1
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Merrill CB, Titos I, Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. Iterative assay for transposase-accessible chromatin by sequencing to isolate functionally relevant neuronal subtypes. SCIENCE ADVANCES 2024; 10:eadi4393. [PMID: 38536919 PMCID: PMC10971406 DOI: 10.1126/sciadv.adi4393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 02/21/2024] [Indexed: 04/18/2024]
Abstract
The Drosophila brain contains tens of thousands of distinct cell types. Thousands of different transgenic lines reproducibly target specific neuron subsets, yet most still express in several cell types. Furthermore, most lines were developed without a priori knowledge of where the transgenes would be expressed. To aid in the development of cell type-specific tools for neuronal identification and manipulation, we developed an iterative assay for transposase-accessible chromatin (ATAC) approach. Open chromatin regions (OCRs) enriched in neurons, compared to whole bodies, drove transgene expression preferentially in subsets of neurons. A second round of ATAC-seq from these specific neuron subsets revealed additional enriched OCR2s that further restricted transgene expression within the chosen neuron subset. This approach allows for continued refinement of transgene expression, and we used it to identify neurons relevant for sleep behavior. Furthermore, this approach is widely applicable to other cell types and to other organisms.
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Affiliation(s)
- Collin B. Merrill
- Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108, USA
| | - Iris Titos
- Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108, USA
| | - Miguel A. Pabon
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Aylin R. Rodan
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Adrian Rothenfluh
- Department of Psychiatry, Huntsman Mental Health Institute, University of Utah, Salt Lake City, UT 84108, USA
- Molecular Medicine Program, University of Utah, Salt Lake City, UT 84112, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Department of Neurobiology, University of Utah, Salt Lake City, UT 84112, USA
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2
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Banks E, Gutekunst CA, Vargish GA, Eaton A, Pelkey KA, McBain CJ, Zheng JQ, Oláh VJ, Rowan MJM. An enhancer-AAV approach selectively targeting dentate granule cells of the mouse hippocampus. CELL REPORTS METHODS 2024; 4:100684. [PMID: 38211592 PMCID: PMC10831952 DOI: 10.1016/j.crmeth.2023.100684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/29/2023] [Accepted: 12/13/2023] [Indexed: 01/13/2024]
Abstract
The mammalian brain contains a diverse array of cell types, including dozens of neuronal subtypes with distinct anatomical and functional characteristics. The brain leverages these neuron-type specializations to perform diverse circuit operations and thus execute different behaviors properly. Through the use of Cre lines, access to specific neuron types has improved over past decades. Despite their extraordinary utility, development and cross-breeding of Cre lines is time consuming and expensive, presenting a significant barrier to entry for investigators. Furthermore, cell-based therapeutics developed in Cre mice are not clinically translatable. Recently, several adeno-associated virus (AAV) vectors utilizing neuron-type-specific regulatory transcriptional sequences (enhancer-AAVs) were developed that overcome these limitations. Using a publicly available RNA sequencing (RNA-seq) dataset, we evaluated the potential of several candidate enhancers for neuron-type-specific targeting in the hippocampus. Here, we demonstrate that a previously identified enhancer-AAV selectively targets dentate granule cells over other excitatory neuron types in the hippocampus of wild-type adult mice.
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Affiliation(s)
- Emmie Banks
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; GDBBS Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Claire-Anne Gutekunst
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Geoffrey A Vargish
- Section on Cellular and Synaptic Physiology, NICHD - Eunice Kennedy Shriver National Institute of Child Health, Bethesda, MD, USA
| | - Anna Eaton
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30322, USA; Human Development, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kenneth A Pelkey
- Section on Cellular and Synaptic Physiology, NICHD - Eunice Kennedy Shriver National Institute of Child Health, Bethesda, MD, USA
| | - Chris J McBain
- Section on Cellular and Synaptic Physiology, NICHD - Eunice Kennedy Shriver National Institute of Child Health, Bethesda, MD, USA
| | - James Q Zheng
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Viktor Janos Oláh
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Matthew J M Rowan
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA.
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3
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Grimstvedt JS, Shelton AM, Hoerder‐Suabedissen A, Oliver DK, Berndtsson CH, Blankvoort S, Nair RR, Packer AM, Witter MP, Kentros CG. A multifaceted architectural framework of the mouse claustrum complex. J Comp Neurol 2023; 531:1772-1795. [PMID: 37782702 PMCID: PMC10953385 DOI: 10.1002/cne.25539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 10/04/2023]
Abstract
Accurate anatomical characterizations are necessary to investigate neural circuitry on a fine scale, but for the rodent claustrum complex (CLCX), this has yet to be fully accomplished. The CLCX is generally considered to comprise two major subdivisions, the claustrum (CL) and the dorsal endopiriform nucleus (DEn), but regional boundaries to these areas are debated. To address this, we conducted a multifaceted analysis of fiber- and cytoarchitecture, genetic marker expression, and connectivity using mice of both sexes, to create a comprehensive guide for identifying and delineating borders to CLCX, including an online reference atlas. Our data indicated four distinct subregions within CLCX, subdividing both CL and DEn into two. Additionally, we conducted brain-wide tracing of inputs to CLCX using a transgenic mouse line. Immunohistochemical staining against myelin basic protein (MBP), parvalbumin (PV), and calbindin (CB) revealed intricate fiber-architectural patterns enabling precise delineations of CLCX and its subregions. Myelinated fibers were abundant dorsally in CL but absent ventrally, whereas PV expressing fibers occupied the entire CL. CB staining revealed a central gap within CL, also visible anterior to the striatum. The Nr2f2, Npsr1, and Cplx3 genes expressed specifically within different subregions of the CLCX, and Rprm helped delineate the CL-insular border. Furthermore, cells in CL projecting to the retrosplenial cortex were located within the myelin sparse area. By combining own experimental data with digitally available datasets of gene expression and input connectivity, we could demonstrate that the proposed delineation scheme allows anchoring of datasets from different origins to a common reference framework.
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Affiliation(s)
- Joachim S. Grimstvedt
- Kavli Institute for Systems NeuroscienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Andrew M. Shelton
- Department of Physiology, Anatomy & GeneticsUniversity of OxfordOxfordUK
| | | | - David K. Oliver
- Department of Physiology, Anatomy & GeneticsUniversity of OxfordOxfordUK
| | - Christin H. Berndtsson
- Kavli Institute for Systems NeuroscienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Stefan Blankvoort
- Kavli Institute for Systems NeuroscienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Rajeevkumar R. Nair
- Kavli Institute for Systems NeuroscienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Adam M. Packer
- Department of Physiology, Anatomy & GeneticsUniversity of OxfordOxfordUK
| | - Menno P. Witter
- Kavli Institute for Systems NeuroscienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Clifford G. Kentros
- Kavli Institute for Systems NeuroscienceNTNU Norwegian University of Science and TechnologyTrondheimNorway
- Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
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4
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Li L, Liu Z. Genetic Approaches for Neural Circuits Dissection in Non-human Primates. Neurosci Bull 2023; 39:1561-1576. [PMID: 37258795 PMCID: PMC10533465 DOI: 10.1007/s12264-023-01067-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/27/2023] [Indexed: 06/02/2023] Open
Abstract
Genetic tools, which can be used for the morphology study of specific neurons, pathway-selective connectome mapping, neuronal activity monitoring, and manipulation with a spatiotemporal resolution, have been widely applied to the understanding of complex neural circuit formation, interactions, and functions in rodents. Recently, similar genetic approaches have been tried in non-human primates (NHPs) in neuroscience studies for dissecting the neural circuits involved in sophisticated behaviors and clinical brain disorders, although they are still very preliminary. In this review, we introduce the progress made in the development and application of genetic tools for brain studies on NHPs. We also discuss the advantages and limitations of each approach and provide a perspective for using genetic tools to study the neural circuits of NHPs.
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Affiliation(s)
- Ling Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Roethler O, Zohar E, Cohen-Kashi Malina K, Bitan L, Gabel HW, Spiegel I. Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex. Neuron 2023; 111:2693-2708.e8. [PMID: 37354902 DOI: 10.1016/j.neuron.2023.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/29/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Experience-dependent plasticity of synapses modulates information processing in neural circuits and is essential for cognitive functions. The genome, via non-coding enhancers, was proposed to control information processing and circuit plasticity by regulating experience-induced transcription of genes that modulate specific sets of synapses. To test this idea, we analyze here the cellular and circuit functions of the genomic mechanisms that control the experience-induced transcription of Igf1 (insulin-like growth factor 1) in vasoactive intestinal peptide (VIP) interneurons (INs) in the visual cortex of adult mice. We find that two sensory-induced enhancers selectively and cooperatively drive the activity-induced transcription of Igf1 to thereby promote GABAergic inputs onto VIP INs and to homeostatically control the ratio between excitation and inhibition (E/I ratio)-in turn, this restricts neural activity in VIP INs and principal excitatory neurons and maintains spatial frequency tuning. Thus, enhancer-mediated activity-induced transcription maintains sensory processing in the adult cortex via homeostatic modulation of E/I ratio.
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Affiliation(s)
- Ori Roethler
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Zohar
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Katayun Cohen-Kashi Malina
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Lidor Bitan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Harrison Wren Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Ivo Spiegel
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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6
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Butola T, Hernández Frausto M, Blankvoort S, Flatset MS, Peng L, Elmaleh M, Hairston A, Hussain F, Clopath C, Kentros C, Basu J. Hippocampus shapes cortical sensory output and novelty coding through a direct feedback circuit. RESEARCH SQUARE 2023:rs.3.rs-3270016. [PMID: 37674706 PMCID: PMC10479401 DOI: 10.21203/rs.3.rs-3270016/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
To extract behaviorally relevant information from our surroundings, our brains constantly integrate and compare incoming sensory information with those stored as memories. Cortico-hippocampal interactions could mediate such interplay between sensory processing and memory recall1-4 but this remains to be demonstrated. Recent work parsing entorhinal cortex-to-hippocampus circuitry show its role in episodic memory formation5-7 and spatial navigation8. However, the organization and function of the hippocampus-to-cortex back-projection circuit remains uncharted. We combined circuit mapping, physiology and behavior with optogenetic manipulations, and computational modeling to reveal how hippocampal feedback modulates cortical sensory activity and behavioral output. Here we show a new direct hippocampal projection to entorhinal cortex layer 2/3, the very layer that projects multisensory input to the hippocampus. Our finding challenges the canonical cortico-hippocampal circuit model where hippocampal feedback only reaches entorhinal cortex layer 2/3 indirectly via layer 5. This direct hippocampal input integrates with cortical sensory inputs in layer 2/3 neurons to drive their plasticity and spike output, and provides an important novelty signal during behavior for coding objects and their locations. Through the sensory-memory feedback loop, hippocampus can update real-time cortical sensory processing, efficiently and iteratively, thereby imparting the salient context for adaptive learned behaviors with new experiences.
