Lee
- Department of Biological Sciences, Konkuk University, Seoul 05029. Korea
| | - Jeong-Hoon Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon 34113, Korea
| | - Sunhong Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Biomolecular Science, University of Science and Technology, Daejeon 34113, Korea
| | - Kyoung Sang Cho
- Department of Biological Sciences, Konkuk University, Seoul 05029. Korea
| | - Sung Bae Lee
- Department of Brain & Cognitive Sciences, DGIST, Daegu 42988. Korea
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27
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Abrahao KP, Lovinger DM. Classification of GABAergic neuron subtypes from the globus pallidus using wild-type and transgenic mice. J Physiol 2018; 596:4219-4235. [PMID: 29917235 PMCID: PMC6117588 DOI: 10.1113/jp276079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/07/2018] [Indexed: 01/08/2023] Open
Abstract
KEY POINTS Classifying different subtypes of neurons in deep brain structures is a challenge and is crucial to better understand brain function. Understanding the diversity of neurons in the globus pallidus (GP), a brain region positioned to influence afferent and efferent information processing within basal ganglia, could help to explain a variety of brain functions. We present a classification of neurons from the GP using electrophysiological data from wild-type mice and confirmation using transgenic mice. This work will help researchers to identify specific neuronal subsets in the GP of wild-type mice when transgenic mice with labelled neurons are lacking. ABSTRACT Classification of the extensive neuronal diversity in the brain is fundamental for neuroscience. The globus pallidus external segment (GPe), also referred to as the globus pallidus in rodents, is a large nucleus located in the core of the basal ganglia whose circuitry is implicated in action control, decision-making and reward. Although considerable progress has been made in characterizing different GPe neuronal subtypes, no work has directly attempted to characterize these neurons in non-transgenic mice. Here, we provide data showing the degree of overlap in expression of neuronal PAS domain protein (Npas1), LIM homeobox 6 (Lhx6), parvalbumin (PV) and transcription factor FoxP2 biomarkers in mouse GPe neurons. We used an unbiased statistical method to classify neurons based on electrophysiological properties from nearly 200 neurons from C57BL/6J mice. In addition, we examined the subregion distribution of the neuronal subtypes. Cluster analysis using firing rate and hyperpolarization-induced membrane potential sag variables revealed three distinct neuronal clusters: type 1, characterized by low firing rate and small sag potential; type 2, with low firing rate and larger sag potential; and type 3, with high firing rate and small sag potential. We used other electrophysiological variables and data from marker-expressing neurons to evaluate the clusters. We propose that the GPe GABAergic neurons should be classified into three subgroups: arkypallidal, low-firing prototypical and high-firing prototypical neurons. This work will help researchers identify GPe neuron subtypes when transgenic mice with labelled neurons cannot be used.
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Affiliation(s)
- Karina P. Abrahao
- Laboratory for Integrative Neuroscience, Division of Intramural Clinical and Biological Research, National Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthBethesdaMDUSA
| | - David M. Lovinger
- Laboratory for Integrative Neuroscience, Division of Intramural Clinical and Biological Research, National Institute on Alcohol Abuse and AlcoholismNational Institutes of HealthBethesdaMDUSA
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28
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Yuan Y, Xie S, Darnell JC, Darnell AJ, Saito Y, Phatnani H, Murphy EA, Zhang C, Maniatis T, Darnell RB. Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons. Genome Biol 2018; 19:117. [PMID: 30111345 PMCID: PMC6092797 DOI: 10.1186/s13059-018-1493-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/24/2018] [Indexed: 12/30/2022] Open
Abstract
Background Alternative RNA processing plays an essential role in shaping cell identity and connectivity in the central nervous system. This is believed to involve differential regulation of RNA processing in various cell types. However, in vivo study of cell type-specific post-transcriptional regulation has been a challenge. Here, we describe a sensitive and stringent method combining genetics and CLIP (crosslinking and immunoprecipitation) to globally identify regulatory interactions between NOVA and RNA in the mouse spinal cord motoneurons. Results We developed a means of undertaking motoneuron-specific CLIP to explore motoneuron-specific protein–RNA interactions relative to studies of the whole spinal cord in mouse. This allowed us to pinpoint differential RNA regulation specific to motoneurons, revealing a major role for NOVA in regulating cytoskeleton interactions in motoneurons. In particular, NOVA specifically promotes the palmitoylated isoform of the cytoskeleton protein Septin 8 in motoneurons, which enhances dendritic arborization. Conclusions Our study demonstrates that cell type-specific RNA regulation is important for fine tuning motoneuron physiology and highlights the value of defining RNA processing regulation at single cell type resolution. Electronic supplementary material The online version of this article (10.1186/s13059-018-1493-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuan Yuan
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA
| | - Shirley Xie
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA
| | - Jennifer C Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA
| | - Andrew J Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA
| | - Yuhki Saito
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA
| | - Hemali Phatnani
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Elisabeth A Murphy
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.,Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.,Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA. .,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave., New York, NY, 10065, USA.
