1
|
Martinetti LE, Autio DM, Crandall SR. Motor Control of Distinct Layer 6 Corticothalamic Feedback Circuits. eNeuro 2024; 11:ENEURO.0255-24.2024. [PMID: 38926084 PMCID: PMC11236587 DOI: 10.1523/eneuro.0255-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024] Open
Abstract
Layer 6 corticothalamic (L6 CT) neurons provide massive input to the thalamus, and these feedback connections enable the cortex to influence its own sensory input by modulating thalamic excitability. However, the functional role(s) feedback serves during sensory processing is unclear. One hypothesis is that CT feedback is under the control of extrasensory signals originating from higher-order cortical areas, yet we know nothing about the mechanisms of such control. It is also unclear whether such regulation is specific to CT neurons with distinct thalamic connectivity. Using mice (either sex) combined with in vitro electrophysiology techniques, optogenetics, and retrograde labeling, we describe studies of vibrissal primary motor cortex (vM1) influences on different CT neurons in the vibrissal primary somatosensory cortex (vS1) with distinct intrathalamic axonal projections. We found that vM1 inputs are highly selective, evoking stronger postsynaptic responses in CT neurons projecting to the dual ventral posterior medial nucleus (VPm) and posterior medial nucleus (POm) located in lower L6a than VPm-only-projecting CT cells in upper L6a. A targeted analysis of the specific cells and synapses involved revealed that the greater responsiveness of Dual CT neurons was due to their distinctive intrinsic membrane properties and synaptic mechanisms. These data demonstrate that vS1 has at least two discrete L6 CT subcircuits distinguished by their thalamic projection patterns, intrinsic physiology, and functional connectivity with vM1. Our results also provide insights into how a distinct CT subcircuit may serve specialized roles specific to contextual modulation of tactile-related sensory signals in the somatosensory thalamus during active vibrissa movements.
Collapse
Affiliation(s)
- Luis E Martinetti
- Neuroscience Program, Michigan State University, East Lansing, Michigan 48824
| | - Dawn M Autio
- Department of Physiology, Michigan State University, East Lansing, Michigan 48824
| | - Shane R Crandall
- Neuroscience Program, Michigan State University, East Lansing, Michigan 48824
- Department of Physiology, Michigan State University, East Lansing, Michigan 48824
| |
Collapse
|
2
|
Martinetti LE, Autio DM, Crandall SR. Motor Control of Distinct Layer 6 Corticothalamic Feedback Circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590613. [PMID: 38712153 PMCID: PMC11071411 DOI: 10.1101/2024.04.22.590613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Layer 6 corticothalamic (L6 CT) neurons provide massive input to the thalamus, and these feedback connections enable the cortex to influence its own sensory input by modulating thalamic excitability. However, the functional role(s) feedback serves during sensory processing is unclear. One hypothesis is that CT feedback is under the control of extra-sensory signals originating from higher-order cortical areas, yet we know nothing about the mechanisms of such control. It is also unclear whether such regulation is specific to CT neurons with distinct thalamic connectivity. Using mice (either sex) combined with in vitro electrophysiology techniques, optogenetics, and retrograde labeling, we describe studies of vibrissal primary motor cortex (vM1) influences on different CT neurons in the vibrissal primary somatosensory cortex (vS1) with distinct intrathalamic axonal projections. We found that vM1 inputs are highly selective, evoking stronger postsynaptic responses in Dual ventral posterior medial nucleus (VPm) and posterior medial nucleus (POm) projecting CT neurons located in lower L6a than VPm-only projecting CT cells in upper L6a. A targeted analysis of the specific cells and synapses involved revealed that the greater responsiveness of Dual CT neurons was due to their distinctive intrinsic membrane properties and synaptic mechanisms. These data demonstrate that vS1 has at least two discrete L6 CT subcircuits distinguished by their thalamic projection patterns, intrinsic physiology, and functional connectivity with vM1. Our results also provide insights into how a distinct CT subcircuit may serve specialized roles specific to contextual modulation of tactile-related sensory signals in the somatosensory thalamus during active vibrissa movements.
Collapse
Affiliation(s)
| | - Dawn M. Autio
- Department of Physiology, Michigan State University, East Lansing, MI 48824
| | - Shane R. Crandall
- Neuroscience Program, Michigan State University, East Lansing, MI 48824
- Department of Physiology, Michigan State University, East Lansing, MI 48824
| |
Collapse
|
3
|
Mahon S. Variation and convergence in the morpho-functional properties of the mammalian neocortex. Front Syst Neurosci 2024; 18:1413780. [PMID: 38966330 PMCID: PMC11222651 DOI: 10.3389/fnsys.2024.1413780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/03/2024] [Indexed: 07/06/2024] Open
Abstract
Man's natural inclination to classify and hierarchize the living world has prompted neurophysiologists to explore possible differences in brain organisation between mammals, with the aim of understanding the diversity of their behavioural repertoires. But what really distinguishes the human brain from that of a platypus, an opossum or a rodent? In this review, we compare the structural and electrical properties of neocortical neurons in the main mammalian radiations and examine their impact on the functioning of the networks they form. We discuss variations in overall brain size, number of neurons, length of their dendritic trees and density of spines, acknowledging their increase in humans as in most large-brained species. Our comparative analysis also highlights a remarkable consistency, particularly pronounced in marsupial and placental mammals, in the cell typology, intrinsic and synaptic electrical properties of pyramidal neuron subtypes, and in their organisation into functional circuits. These shared cellular and network characteristics contribute to the emergence of strikingly similar large-scale physiological and pathological brain dynamics across a wide range of species. These findings support the existence of a core set of neural principles and processes conserved throughout mammalian evolution, from which a number of species-specific adaptations appear, likely allowing distinct functional needs to be met in a variety of environmental contexts.
Collapse
Affiliation(s)
- Séverine Mahon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, Paris, France
| |
Collapse
|
4
|
James RE, Hamilton NR, Huffman LN, Pasterkamp J, Goff LA, Kolodkin AL. Semaphorin 6A in Retinal Ganglion Cells Regulates Functional Specialization of the Inner Retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567662. [PMID: 38014224 PMCID: PMC10680864 DOI: 10.1101/2023.11.18.567662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
To form functional circuits, neurons must settle in their appropriate cellular locations and then project and elaborate neurites to contact their target synaptic neuropils. Laminar organization within the vertebrate retinal inner plexiform layer (IPL) facilitates pre- and postsynaptic neurite targeting, yet, the precise mechanisms underlying establishment of functional IPL subdomains are not well understood. Here we explore mechanisms defining the compartmentalization of OFF and ON neurites generally, and OFF and ON direction-selective neurites specifically, within the developing IPL. We show that semaphorin 6A (Sema6A), a repulsive axon guidance cue, is required for delineation of OFF versus ON circuits within the IPL: in the Sema6a null IPL, the boundary between OFF and ON domains is blurred. Furthermore, Sema6A expressed by retinal ganglion cells (RGCs) directs laminar segregation of OFF and ON starburst amacrine cell (SAC) dendritic scaffolds, which themselves serve as a substrate upon which other retinal neurites elaborate. These results demonstrate for the first time that RGCs, the first neuron-type born within the retina, play an active role in functional specialization of the IPL. Retinal ganglion cell-dependent regulation of OFF and ON starburst amacrine cell dendritic scaffold segregation prevents blurring of OFF versus ON functional domains in the murine inner plexiform layer.