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Affiliation(s)
- T. Butola
- Neuroscience Institute, New York University Langone Health; New York City, 10016, USA
| | - M. Hernández Frausto
- Neuroscience Institute, New York University Langone Health; New York City, 10016, USA
| | - S. Blankvoort
- Centre for Neural Computation, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology; Trondheim, Norway
| | - M. S. Flatset
- Centre for Neural Computation, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology; Trondheim, Norway
| | - L. Peng
- Neuroscience Institute, New York University Langone Health; New York City, 10016, USA
| | - M. Elmaleh
- Neuroscience Institute, New York University Langone Health; New York City, 10016, USA
| | - A. Hairston
- Neuroscience Institute, New York University Langone Health; New York City, 10016, USA
| | - F. Hussain
- Neuroscience Institute, New York University Langone Health; New York City, 10016, USA
| | - C. Clopath
- Department of Bioengineering, Imperial College London; London, SW7 2AZ, UK
| | - C. Kentros
- Centre for Neural Computation, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology; Trondheim, Norway
- Institute of Neuroscience, University of Oregon; Eugene, United States
| | - J. Basu
- Neuroscience Institute, New York University Langone Health; New York City, 10016, USA
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine; New York City, 10016, USA
- Department of Psychiatry, New York University Grossman School of Medicine; New York City, 10016, USA
- Center for Neural Science, New York University, New York, NY 10003, USA
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7
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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8
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Jiang K, Koob J, Chen XD, Krajeski RN, Zhang Y, Volf V, Zhou W, Sgrizzi SR, Villiger L, Gootenberg JS, Chen F, Abudayyeh OO. Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR. Nat Biotechnol 2023; 41:698-707. [PMID: 36302988 DOI: 10.1038/s41587-022-01534-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Programmable approaches to sense and respond to the presence of specific RNAs in biological systems have broad applications in research, diagnostics, and therapeutics. Here we engineer a programmable RNA-sensing technology, reprogrammable ADAR sensors (RADARS), which harnesses RNA editing by adenosine deaminases acting on RNA (ADAR) to gate translation of a cargo protein by the presence of endogenous RNA transcripts. Introduction of a stop codon in a guide upstream of the cargo makes translation contingent on binding of an endogenous transcript to the guide, leading to ADAR editing of the stop codon and allowing translational readthrough. Through systematic sensor engineering, we achieve 277 fold improvement in sensor activation and engineer RADARS with diverse cargo proteins, including luciferases, fluorescent proteins, recombinases, and caspases, enabling detection sensitivity on endogenous transcripts expressed at levels as low as 13 transcripts per million. We show that RADARS are functional as either expressed DNA or synthetic mRNA and with either exogenous or endogenous ADAR. We apply RADARS in multiple contexts, including tracking transcriptional states, RNA-sensing-induced cell death, cell-type identification, and control of synthetic mRNA translation.
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Affiliation(s)
- Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeremy Koob
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Xi Dawn Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Systems, Synthetic, and Quantitative Biology Program, Harvard Medical School, Boston, MA, USA
| | - Rohan N Krajeski
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yifan Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Verena Volf
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samantha R Sgrizzi
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas Villiger
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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9
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Hoerder-Suabedissen A, Ocana-Santero G, Draper TH, Scott SA, Kimani JG, Shelton AM, Butt SJB, Molnár Z, Packer AM. Temporal origin of mouse claustrum and development of its cortical projections. Cereb Cortex 2023; 33:3944-3959. [PMID: 36104852 PMCID: PMC10068282 DOI: 10.1093/cercor/bhac318] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/12/2022] Open
Abstract
The claustrum is known for its extensive connectivity with many other forebrain regions, but its elongated shape and deep location have made further study difficult. We have sought to understand when mouse claustrum neurons are born, where they are located in developing brains, and when they develop their widespread connections to the cortex. We established that a well-characterized parvalbumin plexus, which identifies the claustrum in adults, is only present from postnatal day (P) 21. A myeloarchitectonic outline of the claustrum can be derived from a triangular fiber arrangement from P15. A dense patch of Nurr1+ cells is present at its core and is already evident at birth. Bromodeoxyuridine birth dating of forebrain progenitors reveals that the majority of claustrum neurons are born during a narrow time window centered on embryonic day 12.5, which is later than the adjacent subplate and endopiriform nucleus. Retrograde tracing revealed that claustrum projections to anterior cingulate (ACA) and retrosplenial cortex (RSP) follow distinct developmental trajectories. Claustrum-ACA connectivity matures rapidly and reaches adult-like innervation density by P10, whereas claustrum-RSP innervation emerges later over a protracted time window. This work establishes the timeline of claustrum development and provides a framework for understanding how the claustrum is built and develops its unique connectivity.
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Affiliation(s)
- Anna Hoerder-Suabedissen
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, United Kingdom
| | - Gabriel Ocana-Santero
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, United Kingdom
| | - Thomas H Draper
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, United Kingdom
| | - Sophie A Scott
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, United Kingdom
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London SE5 8AF, UK
| | - Jesse G Kimani
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, United Kingdom
| | - Andrew M Shelton
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, United Kingdom
| | - Simon J B Butt
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, United Kingdom
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, United Kingdom
| | - Adam M Packer
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, United Kingdom
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10
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Winchester EW, Hardy A, Cotney J. Integration of multimodal data in the developing tooth reveals candidate regulatory loci driving human odontogenic phenotypes. FRONTIERS IN DENTAL MEDICINE 2022; 3:1009264. [PMID: 37034481 PMCID: PMC10078798 DOI: 10.3389/fdmed.2022.1009264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Human odontogenic aberrations such as abnormal tooth number and delayed tooth eruption can occur as a symptom of rare syndromes or, more commonly, as nonsyndromic phenotypes. These phenotypes can require extensive and expensive dental treatment, posing a significant burden. While many dental phenotypes are heritable, most nonsyndromic cases have not been linked to causal genes. We demonstrate the novel finding that common sequence variants associated with human odontogenic phenotypes are enriched in developmental craniofacial enhancers conserved between human and mouse. However, the bulk nature of these samples obscures if this finding is due to the tooth itself or the surrounding tissues. We therefore sought to identify enhancers specifically active in the tooth anlagen and quantify their contribution to the observed genetic enrichments. We systematically identified 22,001 conserved enhancers active in E13.5 mouse incisors using ChIP-seq and machine learning pipelines and demonstrated biologically relevant enrichments in putative target genes, transcription factor binding motifs, and in vivo activity. Multi-tissue comparisons of human and mouse enhancers revealed that these putative tooth enhancers had the strongest enrichment of odontogenic phenotype-associated variants, suggesting a role for dysregulation of tooth developmental enhancers in human dental phenotypes. The large number of these regions genome-wide necessitated prioritization of enhancer loci for future investigations. As enhancers modulate gene expression, we prioritized regions based on enhancers' putative target genes. We predicted these target genes and prioritized loci by integrating chromatin state, bulk gene expression and coexpression, GWAS variants, and cell type resolved gene expression to generate a prioritized list of putative odontogenic phenotype-driving loci active in the developing tooth. These genomic regions are of particular interest for downstream experiments determining the role of specific dental enhancer:gene pairs in odontogenesis.
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Affiliation(s)
| | - Alexis Hardy
- Master of Genetics Program, Paris Diderot University,
Paris, France
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of
Connecticut School of Medicine, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut,
Storrs, CT, United States
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11
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Nagayasu K, Andoh C, Shirakawa H, Kaneko S. Diff-ATAC-STARR-Seq: A Method for Genome-Wide Functional Screening of Enhancer Activity in Vivo. Biol Pharm Bull 2022; 45:1590-1595. [PMID: 36184520 DOI: 10.1248/bpb.b22-00400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transcriptional regulatory elements, including promoters and enhancers, play a key role in the cell-type specific regulation of the transcriptome. Application of rapidly evolving genetic tools, such as optogenetic/chemogenetic actuators and fluorescent reporters to elucidate the function of cell subtypes in vivo necessitates cell-type specific promoters or enhancers. In this context, methods for genome-wide functional screening of cis-regulatory elements, including enhancers, are of utmost importance. In this study, we describe a novel method for genome-wide functional screening of enhancer activity in vivo with minimal handling. Application of the method to cells from different brain structures and subsequent differential analysis allow identification of active enhancers in the target tissue or brain structures. To demonstrate proof of concept, we applied this method to samples from the dorsal raphe nucleus (DRN) and the medial prefrontal cortex of the mouse brain and successfully identified six enhancers with highly biased activity towards the dorsal raphe nucleus. Considering that these two structures consist of largely similar cell types whereas serotonin and dopamine neurons exist only in the DRN, our results confirm the validity of this method in identifying cell-type specific and brain-structure specific enhancers. Overall, this method will be helpful in identifying cis-regulatory elements suitable for cell-type specific manipulations.
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Affiliation(s)
- Kazuki Nagayasu
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Chihiro Andoh
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Hisashi Shirakawa
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Shuji Kaneko
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
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12
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Ramirez M, Badayeva Y, Yeung J, Wu J, Abdalla-Wyse A, Yang E, Trost B, Scherer SW, Goldowitz D. Temporal analysis of enhancers during mouse cerebellar development reveals dynamic and novel regulatory functions. eLife 2022; 11:74207. [PMID: 35942939 PMCID: PMC9398453 DOI: 10.7554/elife.74207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
We have identified active enhancers in the mouse cerebellum at embryonic and postnatal stages which provides a view of novel enhancers active during cerebellar development. The majority of cerebellar enhancers have dynamic activity between embryonic and postnatal development. Cerebellar enhancers were enriched for neural transcription factor binding sites with temporally specific expression. Putative gene targets displayed spatially restricted expression patterns, indicating cell-type specific expression regulation. Functional analysis of target genes indicated that enhancers regulate processes spanning several developmental epochs such as specification, differentiation and maturation. We use these analyses to discover one novel regulator and one novel marker of cerebellar development: Bhlhe22 and Pax3, respectively. We identified an enrichment of de novo mutations and variants associated with autism spectrum disorder in cerebellar enhancers. Furthermore, by comparing our data with relevant brain development ENCODE histone profiles and cerebellar single-cell datasets we have been able to generalize and expand on the presented analyses, respectively. We have made the results of our analyses available online in the Developing Mouse Cerebellum Enhancer Atlas (https://goldowitzlab.shinyapps.io/developing_mouse_cerebellum_enhancer_atlas/), where our dataset can be efficiently queried, curated and exported by the scientific community to facilitate future research efforts. Our study provides a valuable resource for studying the dynamics of gene expression regulation by enhancers in the developing cerebellum and delivers a rich dataset of novel gene-enhancer associations providing a basis for future in-depth studies in the cerebellum.