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29
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The sacral autonomic outflow is parasympathetic: Langley got it right. Clin Auton Res 2018; 28:181-185. [PMID: 29453697 PMCID: PMC5859694 DOI: 10.1007/s10286-018-0510-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 02/06/2018] [Indexed: 12/12/2022]
Abstract
A recent developmental study of gene expression by Espinosa-Medina, Brunet and colleagues sparked controversy by asserting a revised nomenclature for divisions of the autonomic motor system. Should we re-classify the sacral autonomic outflow as sympathetic, as now suggested, or does it rightly belong to the parasympathetic system, as defined by Langley nearly 100 years ago? Arguments for rejecting Espinosa-Medina, Brunet et al.’s scheme subsequently appeared in e-letters and brief reviews. A more recent commentary in this journal by Brunet and colleagues responded to these criticisms by labeling Langley’s scheme as a historical myth perpetuated by ignorance. In reaction to this heated exchange, I now examine both sides to the controversy, together with purported errors by the pioneers in the field. I then explain, once more, why the sacral outflow should remain known as parasympathetic, and outline suggestions for future experimentation to advance the understanding of cellular identity in the autonomic motor system.
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30
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Abstract
We revisit the classification of neuronal cell types in the nervous system of the nematode Caenorhabditis elegans. Based on anatomy and synaptic connectivity patterns, the 302 neurons of the nervous system of the hermaphrodite were categorized into 118 neuron classes more than 30 years ago. Analysis of all presently available neuronal gene expression patterns reveals a remarkable congruence of anatomical and molecular classification and further suggests subclassification schemes. Transcription factor expression profiles alone are sufficient to uniquely classify more than 90% of all neuron classes in the C. elegans nervous system. Neuron classification in C. elegans may be paradigmatic for neuron classification schemes in vertebrate nervous systems.
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31
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Zammit V, Baron B, Ayers D. MiRNA Influences in Neuroblast Modulation: An Introspective Analysis. Genes (Basel) 2018; 9:genes9010026. [PMID: 29315268 PMCID: PMC5793179 DOI: 10.3390/genes9010026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/22/2017] [Accepted: 12/29/2017] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma (NB) is the most common occurring solid paediatric cancer in children under the age of five years. Whether of familial or sporadic origin, chromosome abnormalities contribute to the development of NB and cause dysregulation of microRNAs (miRNAs). MiRNAs are small non-coding, single stranded RNAs that target messenger RNAs at the post-transcriptional levels by repressing translation within all facets of human physiology. Such gene 'silencing' activities by miRNAs allows the development of regulatory feedback loops affecting multiple functions within the cell, including the possible differentiation of neural stem cell (NSC) lineage selection. Neurogenesis includes stages of self-renewal and fate specification of NSCs, migration and maturation of young neurones, and functional integration of new neurones into the neural circuitry, all of which are regulated by miRNAs. The role of miRNAs and their interaction in cellular processes are recognised aspects of cancer genetics, and miRNAs are currently employed as biomarkers for prognosis and tumour characterisation in multiple cancer models. Consequently, thorough understanding of the mechanisms of how these miRNAs interplay at the transcriptomic level will definitely lead to the development of novel, bespoke and efficient therapeutic measures, with this review focusing on the influences of miRNAs on neuroblast modulations leading to neuroblastoma.
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Affiliation(s)
- Vanessa Zammit
- National Blood Transfusion Service, St. Luke's Hospital, PTA1010 G'Mangia, Malta.
- School of Biomedical Science and Physiology, University of Wolverhampton, Wolverhampton WV1 1LY, UK.
| | - Byron Baron
- Centre for Molecular Medicine and Biobanking, Faculty of Medicine and Surgery, University of Malta, MSD2080 Msida, Malta.
| | - Duncan Ayers
- Centre for Molecular Medicine and Biobanking, Faculty of Medicine and Surgery, University of Malta, MSD2080 Msida, Malta.
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK.
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32
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Barnett Burns S, Almeida D, Turecki G. The Epigenetics of Early Life Adversity: Current Limitations and Possible Solutions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:343-425. [DOI: 10.1016/bs.pmbts.2018.01.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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33
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Schubert R, Trenholm S, Balint K, Kosche G, Cowan CS, Mohr MA, Munz M, Martinez-Martin D, Fläschner G, Newton R, Krol J, Scherf BG, Yonehara K, Wertz A, Ponti A, Ghanem A, Hillier D, Conzelmann KK, Müller DJ, Roska B. Virus stamping for targeted single-cell infection in vitro and in vivo. Nat Biotechnol 2017; 36:81-88. [DOI: 10.1038/nbt.4034] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/13/2017] [Indexed: 11/09/2022]
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34
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Pfeffer CK, Beltramo R. Correlating Anatomy and Function with Gene Expression in Individual Neurons by Combining in Vivo Labeling, Patch Clamp, and Single Cell RNA-seq. Front Cell Neurosci 2017; 11:376. [PMID: 29249941 PMCID: PMC5714881 DOI: 10.3389/fncel.2017.00376] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/13/2017] [Indexed: 11/13/2022] Open
Abstract
The classification of neurons into distinct types is an ongoing effort aimed at revealing and understanding the diversity of the components of the nervous system. Recently available methods allow us to determine the gene expression pattern of individual neurons in the mammalian cerebral cortex to generate powerful categorization schemes. For a thorough understanding of neuronal diversity such genetic categorization schemes need to be combined with traditional classification parameters like position, axonal projection or response properties to sensory stimulation. Here we describe a method to link the gene expression of individual neurons with their position, axonal projection, or sensory response properties. Neurons are labeled in vivo based on their anatomical or functional properties and, using patch clamp pipettes, their RNA individually harvested in vitro for RNAseq. We validate the methodology using multiple established molecularly and anatomically distinct cell populations and explore molecular differences between uncharacterized neurons in mouse visual cortex. Gene expression patterns between L5 neurons projecting to frontal or contralateral cortex are distinct while L2 neurons differing in position, projection, or function are molecularly similar. With this method we can determine the genetic expression pattern of functionally and anatomically identified individual neurons.