Collapse
|
5
|
Feldmeyer D. Structure and function of neocortical layer 6b. Front Cell Neurosci 2023; 17:1257803. [PMID: 37744882 PMCID: PMC10516558 DOI: 10.3389/fncel.2023.1257803] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023] Open
Abstract
Cortical layer 6b is considered by many to be a remnant of the subplate that forms during early stages of neocortical development, but its role in the adult is not well understood. Its neuronal complement has only recently become the subject of systematic studies, and its axonal projections and synaptic input structures have remained largely unexplored despite decades of research into neocortical function. In recent years, however, layer 6b (L6b) has attracted increasing attention and its functional role is beginning to be elucidated. In this review, I will attempt to provide an overview of what is currently known about the excitatory and inhibitory neurons in this layer, their pre- and postsynaptic connectivity, and their functional implications. Similarities and differences between different cortical areas will be highlighted. Finally, layer 6b neurons are highly responsive to several neuropeptides such as orexin/hypocretin, neurotensin and cholecystokinin, in some cases exclusively. They are also strongly controlled by neurotransmitters such as acetylcholine and norepinephrine. The interaction of these neuromodulators with L6b microcircuitry and its functional consequences will also be discussed.
Collapse
Affiliation(s)
- Dirk Feldmeyer
- Research Centre Jülich, Institute of Neuroscience and Medicine 10 (INM-10), Jülich, Germany
- Department of Psychiatry, Psychotherapy, and Psychosomatics, RWTH Aachen University Hospital, Aachen, Germany
- Jülich-Aachen Research Alliance, Translational Brain Medicine (JARA Brain), Aachen, Germany
| |
Collapse
|
6
|
Galazo MJ, Sweetser DA, Macklis JD. Tle4 controls both developmental acquisition and early post-natal maturation of corticothalamic projection neuron identity. Cell Rep 2023; 42:112957. [PMID: 37561632 PMCID: PMC10542749 DOI: 10.1016/j.celrep.2023.112957] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 04/21/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Identities of distinct neuron subtypes are specified during embryonic development, then maintained during post-natal maturation. In cerebral cortex, mechanisms controlling early acquisition of neuron-subtype identities have become increasingly understood. However, mechanisms controlling neuron-subtype identity stability during post-natal maturation are largely unexplored. We identify that Tle4 is required for both early acquisition and post-natal stability of corticothalamic neuron-subtype identity. Embryonically, Tle4 promotes acquisition of corticothalamic identity and blocks emergence of core characteristics of subcerebral/corticospinal projection neuron identity, including gene expression and connectivity. During the first post-natal week, when corticothalamic innervation is ongoing, Tle4 is required to stabilize corticothalamic neuron identity, limiting interference from differentiation programs of developmentally related neuron classes. We identify a deacetylation-based epigenetic mechanism by which TLE4 controls Fezf2 expression level by corticothalamic neurons. This contributes to distinction of cortical output subtypes and ensures identity stability for appropriate maturation of corticothalamic neurons.
Collapse
Affiliation(s)
- Maria J Galazo
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - David A Sweetser
- Department of Pediatrics, Divisions of Pediatric Hematology/Oncology and Medical Genetics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
7
|
Vincent E, Chatterjee S, Cannon GH, Auer D, Ross H, Chakravarti A, Goff LA. Ret deficiency decreases neural crest progenitor proliferation and restricts fate potential during enteric nervous system development. Proc Natl Acad Sci U S A 2023; 120:e2211986120. [PMID: 37585461 PMCID: PMC10451519 DOI: 10.1073/pnas.2211986120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/18/2023] [Indexed: 08/18/2023] Open
Abstract
The receptor tyrosine kinase RET plays a critical role in the fate specification of enteric neural crest-derived cells (ENCDCs) during enteric nervous system (ENS) development. RET loss of function (LoF) is associated with Hirschsprung disease (HSCR), which is marked by aganglionosis of the gastrointestinal (GI) tract. Although the major phenotypic consequences and the underlying transcriptional changes from Ret LoF in the developing ENS have been described, cell type- and state-specific effects are unknown. We performed single-cell RNA sequencing on an enriched population of ENCDCs from the developing GI tract of Ret null heterozygous and homozygous mice at embryonic day (E)12.5 and E14.5. We demonstrate four significant findings: 1) Ret-expressing ENCDCs are a heterogeneous population comprising ENS progenitors as well as glial- and neuronal-committed cells; 2) neurons committed to a predominantly inhibitory motor neuron developmental trajectory are not produced under Ret LoF, leaving behind a mostly excitatory motor neuron developmental program; 3) expression patterns of HSCR-associated and Ret gene regulatory network genes are impacted by Ret LoF; and 4) Ret deficiency leads to precocious differentiation and reduction in the number of proliferating ENS precursors. Our results support a model in which Ret contributes to multiple distinct cellular phenotypes during development of the ENS, including the specification of inhibitory neuron subtypes, cell cycle dynamics of ENS progenitors, and the developmental timing of neuronal and glial commitment.
Collapse
Affiliation(s)
- Elizabeth Vincent
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Sumantra Chatterjee
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY10016
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY10016
| | - Gabrielle H. Cannon
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Dallas Auer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Holly Ross
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY10016
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY10016
| | - Loyal A. Goff
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD21205
| |
Collapse
|
8
|
Al-Khindi T, Sherman MB, Kodama T, Gopal P, Pan Z, Kiraly JK, Zhang H, Goff LA, du Lac S, Kolodkin AL. The transcription factor Tbx5 regulates direction-selective retinal ganglion cell development and image stabilization. Curr Biol 2022; 32:4286-4298.e5. [PMID: 35998637 PMCID: PMC9560999 DOI: 10.1016/j.cub.2022.07.064] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/05/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022]
Abstract
The diversity of visual input processed by the mammalian visual system requires the generation of many distinct retinal ganglion cell (RGC) types, each tuned to a particular feature. The molecular code needed to generate this cell-type diversity is poorly understood. Here, we focus on the molecules needed to specify one type of retinal cell: the upward-preferring ON direction-selective ganglion cell (up-oDSGC) of the mouse visual system. Single-cell transcriptomic profiling of up- and down-oDSGCs shows that the transcription factor Tbx5 is selectively expressed in up-oDSGCs. The loss of Tbx5 in up-oDSGCs results in a selective defect in the formation of up-oDSGCs and a corresponding inability to detect vertical motion. A downstream effector of Tbx5, Sfrp1, is also critical for vertical motion detection but not up-oDSGC formation. These results advance our understanding of the molecular mechanisms that specify a rare retinal cell type and show how disrupting this specification leads to a corresponding defect in neural circuitry and behavior.
Collapse
Affiliation(s)
- Timour Al-Khindi
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael B Sherman
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Takashi Kodama
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Otolaryngology & Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Preethi Gopal
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhiwei Pan
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James K Kiraly
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hao Zhang
- Department of Microbiology and Immunology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sascha du Lac
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Otolaryngology & Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alex L Kolodkin
- Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
9
|
Navas-Zuloaga MG, Pavlic TP, Smith BH. Alternative model systems for cognitive variation: eusocial-insect colonies. Trends Cogn Sci 2022; 26:836-848. [PMID: 35864031 DOI: 10.1016/j.tics.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/20/2022]
Abstract
Understanding the origins and maintenance of cognitive variation in animal populations is central to the study of the evolution of cognition. However, the brain is itself a complex, hierarchical network of heterogeneous components, from diverse cell types to diverse neuropils, each of which may be of limited use to study in isolation or prohibitively challenging to manipulate in situ. Consequently, highly tractable alternative model systems may be valuable tools. Eusocial-insect colonies display emergent cognitive-like properties from relatively simple social interactions between diverse subunits that can be observed and manipulated while operating collectively. Here, we review the individual-scale mechanisms that cause group-level variation in how colonies solve problems analogous to cognitive challenges faced by brains, like decision-making, attention, and search.
