201
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Urrutia-Piñones J, Morales-Moraga C, Sanguinetti-González N, Escobar AP, Chiu CQ. Long-Range GABAergic Projections of Cortical Origin in Brain Function. Front Syst Neurosci 2022; 16:841869. [PMID: 35392440 PMCID: PMC8981584 DOI: 10.3389/fnsys.2022.841869] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
The study of long-range GABAergic projections has traditionally been focused on those with subcortical origin. In the last few years, cortical GABAergic neurons have been shown to not only mediate local inhibition, but also extend long-range axons to remote cortical and subcortical areas. In this review, we delineate the different types of long-range GABAergic neurons (LRGNs) that have been reported to arise from the hippocampus and neocortex, paying attention to the anatomical and functional circuits they form to understand their role in behavior. Although cortical LRGNs are similar to their interneuron and subcortical counterparts, they comprise distinct populations that show specific patterns of cortico-cortical and cortico-fugal connectivity. Functionally, cortical LRGNs likely induce timed disinhibition in target regions to synchronize network activity. Thus, LRGNs are emerging as a new element of cortical output, acting in concert with long-range excitatory projections to shape brain function in health and disease.
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Affiliation(s)
- Jocelyn Urrutia-Piñones
- Ph.D. Program in Neuroscience, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Facultad de Ciencias, Instituto de Neurociencia, Universidad de Valparaíso, Valparaíso, Chile
| | - Camila Morales-Moraga
- Facultad de Ciencias, Instituto de Neurociencia, Universidad de Valparaíso, Valparaíso, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
| | - Nicole Sanguinetti-González
- Ph.D. Program in Neuroscience, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Facultad de Ciencias, Instituto de Neurociencia, Universidad de Valparaíso, Valparaíso, Chile
| | - Angelica P. Escobar
- Instituto de Fisiología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Neurobiología y Fisiopatología Integrativa, Universidad de Valparaíso, Valparaíso, Chile
| | - Chiayu Q. Chiu
- Facultad de Ciencias, Instituto de Neurociencia, Universidad de Valparaíso, Valparaíso, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
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202
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Suzuki N, Tantirigama MLS, Aung KP, Huang HHY, Bekkers JM. Fast and slow feedforward inhibitory circuits for cortical odor processing. eLife 2022; 11:73406. [PMID: 35297763 PMCID: PMC8929928 DOI: 10.7554/elife.73406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
Feedforward inhibitory circuits are key contributors to the complex interplay between excitation and inhibition in the brain. Little is known about the function of feedforward inhibition in the primary olfactory (piriform) cortex. Using in vivo two-photon-targeted patch clamping and calcium imaging in mice, we find that odors evoke strong excitation in two classes of interneurons – neurogliaform (NG) cells and horizontal (HZ) cells – that provide feedforward inhibition in layer 1 of the piriform cortex. NG cells fire much earlier than HZ cells following odor onset, a difference that can be attributed to the faster odor-driven excitatory synaptic drive that NG cells receive from the olfactory bulb. As a result, NG cells strongly but transiently inhibit odor-evoked excitation in layer 2 principal cells, whereas HZ cells provide more diffuse and prolonged feedforward inhibition. Our findings reveal unexpected complexity in the operation of inhibition in the piriform cortex.
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Affiliation(s)
- Norimitsu Suzuki
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Malinda L S Tantirigama
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, Australia.,Neurocure Center for Excellence, Charité Universitätsmedizin Berlin and Humboldt Universität, Berlin, Germany
| | - K Phyu Aung
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Helena H Y Huang
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - John M Bekkers
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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203
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Campagnola L, Seeman SC, Chartrand T, Kim L, Hoggarth A, Gamlin C, Ito S, Trinh J, Davoudian P, Radaelli C, Kim MH, Hage T, Braun T, Alfiler L, Andrade J, Bohn P, Dalley R, Henry A, Kebede S, Mukora A, Sandman D, Williams G, Larsen R, Teeter C, Daigle TL, Berry K, Dotson N, Enstrom R, Gorham M, Hupp M, Lee SD, Ngo K, Nicovich PR, Potekhina L, Ransford S, Gary A, Goldy J, McMillen D, Pham T, Tieu M, Siverts L, Walker M, Farrell C, Schroedter M, Slaughterbeck C, Cobb C, Ellenbogen R, Gwinn RP, Keene CD, Ko AL, Ojemann JG, Silbergeld DL, Carey D, Casper T, Crichton K, Clark M, Dee N, Ellingwood L, Gloe J, Kroll M, Sulc J, Tung H, Wadhwani K, Brouner K, Egdorf T, Maxwell M, McGraw M, Pom CA, Ruiz A, Bomben J, Feng D, Hejazinia N, Shi S, Szafer A, Wakeman W, Phillips J, Bernard A, Esposito L, D’Orazi FD, Sunkin S, Smith K, Tasic B, Arkhipov A, Sorensen S, Lein E, Koch C, Murphy G, Zeng H, Jarsky T. Local connectivity and synaptic dynamics in mouse and human neocortex. Science 2022; 375:eabj5861. [PMID: 35271334 PMCID: PMC9970277 DOI: 10.1126/science.abj5861] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present a unique, extensive, and open synaptic physiology analysis platform and dataset. Through its application, we reveal principles that relate cell type to synaptic properties and intralaminar circuit organization in the mouse and human cortex. The dynamics of excitatory synapses align with the postsynaptic cell subclass, whereas inhibitory synapse dynamics partly align with presynaptic cell subclass but with considerable overlap. Synaptic properties are heterogeneous in most subclass-to-subclass connections. The two main axes of heterogeneity are strength and variability. Cell subclasses divide along the variability axis, whereas the strength axis accounts for substantial heterogeneity within the subclass. In the human cortex, excitatory-to-excitatory synaptic dynamics are distinct from those in the mouse cortex and vary with depth across layers 2 and 3.
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Affiliation(s)
| | | | | | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Shinya Ito
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Travis Hage
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Phillip Bohn
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Alex Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nadia Dotson
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Charles Cobb
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Richard Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Ryder P Gwinn
- Epilepsy Surgery and Functional Neurosurgery, Swedish Neuroscience Institute, Seattle, WA, USA
| | - C. Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA,Regional Epilepsy Center at Harborview Medical Center, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA,Regional Epilepsy Center at Harborview Medical Center, Seattle, WA, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Shu Shi
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Susan Sunkin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Gabe Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA,Corresponding author:
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204
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Rapti G. Open Frontiers in Neural Cell Type Investigations; Lessons From Caenorhabditis elegans and Beyond, Toward a Multimodal Integration. Front Neurosci 2022; 15:787753. [PMID: 35321480 PMCID: PMC8934944 DOI: 10.3389/fnins.2021.787753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Nervous system cells, the building blocks of circuits, have been studied with ever-progressing resolution, yet neural circuits appear still resistant to schemes of reductionist classification. Due to their sheer numbers, complexity and diversity, their systematic study requires concrete classifications that can serve reduced dimensionality, reproducibility, and information integration. Conventional hierarchical schemes transformed through the history of neuroscience by prioritizing criteria of morphology, (electro)physiological activity, molecular content, and circuit function, influenced by prevailing methodologies of the time. Since the molecular biology revolution and the recent advents in transcriptomics, molecular profiling gains ground toward the classification of neurons and glial cell types. Yet, transcriptomics entails technical challenges and more importantly uncovers unforeseen spatiotemporal heterogeneity, in complex and simpler nervous systems. Cells change states dynamically in space and time, in response to stimuli or throughout their developmental trajectory. Mapping cell type and state heterogeneity uncovers uncharted terrains in neurons and especially in glial cell biology, that remains understudied in many aspects. Examining neurons and glial cells from the perspectives of molecular neuroscience, physiology, development and evolution highlights the advantage of multifaceted classification schemes. Among the amalgam of models contributing to neuroscience research, Caenorhabditis elegans combines nervous system anatomy, lineage, connectivity and molecular content, all mapped at single-cell resolution, and can provide valuable insights for the workflow and challenges of the multimodal integration of cell type features. This review reflects on concepts and practices of neuron and glial cells classification and how research, in C. elegans and beyond, guides nervous system experimentation through integrated multidimensional schemes. It highlights underlying principles, emerging themes, and open frontiers in the study of nervous system development, regulatory logic and evolution. It proposes unified platforms to allow integrated annotation of large-scale datasets, gene-function studies, published or unpublished findings and community feedback. Neuroscience is moving fast toward interdisciplinary, high-throughput approaches for combined mapping of the morphology, physiology, connectivity, molecular function, and the integration of information in multifaceted schemes. A closer look in mapped neural circuits and understudied terrains offers insights for the best implementation of these approaches.
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205
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Transcriptomically-Guided Pharmacological Experiments in Neocortical and Hippocampal NPY-Positive GABAergic Interneurons. eNeuro 2022; 9:ENEURO.0005-22.2022. [PMID: 35437266 PMCID: PMC9045474 DOI: 10.1523/eneuro.0005-22.2022] [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: 01/04/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 12/13/2022] Open
Abstract
Cortical GABAergic interneurons have been shown to fulfil important roles by inhibiting excitatory principal neurons. Recent transcriptomic studies have confirmed seminal discoveries that used anatomic and electrophysiological methods highlighting the existence of multiple different classes of GABAergic interneurons. Although some of these studies have emphasized that inter-regional differences may exist for a given class, the extent of such differences remains unknown. To address this problem, we used single-cell Patch-RNAseq to characterize neuropeptide Y (NPY)-positive GABAergic interneurons in superficial layers of the primary auditory cortex (AC) and in distal layers of area CA3 in mice. We found that more than 300 genes are differentially expressed in NPY-positive neurons between these two brain regions. For example, the AMPA receptor (AMPAR) auxiliary subunit Shisa9/CKAMP44 and the 5HT2a receptor (5HT2aR) are significantly higher expressed in auditory NPY-positive neurons. These findings guided us to perform pharmacological experiments that revealed a role for 5HT2aRs in auditory NPY-positive neurons. Specifically, although the application of 5HT led to a depolarization of both auditory and CA3 NPY-positive neurons, the 5HT2aR antagonist ketanserin only reversed membrane potential changes in auditory NPY-positive neurons. Our study demonstrates the potential of single-cell transcriptomic studies in guiding directed pharmacological experiments.