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Affiliation(s)
- Carsten K Pfeffer
- Neurobiology Section, Center for Neural Circuits and Behavior, University of California, San Diego, La Jolla, CA, United States.,Department of Neuroscience, University of California, San Diego, La Jolla, CA, United States
| | - Riccardo Beltramo
- Neurobiology Section, Center for Neural Circuits and Behavior, University of California, San Diego, La Jolla, CA, United States.,Department of Neuroscience, University of California, San Diego, La Jolla, CA, United States
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35
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Johnson B, Zhao Y, Fasolino M, Lamonica J, Kim Y, Georgakilas G, Wood K, Bu D, Cui Y, Goffin D, Vahedi G, Kim T, Zhou Z. Biotin tagging of MeCP2 in mice reveals contextual insights into the Rett syndrome transcriptome. Nat Med 2017; 23:1203-1214. [PMID: 28920956 PMCID: PMC5630512 DOI: 10.1038/nm.4406] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 08/18/2017] [Indexed: 12/12/2022]
Abstract
Mutations in MECP2 cause Rett syndrome (RTT), an X-linked neurological disorder characterized by regressive loss of neurodevelopmental milestones and acquired psychomotor deficits. However, the cellular heterogeneity of the brain impedes an understanding of how MECP2 mutations contribute to RTT. Here we developed a Cre-inducible method for cell-type-specific biotin tagging of MeCP2 in mice. Combining this approach with an allelic series of knock-in mice carrying frequent RTT-associated mutations (encoding T158M and R106W) enabled the selective profiling of RTT-associated nuclear transcriptomes in excitatory and inhibitory cortical neurons. We found that most gene-expression changes were largely specific to each RTT-associated mutation and cell type. Lowly expressed cell-type-enriched genes were preferentially disrupted by MeCP2 mutations, with upregulated and downregulated genes reflecting distinct functional categories. Subcellular RNA analysis in MeCP2-mutant neurons further revealed reductions in the nascent transcription of long genes and uncovered widespread post-transcriptional compensation at the cellular level. Finally, we overcame X-linked cellular mosaicism in female RTT models and identified distinct gene-expression changes between neighboring wild-type and mutant neurons, providing contextual insights into RTT etiology that support personalized therapeutic interventions.
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Affiliation(s)
- B.S. Johnson
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Y.T. Zhao
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - M. Fasolino
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - J.M. Lamonica
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Y.J. Kim
- Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - G. Georgakilas
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - K.H. Wood
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - D. Bu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Y. Cui
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - D. Goffin
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - G. Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - T.H. Kim
- Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Z. Zhou
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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36
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Neurochemical Heterogeneity Among Lateral Hypothalamic Hypocretin/Orexin and Melanin-Concentrating Hormone Neurons Identified Through Single-Cell Gene Expression Analysis. eNeuro 2017; 4:eN-NWR-0013-17. [PMID: 28966976 PMCID: PMC5617207 DOI: 10.1523/eneuro.0013-17.2017] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 08/14/2017] [Accepted: 08/25/2017] [Indexed: 02/06/2023] Open
Abstract
The lateral hypothalamic area (LHA) lies at the intersection of multiple neural and humoral systems and orchestrates fundamental aspects of behavior. Two neuronal cell types found in the LHA are defined by their expression of hypocretin/orexin (Hcrt/Ox) and melanin-concentrating hormone (MCH) and are both important regulators of arousal, feeding, and metabolism. Conflicting evidence suggests that these cell populations have a more complex signaling repertoire than previously appreciated, particularly in regard to their coexpression of other neuropeptides and the machinery for the synthesis and release of GABA and glutamate. Here, we undertook a single-cell expression profiling approach to decipher the neurochemical phenotype, and heterogeneity therein, of Hcrt/Ox and MCH neurons. In transgenic mouse lines, we used single-cell quantitative polymerase chain reaction (qPCR) to quantify the expression of 48 key genes, which include neuropeptides, fast neurotransmitter components, and other key markers, which revealed unexpected neurochemical diversity. We found that single MCH and Hcrt/Ox neurons express transcripts for multiple neuropeptides and markers of both excitatory and inhibitory fast neurotransmission. Virtually all MCH and approximately half of the Hcrt/Ox neurons sampled express both the machinery for glutamate release and GABA synthesis in the absence of a vesicular GABA release pathway. Furthermore, we found that this profile is characteristic of a subpopulation of LHA glutamatergic neurons but contrasts with a broad population of LHA GABAergic neurons. Identifying the neurochemical diversity of Hcrt/Ox and MCH neurons will further our understanding of how these populations modulate postsynaptic excitability through multiple signaling mechanisms and coordinate diverse behavioral outputs.