Collapse
Affiliation(s)
| | - Theodore P Pavlic
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85287, USA; School of Sustainability, Arizona State University, Tempe, AZ 85287, USA; School of Complex Adaptive Systems, Arizona State University, Tempe, AZ 85287, USA
| | - Brian H Smith
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| |
Collapse
|
10
|
Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. mSystems 2022; 7:e0023222. [PMID: 35638725 PMCID: PMC9239088 DOI: 10.1128/msystems.00232-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Secondary metabolite clusters (SMCs) encode the machinery for fungal toxin production. However, understanding their function and analyzing their products requires investigation of the developmental and environmental conditions in which they are expressed. Gene expression is often restricted to specific and unexamined stages of the life cycle. Therefore, we applied comparative genomics analyses to identify SMCs in Neurospora crassa and analyzed extensive transcriptomic data spanning nine independent experiments from diverse developmental and environmental conditions to reveal their life cycle-specific gene expression patterns. We reported 20 SMCs comprising 177 genes-a manageable set for investigation of the roles of SMCs across the life cycle of the fungal model N. crassa-as well as gene sets coordinately expressed in 18 predicted SMCs during asexual and sexual growth under three nutritional and two temperature conditions. Divergent activity of SMCs between asexual and sexual development was reported. Of 126 SMC genes that we examined for knockout phenotypes, al-2 and al-3 exhibited phenotypes in asexual growth and conidiation, whereas os-5, poi-2, and pmd-1 exhibited phenotypes in sexual development. SMCs with annotated function in mating and crossing were actively regulated during the switch between asexual and sexual growth. Our discoveries call for attention to roles that SMCs may play in the regulatory switches controlling mode of development, as well as the ecological associations of those developmental stages that may influence expression of SMCs. IMPORTANCE Secondary metabolites (SMs) are low-molecular-weight compounds that often mediate interactions between fungi and their environments. Fungi enriched with SMs are of significant research interest to agriculture and medicine, especially from the aspects of pathogen ecology and environmental epidemiology. However, SM clusters (SMCs) that have been predicted by comparative genomics alone have typically been poorly defined and insufficiently functionally annotated. Therefore, we have investigated coordinate expression in SMCs in the model system N. crassa, and our results suggest that SMCs respond to environmental signals and to stress that are associated with development. This study examined SMC regulation at the level of RNA to integrate observations and knowledge of these genes in various growth and development conditions, supporting combining comparative genomics and inclusive transcriptomics to improve computational annotation of SMCs. Our findings call for detailed study of the function of SMCs during the asexual-sexual switch, a key, often-overlooked developmental stage.
Collapse
|
11
|
Marin IA, Gutman-Wei AY, Chew KS, Raissi AJ, Djurisic M, Shatz CJ. The nonclassical MHC class I Qa-1 expressed in layer 6 neurons regulates activity-dependent plasticity via microglial CD94/NKG2 in the cortex. Proc Natl Acad Sci U S A 2022; 119:e2203965119. [PMID: 35648829 PMCID: PMC9191652 DOI: 10.1073/pnas.2203965119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
During developmental critical periods, circuits are sculpted by a process of activity-dependent competition. The molecular machinery involved in regulating the complex process of responding to different levels of activity is now beginning to be identified. Here, we show that the nonclassical major histocompatibility class I (MHCI) molecule Qa-1 is expressed in the healthy brain in layer 6 corticothalamic neurons. In the visual cortex, Qa-1 expression begins during the critical period for ocular dominance (OD) plasticity and is regulated by neuronal activity, suggesting a role in regulating activity-dependent competition. Indeed, in mice lacking Qa-1, OD plasticity is perturbed. Moreover, signaling through CD94/NKG2, a known cognate Qa-1 heterodimeric receptor in the immune system, is implicated: selectively targeting this interaction phenocopies the plasticity perturbation observed in Qa-1 knockouts. In the cortex, CD94/NKG2 is expressed by microglial cells, which undergo activity-dependent changes in their morphology in a Qa-1–dependent manner. Our study thus reveals a neuron–microglial interaction dependent upon a nonclassical MHCI molecule expressed in L6 neurons, which regulates plasticity in the visual cortex. These results also point to an unexpected function for the Qa-1/HLA-E (ligand) and CD94/NKG2 (receptor) interaction in the nervous system, in addition to that described in the immune system.
Collapse
Affiliation(s)
- Ioana A. Marin
- Department of Biology, Stanford University, Stanford, CA 94035
- Department of Neurobiology, Stanford University, Stanford, CA 94035
| | - Alan Y. Gutman-Wei
- Department of Biology, Stanford University, Stanford, CA 94035
- Department of Neurobiology, Stanford University, Stanford, CA 94035
| | - Kylie S. Chew
- Department of Biology, Stanford University, Stanford, CA 94035
- Department of Neurobiology, Stanford University, Stanford, CA 94035
| | - Aram J. Raissi
- Department of Biology, Stanford University, Stanford, CA 94035
- Department of Neurobiology, Stanford University, Stanford, CA 94035
| | - Maja Djurisic
- Department of Biology, Stanford University, Stanford, CA 94035
- Department of Neurobiology, Stanford University, Stanford, CA 94035
| | - Carla J. Shatz
- Department of Biology, Stanford University, Stanford, CA 94035
- Department of Neurobiology, Stanford University, Stanford, CA 94035
| |
Collapse
|
12
|
Pumo GM, Kitazawa T, Rijli FM. Epigenetic and Transcriptional Regulation of Spontaneous and Sensory Activity Dependent Programs During Neuronal Circuit Development. Front Neural Circuits 2022; 16:911023. [PMID: 35664458 PMCID: PMC9158562 DOI: 10.3389/fncir.2022.911023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Spontaneous activity generated before the onset of sensory transduction has a key role in wiring developing sensory circuits. From axonal targeting, to synapse formation and elimination, to the balanced integration of neurons into developing circuits, this type of activity is implicated in a variety of cellular processes. However, little is known about its molecular mechanisms of action, especially at the level of genome regulation. Conversely, sensory experience-dependent activity implements well-characterized transcriptional and epigenetic chromatin programs that underlie heterogeneous but specific genomic responses that shape both postnatal circuit development and neuroplasticity in the adult. In this review, we focus on our knowledge of the developmental processes regulated by spontaneous activity and the underlying transcriptional mechanisms. We also review novel findings on how chromatin regulates the specificity and developmental induction of the experience-dependent program, and speculate their relevance for our understanding of how spontaneous activity may act at the genomic level to instruct circuit assembly and prepare developing neurons for sensory-dependent connectivity refinement and processing.