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Affiliation(s)
- Miguel Ramirez
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Yuliya Badayeva
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Joshua Wu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Ayasha Abdalla-Wyse
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
| | - Erin Yang
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
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- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Brett Trost
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, Hospital for Sick Children, Toronto, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, Canada
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13
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Pouchelon G, Vergara J, McMahon J, Gorissen BL, Lin JD, Vormstein-Schneider D, Niehaus JL, Burbridge TJ, Wester JC, Sherer M, Fernandez-Otero M, Allaway KC, Pelkey K, Chittajallu R, McBain CJ, Fan M, Nasse JS, Wildenberg GA, Fishell G, Dimidschstein J. A versatile viral toolkit for functional discovery in the nervous system. CELL REPORTS METHODS 2022; 2:100225. [PMID: 35784651 PMCID: PMC9243523 DOI: 10.1016/j.crmeth.2022.100225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/21/2022] [Accepted: 05/04/2022] [Indexed: 12/24/2022]
Abstract
The ability to precisely control transgene expression is essential for basic research and clinical applications. Adeno-associated viruses (AAVs) are non-pathogenic and can be used to drive stable expression in virtually any tissue, cell type, or species, but their limited genomic payload results in a trade-off between the transgenes that can be incorporated and the complexity of the regulatory elements controlling their expression. Resolving these competing imperatives in complex experiments inevitably results in compromises. Here, we assemble an optimized viral toolkit (VTK) that addresses these limitations and allows for efficient combinatorial targeting of cell types. Moreover, their modular design explicitly enables further refinements. We achieve this in compact vectors by integrating structural improvements of AAV vectors with innovative molecular tools. We illustrate the potential of this approach through a systematic demonstration of their utility for targeting cell types and querying their biology using a wide array of genetically encoded tools.
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Affiliation(s)
- Gabrielle Pouchelon
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Josselyn Vergara
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Justin McMahon
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Bram L. Gorissen
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Jessica D. Lin
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | | | | | - Timothy J. Burbridge
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Jason C. Wester
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Mia Sherer
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Marian Fernandez-Otero
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Kathryn C. Allaway
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Kenneth Pelkey
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Ramesh Chittajallu
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Chris J. McBain
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | | | | | - Gregg A. Wildenberg
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Gordon Fishell
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
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14
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Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system. Nat Commun 2022; 13:2733. [PMID: 35585070 PMCID: PMC9117226 DOI: 10.1038/s41467-022-30192-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 04/20/2022] [Indexed: 11/08/2022] Open
Abstract
Mammalian genomes comprise largely intergenic noncoding DNA with numerous cis-regulatory elements. Whether and how the size of intergenic DNA affects gene expression in a tissue-specific manner remain unknown. Here we show that genes with extended intergenic regions are preferentially expressed in neural tissues but repressed in other tissues in mice and humans. Extended intergenic regions contain twice as many active enhancers in neural tissues compared to other tissues. Neural genes with extended intergenic regions are globally co-expressed with neighboring neural genes controlled by distinct enhancers in the shared intergenic regions. Moreover, generic neural genes expressed in multiple tissues have significantly longer intergenic regions than neural genes expressed in fewer tissues. The intergenic regions of the generic neural genes have many tissue-specific active enhancers containing distinct transcription factor binding sites specific to each neural tissue. We also show that genes with extended intergenic regions are enriched for neural genes only in vertebrates. The expansion of intergenic regions may reflect the regulatory complexity of tissue-type-specific gene expression in the nervous system.
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15
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Björklund T, Davidsson M. Next-Generation Gene Therapy for Parkinson's Disease Using Engineered Viral Vectors. JOURNAL OF PARKINSON'S DISEASE 2022; 11:S209-S217. [PMID: 34366370 PMCID: PMC8543274 DOI: 10.3233/jpd-212674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/14/2021] [Indexed: 11/23/2022]
Abstract
Recent technological and conceptual advances have resulted in a plethora of exciting novel engineered adeno associated viral (AAV) vector variants. They all have unique characteristics and abilities. This review summarizes the development and their potential in treating Parkinson's disease (PD). Clinical trials in PD have shown over the last decade that AAV is a safe and suitable vector for gene therapy but that it also is a vehicle that can benefit significantly from improvement in specificity and potency. This review provides a concise collection of the state-of-the-art for synthetic capsids and their utility in PD. We also summarize what therapeutical strategies may become feasible with novel engineered vectors, including genome editing and neuronal rejuvenation.
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Affiliation(s)
- Tomas Björklund
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Marcus Davidsson
- Molecular Neuromodulation, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
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16
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Fluorescence imaging of large-scale neural ensemble dynamics. Cell 2022; 185:9-41. [PMID: 34995519 PMCID: PMC8849612 DOI: 10.1016/j.cell.2021.12.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022]
Abstract
Recent progress in fluorescence imaging allows neuroscientists to observe the dynamics of thousands of individual neurons, identified genetically or by their connectivity, across multiple brain areas and for extended durations in awake behaving mammals. We discuss advances in fluorescent indicators of neural activity, viral and genetic methods to express these indicators, chronic animal preparations for long-term imaging studies, and microscopes to monitor and manipulate the activity of large neural ensembles. Ca2+ imaging studies of neural activity can track brain area interactions and distributed information processing at cellular resolution. Across smaller spatial scales, high-speed voltage imaging reveals the distinctive spiking patterns and coding properties of targeted neuron types. Collectively, these innovations will propel studies of brain function and dovetail with ongoing neuroscience initiatives to identify new neuron types and develop widely applicable, non-human primate models. The optical toolkit's growing sophistication also suggests that "brain observatory" facilities would be useful open resources for future brain-imaging studies.
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17
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Closser M, Guo Y, Wang P, Patel T, Jang S, Hammelman J, De Nooij JC, Kopunova R, Mazzoni EO, Ruan Y, Gifford DK, Wichterle H. An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity. Neuron 2022; 110:70-85.e6. [PMID: 34727520 PMCID: PMC8738133 DOI: 10.1016/j.neuron.2021.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/25/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023]
Abstract
Proper assembly and function of the nervous system requires the generation of a uniquely diverse population of neurons expressing a cell-type-specific combination of effector genes that collectively define neuronal morphology, connectivity, and function. How countless partially overlapping but cell-type-specific patterns of gene expression are controlled at the genomic level remains poorly understood. Here we show that neuronal genes are associated with highly complex gene regulatory systems composed of independent cell-type- and cell-stage-specific regulatory elements that reside in expanded non-coding genomic domains. Mapping enhancer-promoter interactions revealed that motor neuron enhancers are broadly distributed across the large chromatin domains. This distributed regulatory architecture is not a unique property of motor neurons but is employed throughout the nervous system. The number of regulatory elements increased dramatically during the transition from invertebrates to vertebrates, suggesting that acquisition of new enhancers might be a fundamental process underlying the evolutionary increase in cellular complexity.
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Affiliation(s)
- Michael Closser
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yuchun Guo
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Tulsi Patel
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sumin Jang
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jennifer Hammelman
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Joriene C De Nooij
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rachel Kopunova
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA.
| | - Hynek Wichterle
- Departments of Pathology and Cell Biology, Neuroscience, and Neurology, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA.
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18
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Nano PR, Nguyen CV, Mil J, Bhaduri A. Cortical Cartography: Mapping Arealization Using Single-Cell Omics Technology. Front Neural Circuits 2021; 15:788560. [PMID: 34955761 PMCID: PMC8707733 DOI: 10.3389/fncir.2021.788560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022] Open
Abstract
The cerebral cortex derives its cognitive power from a modular network of specialized areas processing a multitude of information. The assembly and organization of these regions is vital for human behavior and perception, as evidenced by the prevalence of area-specific phenotypes that manifest in neurodevelopmental and psychiatric disorders. Generations of scientists have examined the architecture of the human cortex, but efforts to capture the gene networks which drive arealization have been hampered by the lack of tractable models of human neurodevelopment. Advancements in "omics" technologies, imaging, and computational power have enabled exciting breakthroughs into the molecular and structural characteristics of cortical areas, including transcriptomic, epigenomic, metabolomic, and proteomic profiles of mammalian models. Here we review the single-omics atlases that have shaped our current understanding of cortical areas, and their potential to fuel a new era of multi-omic single-cell endeavors to interrogate both the developing and adult human cortex.
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Affiliation(s)
| | | | | | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
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19
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Tosches MA. From Cell Types to an Integrated Understanding of Brain Evolution: The Case of the Cerebral Cortex. Annu Rev Cell Dev Biol 2021; 37:495-517. [PMID: 34416113 DOI: 10.1146/annurev-cellbio-120319-112654] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the discovery of the incredible diversity of neurons, Cajal and coworkers laid the foundation of modern neuroscience. Neuron types are not only structural units of nervous systems but also evolutionary units, because their identities are encoded in the genome. With the advent of high-throughput cellular transcriptomics, neuronal identities can be characterized and compared systematically across species. The comparison of neurons in mammals, reptiles, and birds indicates that the mammalian cerebral cortex is a mosaic of deeply conserved and recently evolved neuron types. Using the cerebral cortex as a case study, this review illustrates how comparing neuron types across species is key to reconciling observations on neural development, neuroanatomy, circuit wiring, and physiology for an integrated understanding of brain evolution.