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37
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Abstract
Cortical networks are composed of glutamatergic excitatory projection neurons and local GABAergic inhibitory interneurons that gate signal flow and sculpt network dynamics. Although they represent a minority of the total neocortical neuronal population, GABAergic interneurons are highly heterogeneous, forming functional classes based on their morphological, electrophysiological, and molecular features, as well as connectivity and in vivo patterns of activity. Here we review our current understanding of neocortical interneuron diversity and the properties that distinguish cell types. We then discuss how the involvement of multiple cell types, each with a specific set of cellular properties, plays a crucial role in diversifying and increasing the computational power of a relatively small number of simple circuit motifs forming cortical networks. We illustrate how recent advances in the field have shed light onto the mechanisms by which GABAergic inhibition contributes to network operations.
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38
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Neuronal cell-type classification: challenges, opportunities and the path forward. Nat Rev Neurosci 2017; 18:530-546. [PMID: 28775344 DOI: 10.1038/nrn.2017.85] [Citation(s) in RCA: 476] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neurons have diverse molecular, morphological, connectional and functional properties. We believe that the only realistic way to manage this complexity - and thereby pave the way for understanding the structure, function and development of brain circuits - is to group neurons into types, which can then be analysed systematically and reproducibly. However, neuronal classification has been challenging both technically and conceptually. New high-throughput methods have created opportunities to address the technical challenges associated with neuronal classification by collecting comprehensive information about individual cells. Nonetheless, conceptual difficulties persist. Borrowing from the field of species taxonomy, we propose principles to be followed in the cell-type classification effort, including the incorporation of multiple, quantitative features as criteria, the use of discontinuous variation to define types and the creation of a hierarchical system to represent relationships between cells. We review the progress of classifying cell types in the retina and cerebral cortex and propose a staged approach for moving forward with a systematic cell-type classification in the nervous system.
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39
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Poulin JF, Tasic B, Hjerling-Leffler J, Trimarchi JM, Awatramani R. Disentangling neural cell diversity using single-cell transcriptomics. Nat Neurosci 2017; 19:1131-41. [PMID: 27571192 DOI: 10.1038/nn.4366] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/22/2016] [Indexed: 12/12/2022]
Abstract
Cellular specialization is particularly prominent in mammalian nervous systems, which are composed of millions to billions of neurons that appear in thousands of different 'flavors' and contribute to a variety of functions. Even in a single brain region, individual neurons differ greatly in their morphology, connectivity and electrophysiological properties. Systematic classification of all mammalian neurons is a key goal towards deconstructing the nervous system into its basic components. With the recent advances in single-cell gene expression profiling technologies, it is now possible to undertake the enormous task of disentangling neuronal heterogeneity. High-throughput single-cell RNA sequencing and multiplexed quantitative RT-PCR have become more accessible, and these technologies enable systematic categorization of individual neurons into groups with similar molecular properties. Here we provide a conceptual and practical guide to classification of neural cell types using single-cell gene expression profiling technologies.
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Affiliation(s)
| | - Bosiljka Tasic
- Department of Molecular Genetics, Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jens Hjerling-Leffler
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jeffrey M Trimarchi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
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40
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Feldmeyer D, Qi G, Emmenegger V, Staiger JF. Inhibitory interneurons and their circuit motifs in the many layers of the barrel cortex. Neuroscience 2017; 368:132-151. [PMID: 28528964 DOI: 10.1016/j.neuroscience.2017.05.027] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 10/19/2022]
Abstract
Recent years have seen substantial progress in studying the structural and functional properties of GABAergic interneurons and their roles in the neuronal networks of barrel cortex. Although GABAergic interneurons represent only about 12% of the total number of neocortical neurons, they are extremely diverse with respect to their structural and functional properties. It has become clear that barrel cortex interneurons not only serve the maintenance of an appropriate excitation/inhibition balance but also are directly involved in sensory processing. In this review we present different interneuron types and their axonal projection pattern framework in the context of the laminar and columnar organization of the barrel cortex. The main focus is here on the most prominent interneuron types, i.e. basket cells, chandelier cells, Martinotti cells, bipolar/bitufted cells and neurogliaform cells, but interneurons with more unusual axonal domains will also be mentioned. We describe their developmental origin, their classification with respect to molecular, morphological and intrinsic membrane and synaptic properties. Most importantly, we will highlight the most prominent circuit motifs these interneurons are involved in and in which way they serve feed-forward inhibition, feedback inhibition and disinhibition. Finally, this will be put into context to their functional roles in sensory signal perception and processing in the whisker system and beyond.