Collapse
Affiliation(s)
- Gabriele M. Pumo
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
| | - Taro Kitazawa
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Filippo M. Rijli
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
| |
Collapse
|
13
|
Breuer TM, Krieger P. Sensory deprivation leads to subpopulation-specific changes in layer 6 corticothalamic cells. Eur J Neurosci 2021; 55:566-588. [PMID: 34927292 DOI: 10.1111/ejn.15572] [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: 04/14/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 12/01/2022]
Abstract
The effect of sensory deprivation on anatomical and physiological properties in two genetically defined types of layer 6 corticothalamic pyramidal cells in mouse somatosensory barrel cortex was investigated using in vitro electrophysiology. The two types analysed were the L6-Ntsr1 subtype, found preferentially in the upper region of layer 6 and projecting to both ventral posterior medial nucleus of the thalamus and posterior medial nucleus of the thalamus, and the L6-Drd1a subtype, located mostly in the lower regions of layer 6 and projecting to posterior medial nucleus. We found that the apical dendrite in L6-Ntsr1 cells is longer and more branched, compared to L6-Drd1a cells, and that the increase in firing frequency with increasing current stimulation is steeper in L6-Drd1a cells. Sensory deprivation was achieved clipping one row of whiskers from birth until the day of experiment (16 ± 2 days). Mice of this age are actively exploring. In L6-Ntsr1, but not in L6-Drd1a cells, sensory deprivation decreased apical and basal dendrite outgrowth, and calcium influx evoked by backpropagating action potentials. These results contribute to the ongoing functional characterisation of corticothalamic layer 6 cells and indicate differences in the postnatal cortical refinement of two distinct corticothalamic circuits.
Collapse
Affiliation(s)
| | - Patrik Krieger
- Department of Systems Neuroscience, Faculty of Medicine; Ruhr University Bochum, Germany
| |
Collapse
|
14
|
Whilden CM, Chevée M, An SY, Brown SP. The synaptic inputs and thalamic projections of two classes of layer 6 corticothalamic neurons in primary somatosensory cortex of the mouse. J Comp Neurol 2021; 529:3751-3771. [PMID: 33908623 PMCID: PMC8551307 DOI: 10.1002/cne.25163] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022]
Abstract
Although corticothalamic neurons (CThNs) represent the largest source of synaptic input to thalamic neurons, their role in regulating thalamocortical interactions remains incompletely understood. CThNs in sensory cortex have historically been divided into two types, those with cell bodies in Layer 6 (L6) that project back to primary sensory thalamic nuclei and those with cell bodies in Layer 5 (L5) that project to higher-order thalamic nuclei and subcortical structures. Recently, diversity among L6 CThNs has increasingly been appreciated. In the rodent somatosensory cortex, two major classes of L6 CThNs have been identified: one projecting to the ventral posterior medial nucleus (VPM-only L6 CThNs) and one projecting to both VPM and the posterior medial nucleus (VPM/POm L6 CThNs). Using rabies-based tracing methods in mice, we asked whether these L6 CThN populations integrate similar synaptic inputs. We found that both types of L6 CThNs received local input from somatosensory cortex and thalamic input from VPM and POm. However, VPM/POm L6 CThNs received significantly more input from a number of additional cortical areas, higher order thalamic nuclei, and subcortical structures. We also found that the two types of L6 CThNs target different functional regions within the thalamic reticular nucleus (TRN). Together, our results indicate that these two types of L6 CThNs represent distinct information streams in the somatosensory cortex and suggest that VPM-only L6 CThNs regulate, via their more restricted circuits, sensory responses related to a cortical column while VPM/POm L6 CThNs, which are integrated into more widespread POm-related circuits, relay contextual information.
Collapse
Affiliation(s)
- Courtney Michelle Whilden
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, USA
| | - Maxime Chevée
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Seong Yeol An
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Solange Pezon Brown
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Vaasjo LO, Han X, Thurmon AN, Tiemroth AS, Berndt H, Korn M, Figueroa A, Reyes R, Feliciano-Ramos PA, Galazo MJ. Characterization and manipulation of Corticothalamic neurons in associative cortices using Syt6-Cre transgenic mice. J Comp Neurol 2021; 530:1020-1048. [PMID: 34617601 DOI: 10.1002/cne.25256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 09/02/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022]
Abstract
Corticothalamic interactions between associative cortices and higher order thalamic nuclei are involved in high-cognitive functions such as decision-making and working memory. Corticothalamic neurons (CTn) in the prefrontal cortex and other associative areas have been much less studied than their counterparts in the primary sensory areas. The availability of characterized transgenic tools to study CTn in associative areas will facilitate their study and contribute to overcome the scarcity of data about their properties, network dynamics, and contribution to cognitive functions. Here, we characterized the Syt6-Cre (KI148Gsat/Mmud) transgenic mouse line, by tracking expression of a Cre-mediated reporter. In this line, Cre-reporter is strongly expressed in the prefrontal, motor, cingulate, and retrosplenial cortices, as well as in other brain areas including the cerebellum and the olfactory tubercle. Cortical expression starts embryonically and reaches the adult expression pattern by postnatal day 15. In the cortex, Cre-reporter is expressed by layer 6-CTn and by layer 5-CTn to a lesser extent. We quantified Syt6-Cre+ CTn axon varicosities to estimate the distribution and density of putative corticothalamic driver and modulator inputs to thalamic nuclei in the medial, midline, intralaminar, anterior, and motor groups. Also, we characterized the effect of optogenetic stimulation of Syt6-Cre+ neurons in the activity of the prefrontal cortex. CTn stimulation in the prefrontal cortex induces an oscillatory activity in the local field potential that resembles the cortical downstates typically observed during slow-wave sleep or quiet wake.
Collapse
Affiliation(s)
- Lee O Vaasjo
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
| | - Xiao Han
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
| | - Abbigail N Thurmon
- Department of Cell and Molecular Biology and Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
| | - Alina S Tiemroth
- Department of Cell and Molecular Biology and Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
| | - Hallie Berndt
- Department of Cell and Molecular Biology and Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
| | - Madelyn Korn
- Department of Cell and Molecular Biology and Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
| | - Alexandra Figueroa
- Department of Cell and Molecular Biology and Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
| | - Rosa Reyes
- Department of Cell and Molecular Biology and Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
| | - Pedro A Feliciano-Ramos
- Department Brain and Cognitive Science, Massachusetts Institute of Technology and Picower Institute for Learning and Memory, Cambridge, Massachusetts, USA
| | - Maria J Galazo
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA.,Department of Cell and Molecular Biology and Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
| |
Collapse
|
17
|
Antunes FM, Malmierca MS. Corticothalamic Pathways in Auditory Processing: Recent Advances and Insights From Other Sensory Systems. Front Neural Circuits 2021; 15:721186. [PMID: 34489648 PMCID: PMC8418311 DOI: 10.3389/fncir.2021.721186] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/28/2021] [Indexed: 11/24/2022] Open
Abstract
The corticothalamic (CT) pathways emanate from either Layer 5 (L5) or 6 (L6) of the neocortex and largely outnumber the ascending, thalamocortical pathways. The CT pathways provide the anatomical foundations for an intricate, bidirectional communication between thalamus and cortex. They act as dynamic circuits of information transfer with the ability to modulate or even drive the response properties of target neurons at each synaptic node of the circuit. L6 CT feedback pathways enable the cortex to shape the nature of its driving inputs, by directly modulating the sensory message arriving at the thalamus. L5 CT pathways can drive the postsynaptic neurons and initiate a transthalamic corticocortical circuit by which cortical areas communicate with each other. For this reason, L5 CT pathways place the thalamus at the heart of information transfer through the cortical hierarchy. Recent evidence goes even further to suggest that the thalamus via CT pathways regulates functional connectivity within and across cortical regions, and might be engaged in cognition, behavior, and perceptual inference. As descending pathways that enable reciprocal and context-dependent communication between thalamus and cortex, we venture that CT projections are particularly interesting in the context of hierarchical perceptual inference formulations such as those contemplated in predictive processing schemes, which so far heavily rely on cortical implementations. We discuss recent proposals suggesting that the thalamus, and particularly higher order thalamus via transthalamic pathways, could coordinate and contextualize hierarchical inference in cortical hierarchies. We will explore these ideas with a focus on the auditory system.