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206
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Degro CE, Bolduan F, Vida I, Booker SA. Interneuron diversity in the rat dentate gyrus: An unbiased in vitro classification. Hippocampus 2022; 32:310-331. [PMID: 35171512 PMCID: PMC9306941 DOI: 10.1002/hipo.23408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/24/2022] [Accepted: 01/29/2022] [Indexed: 11/08/2022]
Abstract
Information processing in cortical circuits, including the hippocampus, relies on the dynamic control of neuronal activity by GABAergic interneurons (INs). INs form a heterogenous population with defined types displaying distinct morphological, molecular, and physiological characteristics. In the major input region of the hippocampus, the dentate gyrus (DG), a number of IN types have been described which provide synaptic inhibition to distinct compartments of excitatory principal cells (PrCs) and other INs. In this study, we perform an unbiased classification of GABAergic INs in the DG by combining in vitro whole-cell patch-clamp recordings, intracellular labeling, morphological analysis, and supervised cluster analysis to better define IN type diversity in this region. This analysis reveals that DG INs divide into at least 13 distinct morpho-physiological types which reflect the complexity of the local IN network and serve as a basis for further network analyses.
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Affiliation(s)
- Claudius E Degro
- Institute for Integrative Neuroanatomy, Charité - Universitätmedizin Berlin, Berlin, Germany
| | - Felix Bolduan
- Institute for Integrative Neuroanatomy, Charité - Universitätmedizin Berlin, Berlin, Germany
| | - Imre Vida
- Institute for Integrative Neuroanatomy, Charité - Universitätmedizin Berlin, Berlin, Germany
| | - Sam A Booker
- Institute for Integrative Neuroanatomy, Charité - Universitätmedizin Berlin, Berlin, Germany.,Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
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207
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Hage TA, Bosma-Moody A, Baker CA, Kratz MB, Campagnola L, Jarsky T, Zeng H, Murphy GJ. Synaptic connectivity to L2/3 of primary visual cortex measured by two-photon optogenetic stimulation. eLife 2022; 11:71103. [PMID: 35060903 PMCID: PMC8824465 DOI: 10.7554/elife.71103] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/19/2022] [Indexed: 12/04/2022] Open
Abstract
Understanding cortical microcircuits requires thorough measurement of physiological properties of synaptic connections formed within and between diverse subclasses of neurons. Towards this goal, we combined spatially precise optogenetic stimulation with multicellular recording to deeply characterize intralaminar and translaminar monosynaptic connections to supragranular (L2/3) neurons in the mouse visual cortex. The reliability and specificity of multiphoton optogenetic stimulation were measured across multiple Cre lines, and measurements of connectivity were verified by comparison to paired recordings and targeted patching of optically identified presynaptic cells. With a focus on translaminar pathways, excitatory and inhibitory synaptic connections from genetically defined presynaptic populations were characterized by their relative abundance, spatial profiles, strength, and short-term dynamics. Consistent with the canonical cortical microcircuit, layer 4 excitatory neurons and interneurons within L2/3 represented the most common sources of input to L2/3 pyramidal cells. More surprisingly, we also observed strong excitatory connections from layer 5 intratelencephalic neurons and potent translaminar inhibition from multiple interneuron subclasses. The hybrid approach revealed convergence to and divergence from excitatory and inhibitory neurons within and across cortical layers. Divergent excitatory connections often spanned hundreds of microns of horizontal space. In contrast, divergent inhibitory connections were more frequently measured from postsynaptic targets near each other.
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Affiliation(s)
- Travis A Hage
- Electrophysiology, Allen Institute for Brain Science
| | | | | | - Megan B Kratz
- Electrophysiology, Allen Institute for Brain Science
| | | | - Tim Jarsky
- Synaptic Physiology, Allen Institute for Brain Science
| | - Hongkui Zeng
- Synaptic Physiology, Allen Institute for Brain Science
| | - Gabe J Murphy
- Synaptic Physiology, Allen Institute for Brain Science
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208
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Newmaster KT, Kronman FA, Wu YT, Kim Y. Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain. Front Neuroanat 2022; 15:787601. [PMID: 35095432 PMCID: PMC8794814 DOI: 10.3389/fnana.2021.787601] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/02/2021] [Indexed: 12/14/2022] Open
Abstract
The brain is composed of diverse neuronal and non-neuronal cell types with complex regional connectivity patterns that create the anatomical infrastructure underlying cognition. Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists to examine microscopic details in macroscopic brain circuits. Nevertheless, implementing these tools is fraught with many technical and analytical challenges with a need for high-level data analysis. Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system. Specifically, we provide practical details for choosing methods including cell type specific labeling, sample preparation (e.g., tissue clearing), microscopy modalities, image processing, and data analysis (e.g., image registration to standard atlases). We also highlight the need to develop better 3D atlases with standardized anatomical labels and nomenclature across species and developmental time points to extend the mapping to other species including humans and to facilitate data sharing, confederation, and integrative analysis. In summary, this review provides key elements and currently available resources to consider while developing and implementing high-resolution mapping methods.
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Affiliation(s)
- Kyra T Newmaster
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| | - Fae A Kronman
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| | - Yuan-Ting Wu
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
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209
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Emerging strategies for the genetic dissection of gene functions, cell types, and neural circuits in the mammalian brain. Mol Psychiatry 2022; 27:422-435. [PMID: 34561609 DOI: 10.1038/s41380-021-01292-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
The mammalian brain is composed of a large number of highly diverse cell types with different molecular, anatomical, and functional features. Distinct cellular identities are generated during development under the regulation of intricate genetic programs and manifested through unique combinations of gene expression. Recent advancements in our understanding of the molecular and cellular mechanisms underlying the assembly, function, and pathology of the brain circuitry depend on the invention and application of genetic strategies that engage intrinsic gene regulatory mechanisms. Here we review the strategies for gene regulation on DNA, RNA, and protein levels and their applications in cell type targeting and neural circuit dissection. We highlight newly emerged strategies and emphasize the importance of combinatorial approaches. We also discuss the potential caveats and pitfalls in current methods and suggest future prospects to improve their comprehensiveness and versatility.
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210
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Masaki Y, Yamaguchi M, Takeuchi RF, Osakada F. Monosynaptic rabies virus tracing from projection-targeted single neurons. Neurosci Res 2022; 178:20-32. [DOI: 10.1016/j.neures.2022.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
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211
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Nguyen ND, Huang J, Wang D. A deep manifold-regularized learning model for improving phenotype prediction from multi-modal data. NATURE COMPUTATIONAL SCIENCE 2022; 2:38-46. [PMID: 35480297 PMCID: PMC9038085 DOI: 10.1038/s43588-021-00185-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022]
Abstract
The phenotypes of complex biological systems are fundamentally driven by various multi-scale mechanisms. Multi-modal data, such as single cell multi-omics data, enables a deeper understanding of underlying complex mechanisms across scales for phenotypes. We developed an interpretable regularized learning model, deepManReg, to predict phenotypes from multi-modal data. First, deepManReg employs deep neural networks to learn cross-modal manifolds and then to align multi-modal features onto a common latent space. Second, deepManReg uses cross-modal manifolds as a feature graph to regularize the classifiers for improving phenotype predictions and also for prioritizing the multi-modal features and cross-modal interactions for the phenotypes. We applied deepManReg to (1) an image dataset of handwritten digits with multi-features and (2) single cell multi-modal data (Patch-seq data) including transcriptomics and electrophysiology for neuronal cells in the mouse brain. We show that deepManReg improved phenotype prediction in both datasets, and also prioritized genes and electrophysiological features for the phenotypes of neuronal cells.
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Affiliation(s)
- Nam D. Nguyen
- Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Present address: Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jiawei Huang
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Present address: Carl H. Lindner College of Business, University of Cincinnati, Cincinnati, OH, 45223, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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212
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Tsukahara T, Brann DH, Pashkovski SL, Guitchounts G, Bozza T, Datta SR. A transcriptional rheostat couples past activity to future sensory responses. Cell 2021; 184:6326-6343.e32. [PMID: 34879231 PMCID: PMC8758202 DOI: 10.1016/j.cell.2021.11.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/07/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
Animals traversing different environments encounter both stable background stimuli and novel cues, which are thought to be detected by primary sensory neurons and then distinguished by downstream brain circuits. Here, we show that each of the ∼1,000 olfactory sensory neuron (OSN) subtypes in the mouse harbors a distinct transcriptome whose content is precisely determined by interactions between its odorant receptor and the environment. This transcriptional variation is systematically organized to support sensory adaptation: expression levels of more than 70 genes relevant to transforming odors into spikes continuously vary across OSN subtypes, dynamically adjust to new environments over hours, and accurately predict acute OSN-specific odor responses. The sensory periphery therefore separates salient signals from predictable background via a transcriptional rheostat whose moment-to-moment state reflects the past and constrains the future; these findings suggest a general model in which structured transcriptional variation within a cell type reflects individual experience.
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Affiliation(s)
- Tatsuya Tsukahara
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - David H Brann
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Stan L Pashkovski
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Thomas Bozza
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
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213
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Sousa E, Flames N. Transcriptional regulation of neuronal identity. Eur J Neurosci 2021; 55:645-660. [PMID: 34862697 PMCID: PMC9306894 DOI: 10.1111/ejn.15551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022]
Abstract
Neuronal diversity is an intrinsic feature of the nervous system. Transcription factors (TFs) are key regulators in the establishment of different neuronal identities; how are the actions of different TFs coordinated to orchestrate this diversity? Are there common features shared among the different neuron types of an organism or even among different animal groups? In this review, we provide a brief overview on common traits emerging on the transcriptional regulation of neuron type diversification with a special focus on the comparison between mouse and Caenorhabditis elegans model systems. In the first part, we describe general concepts on neuronal identity and transcriptional regulation of gene expression. In the second part of the review, TFs are classified in different categories according to their key roles at specific steps along the protracted process of neuronal specification and differentiation. The same TF categories can be identified both in mammals and nematodes. Importantly, TFs are very pleiotropic: Depending on the neuron type or the time in development, the same TF can fulfil functions belonging to different categories. Finally, we describe the key role of transcriptional repression at all steps controlling neuronal diversity and propose that acquisition of neuronal identities could be considered a metastable process.