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20
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Nicola FDC, Hua I, Levine AJ. Intersectional genetic tools to study skilled reaching in mice. Exp Neurol 2021; 347:113879. [PMID: 34597682 DOI: 10.1016/j.expneurol.2021.113879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/10/2021] [Accepted: 09/24/2021] [Indexed: 11/25/2022]
Abstract
Reaching to grasp is an evolutionarily conserved behavior and a crucial part of the motor repertoire in mammals. As it is studied in the laboratory, reaching has become the prototypical example of dexterous forelimb movements, illuminating key principles of motor control throughout the spinal cord, brain, and peripheral nervous system. Here, we (1) review the motor elements or phases that comprise the reach, grasp, and retract movements of reaching behavior, (2) highlight the role of intersectional genetic tools in linking these movements to their neuronal substrates, (3) describe spinal cord cell types and their roles in skilled reaching, and (4) how descending pathways from the brain and the sensory systems contribute to skilled reaching. We emphasize that genetic perturbation experiments can pin-point the neuronal substrates of specific phases of reaching behavior.
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Affiliation(s)
- Fabricio do Couto Nicola
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Isabelle Hua
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, United States of America
| | - Ariel J Levine
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, United States of America.
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21
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Chalkiadaki K, Statoulla E, Markou M, Bellou S, Bagli E, Fotsis T, Murphy C, Gkogkas CG. Translational control in neurovascular brain development. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211088. [PMID: 34659781 PMCID: PMC8511748 DOI: 10.1098/rsos.211088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The human brain carries out complex tasks and higher functions and is crucial for organismal survival, as it senses both intrinsic and extrinsic environments. Proper brain development relies on the orchestrated development of different precursor cells, which will give rise to the plethora of mature brain cell-types. Within this process, neuronal cells develop closely to and in coordination with vascular cells (endothelial cells (ECs), pericytes) in a bilateral communication process that relies on neuronal activity, attractive or repulsive guidance cues for both cell types and on tight-regulation of gene expression. Translational control is a master regulator of the gene-expression pathway and in particular for neuronal and ECs, it can be localized in developmentally relevant (axon growth cone, endothelial tip cell) and mature compartments (synapses, axons). Herein, we will review mechanisms of translational control relevant to brain development in neurons and ECs in health and disease.
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Affiliation(s)
- Kleanthi Chalkiadaki
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Elpida Statoulla
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Maria Markou
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Sofia Bellou
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Eleni Bagli
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Theodore Fotsis
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Carol Murphy
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
| | - Christos G. Gkogkas
- Division of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, University Campus, 45110 Ioannina, Greece
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22
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Matho KS, Huilgol D, Galbavy W, He M, Kim G, An X, Lu J, Wu P, Di Bella DJ, Shetty AS, Palaniswamy R, Hatfield J, Raudales R, Narasimhan A, Gamache E, Levine JM, Tucciarone J, Szelenyi E, Harris JA, Mitra PP, Osten P, Arlotta P, Huang ZJ. Genetic dissection of the glutamatergic neuron system in cerebral cortex. Nature 2021; 598:182-187. [PMID: 34616069 PMCID: PMC8494647 DOI: 10.1038/s41586-021-03955-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/25/2021] [Indexed: 11/09/2022]
Abstract
Diverse types of glutamatergic pyramidal neurons mediate the myriad processing streams and output channels of the cerebral cortex1,2, yet all derive from neural progenitors of the embryonic dorsal telencephalon3,4. Here we establish genetic strategies and tools for dissecting and fate-mapping subpopulations of pyramidal neurons on the basis of their developmental and molecular programs. We leverage key transcription factors and effector genes to systematically target temporal patterning programs in progenitors and differentiation programs in postmitotic neurons. We generated over a dozen temporally inducible mouse Cre and Flp knock-in driver lines to enable the combinatorial targeting of major progenitor types and projection classes. Combinatorial strategies confer viral access to subsets of pyramidal neurons defined by developmental origin, marker expression, anatomical location and projection targets. These strategies establish an experimental framework for understanding the hierarchical organization and developmental trajectory of subpopulations of pyramidal neurons that assemble cortical processing networks and output channels.
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Affiliation(s)
- Katherine S Matho
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Dhananjay Huilgol
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - William Galbavy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, USA
| | - Miao He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Gukhan Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Xu An
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Jiangteng Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Shanghai Jiaotong University Medical School, Shanghai, China
| | - Priscilla Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Daniela J Di Bella
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Ashwin S Shetty
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Joshua Hatfield
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Ricardo Raudales
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Program in Neuroscience, Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, USA
| | - Arun Narasimhan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Eric Gamache
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Jesse M Levine
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Program in Neuroscience and Medical Scientist Training Program, Stony Brook University, New York, NY, USA
| | - Jason Tucciarone
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
- Program in Neuroscience and Medical Scientist Training Program, Stony Brook University, New York, NY, USA
- Department of Psychiatry, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Eric Szelenyi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Julie A Harris
- Program in Neuroscience and Medical Scientist Training Program, Stony Brook University, New York, NY, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Partha P Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.
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23
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Iatrou A, Clark EM, Wang Y. Nuclear dynamics and stress responses in Alzheimer's disease. Mol Neurodegener 2021; 16:65. [PMID: 34535174 PMCID: PMC8447732 DOI: 10.1186/s13024-021-00489-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
In response to extracellular and intracellular stressors, the nucleus and nuclear compartments undergo distinct molecular changes to maintain cell homeostasis. In the context of Alzheimer’s disease, misfolded proteins and various cellular stressors lead to profound structural and molecular changes at the nucleus. This review summarizes recent research on nuclear alterations in AD development, from the nuclear envelope changes to chromatin and epigenetic regulation and then to common nuclear stress responses. Finally, we provide our thoughts on the importance of understanding cell-type-specific changes and identifying upstream causal events in AD pathogenesis and highlight novel sequencing and gene perturbation technologies to address those challenges.
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Affiliation(s)
- Artemis Iatrou
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Chicago, IL, 60612, USA
| | - Eric M Clark
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Chicago, IL, 60612, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Chicago, IL, 60612, USA.
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Abulimiti A, Lai MSL, Chang RCC. Applications of adeno-associated virus vector-mediated gene delivery for neurodegenerative diseases and psychiatric diseases: Progress, advances, and challenges. Mech Ageing Dev 2021; 199:111549. [PMID: 34352323 DOI: 10.1016/j.mad.2021.111549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 07/31/2021] [Indexed: 12/19/2022]
Abstract
Neurodegeneration is the most common disease in the elderly population due to its slowly progressive nature of neuronal deterioration, eventually leading to executive dysfunction. The pathological markers of neurological disorders are relatively well-established, however, detailed molecular mechanisms of progression and therapeutic targets are needed to develop novel treatments in human patients. Treating known therapeutic targets of neurological diseases has been aided by recent advancements in adeno-associated virus (AAV) technology. AAVs are known for their low-immunogenicity, blood-brain barrier (BBB) penetrating ability, selective neuronal tropism, stable transgene expression, and pleiotropy. In addition, the usage of AAVs has enormous potential to be optimized. Therefore, AAV can be a powerful tool used to uncover the underlying pathophysiology of neurological disorders and to increase the success in human gene therapy. This review summarizes different optimization approaches of AAV vectors with their current applications in disease modeling, neural tracing and gene therapy, hence exploring progressive mechanisms of neurodegenerative diseases as well as effective therapy. Lastly, this review discusses the limitations and future perspectives of the AAV-mediated transgene delivery system.
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Affiliation(s)
- Amina Abulimiti
- Laboratory of Neurodegenerative Diseases, School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Michael Siu-Lun Lai
- Laboratory of Neurodegenerative Diseases, School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Raymond Chuen-Chung Chang
- Laboratory of Neurodegenerative Diseases, School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region.
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Borodinova AA, Balaban PM, Bezprozvanny IB, Salmina AB, Vlasova OL. Genetic Constructs for the Control of Astrocytes' Activity. Cells 2021; 10:cells10071600. [PMID: 34202359 PMCID: PMC8306323 DOI: 10.3390/cells10071600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 12/20/2022] Open
Abstract
In the current review, we aim to discuss the principles and the perspectives of using the genetic constructs based on AAV vectors to regulate astrocytes’ activity. Practical applications of optogenetic approaches utilizing different genetically encoded opsins to control astroglia activity were evaluated. The diversity of astrocytic cell-types complicates the rational design of an ideal viral vector for particular experimental goals. Therefore, efficient and sufficient targeting of astrocytes is a multiparametric process that requires a combination of specific AAV serotypes naturally predisposed to transduce astroglia with astrocyte-specific promoters in the AAV cassette. Inadequate combinations may result in off-target neuronal transduction to different degrees. Potentially, these constraints may be bypassed with the latest strategies of generating novel synthetic AAV serotypes with specified properties by rational engineering of AAV capsids or using directed evolution approach by searching within a more specific promoter or its replacement with the unique enhancer sequences characterized using modern molecular techniques (ChIP-seq, scATAC-seq, snATAC-seq) to drive the selective transgene expression in the target population of cells or desired brain regions. Realizing these strategies to restrict expression and to efficiently target astrocytic populations in specific brain regions or across the brain has great potential to enable future studies.
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Affiliation(s)
- Anastasia A. Borodinova
- Laboratory of Cellular Neurobiology of Learning, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia;
| | - Pavel M. Balaban
- Laboratory of Cellular Neurobiology of Learning, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 117485 Moscow, Russia;
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (I.B.B.); (A.B.S.); (O.L.V.)
- Correspondence:
| | - Ilya B. Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (I.B.B.); (A.B.S.); (O.L.V.)
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Alla B. Salmina
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (I.B.B.); (A.B.S.); (O.L.V.)
- Research Institute of Molecular Medicine and Pathobiochemistry, V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 660022 Krasnoyarsk, Russia
- Research Center of Neurology, 125367 Moscow, Russia
| | - Olga L. Vlasova
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (I.B.B.); (A.B.S.); (O.L.V.)