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Affiliation(s)
- Dirk Feldmeyer
- Institute of Neuroscience and Medicine, INM-2, Research Center Jülich, D-52425 Jülich, Germany; Department of Psychiatry, Psychotherapy and Psychosomatics, RWTH Aachen University, D-52074 Aachen, Germany; Jülich Aachen Research Alliance, Translational Brain Medicine (JARA Brain), D-52074 Aachen, Germany.
| | - Guanxiao Qi
- Institute of Neuroscience and Medicine, INM-2, Research Center Jülich, D-52425 Jülich, Germany
| | - Vishalini Emmenegger
- Institute of Neuroscience and Medicine, INM-2, Research Center Jülich, D-52425 Jülich, Germany; Department of Psychiatry, Psychotherapy and Psychosomatics, RWTH Aachen University, D-52074 Aachen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center Göttingen, Georg-August-University, Göttingen D-37075, Germany.
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41
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Salatino JW, Winter BM, Drazin MH, Purcell EK. Functional remodeling of subtype-specific markers surrounding implanted neuroprostheses. J Neurophysiol 2017; 118:194-202. [PMID: 28356474 DOI: 10.1152/jn.00162.2017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 03/29/2017] [Accepted: 03/29/2017] [Indexed: 01/04/2023] Open
Abstract
Microelectrode arrays implanted in the brain are increasingly used for the research and treatment of intractable neurological disease. However, local neuronal loss and glial encapsulation are known to interfere with effective integration and communication between implanted devices and brain tissue, where these observations are typically based on assessments of broad neuronal and astroglial markers. However, both neurons and astrocytes comprise heterogeneous cellular populations that can be further divided into subclasses based on unique functional and morphological characteristics. In this study, we investigated whether or not device insertion causes alterations in specific subtypes of these cells. We assessed the expression of both excitatory and inhibitory markers of neurotransmission (vesicular glutamate and GABA transporters, VGLUT1 and VGAT, respectively) surrounding single-shank Michigan-style microelectrode arrays implanted in the motor cortex of adult rats by use of quantitative immunohistochemistry. We found a pronounced shift from significantly elevated VGLUT1 within the initial days following implantation to relatively heightened VGAT by the end of the 4-wk observation period. Unexpectedly, we observed VGAT positivity in a subset of reactive astrocytes during the first week of implantation, indicating heterogeneity in early-responding encapsulating glial cells. We coupled our VGLUT1 data with the evaluation of a second marker of excitatory neurons (CamKiiα); the results closely paralleled each other and underscored a progression from initially heightened to subsequently weakened excitatory tone in the neural tissue proximal to the implanted electrode interface (within 40 μm). Our results provide new evidence for subtype-specific remodeling surrounding brain implants that inform observations of suboptimal integration and performance.NEW & NOTEWORTHY We report novel changes in the local expression of excitatory and inhibitory synaptic markers surrounding microelectrode arrays implanted in the motor cortex of rats, where a progressive shift toward increased inhibitory tone was observed over the 4-wk observation period. The result was driven by declining glutamate transporter expression (VGLUT1) in parallel with increasing GABA transporter expression (VGAT) over time, where a reactive VGAT+ astroglial subtype made an unexpected contribution to our findings.
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Affiliation(s)
- Joseph W Salatino
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan
| | - Bailey M Winter
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan.,Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan
| | - Matthew H Drazin
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan; and
| | - Erin K Purcell
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan; .,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan.,Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan.,Neuroscience Program, Michigan State University, East Lansing, Michigan
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42
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Seymour JP, Wu F, Wise KD, Yoon E. State-of-the-art MEMS and microsystem tools for brain research. MICROSYSTEMS & NANOENGINEERING 2017; 3:16066. [PMID: 31057845 PMCID: PMC6445015 DOI: 10.1038/micronano.2016.66] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/01/2016] [Accepted: 08/23/2016] [Indexed: 05/02/2023]
Abstract
Mapping brain activity has received growing worldwide interest because it is expected to improve disease treatment and allow for the development of important neuromorphic computational methods. MEMS and microsystems are expected to continue to offer new and exciting solutions to meet the need for high-density, high-fidelity neural interfaces. Herein, the state-of-the-art in recording and stimulation tools for brain research is reviewed, and some of the most significant technology trends shaping the field of neurotechnology are discussed.