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Affiliation(s)
- Erick Sousa
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
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214
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Contractor A, Ethell IM, Portera-Cailliau C. Cortical interneurons in autism. Nat Neurosci 2021; 24:1648-1659. [PMID: 34848882 PMCID: PMC9798607 DOI: 10.1038/s41593-021-00967-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 09/21/2021] [Indexed: 01/01/2023]
Abstract
The mechanistic underpinnings of autism remain a subject of debate and controversy. Why do individuals with autism share an overlapping set of atypical behaviors and symptoms, despite having different genetic and environmental risk factors? A major challenge in developing new therapies for autism has been the inability to identify convergent neural phenotypes that could explain the common set of symptoms that result in the diagnosis. Although no striking macroscopic neuropathological changes have been identified in autism, there is growing evidence that inhibitory interneurons (INs) play an important role in its neural basis. In this Review, we evaluate and interpret this evidence, focusing on recent findings showing reduced density and activity of the parvalbumin class of INs. We discuss the need for additional studies that investigate how genes and the environment interact to change the developmental trajectory of INs, permanently altering their numbers, connectivity and circuit engagement.
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Affiliation(s)
- Anis Contractor
- Department of Neuroscience Feinberg School of Medicine, Weinberg College of Arts and Sciences, Northwestern University, Chicago, IL, USA
- Department of Neurobiology, Weinberg College of Arts and Sciences, Northwestern University, Chicago, IL, USA
| | - Iryna M Ethell
- Division of Biomedical Sciences, UC Riverside School of Medicine, Riverside, CA, USA
| | - Carlos Portera-Cailliau
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
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215
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Inhibition in the auditory cortex. Neurosci Biobehav Rev 2021; 132:61-75. [PMID: 34822879 DOI: 10.1016/j.neubiorev.2021.11.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023]
Abstract
The auditory system provides us with extremely rich and precise information about the outside world. Once a sound reaches our ears, the acoustic information it carries travels from the cochlea all the way to the auditory cortex, where its complexity and nuances are integrated. In the auditory cortex, functional circuits are formed by subpopulations of intermingled excitatory and inhibitory cells. In this review, we discuss recent evidence of the specific contributions of inhibitory neurons in sound processing and integration. We first examine intrinsic properties of three main classes of inhibitory interneurons in the auditory cortex. Then, we describe how inhibition shapes the responsiveness of the auditory cortex to sound. Finally, we discuss how inhibitory interneurons contribute to the sensation and perception of sounds. Altogether, this review points out the crucial role of cortical inhibitory interneurons in integrating information about the context, history, or meaning of a sound. It also highlights open questions to be addressed for increasing our understanding of the staggering complexity leading to the subtlest auditory perception.
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216
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Huang J, Sheng J, Wang D. Manifold learning analysis suggests strategies to align single-cell multimodal data of neuronal electrophysiology and transcriptomics. Commun Biol 2021; 4:1308. [PMID: 34799674 PMCID: PMC8604989 DOI: 10.1038/s42003-021-02807-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Recent single-cell multimodal data reveal multi-scale characteristics of single cells, such as transcriptomics, morphology, and electrophysiology. However, integrating and analyzing such multimodal data to deeper understand functional genomics and gene regulation in various cellular characteristics remains elusive. To address this, we applied and benchmarked multiple machine learning methods to align gene expression and electrophysiological data of single neuronal cells in the mouse brain from the Brain Initiative. We found that nonlinear manifold learning outperforms other methods. After manifold alignment, the cells form clusters highly corresponding to transcriptomic and morphological cell types, suggesting a strong nonlinear relationship between gene expression and electrophysiology at the cell-type level. Also, the electrophysiological features are highly predictable by gene expression on the latent space from manifold alignment. The aligned cells further show continuous changes of electrophysiological features, implying cross-cluster gene expression transitions. Functional enrichment and gene regulatory network analyses for those cell clusters revealed potential genome functions and molecular mechanisms from gene expression to neuronal electrophysiology.
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Affiliation(s)
- Jiawei Huang
- Department of Statistics, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Carl H. Lindner College of Business, University of Cincinnati, Cincinnati, OH, 45223, USA
| | - Jie Sheng
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA.
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53706, USA.
- Department of Computer Sciences, University of Wisconsin - Madison, Madison, WI, 53706, USA.
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217
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de la Prida LM, Ascoli GA. Explorers of the cells: Toward cross-platform knowledge integration to evaluate neuronal function. Neuron 2021; 109:3535-3537. [PMID: 34793702 DOI: 10.1016/j.neuron.2021.10.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this issue of Neuron, Petersen et al. (2021) introduce CellExplorer, an open-source tool to integrate neurophysiological metrics of neuronal activity from circuits to behavior. Together with other neuroinformatic resources, it may facilitate community-based multidisciplinary characterization of brain cell types.
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Affiliation(s)
| | - Giorgio A Ascoli
- Bioengineering Department, Volgenau School of Engineering, George Mason University, Fairfax, VA, USA
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218
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Reichard J, Zimmer-Bensch G. The Epigenome in Neurodevelopmental Disorders. Front Neurosci 2021; 15:776809. [PMID: 34803599 PMCID: PMC8595945 DOI: 10.3389/fnins.2021.776809] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
Neurodevelopmental diseases (NDDs), such as autism spectrum disorders, epilepsy, and schizophrenia, are characterized by diverse facets of neurological and psychiatric symptoms, differing in etiology, onset and severity. Such symptoms include mental delay, cognitive and language impairments, or restrictions to adaptive and social behavior. Nevertheless, all have in common that critical milestones of brain development are disrupted, leading to functional deficits of the central nervous system and clinical manifestation in child- or adulthood. To approach how the different development-associated neuropathologies can occur and which risk factors or critical processes are involved in provoking higher susceptibility for such diseases, a detailed understanding of the mechanisms underlying proper brain formation is required. NDDs rely on deficits in neuronal identity, proportion or function, whereby a defective development of the cerebral cortex, the seat of higher cognitive functions, is implicated in numerous disorders. Such deficits can be provoked by genetic and environmental factors during corticogenesis. Thereby, epigenetic mechanisms can act as an interface between external stimuli and the genome, since they are known to be responsive to external stimuli also in cortical neurons. In line with that, DNA methylation, histone modifications/variants, ATP-dependent chromatin remodeling, as well as regulatory non-coding RNAs regulate diverse aspects of neuronal development, and alterations in epigenomic marks have been associated with NDDs of varying phenotypes. Here, we provide an overview of essential steps of mammalian corticogenesis, and discuss the role of epigenetic mechanisms assumed to contribute to pathophysiological aspects of NDDs, when being disrupted.
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Affiliation(s)
- Julia Reichard
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Geraldine Zimmer-Bensch
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
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219
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Maksymetz J, Byun NE, Luessen DJ, Li B, Barry RL, Gore JC, Niswender CM, Lindsley CW, Joffe ME, Conn PJ. mGlu 1 potentiation enhances prelimbic somatostatin interneuron activity to rescue schizophrenia-like physiological and cognitive deficits. Cell Rep 2021; 37:109950. [PMID: 34731619 PMCID: PMC8628371 DOI: 10.1016/j.celrep.2021.109950] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 08/09/2021] [Accepted: 10/14/2021] [Indexed: 01/03/2023] Open
Abstract
Evidence for prefrontal cortical (PFC) GABAergic dysfunction is one of the most consistent findings in schizophrenia and may contribute to cognitive deficits. Recent studies suggest that the mGlu1 subtype of metabotropic glutamate receptor regulates cortical inhibition; however, understanding the mechanisms through which mGlu1 positive allosteric modulators (PAMs) regulate PFC microcircuit function and cognition is essential for advancing these potential therapeutics toward the clinic. We report a series of electrophysiology, optogenetic, pharmacological magnetic resonance imaging, and animal behavior studies demonstrating that activation of mGlu1 receptors increases inhibitory transmission in the prelimbic PFC by selective excitation of somatostatin-expressing interneurons (SST-INs). An mGlu1 PAM reverses cortical hyperactivity and concomitant cognitive deficits induced by N-methyl-d-aspartate (NMDA) receptor antagonists. Using in vivo optogenetics, we show that prelimbic SST-INs are necessary for mGlu1 PAM efficacy. Collectively, these findings suggest that mGlu1 PAMs could reverse cortical GABAergic deficits and exhibit efficacy in treating cognitive dysfunction in schizophrenia.
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Affiliation(s)
- James Maksymetz
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA
| | - Nellie E Byun
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Deborah J Luessen
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA
| | - Brianna Li
- Vanderbilt University, Nashville, TN 37232, USA
| | - Robert L Barry
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Radiology & Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John C Gore
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Radiology & Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Colleen M Niswender
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Craig W Lindsley
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Max E Joffe
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA
| | - P Jeffrey Conn
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA.
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220
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Dudok B, Klein PM, Soltesz I. Toward Understanding the Diverse Roles of Perisomatic Interneurons in Epilepsy. Epilepsy Curr 2021; 22:54-60. [PMID: 35233202 PMCID: PMC8832350 DOI: 10.1177/15357597211053687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Epileptic seizures are associated with excessive neuronal spiking. Perisomatic
γ-aminobutyric acid (GABA)ergic interneurons specifically innervate the subcellular
domains of postsynaptic excitatory cells that are critical for spike generation. With a
revolution in transcriptomics-based cell taxonomy driving the development of novel
transgenic mouse lines, selectively monitoring and modulating previously elusive
interneuron types is becoming increasingly feasible. Emerging evidence suggests that the
three types of hippocampal perisomatic interneurons, axo-axonic cells, along with
parvalbumin- and cholecystokinin-expressing basket cells, each follow unique activity
patterns in vivo, suggesting distinctive roles in regulating epileptic networks.
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Affiliation(s)
- Barna Dudok
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Peter M. Klein
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
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221
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Chang CW, Evans MD, Yu X, Yu GQ, Mucke L. Tau reduction affects excitatory and inhibitory neurons differently, reduces excitation/inhibition ratios, and counteracts network hypersynchrony. Cell Rep 2021; 37:109855. [PMID: 34686344 PMCID: PMC8648275 DOI: 10.1016/j.celrep.2021.109855] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/04/2021] [Accepted: 09/27/2021] [Indexed: 11/27/2022] Open
Abstract
The protein tau has been implicated in many brain disorders. In animal models, tau reduction suppresses epileptogenesis of diverse causes and ameliorates synaptic and behavioral abnormalities in various conditions associated with excessive excitation-inhibition (E/I) ratios. However, the underlying mechanisms are unknown. Global genetic ablation of tau in mice reduces the action potential (AP) firing and E/I ratio of pyramidal cells in acute cortical slices without affecting the excitability of these cells. Tau ablation reduces the excitatory inputs to inhibitory neurons, increases the excitability of these cells, and structurally alters their axon initial segments (AISs). In primary neuronal cultures subjected to prolonged overstimulation, tau ablation diminishes the homeostatic response of AISs in inhibitory neurons, promotes inhibition, and suppresses hypersynchrony. Together, these differential alterations in excitatory and inhibitory neurons help explain how tau reduction prevents network hypersynchrony and counteracts brain disorders causing abnormally increased E/I ratios.