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Liu Y, Bergmann T, Mori Y, Peralvo Vidal JM, Pihl M, Vasistha NA, Thomsen PD, Seemann SE, Gorodkin J, Hyttel P, Khodosevich K, Witter MP, Hall VJ. Development of the Entorhinal Cortex Occurs via Parallel Lamination During Neurogenesis. Front Neuroanat 2021; 15:663667. [PMID: 34025365 PMCID: PMC8139189 DOI: 10.3389/fnana.2021.663667] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/08/2021] [Indexed: 11/13/2022] Open
Abstract
The entorhinal cortex (EC) is the spatial processing center of the brain and structurally is an interface between the three layered paleocortex and six layered neocortex, known as the periarchicortex. Limited studies indicate peculiarities in the formation of the EC such as early emergence of cells in layers (L) II and late deposition of LIII, as well as divergence in the timing of maturation of cell types in the superficial layers. In this study, we examine developmental events in the entorhinal cortex using an understudied model in neuroanatomy and development, the pig and supplement the research with BrdU labeling in the developing mouse EC. We determine the pig serves as an excellent anatomical model for studying human neurogenesis, given its long gestational length, presence of a moderate sized outer subventricular zone and early cessation of neurogenesis during gestation. Immunohistochemistry identified prominent clusters of OLIG2+ oligoprogenitor-like cells in the superficial layers of the lateral EC (LEC) that are sparser in the medial EC (MEC). These are first detected in the subplate during the early second trimester. MRI analyses reveal an acceleration of EC growth at the end of the second trimester. BrdU labeling of the developing MEC, shows the deeper layers form first and prior to the superficial layers, but the LV/VI emerges in parallel and the LII/III emerges later, but also in parallel. We coin this lamination pattern parallel lamination. The early born Reln+ stellate cells in the superficial layers express the classic LV marker, Bcl11b (Ctip2) and arise from a common progenitor that forms the late deep layer LV neurons. In summary, we characterize the developing EC in a novel animal model and outline in detail the formation of the EC. We further provide insight into how the periarchicortex forms in the brain, which differs remarkably to the inside-out lamination of the neocortex.
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Affiliation(s)
- Yong Liu
- Group of Brain Development and Disease, Section Pathobiological Sciences, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Bergmann
- Group of Brain Development and Disease, Section Pathobiological Sciences, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yuki Mori
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juan Miguel Peralvo Vidal
- Group of Brain Development and Disease, Section Pathobiological Sciences, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pihl
- Disease Stem Cell Models and Embryology, Section Pathobiological Sciences, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Navneet A. Vasistha
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Preben Dybdahl Thomsen
- Disease Stem Cell Models and Embryology, Section Pathobiological Sciences, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stefan E. Seemann
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Poul Hyttel
- Disease Stem Cell Models and Embryology, Section Pathobiological Sciences, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Menno P. Witter
- Kavli Institute for Systems Neuroscience, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Vanessa Jane Hall
- Group of Brain Development and Disease, Section Pathobiological Sciences, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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27
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Enhancer viruses for combinatorial cell-subclass-specific labeling. Neuron 2021; 109:1449-1464.e13. [PMID: 33789083 DOI: 10.1016/j.neuron.2021.03.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 12/14/2020] [Accepted: 03/08/2021] [Indexed: 12/21/2022]
Abstract
Rapid cell type identification by new genomic single-cell analysis methods has not been met with efficient experimental access to these cell types. To facilitate access to specific neural populations in mouse cortex, we collected chromatin accessibility data from individual cells and identified enhancers specific for cell subclasses and types. When cloned into recombinant adeno-associated viruses (AAVs) and delivered to the brain, these enhancers drive transgene expression in specific cortical cell subclasses. We extensively characterized several enhancer AAVs to show that they label different projection neuron subclasses as well as a homologous neuron subclass in human cortical slices. We also show how coupling enhancer viruses expressing recombinases to a newly generated transgenic mouse, Ai213, enables strong labeling of three different neuronal classes/subclasses in the brain of a single transgenic animal. This approach combines unprecedented flexibility with specificity for investigation of cell types in the mouse brain and beyond.
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Ohara S, Blankvoort S, Nair RR, Nigro MJ, Nilssen ES, Kentros C, Witter MP. Local projections of layer Vb-to-Va are more prominent in lateral than in medial entorhinal cortex. eLife 2021; 10:e67262. [PMID: 33769282 PMCID: PMC8051944 DOI: 10.7554/elife.67262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
The entorhinal cortex, in particular neurons in layer V, allegedly mediate transfer of information from the hippocampus to the neocortex, underlying long-term memory. Recently, this circuit has been shown to comprise a hippocampal output recipient layer Vb and a cortical projecting layer Va. With the use of in vitro electrophysiology in transgenic mice specific for layer Vb, we assessed the presence of the thus necessary connection from layer Vb-to-Va in the functionally distinct medial (MEC) and lateral (LEC) subdivisions; MEC, particularly its dorsal part, processes allocentric spatial information, whereas the corresponding part of LEC processes information representing elements of episodes. Using identical experimental approaches, we show that connections from layer Vb-to-Va neurons are stronger in dorsal LEC compared with dorsal MEC, suggesting different operating principles in these two regions. Although further in vivo experiments are needed, our findings imply a potential difference in how LEC and MEC mediate episodic systems consolidation.
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Grants
- endowment Kavli Foundation
- infrastructure grant NORBRAIN,#197467 Norwegian Research Council
- the Centre of Excellence scheme - Centre for Neural Computation,#223262 Norwegian Research Council
- research grant,# 227769 Norwegian Research Council
- KAKENHI,#19K06917 Ministry of Education, Culture, Sports, Science and Technology
- KAKENHI (#19K06917) Ministry of Education, Culture, Sports, Science and Technology
- #197467 Norwegian Research Council
- #223262 Norwegian Research Council
- #227769 Norwegian Research Council
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Affiliation(s)
- Shinya Ohara
- Kavli institute for Systems Neuroscience, Center for Computational Neuroscience, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, NTNU Norwegian University of Science and TechnologyTrondheimNorway
- Laboratory of Systems Neuroscience, Tohoku University Graduate School of Life SciencesTohokuJapan
| | - Stefan Blankvoort
- Kavli institute for Systems Neuroscience, Center for Computational Neuroscience, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, NTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Rajeevkumar Raveendran Nair
- Kavli institute for Systems Neuroscience, Center for Computational Neuroscience, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, NTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Maximiliano J Nigro
- Kavli institute for Systems Neuroscience, Center for Computational Neuroscience, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, NTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Eirik S Nilssen
- Kavli institute for Systems Neuroscience, Center for Computational Neuroscience, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, NTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Clifford Kentros
- Kavli institute for Systems Neuroscience, Center for Computational Neuroscience, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, NTNU Norwegian University of Science and TechnologyTrondheimNorway
| | - Menno P Witter
- Kavli institute for Systems Neuroscience, Center for Computational Neuroscience, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, NTNU Norwegian University of Science and TechnologyTrondheimNorway
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Chadney OMT, Blankvoort S, Grimstvedt JS, Utz A, Kentros CG. Multiplexing viral approaches to the study of the neuronal circuits. J Neurosci Methods 2021; 357:109142. [PMID: 33753126 DOI: 10.1016/j.jneumeth.2021.109142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/27/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022]
Abstract
Neural circuits are composed of multitudes of elaborately interconnected cell types. Understanding neural circuit function requires not only cell-specific knowledge of connectivity, but the ability to record and manipulate distinct cell types independently. Recent advances in viral vectors promise the requisite specificity to perform true "circuit-breaking" experiments. However, such new avenues of multiplexed, cell-specific investigation raise new technical issues: one must ensure that both the viral vectors and their transgene payloads do not overlap with each other in both an anatomical and a functional sense. This review describes benefits and issues regarding the use of viral vectors to analyse the function of neural circuits and provides a resource for the design and implementation of such multiplexing experiments.
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Affiliation(s)
- Oscar M T Chadney
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway.
| | - Stefan Blankvoort
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - Joachim S Grimstvedt
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - Annika Utz
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - Clifford G Kentros
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway.
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Mulvey B, Lagunas T, Dougherty JD. Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts. Biol Psychiatry 2021; 89:76-89. [PMID: 32843144 PMCID: PMC7938388 DOI: 10.1016/j.biopsych.2020.06.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/18/2022]
Abstract
Neuropsychiatric phenotypes have long been known to be influenced by heritable risk factors, directly confirmed by the past decade of genetic studies that have revealed specific genetic variants enriched in disease cohorts. However, the initial hope that a small set of genes would be responsible for a given disorder proved false. The more complex reality is that a given disorder may be influenced by myriad small-effect noncoding variants and/or by rare but severe coding variants, many de novo. Noncoding genomic sequences-for which molecular functions cannot usually be inferred-harbor a large portion of these variants, creating a substantial barrier to understanding higher-order molecular and biological systems of disease. Fortunately, novel genetic technologies-scalable oligonucleotide synthesis, RNA sequencing, and CRISPR (clustered regularly interspaced short palindromic repeats)-have opened novel avenues to experimentally identify biologically significant variants en masse. Massively parallel reporter assays (MPRAs) are an especially versatile technique resulting from such innovations. MPRAs are powerful molecular genetics tools that can be used to screen thousands of untranscribed or untranslated sequences and their variants for functional effects in a single experiment. This approach, though underutilized in psychiatric genetics, has several useful features for the field. We review methods for assaying putatively functional genetic variants and regions, emphasizing MPRAs and the opportunities they hold for dissection of psychiatric polygenicity. We discuss literature applying functional assays in neurogenetics, highlighting strengths, caveats, and design considerations-especially regarding disease-relevant variables (cell type, neurodevelopment, and sex), and we ultimately propose applications of MPRA to both computational and experimental neurogenetics of polygenic disease risk.
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Affiliation(s)
- Bernard Mulvey
- Division of Biology and Biomedical Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Tomás Lagunas
- Division of Biology and Biomedical Sciences, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, Missouri; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, Missouri.