Collapse
Affiliation(s)
- Flora M. Antunes
- Cognitive and Auditory Neuroscience Laboratory (CANELAB), Institute of Neuroscience of Castilla y León (INCYL), University of Salamanca, Salamanca, Spain
- Institute for Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain
| | - Manuel S. Malmierca
- Cognitive and Auditory Neuroscience Laboratory (CANELAB), Institute of Neuroscience of Castilla y León (INCYL), University of Salamanca, Salamanca, Spain
- Institute for Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain
- Department of Cell Biology and Pathology, School of Medicine, University of Salamanca, Salamanca, Spain
| |
Collapse
|
18
|
Differential Expression Levels of Sox9 in Early Neocortical Radial Glial Cells Regulate the Decision between Stem Cell Maintenance and Differentiation. J Neurosci 2021; 41:6969-6986. [PMID: 34266896 PMCID: PMC8372026 DOI: 10.1523/jneurosci.2905-20.2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022] Open
Abstract
Radial glial progenitor cells (RGCs) in the dorsal telencephalon directly or indirectly produce excitatory projection neurons and macroglia of the neocortex. Recent evidence shows that the pool of RGCs is more heterogeneous than originally thought and that progenitor subpopulations can generate particular neuronal cell types. Using single-cell RNA sequencing, we have studied gene expression patterns of RGCs with different neurogenic behavior at early stages of cortical development. At this early age, some RGCs rapidly produce postmitotic neurons, whereas others self-renew and undergo neurogenic divisions at a later age. We have identified candidate genes that are differentially expressed among these early RGC subpopulations, including the transcription factor Sox9. Using in utero electroporation in embryonic mice of either sex, we demonstrate that elevated Sox9 expression in progenitors affects RGC cell cycle duration and leads to the generation of upper layer cortical neurons. Our data thus reveal molecular differences between progenitor cells with different neurogenic behavior at early stages of corticogenesis and indicates that Sox9 is critical for the maintenance of RGCs to regulate the generation of upper layer neurons. SIGNIFICANCE STATEMENT The existence of heterogeneity in the pool of RGCs and its relationship with the generation of cellular diversity in the cerebral cortex has been an interesting topic of debate for many years. Here we describe the existence of RGCs with reduced neurogenic behavior at early embryonic ages presenting a particular molecular signature. This molecular signature consists of differential expression of some genes including the transcription factor Sox9, which has been found to be a specific regulator of this subpopulation of progenitor cells. Functional experiments perturbing expression levels of Sox9 reveal its instructive role in the regulation of the neurogenic behavior of RGCs and its relationship with the generation of upper layer projection neurons at later ages.
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Marcovich I, Moglie MJ, Carpaneto Freixas AE, Trigila AP, Franchini LF, Plazas PV, Lipovsek M, Elgoyhen AB. Distinct Evolutionary Trajectories of Neuronal and Hair Cell Nicotinic Acetylcholine Receptors. Mol Biol Evol 2021; 37:1070-1089. [PMID: 31821508 PMCID: PMC7086180 DOI: 10.1093/molbev/msz290] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The expansion and pruning of ion channel families has played a crucial role in the evolution of nervous systems. Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels with distinct roles in synaptic transmission at the neuromuscular junction, the central and peripheral nervous system, and the inner ear. Remarkably, the complement of nAChR subunits has been highly conserved along vertebrate phylogeny. To ask whether the different subtypes of receptors underwent different evolutionary trajectories, we performed a comprehensive analysis of vertebrate nAChRs coding sequences, mouse single-cell expression patterns, and comparative functional properties of receptors from three representative tetrapod species. We found significant differences between hair cell and neuronal receptors that were most likely shaped by the differences in coexpression patterns and coassembly rules of component subunits. Thus, neuronal nAChRs showed high degree of coding sequence conservation, coupled to greater coexpression variance and conservation of functional properties across tetrapod clades. In contrast, hair cell α9α10 nAChRs exhibited greater sequence divergence, narrow coexpression pattern, and great variability of functional properties across species. These results point to differential substrates for random change within the family of gene paralogs that relate to the segregated roles of nAChRs in synaptic transmission.
Collapse
Affiliation(s)
- Irina Marcovich
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcelo J Moglie
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Agustín E Carpaneto Freixas
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Anabella P Trigila
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lucia F Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Paola V Plazas
- Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marcela Lipovsek
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Centre for Developmental Neurobiology, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Guy's Campus, London, United Kingdom
| | - Ana Belén Elgoyhen
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
21
|
Uncovering Statistical Links Between Gene Expression and Structural Connectivity Patterns in the Mouse Brain. Neuroinformatics 2021; 19:649-667. [PMID: 33704701 PMCID: PMC8566442 DOI: 10.1007/s12021-021-09511-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
Finding links between genes and structural connectivity is of the utmost importance for unravelling the underlying mechanism of the brain connectome. In this study we identify links between the gene expression and the axonal projection density in the mouse brain, by applying a modified version of the Linked ICA method to volumetric data from the Allen Institute for Brain Science for identifying independent sources of information that link both modalities at the voxel level. We performed separate analyses on sets of projections from the visual cortex, the caudoputamen and the midbrain reticular nucleus, and we determined those brain areas, injections and genes that were most involved in independent components that link both gene expression and projection density data, while we validated their biological context through enrichment analysis. We identified representative and literature-validated cortico-midbrain and cortico-striatal projections, whose gene subsets were enriched with annotations for neuronal and synaptic function and related developmental and metabolic processes. The results were highly reproducible when including all available projections, as well as consistent with factorisations obtained using the Dictionary Learning and Sparse Coding technique. Hence, Linked ICA yielded reproducible independent components that were preserved under increasing data variance. Taken together, we have developed and validated a novel paradigm for linking gene expression and structural projection patterns in the mouse mesoconnectome, which can power future studies aiming to relate genes to brain function.
Collapse
|
22
|
Lipovsek M, Bardy C, Cadwell CR, Hadley K, Kobak D, Tripathy SJ. Patch-seq: Past, Present, and Future. J Neurosci 2021; 41:937-946. [PMID: 33431632 PMCID: PMC7880286 DOI: 10.1523/jneurosci.1653-20.2020] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/11/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Single-cell transcriptomic approaches are revolutionizing neuroscience. Integrating this wealth of data with morphology and physiology, for the comprehensive study of neuronal biology, requires multiplexing gene expression data with complementary techniques. To meet this need, multiple groups in parallel have developed "Patch-seq," a modification of whole-cell patch-clamp protocols that enables mRNA sequencing of cell contents after electrophysiological recordings from individual neurons and morphologic reconstruction of the same cells. In this review, we first outline the critical technical developments that enabled robust Patch-seq experimental efforts and analytical solutions to interpret the rich multimodal data generated. We then review recent applications of Patch-seq that address novel and long-standing questions in neuroscience. These include the following: (1) targeted study of specific neuronal populations based on their anatomic location, functional properties, lineage, or a combination of these factors; (2) the compilation and integration of multimodal cell type atlases; and (3) the investigation of the molecular basis of morphologic and functional diversity. Finally, we highlight potential opportunities for further technical development and lines of research that may benefit from implementing the Patch-seq technique. As a multimodal approach at the intersection of molecular neurobiology and physiology, Patch-seq is uniquely positioned to directly link gene expression to brain function.