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Affiliation(s)
- Che-Wei Chang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Mark D Evans
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Xinxing Yu
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Gui-Qiu Yu
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Lennart Mucke
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA.
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222
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Yang D, Qi G, Ding C, Feldmeyer D. Layer 6A Pyramidal Cell Subtypes Form Synaptic Microcircuits with Distinct Functional and Structural Properties. Cereb Cortex 2021; 32:2095-2111. [PMID: 34628499 PMCID: PMC9113278 DOI: 10.1093/cercor/bhab340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/03/2021] [Accepted: 08/25/2021] [Indexed: 11/27/2022] Open
Abstract
Neocortical layer 6 plays a crucial role in sensorimotor co-ordination and integration through functionally segregated circuits linking intracortical and subcortical areas. We performed whole-cell recordings combined with morphological reconstructions to identify morpho-electric types of layer 6A pyramidal cells (PCs) in rat barrel cortex. Cortico-thalamic (CT), cortico-cortical (CC), and cortico-claustral (CCla) PCs were classified based on their distinct morphologies and have been shown to exhibit different electrophysiological properties. We demonstrate that these three types of layer 6A PCs innervate neighboring excitatory neurons with distinct synaptic properties: CT PCs establish weak facilitating synapses onto other L6A PCs; CC PCs form synapses of moderate efficacy, while synapses made by putative CCla PCs display the highest release probability and a marked short-term depression. For excitatory-inhibitory synaptic connections in layer 6, both the presynaptic PC type and the postsynaptic interneuron type govern the dynamic properties of the respective synaptic connections. We have identified a functional division of local layer 6A excitatory microcircuits which may be responsible for the differential temporal engagement of layer 6 feed-forward and feedback networks. Our results provide a basis for further investigations on the long-range CC, CT, and CCla pathways.
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Affiliation(s)
- Danqing Yang
- Research Center Juelich, Institute of Neuroscience and Medicine 10, 52425 Juelich, Germany
| | - Guanxiao Qi
- Research Center Juelich, Institute of Neuroscience and Medicine 10, 52425 Juelich, Germany
| | - Chao Ding
- Research Center Juelich, Institute of Neuroscience and Medicine 10, 52425 Juelich, Germany
| | - Dirk Feldmeyer
- Research Center Juelich, Institute of Neuroscience and Medicine 10, 52425 Juelich, Germany.,RWTH Aachen University Hospital, Dept of Psychiatry, Psychotherapy, and Psychosomatics, 52074 Aachen, Germany.,Jülich-Aachen Research Alliance, Translational Brain Medicine (JARA Brain), Aachen, Germany
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223
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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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224
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Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 2021; 598:111-119. [PMID: 34616062 PMCID: PMC8494640 DOI: 10.1038/s41586-021-03465-8] [Citation(s) in RCA: 299] [Impact Index Per Article: 99.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 03/17/2021] [Indexed: 12/11/2022]
Abstract
The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.
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Affiliation(s)
| | | | - Qiwen Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Wei Tian
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Brian E Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Megan Crow
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Fenna M Krienen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Jeroen Eggermont
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Andrew I Aldridge
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Rosa G Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nikolai Dembrow
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Epilepsy Center of Excellence, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Weixiu Dong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Rongxin Fang
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Stephan Fischer
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Melissa Goldman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Brian R Herb
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Xiaomeng Hou
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jayaram Kancherla
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Baldur van Lew
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Yang Eric Li
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Christine S Liu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Anup Mahurkar
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Sheng-Yong Niu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Computer Science and Engineering Program, University of California, San Diego, La Jolla, CA, USA
| | - Joshua Orvis
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Julia K Osteen
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Scott Owen
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Carter R Palmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivier Poirion
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nora M Reed
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Angeline Rivkin
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - William J Romanow
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Xinxin Wang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Fangming Xie
- Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | | | - Renee Zhang
- J. Craig Venter Institute, La Jolla, CA, USA
| | - Seth A Ament
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Hector Corrada Bravo
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ronna Hertzano
- Departments of Otorhinolaryngology, Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Höllt
- Computer Graphics and Visualization Group, Delt University of Technology, Delft, The Netherlands
| | - Gregory D Horwitz
- Department of Physiology and Biophysics, Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA
- Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA
| | - Boudewijn P Lelieveldt
- LKEB, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Pattern Recognition and Bioinformatics group, Delft University of Technology, Delft, The Netherlands
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | | | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - William J Spain
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Epilepsy Center of Excellence, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Owen R White
- Institute for Genomes Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | | | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
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225
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Nomura T. Interneuron Dysfunction and Inhibitory Deficits in Autism and Fragile X Syndrome. Cells 2021; 10:cells10102610. [PMID: 34685590 PMCID: PMC8534049 DOI: 10.3390/cells10102610] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 01/18/2023] Open
Abstract
The alteration of excitatory–inhibitory (E–I) balance has been implicated in various neurological and psychiatric diseases, including autism spectrum disorder (ASD). Fragile X syndrome (FXS) is a single-gene disorder that is the most common known cause of ASD. Understanding the molecular and physiological features of FXS is thought to enhance our knowledge of the pathophysiology of ASD. Accumulated evidence implicates deficits in the inhibitory circuits in FXS that tips E–I balance toward excitation. Deficits in interneurons, the main source of an inhibitory neurotransmitter, gamma-aminobutyric acid (GABA), have been reported in FXS, including a reduced number of cells, reduction in intrinsic cellular excitability, or weaker synaptic connectivity. Manipulating the interneuron activity ameliorated the symptoms in the FXS mouse model, which makes it reasonable to conceptualize FXS as an interneuronopathy. While it is still poorly understood how the developmental profiles of the inhibitory circuit go awry in FXS, recent works have uncovered several developmental alterations in the functional properties of interneurons. Correcting disrupted E–I balance by potentiating the inhibitory circuit by targeting interneurons may have a therapeutic potential in FXS. I will review the recent evidence about the inhibitory alterations and interneuron dysfunction in ASD and FXS and will discuss the future directions of this field.
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Affiliation(s)
- Toshihiro Nomura
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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226
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Peng H, Xie P, Liu L, Kuang X, Wang Y, Qu L, Gong H, Jiang S, Li A, Ruan Z, Ding L, Yao Z, Chen C, Chen M, Daigle TL, Dalley R, Ding Z, Duan Y, Feiner A, He P, Hill C, Hirokawa KE, Hong G, Huang L, Kebede S, Kuo HC, Larsen R, Lesnar P, Li L, Li Q, Li X, Li Y, Li Y, Liu A, Lu D, Mok S, Ng L, Nguyen TN, Ouyang Q, Pan J, Shen E, Song Y, Sunkin SM, Tasic B, Veldman MB, Wakeman W, Wan W, Wang P, Wang Q, Wang T, Wang Y, Xiong F, Xiong W, Xu W, Ye M, Yin L, Yu Y, Yuan J, Yuan J, Yun Z, Zeng S, Zhang S, Zhao S, Zhao Z, Zhou Z, Huang ZJ, Esposito L, Hawrylycz MJ, Sorensen SA, Yang XW, Zheng Y, Gu Z, Xie W, Koch C, Luo Q, Harris JA, Wang Y, Zeng H. Morphological diversity of single neurons in molecularly defined cell types. Nature 2021; 598:174-181. [PMID: 34616072 PMCID: PMC8494643 DOI: 10.1038/s41586-021-03941-1] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 08/24/2021] [Indexed: 12/23/2022]
Abstract
Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits.
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Affiliation(s)
- Hanchuan Peng
- Allen Institute for Brain Science, Seattle, WA, USA.
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China.
| | - Peng Xie
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Lijuan Liu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Ministry of Education Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Xiuli Kuang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Yimin Wang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Lei Qu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Key Laboratory of Intelligent Computation and Signal Processing, Ministry of Education, Anhui University, Hefei, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Shengdian Jiang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Zongcai Ruan
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Liya Ding
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chao Chen
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Mengya Chen
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | | | | | - Zhangcan Ding
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yanjun Duan
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Aaron Feiner
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ping He
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Karla E Hirokawa
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | - Guodong Hong
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Ministry of Education Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Lei Huang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Phil Lesnar
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Longfei Li
- Key Laboratory of Intelligent Computation and Signal Processing, Ministry of Education, Anhui University, Hefei, China
| | - Qi Li
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Yaoyao Li
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Yuanyuan Li
- Key Laboratory of Intelligent Computation and Signal Processing, Ministry of Education, Anhui University, Hefei, China
| | - An Liu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Ministry of Education Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | | | | | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Thuc Nghi Nguyen
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | - Qiang Ouyang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Jintao Pan
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Elise Shen
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Yuanyuan Song
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | | | | | - Matthew B Veldman
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Wan Wan
- Key Laboratory of Intelligent Computation and Signal Processing, Ministry of Education, Anhui University, Hefei, China
| | - Peng Wang
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tao Wang
- Key Laboratory of Intelligent Computation and Signal Processing, Ministry of Education, Anhui University, Hefei, China
| | - Yaping Wang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Feng Xiong
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Wei Xiong
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Wenjie Xu
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Min Ye
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Lulu Yin
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yang Yu
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jia Yuan
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Ministry of Education Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Zhixi Yun
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Shaoqun Zeng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
| | - Shichen Zhang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Sujun Zhao
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Zijun Zhao
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Zhi Zhou
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | | | | | | | - X William Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Zhongze Gu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Wei Xie
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Ministry of Education Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | | | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | - Yun Wang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
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227
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Diez D, Morte B, Bernal J. Single-Cell Transcriptome Profiling of Thyroid Hormone Effectors in the Human Fetal Neocortex: Expression of SLCO1C1, DIO2, and THRB in Specific Cell Types. Thyroid 2021; 31:1577-1588. [PMID: 34114484 DOI: 10.1089/thy.2021.0057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Background: Thyroid hormones are crucial for brain development, acting through the thyroid hormone nuclear receptors (TR)α1 and β to control gene expression. Triiodothyronine (T3), the receptor-ligand, is transported into the brain from the blood by the monocarboxylate transporter 8 (MCT8). Another source of brain T3 is from the local deiodination of thyroxine (T4) by type 2 deiodinase (DIO2). While these mechanisms are very similar in mice and humans, important species-specific differences confound our understanding of disease using mouse models. To fill this knowledge gap on thyroid hormone action in the human fetal brain, we analyzed the expression of transporters, DIO2, and TRs, which we call thyroid hormone effectors, at single-cell resolution. Methods: We analyzed publicly available single-cell transcriptome data sets of isolated cerebral cortex neural cells from three different studies, with expression data from 393 to almost 40,000 cells. We generated Uniform Manifold Approximation and Projection scatterplots and cell clusters to identify differentially expressed genes between clusters, and correlated their gene signatures with the expression of thyroid effectors. Results: The radial glia, mainly the outer radial glia, and astrocytes coexpress SLCO1C1 and DIO2, indicating close cooperation between the T4 transporter OATP1C1 and DIO2 in local T3 formation. Strikingly, THRB was mainly present in two classes of interneurons: a majority expressing CALB2/calretinin, from the caudal ganglionic eminence, and in somatostatin-expressing interneurons from the medial ganglionic eminence. By contrast, many cell types express SLC16A2 and THRA. Conclusions:SLCO1C1 and DIO2 coexpression in the outer radial glia, the universal stem cell of the cerebral cortex, highlights the likely importance of brain-generated T3 in neurogenesis. The unique expression of THRB in discrete subsets of interneurons is a novel finding whose pathophysiological meaning deserves further investigation.