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Affiliation(s)
- John P. Seymour
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48105, USA
| | - Fan Wu
- Diagnostic Biochips, Inc., Glen Burnie, MD 21061, USA
| | - Kensall D. Wise
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48105, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48105, USA
| | - Euisik Yoon
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48105, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48105, USA
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43
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O'Toole SM, Ferrer MM, Mekonnen J, Zhang H, Shima Y, Ladle DR, Nelson SB. Dicer maintains the identity and function of proprioceptive sensory neurons. J Neurophysiol 2016; 117:1057-1069. [PMID: 28003412 DOI: 10.1152/jn.00763.2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 11/22/2022] Open
Abstract
Neuronal cell identity is established during development and must be maintained throughout an animal's life (Fishell G, Heintz N. Neuron 80: 602-612, 2013). Transcription factors critical for establishing neuronal identity can be required for maintaining it (Deneris ES, Hobert O. Nat Neurosci 17: 899-907, 2014). Posttranscriptional regulation also plays an important role in neuronal differentiation (Bian S, Sun T. Mol Neurobiol 44: 359-373, 2011), but its role in maintaining cell identity is less established. To better understand how posttranscriptional regulation might contribute to cell identity, we examined the proprioceptive neurons in the dorsal root ganglion (DRG), a highly specialized sensory neuron class, with well-established properties that distinguish them from other neurons in the ganglion. By conditionally ablating Dicer in mice, using parvalbumin (Pvalb)-driven Cre recombinase, we impaired posttranscriptional regulation in the proprioceptive sensory neuron population. Knockout (KO) animals display a progressive form of ataxia at the beginning of the fourth postnatal week that is accompanied by a cell death within the DRG. Before cell loss, expression profiling shows a reduction of proprioceptor specific genes and an increased expression of nonproprioceptive genes normally enriched in other ganglion neurons. Furthermore, although central connections of these neurons are intact, the peripheral connections to the muscle are functionally impaired. Posttranscriptional regulation is therefore necessary to retain the transcriptional identity and support functional specialization of the proprioceptive sensory neurons.NEW & NOTEWORTHY We have demonstrated that selectively impairing Dicer in parvalbumin-positive neurons, which include the proprioceptors, triggers behavioral changes, a lack of muscle connectivity, and a loss of transcriptional identity as observed through RNA sequencing. These results suggest that Dicer and, most likely by extension, microRNAs are crucially important for maintaining proprioception. Additionally, this study hints at the larger question of how neurons maintain their functional and molecular specificity.
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Affiliation(s)
- Sean M O'Toole
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - Monica M Ferrer
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - Jennifer Mekonnen
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - Haihan Zhang
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - Yasuyuki Shima
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
| | - David R Ladle
- Department of Neuroscience, Cell Biology, and Physiology, Wright State University, Dayton, Ohio
| | - Sacha B Nelson
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts; and
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44
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Tramacere A, Pievani T, Ferrari PF. Mirror neurons in the tree of life: mosaic evolution, plasticity and exaptation of sensorimotor matching responses. Biol Rev Camb Philos Soc 2016; 92:1819-1841. [PMID: 27862868 DOI: 10.1111/brv.12310] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 12/31/2022]
Abstract
Considering the properties of mirror neurons (MNs) in terms of development and phylogeny, we offer a novel, unifying, and testable account of their evolution according to the available data and try to unify apparently discordant research, including the plasticity of MNs during development, their adaptive value and their phylogenetic relationships and continuity. We hypothesize that the MN system reflects a set of interrelated traits, each with an independent natural history due to unique selective pressures, and propose that there are at least three evolutionarily significant trends that gave raise to three subtypes: hand visuomotor, mouth visuomotor, and audio-vocal. Specifically, we put forward a mosaic evolution hypothesis, which posits that different types of MNs may have evolved at different rates within and among species. This evolutionary hypothesis represents an alternative to both adaptationist and associative models. Finally, the review offers a strong heuristic potential in predicting the circumstances under which specific variations and properties of MNs are expected. Such predictive value is critical to test new hypotheses about MN activity and its plastic changes, depending on the species, the neuroanatomical substrates, and the ecological niche.
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Affiliation(s)
- Antonella Tramacere
- Department of Neuroscience, University of Parma, Parma, 43100, Italy.,Deutsche Primaten Zentrum - Lichtenberg-Kolleg, Institute for Advanced Study, 37083, Göttingen, Germany
| | - Telmo Pievani
- Department of Biology, University of Padua, Padua, 35131, Italy
| | - Pier F Ferrari
- Department of Neuroscience, University of Parma, Parma, 43100, Italy.,Institut des Sciences Cognitives 'Marc Jeannerod', CNRS/Université Claude Bernard Lyon, 69675, Bron Cedex, France
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45
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Protein characterization of intracellular target-sorted, formalin-fixed cell subpopulations. Sci Rep 2016; 6:33999. [PMID: 27666089 PMCID: PMC5036045 DOI: 10.1038/srep33999] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/01/2016] [Indexed: 12/14/2022] Open
Abstract
Cellular heterogeneity is inherent in most human tissues, making the investigation of specific cell types challenging. Here, we describe a novel, fixation/intracellular target-based sorting and protein extraction method to provide accurate protein characterization for cell subpopulations. Validation and feasibility tests were conducted using homogeneous, neural cell lines and heterogeneous, rat brain cells, respectively. Intracellular proteins of interest were labeled with fluorescent antibodies for fluorescence-activated cell sorting. Reproducible protein extraction from fresh and fixed samples required lysis buffer with high concentrations of Tris-HCl and sodium dodecyl sulfate as well as exposure to high heat. No deterioration in protein amount or quality was observed for fixed, sorted samples. For the feasibility experiment, a primary rat subpopulation of neuronal cells was selected for based on high, intracellular β-III tubulin signal. These cells showed distinct protein expression differences from the unsorted population for specific (phosphorylated tau) and non-specific (total tau) protein targets. Our approach allows for determining more accurate protein profiles directly from cell types of interest and provides a platform technology in which any cell subpopulation can be biochemically investigated.