Collapse
Affiliation(s)
- Marcela Lipovsek
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Cedric Bardy
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI), Adelaide 5000, SA, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park 5042, SA, Australia
| | - Cathryn R Cadwell
- Department of Pathology, University of California San Francisco, San Francisco, California 94143
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, Washington 98109
| | - Dmitry Kobak
- Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Shreejoy J Tripathy
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
23
|
Rockland KS. A Closer Look at Corticothalamic "Loops". Front Neural Circuits 2021; 15:632668. [PMID: 33603649 PMCID: PMC7884447 DOI: 10.3389/fncir.2021.632668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kathleen S Rockland
- Department of Anatomy & Neurobiology, Boston University School of Medicine, Boston, MA, United States
| |
Collapse
|
24
|
Lewis EM, Stein-O'Brien GL, Patino AV, Nardou R, Grossman CD, Brown M, Bangamwabo B, Ndiaye N, Giovinazzo D, Dardani I, Jiang C, Goff LA, Dölen G. Parallel Social Information Processing Circuits Are Differentially Impacted in Autism. Neuron 2020; 108:659-675.e6. [PMID: 33113347 PMCID: PMC8033501 DOI: 10.1016/j.neuron.2020.10.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/21/2020] [Accepted: 10/03/2020] [Indexed: 02/07/2023]
Abstract
Parallel processing circuits are thought to dramatically expand the network capabilities of the nervous system. Magnocellular and parvocellular oxytocin neurons have been proposed to subserve two parallel streams of social information processing, which allow a single molecule to encode a diverse array of ethologically distinct behaviors. Here we provide the first comprehensive characterization of magnocellular and parvocellular oxytocin neurons in male mice, validated across anatomical, projection target, electrophysiological, and transcriptional criteria. We next use novel multiple feature selection tools in Fmr1-KO mice to provide direct evidence that normal functioning of the parvocellular but not magnocellular oxytocin pathway is required for autism-relevant social reward behavior. Finally, we demonstrate that autism risk genes are enriched in parvocellular compared with magnocellular oxytocin neurons. Taken together, these results provide the first evidence that oxytocin-pathway-specific pathogenic mechanisms account for social impairments across a broad range of autism etiologies.
Collapse
Affiliation(s)
- Eastman M Lewis
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Brain Science Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Kavli Neuroscience Discovery Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Wendy Klag Institute for Autism and Developmental Disabilities, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Genevieve L Stein-O'Brien
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Kavli Neuroscience Discovery Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205; McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Alejandra V Patino
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Brain Science Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Kavli Neuroscience Discovery Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Wendy Klag Institute for Autism and Developmental Disabilities, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Romain Nardou
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Brain Science Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Kavli Neuroscience Discovery Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Wendy Klag Institute for Autism and Developmental Disabilities, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Cooper D Grossman
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Brain Science Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Kavli Neuroscience Discovery Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Matthew Brown
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Bidii Bangamwabo
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Ndeye Ndiaye
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Daniel Giovinazzo
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Ian Dardani
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Connie Jiang
- Cell and Molecular Biology Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Loyal A Goff
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Kavli Neuroscience Discovery Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA.
| | - Gül Dölen
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Brain Science Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Kavli Neuroscience Discovery Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; The Wendy Klag Institute for Autism and Developmental Disabilities, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
25
|
Frandolig JE, Matney CJ, Lee K, Kim J, Chevée M, Kim SJ, Bickert AA, Brown SP. The Synaptic Organization of Layer 6 Circuits Reveals Inhibition as a Major Output of a Neocortical Sublamina. Cell Rep 2020; 28:3131-3143.e5. [PMID: 31533036 DOI: 10.1016/j.celrep.2019.08.048] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/24/2019] [Accepted: 08/13/2019] [Indexed: 12/21/2022] Open
Abstract
The canonical cortical microcircuit has principally been defined by interlaminar excitatory connections among the six layers of the neocortex. However, excitatory neurons in layer 6 (L6), a layer whose functional organization is poorly understood, form relatively rare synaptic connections with other cortical excitatory neurons. Here, we show that the vast majority of parvalbumin inhibitory neurons in a sublamina within L6 send axons through the cortical layers toward the pia. These interlaminar inhibitory neurons receive local synaptic inputs from both major types of L6 excitatory neurons and receive stronger input from thalamocortical afferents than do neighboring pyramidal neurons. The distribution of these interlaminar interneurons and their synaptic connectivity further support a functional subdivision within the standard six layers of the cortex. Positioned to integrate local and long-distance inputs in this sublayer, these interneurons generate an inhibitory interlaminar output. These findings call for a revision to the canonical cortical microcircuit.
Collapse
Affiliation(s)
- Jaclyn Ellen Frandolig
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chanel Joylae Matney
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kihwan Lee
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Juhyun Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Maxime Chevée
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Su-Jeong Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aaron Andrew Bickert
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Solange Pezon Brown
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
26
|
Brann DH, Tsukahara T, Weinreb C, Lipovsek M, Van den Berge K, Gong B, Chance R, Macaulay IC, Chou HJ, Fletcher RB, Das D, Street K, de Bezieux HR, Choi YG, Risso D, Dudoit S, Purdom E, Mill J, Hachem RA, Matsunami H, Logan DW, Goldstein BJ, Grubb MS, Ngai J, Datta SR. Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. SCIENCE ADVANCES 2020; 6:eabc5801. [PMID: 32937591 PMCID: PMC10715684 DOI: 10.1126/sciadv.abc5801] [Citation(s) in RCA: 690] [Impact Index Per Article: 172.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly, by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing demonstrated that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing revealed that ACE2 is expressed in support cells, stem cells, and perivascular cells, rather than in neurons. Immunostaining confirmed these results and revealed pervasive expression of ACE2 protein in dorsally-located olfactory epithelial sustentacular cells and olfactory bulb pericytes in the mouse. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.