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Affiliation(s)
- Diego Diez
- Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Beatriz Morte
- Center for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Investigaciones Biomedicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Bernal
- Instituto de Investigaciones Biomedicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid, Madrid, Spain
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228
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Scala F, Kobak D, Bernabucci M, Bernaerts Y, Cadwell CR, Castro JR, Hartmanis L, Jiang X, Laturnus S, Miranda E, Mulherkar S, Tan ZH, Yao Z, Zeng H, Sandberg R, Berens P, Tolias AS. Phenotypic variation of transcriptomic cell types in mouse motor cortex. Nature 2021; 598:144-150. [PMID: 33184512 PMCID: PMC8113357 DOI: 10.1038/s41586-020-2907-3] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022]
Abstract
Cortical neurons exhibit extreme diversity in gene expression as well as in morphological and electrophysiological properties1,2. Most existing neural taxonomies are based on either transcriptomic3,4 or morpho-electric5,6 criteria, as it has been technically challenging to study both aspects of neuronal diversity in the same set of cells7. Here we used Patch-seq8 to combine patch-clamp recording, biocytin staining, and single-cell RNA sequencing of more than 1,300 neurons in adult mouse primary motor cortex, providing a morpho-electric annotation of almost all transcriptomically defined neural cell types. We found that, although broad families of transcriptomic types (those expressing Vip, Pvalb, Sst and so on) had distinct and essentially non-overlapping morpho-electric phenotypes, individual transcriptomic types within the same family were not well separated in the morpho-electric space. Instead, there was a continuum of variability in morphology and electrophysiology, with neighbouring transcriptomic cell types showing similar morpho-electric features, often without clear boundaries between them. Our results suggest that neuronal types in the neocortex do not always form discrete entities. Instead, neurons form a hierarchy that consists of distinct non-overlapping branches at the level of families, but can form continuous and correlated transcriptomic and morpho-electrical landscapes within families.
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Affiliation(s)
- Federico Scala
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Dmitry Kobak
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Matteo Bernabucci
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Yves Bernaerts
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
- International Max Planck Research School for Intelligent Systems, Tübingen, Germany
| | - Cathryn René Cadwell
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Jesus Ramon Castro
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Leonard Hartmanis
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xiaolong Jiang
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA
| | - Sophie Laturnus
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Elanine Miranda
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shalaka Mulherkar
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Zheng Huan Tan
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Philipp Berens
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.
- Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
- Bernstein Center for Computational Neuroscience, University of Tübingen, Tübingen, Germany.
| | - Andreas S Tolias
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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229
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A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 2021; 598:86-102. [PMID: 34616075 DOI: 10.1101/2020.10.19.343129v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 08/25/2021] [Indexed: 05/26/2023]
Abstract
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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230
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Callaway EM, Dong HW, Ecker JR, Hawrylycz MJ, Huang ZJ, Lein ES, Ngai J, Osten P, Ren B, Tolias AS, White O, Zeng H, Zhuang X, Ascoli GA, Behrens MM, Chun J, Feng G, Gee JC, Ghosh SS, Halchenko YO, Hertzano R, Lim BK, Martone ME, Ng L, Pachter L, Ropelewski AJ, Tickle TL, Yang XW, Zhang K, Bakken TE, Berens P, Daigle TL, Harris JA, Jorstad NL, Kalmbach BE, Kobak D, Li YE, Liu H, Matho KS, Mukamel EA, Naeemi M, Scala F, Tan P, Ting JT, Xie F, Zhang M, Zhang Z, Zhou J, Zingg B, Armand E, Yao Z, Bertagnolli D, Casper T, Crichton K, Dee N, Diep D, Ding SL, Dong W, Dougherty EL, Fong O, Goldman M, Goldy J, Hodge RD, Hu L, Keene CD, Krienen FM, Kroll M, Lake BB, Lathia K, Linnarsson S, Liu CS, Macosko EZ, McCarroll SA, McMillen D, Nadaf NM, Nguyen TN, Palmer CR, Pham T, Plongthongkum N, Reed NM, Regev A, Rimorin C, Romanow WJ, Savoia S, Siletti K, Smith K, Sulc J, Tasic B, Tieu M, Torkelson A, Tung H, van Velthoven CTJ, Vanderburg CR, Yanny AM, Fang R, Hou X, Lucero JD, Osteen JK, Pinto-Duarte A, Poirion O, Preissl S, Wang X, Aldridge AI, Bartlett A, Boggeman L, O’Connor C, Castanon RG, Chen H, Fitzpatrick C, Luo C, Nery JR, Nunn M, Rivkin AC, Tian W, Dominguez B, Ito-Cole T, Jacobs M, Jin X, Lee CT, Lee KF, Miyazaki PA, Pang Y, Rashid M, Smith JB, Vu M, Williams E, Biancalani T, Booeshaghi AS, Crow M, Dudoit S, Fischer S, Gillis J, Hu Q, Kharchenko PV, Niu SY, Ntranos V, Purdom E, Risso D, de Bézieux HR, Somasundaram S, Street K, Svensson V, Vaishnav ED, Van den Berge K, Welch JD, An X, Bateup HS, Bowman I, Chance RK, Foster NN, Galbavy W, Gong H, Gou L, Hatfield JT, Hintiryan H, Hirokawa KE, Kim G, Kramer DJ, Li A, Li X, Luo Q, Muñoz-Castañeda R, Stafford DA, Feng Z, Jia X, Jiang S, Jiang T, Kuang X, Larsen R, Lesnar P, Li Y, Li Y, Liu L, Peng H, Qu L, Ren M, Ruan Z, Shen E, Song Y, Wakeman W, Wang P, Wang Y, Wang Y, Yin L, Yuan J, Zhao S, Zhao X, Narasimhan A, Palaniswamy R, Banerjee S, Ding L, Huilgol D, Huo B, Kuo HC, Laturnus S, Li X, Mitra PP, Mizrachi J, Wang Q, Xie P, Xiong F, Yu Y, Eichhorn SW, Berg J, Bernabucci M, Bernaerts Y, Cadwell CR, Castro JR, Dalley R, Hartmanis L, Horwitz GD, Jiang X, Ko AL, Miranda E, Mulherkar S, Nicovich PR, Owen SF, Sandberg R, Sorensen SA, Tan ZH, Allen S, Hockemeyer D, Lee AY, Veldman MB, Adkins RS, Ament SA, Bravo HC, Carter R, Chatterjee A, Colantuoni C, Crabtree J, Creasy H, Felix V, Giglio M, Herb BR, Kancherla J, Mahurkar A, McCracken C, Nickel L, Olley D, Orvis J, Schor M, Hood G, Dichter B, Grauer M, Helba B, Bandrowski A, Barkas N, Carlin B, D’Orazi FD, Degatano K, Gillespie TH, Khajouei F, Konwar K, Thompson C, Kelly K, Mok S, Sunkin S. A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 2021; 598:86-102. [PMID: 34616075 PMCID: PMC8494634 DOI: 10.1038/s41586-021-03950-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 08/25/2021] [Indexed: 12/14/2022]
Abstract
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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231
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Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Human neocortical expansion involves glutamatergic neuron diversification. Nature 2021; 598:151-158. [PMID: 34616067 PMCID: PMC8494638 DOI: 10.1038/s41586-021-03813-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/07/2021] [Indexed: 11/09/2022]
Abstract
The neocortex is disproportionately expanded in human compared with mouse1,2, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers composed of neurons that selectively make connections within the neocortex and with other telencephalic structures. Single-cell transcriptomic analyses of human and mouse neocortex show an increased diversity of glutamatergic neuron types in supragranular layers in human neocortex and pronounced gradients as a function of cortical depth3. Here, to probe the functional and anatomical correlates of this transcriptomic diversity, we developed a robust platform combining patch clamp recording, biocytin staining and single-cell RNA-sequencing (Patch-seq) to examine neurosurgically resected human tissues. We demonstrate a strong correspondence between morphological, physiological and transcriptomic phenotypes of five human glutamatergic supragranular neuron types. These were enriched in but not restricted to layers, with one type varying continuously in all phenotypes across layers 2 and 3. The deep portion of layer 3 contained highly distinctive cell types, two of which express a neurofilament protein that labels long-range projection neurons in primates that are selectively depleted in Alzheimer's disease4,5. Together, these results demonstrate the explanatory power of transcriptomic cell-type classification, provide a structural underpinning for increased complexity of cortical function in humans, and implicate discrete transcriptomic neuron types as selectively vulnerable in disease.