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31
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Lawler AJ, Brown AR, Bouchard RS, Toong N, Kim Y, Velraj N, Fox G, Kleyman M, Kang B, Gittis AH, Pfenning AR. Cell Type-Specific Oxidative Stress Genomic Signatures in the Globus Pallidus of Dopamine-Depleted Mice. J Neurosci 2020; 40:9772-9783. [PMID: 33188066 PMCID: PMC7726543 DOI: 10.1523/jneurosci.1634-20.2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022] Open
Abstract
Neuron subtype dysfunction is a key contributor to neurologic disease circuits, but identifying associated gene regulatory pathways is complicated by the molecular complexity of the brain. For example, parvalbumin-expressing (PV+) neurons in the external globus pallidus (GPe) are critically involved in the motor deficits of dopamine-depleted mouse models of Parkinson's disease, where cell type-specific optogenetic stimulation of PV+ neurons over other neuron populations rescues locomotion. Despite the distinct roles these cell types play in the neural circuit, the molecular correlates remain unknown because of the difficulty of isolating rare neuron subtypes. To address this issue, we developed a new viral affinity purification strategy, Cre-Specific Nuclear Anchored Independent Labeling, to isolate Cre recombinase-expressing (Cre+) nuclei from the adult mouse brain. Applying this technology, we performed targeted assessments of the cell type-specific transcriptomic and epigenetic effects of dopamine depletion on PV+ and PV- cells within three brain regions of male and female mice: GPe, striatum, and cortex. We found GPe PV+ neuron-specific gene expression changes that suggested increased hypoxia-inducible factor 2α signaling. Consistent with transcriptomic data, regions of open chromatin affected by dopamine depletion within GPe PV+ neurons were enriched for hypoxia-inducible factor family binding motifs. The gene expression and epigenomic experiments performed on PV+ neurons isolated by Cre-Specific Nuclear Anchored Independent Labeling identified a transcriptional regulatory network mediated by the neuroprotective factor Hif2a as underlying neural circuit differences in response to dopamine depletion.SIGNIFICANCE STATEMENT Cre-Specific Nuclear Anchored Independent Labeling is an enhanced, virus-based approach to isolate nuclei of a specific cell type for transcriptome and epigenome interrogation that decreases dependency on transgenic animals. Applying this technology to GPe parvalbumin-expressing neurons in a mouse model of Parkinson's disease, we discovered evidence for an upregulation of the oxygen homeostasis maintaining pathway involving Hypoxia-inducible factor 2α. These results provide new insight into how neuron subtypes outside the substantia nigra pars compacta may be compensating at a molecular level for differences in the motor production neural circuit during the progression of Parkinson's disease. Furthermore, they emphasize the utility of cell type-specific technologies, such as Cre-Specific Nuclear Anchored Independent Labeling, for isolated assessment of specific neuron subtypes in complex systems.
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Affiliation(s)
- Alyssa J Lawler
- Computational Biology
- Biological Sciences
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Ashley R Brown
- Computational Biology
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Rachel S Bouchard
- Biological Sciences
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Noelle Toong
- Computational Biology
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Yeonju Kim
- Computational Biology
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Nitinram Velraj
- Computational Biology
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Grant Fox
- Computational Biology
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Michael Kleyman
- Computational Biology
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Byungsoo Kang
- Computational Biology
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Aryn H Gittis
- Biological Sciences
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Andreas R Pfenning
- Computational Biology
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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32
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Ross JM, Kim C, Allen D, Crouch EE, Narsinh K, Cooke DL, Abla AA, Nowakowski TJ, Winkler EA. The Expanding Cell Diversity of the Brain Vasculature. Front Physiol 2020; 11:600767. [PMID: 33343397 PMCID: PMC7744630 DOI: 10.3389/fphys.2020.600767] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
The cerebrovasculature is essential to brain health and is tasked with ensuring adequate delivery of oxygen and metabolic precursors to ensure normal neurologic function. This is coordinated through a dynamic, multi-directional cellular interplay between vascular, neuronal, and glial cells. Molecular exchanges across the blood-brain barrier or the close matching of regional blood flow with brain activation are not uniformly assigned to arteries, capillaries, and veins. Evidence has supported functional segmentation of the brain vasculature. This is achieved in part through morphologic or transcriptional heterogeneity of brain vascular cells-including endothelium, pericytes, and vascular smooth muscle. Advances with single cell genomic technologies have shown increasing cell complexity of the brain vasculature identifying previously unknown cell types and further subclassifying transcriptional diversity in cardinal vascular cell types. Cell-type specific molecular transitions or zonations have been identified. In this review, we summarize emerging evidence for the expanding vascular cell diversity in the brain and how this may provide a cellular basis for functional segmentation along the arterial-venous axis.
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Affiliation(s)
- Jayden M. Ross
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
| | - Chang Kim
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
| | - Denise Allen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
| | - Elizabeth E. Crouch
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Kazim Narsinh
- Department of Radiology, University of California, San Francisco, San Francisco, CA, United States
| | - Daniel L. Cooke
- Department of Radiology, University of California, San Francisco, San Francisco, CA, United States
| | - Adib A. Abla
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Tomasz J. Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiology, University of California, San Francisco, San Francisco, CA, United States
| | - Ethan A. Winkler
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
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Bernard C. Circadian/multidien Molecular Oscillations and Rhythmicity of Epilepsy (MORE). Epilepsia 2020; 62 Suppl 1:S49-S68. [PMID: 33063860 DOI: 10.1111/epi.16716] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 12/26/2022]
Abstract
The occurrence of seizures at specific times of the day has been consistently observed for centuries in individuals with epilepsy. Electrophysiological recordings provide evidence that seizures have a higher probability of occurring at a given time during the night and day cycle in individuals with epilepsy here referred to as the seizure rush hour. Which mechanisms underlie such circadian rhythmicity of seizures? Why don't they occur every day at the same time? Which mechanisms may underlie their occurrence outside the rush hour? In this commentary, I present a hypothesis: MORE - Molecular Oscillations and Rhythmicity of Epilepsy, a conceptual framework to study and understand the mechanisms underlying the circadian rhythmicity of seizures and their probabilistic nature. The core of the hypothesis is the existence of ~24-hour oscillations of gene and protein expression throughout the body in different cells and organs. The orchestrated molecular oscillations control the rhythmicity of numerous body events, such as feeding and sleep. The concept developed here is that molecular oscillations may favor seizure genesis at preferred times, generating the condition for a seizure rush hour. However, the condition is not sufficient, as other factors are necessary for a seizure to occur. Studying these molecular oscillations may help us understand seizure genesis mechanisms and find new therapeutic targets and predictive biomarkers. The MORE hypothesis can be generalized to comorbidities and the slower multidien (week/month period) rhythmicity of seizures, a phenomenon addressed in another article in this issue of Epilepsia.
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Affiliation(s)
- Christophe Bernard
- Inserm, INS, Institut de Neurosciences des Systèmes, Aix Marseille Univ, Marseille, France
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Abstract
RATIONALE There is growing evidence that common variants and rare sequence alterations in regulatory sequences can result in birth defects or predisposition to disease. Congenital heart defects are the most common birth defect and have a clear genetic component, yet only a third of cases can be attributed to structural variation in the genome or a mutation in a gene. The remaining unknown cases could be caused by alterations in regulatory sequences. OBJECTIVE Identify regulatory sequences and gene expression networks that are active during organogenesis of the human heart. Determine whether these sites and networks are enriched for disease-relevant genes and associated genetic variation. METHODS AND RESULTS We characterized ChromHMM (chromatin state) and gene expression dynamics during human heart organogenesis. We profiled 7 histone modifications in embryonic hearts from each of 9 distinct Carnegie stages (13-14, 16-21, and 23), annotated chromatin states, and compared these maps to over 100 human tissues and cell types. We also generated RNA-sequencing data, performed differential expression, and constructed weighted gene coexpression networks. We identified 177 412 heart enhancers; 12 395 had not been previously annotated as strong enhancers. We identified 92% of all functionally validated heart-positive enhancers (n=281; 7.5× enrichment; P<2.2×10-16). Integration of these data demonstrated novel heart enhancers are enriched near genes expressed more strongly in cardiac tissue and are enriched for variants associated with ECG measures and atrial fibrillation. Our gene expression network analysis identified gene modules strongly enriched for heart-related functions, regulatory control by heart-specific enhancers, and putative disease genes. CONCLUSIONS Well-connected hub genes with heart-specific expression targeted by embryonic heart-specific enhancers are likely disease candidates. Our functional annotations will allow for better interpretation of whole genome sequencing data in the large number of patients affected by congenital heart defects.
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Affiliation(s)
- Jennifer VanOudenhove
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
| | - Tara N. Yankee
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington CT, USA
| | - Andrea Wilderman
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington CT, USA
| | - Justin Cotney
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
- Institute for Systems Genomics, UConn, Storrs CT, USA
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Liang L, Chen C. Organization, Function, and Development of the Mouse Retinogeniculate Synapse. Annu Rev Vis Sci 2020; 6:261-285. [DOI: 10.1146/annurev-vision-121219-081753] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Visual information is encoded in distinct retinal ganglion cell (RGC) types in the eye tuned to specific features of the visual space. These streams of information project to the visual thalamus, the first station of the image-forming pathway. In the mouse, this connection between RGCs and thalamocortical neurons, the retinogeniculate synapse, has become a powerful experimental model for understanding how circuits in the thalamus are constructed to process these incoming lines of information. Using modern molecular and genetic tools, recent studies have suggested a more complex circuit organization than was previously understood. In this review, we summarize the current understanding of the structural and functional organization of the retinogeniculate synapse in the mouse. We discuss a framework by which a seemingly complex circuit can effectively integrate and parse information to downstream stations of the visual pathway. Finally, we review how activity and visual experience can sculpt this exquisite connectivity.
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Affiliation(s)
- Liang Liang
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Department of Neuroscience, Yale University, New Haven, Connecticut 06520, USA
| | - Chinfei Chen
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts 02115, USA
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Vormstein-Schneider D, Lin JD, Pelkey KA, Chittajallu R, Guo B, Arias-Garcia MA, Allaway K, Sakopoulos S, Schneider G, Stevenson O, Vergara J, Sharma J, Zhang Q, Franken TP, Smith J, Ibrahim LA, M Astro KJ, Sabri E, Huang S, Favuzzi E, Burbridge T, Xu Q, Guo L, Vogel I, Sanchez V, Saldi GA, Gorissen BL, Yuan X, Zaghloul KA, Devinsky O, Sabatini BL, Batista-Brito R, Reynolds J, Feng G, Fu Z, McBain CJ, Fishell G, Dimidschstein J. Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans. Nat Neurosci 2020; 23:1629-1636. [PMID: 32807948 DOI: 10.1038/s41593-020-0692-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Recent success in identifying gene-regulatory elements in the context of recombinant adeno-associated virus vectors has enabled cell-type-restricted gene expression. However, within the cerebral cortex these tools are largely limited to broad classes of neurons. To overcome this limitation, we developed a strategy that led to the identification of multiple new enhancers to target functionally distinct neuronal subtypes. By investigating the regulatory landscape of the disease gene Scn1a, we discovered enhancers selective for parvalbumin (PV) and vasoactive intestinal peptide-expressing interneurons. Demonstrating the functional utility of these elements, we show that the PV-specific enhancer allowed for the selective targeting and manipulation of these neurons across vertebrate species, including humans. Finally, we demonstrate that our selection method is generalizable and characterizes additional PV-specific enhancers with exquisite specificity within distinct brain regions. Altogether, these viral tools can be used for cell-type-specific circuit manipulation and hold considerable promise for use in therapeutic interventions.