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46
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Lin CY, Huang SC, Tung CC, Chou CH, Gau SSF, Huang HS. Analysis of Genome-Wide Monoallelic Expression Patterns in Three Major Cell Types of Mouse Visual Cortex Using Laser Capture Microdissection. PLoS One 2016; 11:e0163663. [PMID: 27662371 PMCID: PMC5035046 DOI: 10.1371/journal.pone.0163663] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022] Open
Abstract
Genomic imprinting is an epigenetic mechanism causing monoallelic expression in a parent-of-origin-specific manner. Disruption of imprinted genes causes various neurological and psychiatric disorders. However, the role of imprinted genes in the brain is largely unknown. Different cell types within distinct brain regions can influence the genomic imprinting status, but imprinted genes in single cell types within distinct brain regions have not been characterized on a genome-wide scale. To address this critical question, we used a multi-stage approach, which combined genetically engineered mice with fluorescence-based laser capture microdissection (LCM) to capture excitatory neurons, inhibitory neurons and astrocytes as single cells in layer 2/3 of mouse visual cortex. RNA sequencing determined parental expression patterns on a genome-wide scale in the captured cells within specific brain regions. The expression level of cell-type-specific genes for excitatory neurons (13 genes), inhibitory neurons (16 genes) and astrocytes (20 genes) confirmed the LCM-captured cells maintained their cellular identities. The parent-of-origin-specific expression pattern of imprinted genes, including maternally expressed Meg3 and paternally expressed Peg3, provided evidence that the status of known imprinted genes was also maintained. Although our platform remains to be improved, our findings demonstrate the parental expression pattern can be analysed not only at the level of a single cell type but also at the level of specific cortical layers. Our approach has the potential to reveal novel regulatory modules associated with plasticity through genomic imprinting mechanisms in different cell types, not only in the visual cortex but also in other brain regions.
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Affiliation(s)
- Chia-Yi Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Chuan Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Che Tung
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-Hsuan Chou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Susan Shur-Fen Gau
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Taiwan University, Taipei, Taiwan
- Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
- Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Neurodevelopment Club in Taiwan, Taipei, Taiwan
- * E-mail:
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47
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Sun MA, Sun Z, Wu X, Rajaram V, Keimig D, Lim J, Zhu H, Xie H. Mammalian Brain Development is Accompanied by a Dramatic Increase in Bipolar DNA Methylation. Sci Rep 2016; 6:32298. [PMID: 27585862 PMCID: PMC5010034 DOI: 10.1038/srep32298] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 08/02/2016] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic mechanism critical for tissue development and cell specification. Mammalian brains consist of many different types of cells with assumedly distinct DNA methylation profiles, and thus some genomic loci may demonstrate bipolar DNA methylation pattern, i.e. hypermethylated in one cell subset but hypomethylated in others. Currently, how extensive methylation patterns vary among brain cells is unknown and bipolar methylated genomic loci remain largely unexplored. In this study, we implemented a procedure to infer cell-subset specific methylated (CSM) loci from the methylomes of human and mouse frontal cortices at different developmental stages. With the genome-scale hairpin bisulfite sequencing approach, we demonstrated that the majority of CSM loci predicted likely resulted from the methylation differences among brain cells rather than from asymmetric DNA methylation between DNA double strands. Correlated with enhancer-associated histone modifications, putative CSM loci increased dramatically during early stages of brain development and were enriched for GWAS variants associated with neurological disorder-related diseases/traits. Altogether, this study provides a procedure to identify genomic regions showing methylation differences in a mixed cell population and our results suggest that a set of cis-regulatory elements are primed in early postnatal life whose functions may be compromised in human neurological disorders.
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Affiliation(s)
- Ming-An Sun
- Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA
| | - Zhixiong Sun
- Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Xiaowei Wu
- Department of Statistics, Virginia Tech, Blacksburg, VA, USA
| | - Veena Rajaram
- Department of Pathology, Children's Medical center, Dallas 75235 , USA.,Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - David Keimig
- Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA
| | - Jessica Lim
- Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Hongxiao Zhu
- Department of Statistics, Virginia Tech, Blacksburg, VA, USA
| | - Hehuang Xie
- Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,School of Neuroscience, Virginia Tech, Blacksburg, VA, USA.,Interdisciplinary Ph.D. Program in Genomics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA.,Ph.D. Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksbury, VA 24061, USA
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48
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Mullins C, Fishell G, Tsien RW. Unifying Views of Autism Spectrum Disorders: A Consideration of Autoregulatory Feedback Loops. Neuron 2016; 89:1131-1156. [PMID: 26985722 DOI: 10.1016/j.neuron.2016.02.017] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2016] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms underlying autism spectrum disorders (ASDs) is a challenging goal. Here we review recent progress on several fronts, including genetics, proteomics, biochemistry, and electrophysiology, that raise motivation for forming a viable pathophysiological hypothesis. In place of a traditionally unidirectional progression, we put forward a framework that extends homeostatic hypotheses by explicitly emphasizing autoregulatory feedback loops and known synaptic biology. The regulated biological feature can be neuronal electrical activity, the collective strength of synapses onto a dendritic branch, the local concentration of a signaling molecule, or the relative strengths of synaptic excitation and inhibition. The sensor of the biological variable (which we have termed the homeostat) engages mechanisms that operate as negative feedback elements to keep the biological variable tightly confined. We categorize known ASD-associated gene products according to their roles in such feedback loops and provide detailed commentary for exemplar genes within each module.