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Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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232
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Ter Wal M, Tiesinga PHE. Comprehensive characterization of oscillatory signatures in a model circuit with PV- and SOM-expressing interneurons. BIOLOGICAL CYBERNETICS 2021; 115:487-517. [PMID: 34628539 PMCID: PMC8551150 DOI: 10.1007/s00422-021-00894-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 09/06/2021] [Indexed: 05/06/2023]
Abstract
Neural circuits contain a wide variety of interneuron types, which differ in their biophysical properties and connectivity patterns. The two most common interneuron types, parvalbumin-expressing and somatostatin-expressing cells, have been shown to be differentially involved in many cognitive functions. These cell types also show different relationships with the power and phase of oscillations in local field potentials. The mechanisms that underlie the emergence of different oscillatory rhythms in neural circuits with more than one interneuron subtype, and the roles specific interneurons play in those mechanisms, are not fully understood. Here, we present a comprehensive analysis of all possible circuit motifs and input regimes that can be achieved in circuits comprised of excitatory cells, PV-like fast-spiking interneurons and SOM-like low-threshold spiking interneurons. We identify 18 unique motifs and simulate their dynamics over a range of input strengths. Using several characteristics, such as oscillation frequency, firing rates, phase of firing and burst fraction, we cluster the resulting circuit dynamics across motifs in order to identify patterns of activity and compare these patterns to behaviors that were generated in circuits with one interneuron type. In addition to the well-known PING and ING gamma oscillations and an asynchronous state, our analysis identified three oscillatory behaviors that were generated by the three-cell-type motifs only: theta-nested gamma oscillations, stable beta oscillations and theta-locked bursting behavior, which have also been observed in experiments. Our characterization provides a map to interpret experimental activity patterns and suggests pharmacological manipulations or optogenetics approaches to validate these conclusions.
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Affiliation(s)
- Marije Ter Wal
- Department of Neuroinformatics, Donders Institute, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
- School of Psychology, University of Birmingham, Edgbaston, B15 2TT, UK.
| | - Paul H E Tiesinga
- Department of Neuroinformatics, Donders Institute, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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233
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Samarasinghe RA, Miranda OA, Buth JE, Mitchell S, Ferando I, Watanabe M, Allison TF, Kurdian A, Fotion NN, Gandal MJ, Golshani P, Plath K, Lowry WE, Parent JM, Mody I, Novitch BG. Identification of neural oscillations and epileptiform changes in human brain organoids. Nat Neurosci 2021; 24:1488-1500. [PMID: 34426698 PMCID: PMC9070733 DOI: 10.1038/s41593-021-00906-5] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 07/08/2021] [Indexed: 02/06/2023]
Abstract
Brain organoids represent a powerful tool for studying human neurological diseases, particularly those that affect brain growth and structure. However, many diseases manifest with clear evidence of physiological and network abnormality in the absence of anatomical changes, raising the question of whether organoids possess sufficient neural network complexity to model these conditions. Here, we explore the network-level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex network dynamics reminiscent of intact brain preparations. We demonstrate highly abnormal and epileptiform-like activity in organoids derived from induced pluripotent stem cells from individuals with Rett syndrome, accompanied by transcriptomic differences revealed by single-cell analyses. We also rescue key physiological activities with an unconventional neuroregulatory drug, pifithrin-α. Together, these findings provide an essential foundation for the utilization of brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.
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Affiliation(s)
- Ranmal A Samarasinghe
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Osvaldo A Miranda
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jessie E Buth
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Simon Mitchell
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Brighton and Sussex Medical School, Falmer, United Kingdom
| | - Isabella Ferando
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Momoko Watanabe
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Anatomy & Neurobiology, Sue & Bill Gross Stem Cell Research Center, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Thomas F Allison
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Arinnae Kurdian
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- CIRM CSUN-UCLA Stem Cell Training Program, California State University, Northridge, CA, USA
| | - Namie N Fotion
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Michael J Gandal
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Peyman Golshani
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- West Los Angeles VA Medical Center, Los Angeles, CA, USA
| | - Kathrin Plath
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - William E Lowry
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jack M Parent
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor VA Healthcare System, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Istvan Mody
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Bennett G Novitch
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
- Intellectual Development and Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
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234
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Gutman-Wei AY, Brown SP. Mechanisms Underlying Target Selectivity for Cell Types and Subcellular Domains in Developing Neocortical Circuits. Front Neural Circuits 2021; 15:728832. [PMID: 34630048 PMCID: PMC8497978 DOI: 10.3389/fncir.2021.728832] [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: 06/22/2021] [Accepted: 08/25/2021] [Indexed: 11/25/2022] Open
Abstract
The cerebral cortex contains numerous neuronal cell types, distinguished by their molecular identity as well as their electrophysiological and morphological properties. Cortical function is reliant on stereotyped patterns of synaptic connectivity and synaptic function among these neuron types, but how these patterns are established during development remains poorly understood. Selective targeting not only of different cell types but also of distinct postsynaptic neuronal domains occurs in many brain circuits and is directed by multiple mechanisms. These mechanisms include the regulation of axonal and dendritic guidance and fine-scale morphogenesis of pre- and postsynaptic processes, lineage relationships, activity dependent mechanisms and intercellular molecular determinants such as transmembrane and secreted molecules, many of which have also been implicated in neurodevelopmental disorders. However, many studies of synaptic targeting have focused on circuits in which neuronal processes target different lamina, such that cell-type-biased connectivity may be confounded with mechanisms of laminar specificity. In the cerebral cortex, each cortical layer contains cell bodies and processes from intermingled neuronal cell types, an arrangement that presents a challenge for the development of target-selective synapse formation. Here, we address progress and future directions in the study of cell-type-biased synaptic targeting in the cerebral cortex. We highlight challenges to identifying developmental mechanisms generating stereotyped patterns of intracortical connectivity, recent developments in uncovering the determinants of synaptic target selection during cortical synapse formation, and current gaps in the understanding of cortical synapse specificity.
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Affiliation(s)
- Alan Y. Gutman-Wei
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Solange P. Brown
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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235
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Kalmbach BE, Hodge RD, Jorstad NL, Owen S, de Frates R, Yanny AM, Dalley R, Mallory M, Graybuck LT, Radaelli C, Keene CD, Gwinn RP, Silbergeld DL, Cobbs C, Ojemann JG, Ko AL, Patel AP, Ellenbogen RG, Bakken TE, Daigle TL, Dee N, Lee BR, McGraw M, Nicovich PR, Smith K, Sorensen SA, Tasic B, Zeng H, Koch C, Lein ES, Ting JT. Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons. Neuron 2021; 109:2914-2927.e5. [PMID: 34534454 PMCID: PMC8570452 DOI: 10.1016/j.neuron.2021.08.030] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/20/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022]
Abstract
In the neocortex, subcerebral axonal projections originate largely from layer 5 (L5) extratelencephalic-projecting (ET) neurons. The unique morpho-electric properties of these neurons have been mainly described in rodents, where retrograde tracers or transgenic lines can label them. Similar labeling strategies are infeasible in the human neocortex, rendering the translational relevance of findings in rodents unclear. We leveraged the recent discovery of a transcriptomically defined L5 ET neuron type to study the properties of human L5 ET neurons in neocortical brain slices derived from neurosurgeries. Patch-seq recordings, where transcriptome, physiology, and morphology were assayed from the same cell, revealed many conserved morpho-electric properties of human and rodent L5 ET neurons. Divergent properties were often subtler than differences between L5 cell types within these two species. These data suggest a conserved function of L5 ET neurons in the neocortical hierarchy but also highlight phenotypic divergence possibly related to functional specialization of human neocortex.
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Affiliation(s)
- Brian E Kalmbach
- Allen Institute for Brain Science, Seattle, WA 98109, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA.
| | | | | | - Scott Owen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Matt Mallory
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Ryder P Gwinn
- Epilepsy Surgery and Functional Neurosurgery, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery and Alvord Brain Tumor Center, University of Washington, Seattle, WA 98195, USA
| | - Charles Cobbs
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA 98104, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA 98104, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Tanya L Daigle
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA; Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA 98109, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA; The Washington National Primate Research Center, University of Washington, Seattle, WA 98195, USA.
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236
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Development, Diversity, and Death of MGE-Derived Cortical Interneurons. Int J Mol Sci 2021; 22:ijms22179297. [PMID: 34502208 PMCID: PMC8430628 DOI: 10.3390/ijms22179297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 12/17/2022] Open
Abstract
In the mammalian brain, cortical interneurons (INs) are a highly diverse group of cells. A key neurophysiological question concerns how each class of INs contributes to cortical circuit function and whether specific roles can be attributed to a selective cell type. To address this question, researchers are integrating knowledge derived from transcriptomic, histological, electrophysiological, developmental, and functional experiments to extensively characterise the different classes of INs. Our hope is that such knowledge permits the selective targeting of cell types for therapeutic endeavours. This review will focus on two of the main types of INs, namely the parvalbumin (PV+) or somatostatin (SOM+)-containing cells, and summarise the research to date on these classes.
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237
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Ihbe N, Le Prieult F, Wang Q, Distler U, Sielaff M, Tenzer S, Thal SC, Mittmann T. Adaptive Mechanisms of Somatostatin-Positive Interneurons after Traumatic Brain Injury through a Switch of α Subunits in L-Type Voltage-Gated Calcium Channels. Cereb Cortex 2021; 32:1093-1109. [PMID: 34411234 DOI: 10.1093/cercor/bhab268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/28/2022] Open
Abstract
Unilateral traumatic brain injury (TBI) causes cortical dysfunctions spreading to the primarily undamaged hemisphere. This phenomenon, called transhemispheric diaschisis, is mediated by an imbalance of glutamatergic versus GABAergic neurotransmission. This study investigated the role of GABAergic, somatostatin-positive (SST) interneurons in the contralateral hemisphere 72 h after unilateral TBI. The brain injury was induced to the primary motor/somatosensory cortex of glutamate decarboxylase 67-green fluorescent protein (GAD67-GFP) knock-in mice at postnatal days 19-21 under anesthesia in vivo. Single GFP+ interneurons of the undamaged, contralateral cortex were isolated by fluorescence-activated cell sorting and analyzed by mass spectrometry. TBI caused a switch of 2 α subunits of pore-forming L-type voltage-gated calcium channels (VGCC) in GABAergic interneurons, an increased expression of CaV1.3, and simultaneous ablation of CaV1.2. This switch was associated with 1) increased excitability of single SST interneurons in patch-clamp recordings and (2) a recovery from early network hyperactivity in the contralateral hemisphere in microelectrode array recordings of acute slices. The electrophysiological changes were sensitive to pharmacological blockade of CaV1.3 (isradipine, 100 nM). These data identify a switch of 2 α subunits of VGCCs in SST interneurons early after TBI as a mechanism to counterbalance post-traumatic hyperexcitability.