Collapse
Affiliation(s)
- David H Brann
- Harvard Medical School Department of Neurobiology, Boston MA 02115 USA
| | - Tatsuya Tsukahara
- Harvard Medical School Department of Neurobiology, Boston MA 02115 USA
| | - Caleb Weinreb
- Harvard Medical School Department of Neurobiology, Boston MA 02115 USA
| | - Marcela Lipovsek
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London SE1 1UL, UK
| | - Koen Van den Berge
- Department of Statistics, University of California, Berkeley, CA 94720
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Boying Gong
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720
| | - Rebecca Chance
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Hsin-Jung Chou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Russell B Fletcher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Present address: Surrozen, Inc., South San Francisco, CA 94080
| | - Diya Das
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Berkeley Institute for Data Science, University of California, Berkeley
- Present address: Genentech, Inc., South San Francisco, CA 94080
| | - Kelly Street
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Hector Roux de Bezieux
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720
- Center for Computational Biology, University of California, Berkeley, CA 94720
| | - Yoon-Gi Choi
- QB3 Functional Genomics Laboratory, University of California, Berkeley, CA 94720
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Sandrine Dudoit
- Department of Statistics, University of California, Berkeley, CA 94720
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA 94720
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine & Health, University of Exeter, Exeter EX2 5DW, UK
| | - Ralph Abi Hachem
- Duke University School of Medicine Department of Head and Neck Surgery & Communication Sciences, Durham, NC 27717 USA
| | - Hiroaki Matsunami
- Duke University School of Medicine Department of Molecular Genetics and Microbiology, Department of Neurobiology, Duke Institute for Brain Sciences, Durham, NC 27717 US
| | - Darren W Logan
- Waltham Petcare Science Institute, Leicestershire LE14 4RT, UK
| | - Bradley J Goldstein
- Duke University School of Medicine Department of Head and Neck Surgery & Communication Sciences, Durham, NC 27717 USA
| | - Matthew S Grubb
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London SE1 1UL, UK
| | - John Ngai
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- QB3 Functional Genomics Laboratory, University of California, Berkeley, CA 94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
- Present address: National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | | |
Collapse
|
27
|
Ansorge J, Humanes‐Valera D, Pauzin FP, Schwarz MK, Krieger P. Cortical layer 6 control of sensory responses in higher‐order thalamus. J Physiol 2020; 598:3973-4001. [DOI: 10.1113/jp279915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/22/2020] [Indexed: 12/29/2022] Open
Affiliation(s)
- Josephine Ansorge
- Faculty of Medicine, Department of Systems Neuroscience Ruhr University Bochum Bochum Germany
| | - Desire Humanes‐Valera
- Faculty of Medicine, Department of Systems Neuroscience Ruhr University Bochum Bochum Germany
| | - François P. Pauzin
- Faculty of Medicine, Department of Systems Neuroscience Ruhr University Bochum Bochum Germany
| | - Martin K. Schwarz
- Institute of Experimental Epileptology and Cognition Research University of Bonn Medical School Bonn Germany
| | - Patrik Krieger
- Faculty of Medicine, Department of Systems Neuroscience Ruhr University Bochum Bochum Germany
| |
Collapse
|
28
|
Context-dependent and dynamic functional influence of corticothalamic pathways to first- and higher-order visual thalamus. Proc Natl Acad Sci U S A 2020; 117:13066-13077. [PMID: 32461374 DOI: 10.1073/pnas.2002080117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Layer 6 (L6) is the sole purveyor of corticothalamic (CT) feedback to first-order thalamus and also sends projections to higher-order thalamus, yet how it engages the full corticothalamic circuit to contribute to sensory processing in an awake animal remains unknown. We sought to elucidate the functional impact of L6CT projections from the primary visual cortex to the dorsolateral geniculate nucleus (first-order) and pulvinar (higher-order) using optogenetics and extracellular electrophysiology in awake mice. While sustained L6CT photostimulation suppresses activity in both visual thalamic nuclei in vivo, moderate-frequency (10 Hz) stimulation powerfully facilitates thalamic spiking. We show that each stimulation paradigm differentially influences the balance between monosynaptic excitatory and disynaptic inhibitory corticothalamic pathways to the dorsolateral geniculate nucleus and pulvinar, as well as the prevalence of burst versus tonic firing. Altogether, our results support a model in which L6CTs modulate first- and higher-order thalamus through parallel excitatory and inhibitory pathways that are highly dynamic and context-dependent.
Collapse
|
29
|
Ofer N, Shefi O, Yaari G. Axonal Tree Morphology and Signal Propagation Dynamics Improve Interneuron Classification. Neuroinformatics 2020; 18:581-590. [PMID: 32346847 DOI: 10.1007/s12021-020-09466-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Neurons are diverse and can be differentiated by their morphological, electrophysiological, and molecular properties. Current morphology-based classification approaches largely rely on the dendritic tree structure or on the overall axonal projection layout. Here, we use data from public databases of neuronal reconstructions and membrane properties to study the characteristics of the axonal and dendritic trees for interneuron classification. We show that combining signal propagation patterns observed by biophysical simulations of the activity along ramified axonal trees with morphological parameters of the axonal and dendritic trees, significantly improve classification results compared to previous approaches. The classification schemes introduced here can be utilized for robust neuronal classification. Our work paves the way for understanding and utilizing form-function principles in realistic neuronal reconstructions.
Collapse
Affiliation(s)
- Netanel Ofer
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel.,Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Orit Shefi
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel. .,Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel.
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel.
| |
Collapse
|
30
|
Guo K, Yamawaki N, Barrett JM, Tapies M, Shepherd GMG. Cortico-Thalamo-Cortical Circuits of Mouse Forelimb S1 Are Organized Primarily as Recurrent Loops. J Neurosci 2020; 40:2849-2858. [PMID: 32075900 PMCID: PMC7117898 DOI: 10.1523/jneurosci.2277-19.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/21/2022] Open
Abstract
Cortical projections to the thalamus arise from corticothalamic (CT) neurons in layer 6 and pyramidal tract-type (PT) neurons in layer 5B. We dissected the excitatory synaptic connections in the somatosensory thalamus formed by CT and PT neurons of the primary somatosensory (S1) cortex, focusing on mouse forelimb S1. Mice of both sexes were studied. The CT neurons in S1 synaptically excited S1-projecting thalamocortical (TC) neurons in subregions of both the ventral posterior lateral and posterior (PO) nuclei, forming a pair of recurrent cortico-thalamo-cortical (C-T-C) loops. The PT neurons in S1 also formed a recurrent loop with S1-projecting TC neurons in the same subregion of the PO. The PT neurons in the adjacent primary motor (M1) cortex formed a separate recurrent loop with M1-projecting TC neurons in a nearby subregion of the PO. Collectively, our results reveal that C-T-C circuits of mouse forelimb S1 are primarily organized as multiple cortical cell-type-specific and thalamic subnucleus-specific recurrent loops, with both CT and PT neurons providing the strongest excitatory input to TC neurons that project back to S1. The findings, together with those of related studies of C-T-C circuits, thus suggest that recurrently projecting thalamocortical neurons are the principal targets of cortical excitatory input to the mouse somatosensory and motor thalamus.SIGNIFICANCE STATEMENT Bidirectional cortical communication with the thalamus is considered an important aspect of sensorimotor integration for active touch in the somatosensory system, but the cellular organization of the circuits mediating this process is not well understood. We used an approach combining cell-type-specific anterograde optogenetic excitation with single-cell recordings targeted to retrogradely labeled thalamocortical neurons to dissect these circuits. The findings reveal a consistent pattern: cortical projections to the somatosensory thalamus target thalamocortical neurons that project back to the same cortical area. Commonalities of these findings to previous descriptions of related circuits in other areas suggest that cortico-thalamo-cortical circuits may generally be organized primarily as recurrent loops.