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Affiliation(s)
- Caitlin Mullins
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | - Gord Fishell
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA
| | - Richard W Tsien
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, NY 10016, USA.
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49
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Pet-1 Switches Transcriptional Targets Postnatally to Regulate Maturation of Serotonin Neuron Excitability. J Neurosci 2016; 36:1758-74. [PMID: 26843655 DOI: 10.1523/jneurosci.3798-15.2016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED Newborn neurons enter an extended maturation stage, during which they acquire excitability characteristics crucial for development of presynaptic and postsynaptic connectivity. In contrast to earlier specification programs, little is known about the regulatory mechanisms that control neuronal maturation. The Pet-1 ETS (E26 transformation-specific) factor is continuously expressed in serotonin (5-HT) neurons and initially acts in postmitotic precursors to control acquisition of 5-HT transmitter identity. Using a combination of RNA sequencing, electrophysiology, and conditional targeting approaches, we determined gene expression patterns in maturing flow-sorted 5-HT neurons and the temporal requirements for Pet-1 in shaping these patterns for functional maturation of mouse 5-HT neurons. We report a profound disruption of postmitotic expression trajectories in Pet-1(-/-) neurons, which prevented postnatal maturation of 5-HT neuron passive and active intrinsic membrane properties, G-protein signaling, and synaptic responses to glutamatergic, lysophosphatidic, and adrenergic agonists. Unexpectedly, conditional targeting revealed a postnatal stage-specific switch in Pet-1 targets from 5-HT synthesis genes to transmitter receptor genes required for afferent modulation of 5-HT neuron excitability. Five-HT1a autoreceptor expression depended transiently on Pet-1, thus revealing an early postnatal sensitive period for control of 5-HT excitability genes. Chromatin immunoprecipitation followed by sequencing revealed that Pet-1 regulates 5-HT neuron maturation through direct gene activation and repression. Moreover, Pet-1 directly regulates the 5-HT neuron maturation factor Engrailed 1, which suggests Pet-1 orchestrates maturation through secondary postmitotic regulatory factors. The early postnatal switch in Pet-1 targets uncovers a distinct neonatal stage-specific function for Pet-1, during which it promotes maturation of 5-HT neuron excitability. SIGNIFICANCE STATEMENT The regulatory mechanisms that control functional maturation of neurons are poorly understood. We show that in addition to inducing brain serotonin (5-HT) synthesis and reuptake, the Pet-1 ETS (E26 transformation-specific) factor subsequently globally coordinates postmitotic expression trajectories of genes necessary for maturation of 5-HT neuron excitability. Further, Pet-1 switches its transcriptional targets as 5-HT neurons mature from 5-HT synthesis genes to G-protein-coupled receptors, which are necessary for afferent synaptic modulation of 5-HT neuron excitability. Our findings uncover gene-specific switching of downstream targets as a previously unrecognized regulatory strategy through which continuously expressed transcription factors control acquisition of neuronal identity at different stages of development.
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Mungenast AE, Siegert S, Tsai LH. Modeling Alzheimer's disease with human induced pluripotent stem (iPS) cells. Mol Cell Neurosci 2016; 73:13-31. [PMID: 26657644 PMCID: PMC5930170 DOI: 10.1016/j.mcn.2015.11.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 11/05/2015] [Accepted: 11/25/2015] [Indexed: 02/08/2023] Open
Abstract
In the last decade, induced pluripotent stem (iPS) cells have revolutionized the utility of human in vitro models of neurological disease. The iPS-derived and differentiated cells allow researchers to study the impact of a distinct cell type in health and disease as well as performing therapeutic drug screens on a human genetic background. In particular, clinical trials for Alzheimer's disease (AD) have been failing. Two of the potential reasons are first, the species gap involved in proceeding from initial discoveries in rodent models to human studies, and second, an unsatisfying patient stratification, meaning subgrouping patients based on the disease severity due to the lack of phenotypic and genetic markers. iPS cells overcome this obstacles and will improve our understanding of disease subtypes in AD. They allow researchers conducting in depth characterization of neural cells from both familial and sporadic AD patients as well as preclinical screens on human cells. In this review, we briefly outline the status quo of iPS cell research in neurological diseases along with the general advantages and pitfalls of these models. We summarize how genome-editing techniques such as CRISPR/Cas9 will allow researchers to reduce the problem of genomic variability inherent to human studies, followed by recent iPS cell studies relevant to AD. We then focus on current techniques for the differentiation of iPS cells into neural cell types that are relevant to AD research. Finally, we discuss how the generation of three-dimensional cell culture systems will be important for understanding AD phenotypes in a complex cellular milieu, and how both two- and three-dimensional iPS cell models can provide platforms for drug discovery and translational studies into the treatment of AD.
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Affiliation(s)
- Alison E Mungenast
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Sandra Siegert
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
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