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Affiliation(s)
- Natascha Ihbe
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Florie Le Prieult
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Qi Wang
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Malte Sielaff
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Serge C Thal
- Clinic for Anesthesiology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Thomas Mittmann
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
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238
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Lee BR, Budzillo A, Hadley K, Miller JA, Jarsky T, Baker K, Hill D, Kim L, Mann R, Ng L, Oldre A, Rajanbabu R, Trinh J, Vargas S, Braun T, Dalley RA, Gouwens NW, Kalmbach BE, Kim TK, Smith KA, Soler-Llavina G, Sorensen S, Tasic B, Ting JT, Lein E, Zeng H, Murphy GJ, Berg J. Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization. eLife 2021; 10:e65482. [PMID: 34387544 PMCID: PMC8428855 DOI: 10.7554/elife.65482] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
The Patch-seq approach is a powerful variation of the patch-clamp technique that allows for the combined electrophysiological, morphological, and transcriptomic characterization of individual neurons. To generate Patch-seq datasets at scale, we identified and refined key factors that contribute to the efficient collection of high-quality data. We developed patch-clamp electrophysiology software with analysis functions specifically designed to automate acquisition with online quality control. We recognized the importance of extracting the nucleus for transcriptomic success and maximizing membrane integrity during nucleus extraction for morphology success. The protocol is generalizable to different species and brain regions, as demonstrated by capturing multimodal data from human and macaque brain slices. The protocol, analysis and acquisition software are compiled at https://githubcom/AllenInstitute/patchseqtools. This resource can be used by individual labs to generate data across diverse mammalian species and that is compatible with large publicly available Patch-seq datasets.
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Affiliation(s)
- Brian R Lee
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Tim Jarsky
- Allen Institute for Brain ScienceSeattleUnited States
| | | | - DiJon Hill
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lisa Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | - Rusty Mann
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lindsay Ng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Aaron Oldre
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ram Rajanbabu
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jessica Trinh
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sara Vargas
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Brian E Kalmbach
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Tae Kyung Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | | | - Jonathan T Ting
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Hongkui Zeng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Gabe J Murphy
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Jim Berg
- Allen Institute for Brain ScienceSeattleUnited States
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239
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Lee EK, Balasubramanian H, Tsolias A, Anakwe SU, Medalla M, Shenoy KV, Chandrasekaran C. Non-linear dimensionality reduction on extracellular waveforms reveals cell type diversity in premotor cortex. eLife 2021; 10:e67490. [PMID: 34355695 PMCID: PMC8452311 DOI: 10.7554/elife.67490] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Cortical circuits are thought to contain a large number of cell types that coordinate to produce behavior. Current in vivo methods rely on clustering of specified features of extracellular waveforms to identify putative cell types, but these capture only a small amount of variation. Here, we develop a new method (WaveMAP) that combines non-linear dimensionality reduction with graph clustering to identify putative cell types. We apply WaveMAP to extracellular waveforms recorded from dorsal premotor cortex of macaque monkeys performing a decision-making task. Using WaveMAP, we robustly establish eight waveform clusters and show that these clusters recapitulate previously identified narrow- and broad-spiking types while revealing previously unknown diversity within these subtypes. The eight clusters exhibited distinct laminar distributions, characteristic firing rate patterns, and decision-related dynamics. Such insights were weaker when using feature-based approaches. WaveMAP therefore provides a more nuanced understanding of the dynamics of cell types in cortical circuits.
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Affiliation(s)
- Eric Kenji Lee
- Psychological and Brain Sciences, Boston UniversityBostonUnited States
| | - Hymavathy Balasubramanian
- Bernstein Center for Computational Neuroscience, Bernstein Center for Computational NeuroscienceBerlinGermany
| | - Alexandra Tsolias
- Department of Anatomy and Neurobiology, Boston UniversityBostonUnited States
| | | | - Maria Medalla
- Department of Anatomy and Neurobiology, Boston UniversityBostonUnited States
| | - Krishna V Shenoy
- Department of Electrical Engineering, Stanford UniversityStanfordUnited States
- Department of Bioengineering, Stanford UniversityStanfordUnited States
- Department of Neurobiology, Stanford UniversityStanfordUnited States
- Wu Tsai Neurosciences Institute, Stanford UniversityStanfordUnited States
- Bio-X Institute, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Chandramouli Chandrasekaran
- Psychological and Brain Sciences, Boston UniversityBostonUnited States
- Department of Anatomy and Neurobiology, Boston UniversityBostonUnited States
- Center for Systems Neuroscience, Boston UniversityBostonUnited States
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
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240
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Pérez-Ortega J, Alejandre-García T, Yuste R. Long-term stability of cortical ensembles. eLife 2021; 10:e64449. [PMID: 34328414 PMCID: PMC8376248 DOI: 10.7554/elife.64449] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 07/29/2021] [Indexed: 12/25/2022] Open
Abstract
Neuronal ensembles, coactive groups of neurons found in spontaneous and evoked cortical activity, are causally related to memories and perception, but it is still unknown how stable or flexible they are over time. We used two-photon multiplane calcium imaging to track over weeks the activity of the same pyramidal neurons in layer 2/3 of the visual cortex from awake mice and recorded their spontaneous and visually evoked responses. Less than half of the neurons remained active across any two imaging sessions. These stable neurons formed ensembles that lasted weeks, but some ensembles were also transient and appeared only in one single session. Stable ensembles preserved most of their neurons for up to 46 days, our longest imaged period, and these 'core' cells had stronger functional connectivity. Our results demonstrate that neuronal ensembles can last for weeks and could, in principle, serve as a substrate for long-lasting representation of perceptual states or memories.
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Affiliation(s)
- Jesús Pérez-Ortega
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | | | - Rafael Yuste
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
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241
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Rodríguez-Collado A, Rueda C. Electrophysiological and Transcriptomic Features Reveal a Circular Taxonomy of Cortical Neurons. Front Hum Neurosci 2021; 15:684950. [PMID: 34381341 PMCID: PMC8350032 DOI: 10.3389/fnhum.2021.684950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/28/2021] [Indexed: 11/24/2022] Open
Abstract
The complete understanding of the mammalian brain requires exact knowledge of the function of each neuron subpopulation composing its parts. To achieve this goal, an exhaustive, precise, reproducible, and robust neuronal taxonomy should be defined. In this paper, a new circular taxonomy based on transcriptomic features and novel electrophysiological features is proposed. The approach is validated by analysing more than 1850 electrophysiological signals of different mouse visual cortex neurons proceeding from the Allen Cell Types database. The study is conducted on two different levels: neurons and their cell-type aggregation into Cre lines. At the neuronal level, electrophysiological features have been extracted with a promising model that has already proved its worth in neuronal dynamics. At the Cre line level, electrophysiological and transcriptomic features are joined on cell types with available genetic information. A taxonomy with a circular order is revealed by a simple transformation of the first two principal components that allow the characterization of the different Cre lines. Moreover, the proposed methodology locates other Cre lines in the taxonomy that do not have transcriptomic features available. Finally, the taxonomy is validated by Machine Learning methods which are able to discriminate the different neuron types with the proposed electrophysiological features.
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242
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Abstract
It has been known for over a century that the basic organization of the retina is conserved across vertebrates. It has been equally clear that retinal cells can be classified into numerous types, but only recently have methods been devised to explore this diversity in unbiased, scalable, and comprehensive ways. Advances in high-throughput single-cell RNA-sequencing (scRNA-seq) have played a pivotal role in this effort. In this article, we outline the experimental and computational components of scRNA-seq and review studies that have used them to generate retinal atlases of cell types in several vertebrate species. These atlases have enabled studies of retinal development, responses of retinal cells to injury, expression patterns of genes implicated in retinal disease, and the evolution of cell types. Recently, the inquiry has expanded to include the entire eye and visual centers in the brain. These studies have enhanced our understanding of retinal function and dysfunction and provided tools and insights for exploring neural diversity throughout the brain. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; and California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, USA;
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cell Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
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243
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Nagaeva E, Zubarev I, Korpi ER. Electrophysiological Properties of Neurons: Current-Clamp Recordings in Mouse Brain Slices and Firing-Pattern Analysis. Bio Protoc 2021; 11:e4061. [PMID: 34263004 DOI: 10.21769/bioprotoc.4061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/24/2021] [Accepted: 04/12/2021] [Indexed: 11/02/2022] Open
Abstract
Characterization of an electrically active cell, such as a neuron, demands measurement of its electrical properties. Due to differences in gene activation, location, innervation patterns, and functions, the millions of neurons in the mammalian brain are tremendously diverse in their membrane characteristics and abilities to generate action potentials. These features can be measured with a patch-clamp technique in whole-cell current-clamp configuration followed by detailed post-hoc analysis of firing patterns. This analysis can be time-consuming, and different laboratories have their own methods to perform it, either manually or with custom-written scripts. Here, we describe in detail a protocol for firing-pattern registration in neurons of the ventral tegmental area (VTA) as an example and introduce a software for its fast and convenient analysis. With the help of this article, other research groups can easily apply this method and generate unified types of data that are comparable between brain regions and various studies. Graphic abstract: Workflow of the Protocol.
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Affiliation(s)
- Elina Nagaeva
- Department of Pharmacology, Faculty of Medicine, FI-00014 University of Helsinki, Helsinki, Finland
| | - Ivan Zubarev
- Department of Neuroscience and Biomedical Engineering, Aalto University, 11000 Espoo, Finland
| | - Esa R Korpi
- Department of Pharmacology, Faculty of Medicine, FI-00014 University of Helsinki, Helsinki, Finland
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244
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Timonidis N, Tiesinga PHE. Progress towards a cellularly resolved mouse mesoconnectome is empowered by data fusion and new neuroanatomy techniques. Neurosci Biobehav Rev 2021; 128:569-591. [PMID: 34119523 DOI: 10.1016/j.neubiorev.2021.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/02/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
Over the past decade there has been a rapid improvement in techniques for obtaining large-scale cellular level data related to the mouse brain connectome. However, a detailed mapping of cell-type-specific projection patterns is lacking, which would, for instance, allow us to study the role of circuit motifs in cognitive processes. In this work, we review advanced neuroanatomical and data fusion techniques within the context of a proposed Multimodal Connectomic Integration Framework for augmenting the cellularly resolved mouse mesoconnectome. First, we emphasize the importance of registering data modalities to a common reference atlas. We then review a number of novel experimental techniques that can provide data for characterizing cell-types in the mouse brain. Furthermore, we examine a number of data integration strategies, which involve fine-grained cell-type classification, spatial inference of cell densities, latent variable models for the mesoconnectome and multi-modal factorisation. Finally, we discuss a number of use cases which depend on connectome augmentation techniques, such as model simulations of functional connectivity and generating mechanistic hypotheses for animal disease models.