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Affiliation(s)
| | - Jessica D Lin
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kenneth A Pelkey
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ramesh Chittajallu
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Baolin Guo
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mario A Arias-Garcia
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kathryn Allaway
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,NYU Langone Medical Center, New York University, New York, NY, USA
| | - Sofia Sakopoulos
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gates Schneider
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olivia Stevenson
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Josselyn Vergara
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jitendra Sharma
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qiangge Zhang
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tom P Franken
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jared Smith
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Leena A Ibrahim
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Kevin J M Astro
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ehsan Sabri
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Shuhan Huang
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Emilia Favuzzi
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Timothy Burbridge
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Qing Xu
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - Lihua Guo
- Center for Genomics & Systems Biology, New York University, Abu Dhabi, UAE
| | - Ian Vogel
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Vanessa Sanchez
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Giuseppe A Saldi
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Bram L Gorissen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xiaoqing Yuan
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kareem A Zaghloul
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University School of Medicine, New York, NY, USA
| | - Bernardo L Sabatini
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | | | - John Reynolds
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhanyan Fu
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chris J McBain
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Gord Fishell
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Jordane Dimidschstein
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Shen Y, Campbell RE, Côté DC, Paquet ME. Challenges for Therapeutic Applications of Opsin-Based Optogenetic Tools in Humans. Front Neural Circuits 2020; 14:41. [PMID: 32760252 PMCID: PMC7373823 DOI: 10.3389/fncir.2020.00041] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/16/2020] [Indexed: 12/29/2022] Open
Abstract
As the technological hurdles are overcome and optogenetic techniques advance to have more control over neurons, therapies based on these approaches will begin to emerge in the clinic. Here, we consider the technical challenges surrounding the transition of this breakthrough technology from an investigative tool to a true therapeutic avenue. The emerging strategies and remaining tasks surrounding genetically encoded molecules which respond to light as well as the vehicles required to deliver them are discussed.The use of optogenetics in humans would represent a completely new paradigm in medicine and would be associated with unprecedented technical considerations. To be applied for stimulation of neurons in humans, an ideal optogenetic tool would need to be non-immunogenic, highly sensitive, and activatable with red light or near-infrared light (to maximize light penetration while minimizing photodamage). To enable sophisticated levels of neuronal control, the combined use of optogenetic actuators and indicators could enable closed-loop all-optical neuromodulation. Such systems would introduce additional challenges related to spectral orthogonality between actuator and indicator, the need for decision making computational algorithms and requirements for large gene cassettes. As in any gene therapy, the therapeutic efficiency of optogenetics will rely on vector delivery and expression in the appropriate cell type. Although viral vectors such as those based on AAVs are showing great potential in human trials, barriers to their general use remain, including immune responses, delivery/transport, and liver clearance. Limitations associated with the gene cassette size which can be packaged in currently approved vectors also need to be addressed.
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Affiliation(s)
- Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada.,Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Daniel C Côté
- Centre de Recherche CERVO, Université Laval, Quebec City, QC, Canada.,Département de Physique et Génie Physique, Université Laval, Quebec City, QC, Canada
| | - Marie-Eve Paquet
- Centre de Recherche CERVO, Université Laval, Quebec City, QC, Canada.,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Quebec City, QC, Canada
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Castañer M, Aiello S, Prat Q, Andueza J, Crescimanno G, Camerino O. Impulsivity and physical activity: A T-Pattern detection of motor behavior profiles. Physiol Behav 2020; 219:112849. [PMID: 32088173 DOI: 10.1016/j.physbeh.2020.112849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 10/25/2022]
Abstract
The relation between impulsivity and physical activity has been scantly investigated. Actually, during physical activity, several goals are achieved on the basis of a certain dose of impulsiveness. This study detects motor and interactive behavior profiles from athletes with traits of impulsiveness, moderate impulsiveness and non-impulsiveness, performing open motor tasks concerning material, space and interaction behaviors. A specific test was administered to assess the impulsivity profiles of athletes; then the Observational System of Motor Skills, Space, Time and Interaction (OSMOSTI), was used to observe and detect movement sequences patterns throughout T-Pattern detection and analysis (TPA). Recent researches have shown that TPA is a suitable approach to study physical activity in different contexts related, for instance, to sport, dance or exergames. Results of TPA revealed that open motor situations enhance motor behavior profiles especially by comparing participants with different impulsiveness. T-Patterns of non-impulsiveness and moderate impulsiveness traits emphasized much more the executive functions of response inhibition, working memory and mental shifting. In this study we pointed out on how impulsiveness, as a candent trait, traditionally considered that leads to a precipitation, unplanned and risky actions could enhance adequate responses to goal achievements if we consider it far to be a disorder on sport and similar subjects. The tool OSMOSTI and TPA used to observe diverse degrees of impulsivity have evidenced objectively the aim of the study.
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Affiliation(s)
- Marta Castañer
- National Institute of Physical Education of Catalonia (INEFC), University of Lleida (UdL), Spain; Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLLEIDA), Lleida, Spain.
| | - Stefania Aiello
- Laboratory of Behavioral Physiology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Human Physiology Section "Giuseppe Pagano," University of Palermo, Palermo, Italy.
| | - Queralt Prat
- National Institute of Physical Education of Catalonia (INEFC), University of Lleida (UdL), Spain.
| | - Juan Andueza
- National Institute of Physical Education of Catalonia (INEFC), University of Lleida (UdL), Spain.
| | - Giuseppe Crescimanno
- Laboratory of Behavioral Physiology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Human Physiology Section "Giuseppe Pagano," University of Palermo, Palermo, Italy.
| | - Oleguer Camerino
- National Institute of Physical Education of Catalonia (INEFC), University of Lleida (UdL), Spain; Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLLEIDA), Lleida, Spain.
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Poirazi P, Papoutsi A. Illuminating dendritic function with computational models. Nat Rev Neurosci 2020; 21:303-321. [PMID: 32393820 DOI: 10.1038/s41583-020-0301-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2020] [Indexed: 02/06/2023]
Abstract
Dendrites have always fascinated researchers: from the artistic drawings by Ramon y Cajal to the beautiful recordings of today, neuroscientists have been striving to unravel the mysteries of these structures. Theoretical work in the 1960s predicted important dendritic effects on neuronal processing, establishing computational modelling as a powerful technique for their investigation. Since then, modelling of dendrites has been instrumental in driving neuroscience research in a targeted manner, providing experimentally testable predictions that range from the subcellular level to the systems level, and their relevance extends to fields beyond neuroscience, such as machine learning and artificial intelligence. Validation of modelling predictions often requires - and drives - new technological advances, thus closing the loop with theory-driven experimentation that moves the field forward. This Review features the most important, to our understanding, contributions of modelling of dendritic computations, including those pending experimental verification, and highlights studies of successful interactions between the modelling and experimental neuroscience communities.
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Affiliation(s)
- Panayiota Poirazi
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology - Hellas, Heraklion, Crete, Greece.
| | - Athanasia Papoutsi
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology - Hellas, Heraklion, Crete, Greece
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40
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Yamakawa M, Santosa SM, Chawla N, Ivakhnitskaia E, Del Pino M, Giakas S, Nadel A, Bontu S, Tambe A, Guo K, Han KY, Cortina MS, Yu C, Rosenblatt MI, Chang JH, Azar DT. Transgenic models for investigating the nervous system: Currently available neurofluorescent reporters and potential neuronal markers. Biochim Biophys Acta Gen Subj 2020; 1864:129595. [PMID: 32173376 DOI: 10.1016/j.bbagen.2020.129595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/24/2020] [Accepted: 03/03/2020] [Indexed: 02/06/2023]
Abstract
Recombinant DNA technologies have enabled the development of transgenic animal models for use in studying a myriad of diseases and biological states. By placing fluorescent reporters under the direct regulation of the promoter region of specific marker proteins, these models can localize and characterize very specific cell types. One important application of transgenic species is the study of the cytoarchitecture of the nervous system. Neurofluorescent reporters can be used to study the structural patterns of nerves in the central or peripheral nervous system in vivo, as well as phenomena involving embryologic or adult neurogenesis, injury, degeneration, and recovery. Furthermore, crucial molecular factors can also be screened via the transgenic approach, which may eventually play a major role in the development of therapeutic strategies against diseases like Alzheimer's or Parkinson's. This review describes currently available reporters and their uses in the literature as well as potential neural markers that can be leveraged to create additional, robust transgenic models for future studies.
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Affiliation(s)
- Michael Yamakawa
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Samuel M Santosa
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Neeraj Chawla
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Evguenia Ivakhnitskaia
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Matthew Del Pino
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Sebastian Giakas
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Arnold Nadel
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Sneha Bontu
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Arjun Tambe
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Kai Guo
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Kyu-Yeon Han
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Maria Soledad Cortina
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Charles Yu
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Mark I Rosenblatt
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Jin-Hong Chang
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America.
| | - Dimitri T Azar
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America.
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Powell SK, Samulski RJ, McCown TJ. AAV Capsid-Promoter Interactions Determine CNS Cell-Selective Gene Expression In Vivo. Mol Ther 2020; 28:1373-1380. [PMID: 32213322 DOI: 10.1016/j.ymthe.2020.03.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/03/2020] [Accepted: 03/12/2020] [Indexed: 11/30/2022] Open
Abstract
Cell-selective gene expression comprises a critical element of many adeno-associated virus (AAV) vector-based gene therapies, and to date achieving this goal has focused on AAV capsid engineering, cell-specific promoters, or cell-specific enhancers. Recently, we discovered that the capsid of AAV9 exerts a differential influence on constitutive promoters of sufficient magnitude to alter cell type gene expression in the rat CNS. For AAV9 vectors chicken β-actin (CBA) promoter-driven gene expression exhibited a dominant neuronal gene expression in the rat striatum. Surprisingly, for otherwise identical AAV9 vectors, the truncated CBA hybrid (CBh) promoter shifted gene expression toward striatal oligodendrocytes. In contrast, AAV2 vector gene expression was restricted to striatal neurons, regardless of the constitutive promoter used. Furthermore, a six-glutamate residue insertion immediately after the VP2 start residue shifted CBA-driven cellular gene expression from neurons to oligodendrocytes. Conversely, a six-alanine insertion in the same AAV9 capsid region reversed the CBh-mediated oligodendrocyte expression back to neurons without changing AAV9 capsid access to oligodendrocytes. Given the preponderance of AAV9 in ongoing clinical trials and AAV capsid engineering, this AAV9 capsid-promoter interaction reveals a previously unknown novel contribution to cell-selective AAV-mediated gene expression in the CNS.