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Affiliation(s)
- Nestor Timonidis
- Neuroinformatics department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Paul H E Tiesinga
- Neuroinformatics department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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245
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de Kock CPJ, Pie J, Pieneman AW, Mease RA, Bast A, Guest JM, Oberlaender M, Mansvelder HD, Sakmann B. High-frequency burst spiking in layer 5 thick-tufted pyramids of rat primary somatosensory cortex encodes exploratory touch. Commun Biol 2021; 4:709. [PMID: 34112934 PMCID: PMC8192911 DOI: 10.1038/s42003-021-02241-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 05/18/2021] [Indexed: 01/14/2023] Open
Abstract
Diversity of cell-types that collectively shape the cortical microcircuit ensures the necessary computational richness to orchestrate a wide variety of behaviors. The information content embedded in spiking activity of identified cell-types remain unclear to a large extent. Here, we recorded spike responses upon whisker touch of anatomically identified excitatory cell-types in primary somatosensory cortex in naive, untrained rats. We find major differences across layers and cell-types. The temporal structure of spontaneous spiking contains high-frequency bursts (≥100 Hz) in all morphological cell-types but a significant increase upon whisker touch is restricted to layer L5 thick-tufted pyramids (L5tts) and thus provides a distinct neurophysiological signature. We find that whisker touch can also be decoded from L5tt bursting, but not from other cell-types. We observed high-frequency bursts in L5tts projecting to different subcortical regions, including thalamus, midbrain and brainstem. We conclude that bursts in L5tts allow accurate coding and decoding of exploratory whisker touch. In order to investigate the information encoded by spiking activity in different neuronal cell types in the primary somatosensory cortex, de Kock et al performed electrophysiological recordings in untrained rats. They demonstrated that an increase in high-frequency burst spiking in thick tufted pyramids in layer 5 of the cortex allow accurate encoding of exploratory whisker touch.
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Affiliation(s)
- Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU, Amsterdam, the Netherlands.
| | - Jean Pie
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU, Amsterdam, the Netherlands.,University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, Netherlands
| | - Anton W Pieneman
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU, Amsterdam, the Netherlands
| | - Rebecca A Mease
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Arco Bast
- Max Planck Group: In Silico Brain Sciences, Center of Advanced European Studies and Research, Bonn, Germany
| | - Jason M Guest
- Max Planck Group: In Silico Brain Sciences, Center of Advanced European Studies and Research, Bonn, Germany
| | - Marcel Oberlaender
- Max Planck Group: In Silico Brain Sciences, Center of Advanced European Studies and Research, Bonn, Germany
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU, Amsterdam, the Netherlands
| | - Bert Sakmann
- Max Planck Institute for Neurobiology, Martinsried, Germany
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246
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Yao Z, van Velthoven CTJ, Nguyen TN, Goldy J, Sedeno-Cortes AE, Baftizadeh F, Bertagnolli D, Casper T, Chiang M, Crichton K, Ding SL, Fong O, Garren E, Glandon A, Gouwens NW, Gray J, Graybuck LT, Hawrylycz MJ, Hirschstein D, Kroll M, Lathia K, Lee C, Levi B, McMillen D, Mok S, Pham T, Ren Q, Rimorin C, Shapovalova N, Sulc J, Sunkin SM, Tieu M, Torkelson A, Tung H, Ward K, Dee N, Smith KA, Tasic B, Zeng H. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. Cell 2021; 184:3222-3241.e26. [PMID: 34004146 PMCID: PMC8195859 DOI: 10.1016/j.cell.2021.04.021] [Citation(s) in RCA: 445] [Impact Index Per Article: 148.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 02/09/2021] [Accepted: 04/14/2021] [Indexed: 12/23/2022]
Abstract
The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion, and learning. We profiled ∼1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic cell-type taxonomy revealing a comprehensive repertoire of glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and the isocortex share a common circuit organization. We also identify large-scale continuous and graded variations of cell types along isocortical depth, across the isocortical sheet, and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of the mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity, and function of these two brain structures.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Megan Chiang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Matthew Kroll
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Stephanie Mok
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Qingzhong Ren
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
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247
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Mazuir E, Richevaux L, Nassar M, Robil N, de la Grange P, Lubetzki C, Fricker D, Sol-Foulon N. Oligodendrocyte Secreted Factors Shape Hippocampal GABAergic Neuron Transcriptome and Physiology. Cereb Cortex 2021; 31:5024-5041. [PMID: 34023893 DOI: 10.1093/cercor/bhab139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/26/2021] [Accepted: 04/17/2021] [Indexed: 11/14/2022] Open
Abstract
Oligodendrocytes form myelin for central nervous system axons and release factors which signal to neurons during myelination. Here, we ask how oligodendroglial factors influence hippocampal GABAergic neuron physiology. In mixed hippocampal cultures, GABAergic neurons fired action potentials (APs) of short duration and received high frequencies of excitatory synaptic events. In purified neuronal cultures without glial cells, GABAergic neuron excitability increased and the frequency of synaptic events decreased. These effects were largely reversed by adding oligodendrocyte conditioned medium (OCM). We compared the transcriptomic signature with the electrophysiological phenotype of single neurons in these three culture conditions. Genes expressed by single pyramidal or GABAergic neurons largely conformed to expected cell-type specific patterns. Multiple genes of GABAergic neurons were significantly downregulated by the transition from mixed cultures containing glial cells to purified neuronal cultures. Levels of these genes were restored by the addition of OCM to purified cultures. Clustering genes with similar changes in expression between different culture conditions revealed processes affected by oligodendroglial factors. Enriched genes are linked to roles in synapse assembly, AP generation, and transmembrane ion transport, including of zinc. These results provide new insight into the molecular targets by which oligodendrocytes influence neuron excitability and synaptic function.
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Affiliation(s)
- Elisa Mazuir
- Sorbonne University, Inserm, CNRS, Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, F-75013 Paris, France
| | | | - Merie Nassar
- Université de Paris, INCC UMR 8002, CNRS, F-75006 Paris
| | | | | | - Catherine Lubetzki
- Sorbonne University, Inserm, CNRS, Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, F-75013 Paris, France.,Assistance Publique des Hôpitaux de Paris (APHP), Neurology Department, Pitié-Salpêtrière hospital, Paris 75013, France
| | | | - Nathalie Sol-Foulon
- Sorbonne University, Inserm, CNRS, Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, F-75013 Paris, France
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248
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Kobak D, Bernaerts Y, Weis MA, Scala F, Tolias AS, Berens P. Sparse reduced‐rank regression for exploratory visualisation of paired multivariate data. J R Stat Soc Ser C Appl Stat 2021. [DOI: 10.1111/rssc.12494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dmitry Kobak
- Institute for Ophthalmic Research University of Tübingen Tübingen Germany
| | - Yves Bernaerts
- Institute for Ophthalmic Research University of Tübingen Tübingen Germany
- International Max Planck Research School for Intelligent Systems Germany
| | - Marissa A. Weis
- Institute for Ophthalmic Research University of Tübingen Tübingen Germany
| | - Federico Scala
- Department of Neuroscience Baylor College of Medicine Houston Texas USA
| | - Andreas S. Tolias
- Department of Neuroscience Baylor College of Medicine Houston Texas USA
| | - Philipp Berens
- Institute for Ophthalmic Research University of Tübingen Tübingen Germany
- Department of Computer Science University of Tübingen Tübingen Germany
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249
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Kullander K, Topolnik L. Cortical disinhibitory circuits: cell types, connectivity and function. Trends Neurosci 2021; 44:643-657. [PMID: 34006387 DOI: 10.1016/j.tins.2021.04.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022]
Abstract
The concept of a dynamic excitation/inhibition balance tuned by circuit disinhibition, which can shape information flow during complex behavioral tasks, has arisen as an important and conserved information-processing motif. In cortical circuits, different subtypes of GABAergic inhibitory interneurons are connected to each other, offering an anatomical foundation for disinhibitory processes. Moreover, a subpopulation of GABAergic cells that express vasoactive intestinal polypeptide (VIP) preferentially innervates inhibitory interneurons, highlighting their central role in disinhibitory modulation. We discuss inhibitory neuron subtypes involved in disinhibition, with a focus on local circuits and long-range synaptic connections that drive disinhibitory function. We highlight multiple layers of disinhibition across cortical circuits that regulate behavior and serve to maintain an excitation/inhibition balance.
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Affiliation(s)
- Klas Kullander
- Department of Neuroscience, Uppsala University, Uppsala, Sweden.
| | - Lisa Topolnik
- Department of Biochemistry, Microbiology, and Bioinformatics, Laval University, Québec, QC, Canada; Neuroscience Axis, Centre de Recherche du Centre Hospitalier Universitaire de Québec (CRCHUQ), Laval University, Québec, QC, Canada.
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250
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Booker SA, Wyllie DJA. NMDA receptor function in inhibitory neurons. Neuropharmacology 2021; 196:108609. [PMID: 34000273 DOI: 10.1016/j.neuropharm.2021.108609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/26/2022]
Abstract
N-methyl-d-aspartate receptors (NMDARs) are present in the majority of brain circuits and play a key role in synaptic information transfer and synaptic plasticity. A key element of many brain circuits are inhibitory GABAergic interneurons that in themselves show diverse and cell-type-specific NMDAR expression and function. Indeed, NMDARs located on interneurons control cellular excitation in a synapse-type specific manner which leads to divergent dendritic integration properties amongst the plethora of interneuron subtypes known to exist. In this review, we explore the documented diversity of NMDAR subunit expression in identified subpopulations of interneurons and assess the NMDAR subtype-specific control of their function. We also highlight where knowledge still needs to be obtained, if a full appreciation is to be gained of roles played by NMDARs in controlling GABAergic modulation of synaptic and circuit function. This article is part of the 'Special Issue on Glutamate Receptors - NMDA receptors'.
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Affiliation(s)
- Sam A Booker
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, EH8 9XD, UK; Patrick Wild Centre for Research into Autism, Fragile X Syndrome & Intellectual Disabilities, University of Edinburgh, Edinburgh, EH8 9XD, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK.
| | - David J A Wyllie
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, EH8 9XD, UK; Patrick Wild Centre for Research into Autism, Fragile X Syndrome & Intellectual Disabilities, University of Edinburgh, Edinburgh, EH8 9XD, UK; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK; Centre for Brain Development and Repair, InStem, Bangalore, 560065, India.
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