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Affiliation(s)
- Sara K Powell
- UNC Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - R Jude Samulski
- UNC Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas J McCown
- UNC Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Nair RR, Blankvoort S, Lagartos MJ, Kentros C. Enhancer-Driven Gene Expression (EDGE) Enables the Generation of Viral Vectors Specific to Neuronal Subtypes. iScience 2020; 23:100888. [PMID: 32087575 PMCID: PMC7033522 DOI: 10.1016/j.isci.2020.100888] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/03/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
Although a variety of remarkable molecular tools for studying neural circuits have recently been developed, the ability to deploy them in particular neuronal subtypes is limited by the fact that native promoters are almost never specific enough. We recently showed that one can generate transgenic mice with anatomical specificity surpassing that of native promoters by combining enhancers uniquely active in particular brain regions with a heterologous minimal promoter, an approach we call EDGE (Enhancer-Driven Gene Expression). Here we extend this strategy to the generation of viral (rAAV) vectors, showing that some EDGE rAAVs can recapitulate the specificity of the corresponding transgenic lines in wild-type animals, even of another species. This approach thus holds the promise of enabling circuit-specific manipulations in wild-type animals, not only enhancing our understanding of brain function, but perhaps one day even providing novel therapeutic avenues to approach disorders of the brain. rAAVs with enhancers unique to a brain region specify cell types of that brain region This requires viral constructs optimized to express only with enhancers One rAAV distinguishes distinct subtypes of excitatory neurons in a cortical layer The same specificity is seen in wild-type animals of at least two species
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Affiliation(s)
| | - Stefan Blankvoort
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway
| | - Maria Jose Lagartos
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway
| | - Cliff Kentros
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Norway; Institute of Neuroscience, University of Oregon, Eugene OR, USA.
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Gogola JV, Gores EO, London SE. Inhibitory cell populations depend on age, sex, and prior experience across a neural network for Critical Period learning. Sci Rep 2019; 9:19867. [PMID: 31882750 PMCID: PMC6934704 DOI: 10.1038/s41598-019-56293-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
In many ways, the complement of cell subtypes determines the information processing that a local brain circuit can perform. For example, the balance of excitatory and inhibitory (E/I) signaling within a brain region contributes to response magnitude and specificity in ways that influence the effectiveness of information processing. An extreme example of response changes to sensory information occur across Critical Periods (CPs). In primary mammalian visual cortex, GAD65 and parvalbumin inhibitory cell types in particular control experience-dependent responses during a CP. Here, we test how the density of GAD65- and parvalbumin-expressing cells may inform on a CP for complex behavioral learning. Juvenile male zebra finch songbirds (females cannot sing) learn to sing through coordinated sensory, sensorimotor, and motor learning processes distributed throughout a well-defined neural network. There is a CP for sensory learning, the process by which a young male forms a memory of his “tutor’s” song, which is then used to guide the young bird’s emerging song structure. We quantified the effect of sex and experience with a tutor on the cell densities of GAD65- and parvalbumin-expressing cells across major nodes of the song network, using ages that span the CP for tutor song memorization. As a resource, we also include whole-brain mapping data for both genes. Results indicate that inhibitory cell populations differ across sex, age, and experiential conditions, but not always in the ways we predicted.
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Affiliation(s)
- Joseph V Gogola
- Department of Psychology, Institute for Mind and Biology, Chicago, USA
| | - Elisa O Gores
- Department of Psychology, Institute for Mind and Biology, Chicago, USA
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, Chicago, USA. .,Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, Committee on Neurobiology, Committee on Evolutionary Biology, The University of Chicago, Chicago, IL, USA.
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Nilssen ES, Doan TP, Nigro MJ, Ohara S, Witter MP. Neurons and networks in the entorhinal cortex: A reappraisal of the lateral and medial entorhinal subdivisions mediating parallel cortical pathways. Hippocampus 2019; 29:1238-1254. [PMID: 31408260 DOI: 10.1002/hipo.23145] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/29/2019] [Accepted: 07/11/2019] [Indexed: 12/31/2022]
Abstract
In this review, we aim to reappraise the organization of intrinsic and extrinsic networks of the entorhinal cortex with a focus on the concept of parallel cortical connectivity streams. The concept of two entorhinal areas, the lateral and medial entorhinal cortex, belonging to two parallel input-output streams mediating the encoding and storage of respectively what and where information hinges on the claim that a major component of their cortical connections is with the perirhinal cortex and postrhinal or parahippocampal cortex in, respectively, rodents or primates. In this scenario, the lateral entorhinal cortex and the perirhinal cortex are connectionally associated and likewise the postrhinal/parahippocampal cortex and the medial entorhinal cortex are partners. In contrast, here we argue that the connectivity matrix emphasizes the potential of substantial integration of cortical information through interactions between the two entorhinal subdivisions and between the perirhinal and postrhinal/parahippocampal cortices, but most importantly through a new observation that the postrhinal/parahippocampal cortex projects to both lateral and medial entorhinal cortex. We suggest that entorhinal inputs provide the hippocampus with high-order complex representations of the external environment, its stability, as well as apparent changes either as an inherent feature of a biological environment or as the result of navigating the environment. This thus indicates that the current connectional model of the parahippocampal region as part of the medial temporal lobe memory system needs to be revised.
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Affiliation(s)
- Eirik S Nilssen
- Kavli Institute for Systems Neuroscience, Centre for Neural Computation, Egil and Pauline Braathen and Fred Kavli Centre for Cortical Microcircuits, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Thanh P Doan
- Kavli Institute for Systems Neuroscience, Centre for Neural Computation, Egil and Pauline Braathen and Fred Kavli Centre for Cortical Microcircuits, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Maximiliano J Nigro
- Kavli Institute for Systems Neuroscience, Centre for Neural Computation, Egil and Pauline Braathen and Fred Kavli Centre for Cortical Microcircuits, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Shinya Ohara
- Kavli Institute for Systems Neuroscience, Centre for Neural Computation, Egil and Pauline Braathen and Fred Kavli Centre for Cortical Microcircuits, NTNU Norwegian University of Science and Technology, Trondheim, Norway
- Laboratory of Systems Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai, Japan
| | - Menno P Witter
- Kavli Institute for Systems Neuroscience, Centre for Neural Computation, Egil and Pauline Braathen and Fred Kavli Centre for Cortical Microcircuits, NTNU Norwegian University of Science and Technology, Trondheim, Norway
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Carullo NVN, Day JJ. Genomic Enhancers in Brain Health and Disease. Genes (Basel) 2019; 10:E43. [PMID: 30646598 PMCID: PMC6357130 DOI: 10.3390/genes10010043] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 01/18/2023] Open
Abstract
Enhancers are non-coding DNA elements that function in cis to regulate transcription from nearby genes. Through direct interactions with gene promoters, enhancers give rise to spatially and temporally precise gene expression profiles in distinct cell or tissue types. In the brain, the accurate regulation of these intricate expression programs across different neuronal classes gives rise to an incredible cellular and functional diversity. Newly developed technologies have recently allowed more accurate enhancer mapping and more sophisticated enhancer manipulation, producing rapid progress in our understanding of enhancer biology. Furthermore, identification of disease-linked genetic variation in enhancer regions has highlighted the potential influence of enhancers in brain health and disease. This review outlines the key role of enhancers as transcriptional regulators, reviews the current understanding of enhancer regulation in neuronal development, function and dysfunction and provides our thoughts on how enhancers can be targeted for technological and therapeutic goals.
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Affiliation(s)
- Nancy V N Carullo
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Inhibitory Connectivity Dominates the Fan Cell Network in Layer II of Lateral Entorhinal Cortex. J Neurosci 2018; 38:9712-9727. [PMID: 30249791 DOI: 10.1523/jneurosci.1290-18.2018] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 11/21/2022] Open
Abstract
Fan cells in layer II of the lateral entorhinal cortex (LEC) form a main component of the projection to the dentate gyrus, CA3 and CA2 of the hippocampal formation. This projection has a counterpart originating from stellate cells in layer II of the medial entorhinal cortex (MEC). Available evidence suggests that the two pathways carry different information, exemplified by a difference in spatial tuning of cells in LEC and MEC. The grid cell, a prominent position-modulated cell type present in MEC, has been postulated to derive its characteristic hexagonal firing pattern from dominant disynaptic inhibitory connections between hippocampal-projecting stellate cells. Given that grid cells have not been described in LEC, we aim to describe the local synaptic connectivity of fan cells, to explore whether the network architecture is similar to that of the MEC stellate cell. Using a combination of in vitro multicell electrophysiological and optogenetic approaches in acute slices from rodents of either sex, we show that excitatory connectivity between fan cells is very sparse. Fan cells connect preferentially with two distinct types of inhibitory interneurons, suggesting disynaptic inhibitory coupling as the main form of communication among fan cells. These principles are similar to those reported for stellate cells in MEC, indicating an overall comparable local circuit architecture of the main hippocampal-projecting cell types in the lateral and medial entorhinal cortex.SIGNIFICANCE STATEMENT Our data provide the first description of the synaptic microcircuit of hippocampal-projecting layer II cells in the lateral entorhinal cortex. We show that these cells make infrequent monosynaptic connections with each other, and that they preferentially communicate through a disynaptic inhibitory network. This is similar to the microcircuit of hippocampal-projecting stellate cells in layer II of the medial entorhinal cortex, but dissimilar to the connectivity observed in layer 2 of neocortex. In medial entorhinal cortex, the observed network structure has been proposed to underlie the firing pattern of grid cells. This opens the possibility that layer II cells in lateral entorhinal cortex exhibit regular firing patterns in an unexplored domain.
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