Collapse
Affiliation(s)
- KuangHua Guo
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Naoki Yamawaki
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - John M Barrett
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Martinna Tapies
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Gordon M G Shepherd
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| |
Collapse
|
31
|
Pauzin FP, Schwarz N, Krieger P. Activation of Corticothalamic Layer 6 Cells Decreases Angular Tuning in Mouse Barrel Cortex. Front Neural Circuits 2019; 13:67. [PMID: 31736714 PMCID: PMC6838007 DOI: 10.3389/fncir.2019.00067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/30/2019] [Indexed: 01/21/2023] Open
Abstract
In the mouse whisker system, the contribution of L6 corticothalamic cells (L6 CT) to cortical and thalamic processing of the whisker deflection direction was investigated. A genetically defined population of L6 CT cells project to infragranular GABAergic interneurons that hyperpolarize neurons in somatosensory barrel cortex (BC). Optogenetic activation of these neurons switched BC to an adapted mode in which excitatory cells lost their angular tuning. In contrast, however, this was not the case with a general activation of inhibitory interneurons via optogenetic activation of Gad2-expressing cells. The decrease in angular tuning, when L6 CT cells were activated, was due to changes in cortical inhibition, and not inherited from changes in the thalamic output. Furthermore, L6 CT driven cortical inhibition, but not the general activation of GABAergic interneurons, abolished adaptation to whisker responses. In the present study, evidence is presented that a subpopulation of L6 CT activates a specific circuit of GABAergic interneurons that will predispose neocortex toward processing of tactile information requiring multiple whisker touches, such as in a texture discrimination task.
Collapse
Affiliation(s)
- François Philippe Pauzin
- Department of Systems Neuroscience, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Nadja Schwarz
- Department of Systems Neuroscience, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Patrik Krieger
- Department of Systems Neuroscience, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| |
Collapse
|
32
|
Chen X, Sun YC, Zhan H, Kebschull JM, Fischer S, Matho K, Huang ZJ, Gillis J, Zador AM. High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing. Cell 2019; 179:772-786.e19. [PMID: 31626774 PMCID: PMC7836778 DOI: 10.1016/j.cell.2019.09.023] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 07/30/2019] [Accepted: 09/20/2019] [Indexed: 01/08/2023]
Abstract
Understanding neural circuits requires deciphering interactions among myriad cell types defined by spatial organization, connectivity, gene expression, and other properties. Resolving these cell types requires both single-neuron resolution and high throughput, a challenging combination with conventional methods. Here, we introduce barcoded anatomy resolved by sequencing (BARseq), a multiplexed method based on RNA barcoding for mapping projections of thousands of spatially resolved neurons in a single brain and relating those projections to other properties such as gene or Cre expression. Mapping the projections to 11 areas of 3,579 neurons in mouse auditory cortex using BARseq confirmed the laminar organization of the three top classes (intratelencephalic [IT], pyramidal tract-like [PT-like], and corticothalamic [CT]) of projection neurons. In depth analysis uncovered a projection type restricted almost exclusively to transcriptionally defined subtypes of IT neurons. By bridging anatomical and transcriptomic approaches at cellular resolution with high throughput, BARseq can potentially uncover the organizing principles underlying the structure and formation of neural circuits.
Collapse
Affiliation(s)
- Xiaoyin Chen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yu-Chi Sun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Huiqing Zhan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justus M Kebschull
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Stephan Fischer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Katherine Matho
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Anthony M Zador
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
33
|
Tarashansky AJ, Xue Y, Li P, Quake SR, Wang B. Self-assembling manifolds in single-cell RNA sequencing data. eLife 2019; 8:e48994. [PMID: 31524596 PMCID: PMC6795480 DOI: 10.7554/elife.48994] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/16/2019] [Indexed: 12/14/2022] Open
Abstract
Single-cell RNA sequencing has spurred the development of computational methods that enable researchers to classify cell types, delineate developmental trajectories, and measure molecular responses to external perturbations. Many of these technologies rely on their ability to detect genes whose cell-to-cell variations arise from the biological processes of interest rather than transcriptional or technical noise. However, for datasets in which the biologically relevant differences between cells are subtle, identifying these genes is challenging. We present the self-assembling manifold (SAM) algorithm, an iterative soft feature selection strategy to quantify gene relevance and improve dimensionality reduction. We demonstrate its advantages over other state-of-the-art methods with experimental validation in identifying novel stem cell populations of Schistosoma mansoni, a prevalent parasite that infects hundreds of millions of people. Extending our analysis to a total of 56 datasets, we show that SAM is generalizable and consistently outperforms other methods in a variety of biological and quantitative benchmarks.
Collapse
Affiliation(s)
| | - Yuan Xue
- Department of BioengineeringStanford UniversityStanfordUnited States
| | - Pengyang Li
- Department of BioengineeringStanford UniversityStanfordUnited States
| | - Stephen R Quake
- Department of BioengineeringStanford UniversityStanfordUnited States
- Department of Applied PhysicsStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Bo Wang
- Department of BioengineeringStanford UniversityStanfordUnited States
- Department of Developmental BiologyStanford University School of MedicineStanfordUnited States
| |
Collapse
|
34
|
Distinct Properties of Layer 3 Pyramidal Neurons from Prefrontal and Parietal Areas of the Monkey Neocortex. J Neurosci 2019; 39:7277-7290. [PMID: 31341029 DOI: 10.1523/jneurosci.1210-19.2019] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/25/2019] [Indexed: 12/31/2022] Open
Abstract
In primates, working memory function depends on activity in a distributed network of cortical areas that display different patterns of delay task-related activity. These differences are correlated with, and might depend on, distinctive properties of the neurons located in each area. For example, layer 3 pyramidal neurons (L3PNs) differ significantly between primary visual and dorsolateral prefrontal (DLPFC) cortices. However, to what extent L3PNs differ between DLPFC and other association cortical areas is less clear. Hence, we compared the properties of L3PNs in monkey DLPFC versus posterior parietal cortex (PPC), a key node in the cortical working memory network. Using patch-clamp recordings and biocytin cell filling in acute brain slices, we assessed the physiology and morphology of L3PNs from monkey DLPFC and PPC. The L3PN transcriptome was studied using laser microdissection combined with DNA microarray or quantitative PCR. We found that in both DLPFC and PPC, L3PNs were divided into regular spiking (RS-L3PNs) and bursting (B-L3PNs) physiological subtypes. Whereas regional differences in single-cell excitability were modest, B-L3PNs were rare in PPC (RS-L3PN:B-L3PN, 94:6), but were abundant in DLPFC (50:50), showing greater physiological diversity. Moreover, DLPFC L3PNs display larger and more complex basal dendrites with higher dendritic spine density. Additionally, we found differential expression of hundreds of genes, suggesting a transcriptional basis for the differences in L3PN phenotype between DLPFC and PPC. These data show that the previously observed differences between DLPFC and PPC neuron activity during working memory tasks are associated with diversity in the cellular/molecular properties of L3PNs.SIGNIFICANCE STATEMENT In the human and nonhuman primate neocortex, layer 3 pyramidal neurons (L3PNs) differ significantly between dorsolateral prefrontal (DLPFC) and sensory areas. Hence, L3PN properties reflect, and may contribute to, a greater complexity of computations performed in DLPFC. However, across association cortical areas, L3PN properties are largely unexplored. We studied the physiology, dendrite morphology and transcriptome of L3PNs from macaque monkey DLPFC and posterior parietal cortex (PPC), two key nodes in the cortical working memory network. L3PNs from DLPFC had greater diversity of physiological properties and larger basal dendrites with higher spine density. Moreover, transcriptome analysis suggested a molecular basis for the differences in the physiological and morphological phenotypes of L3PNs from DLPFC and PPC.
Collapse
|
35
|
Clark BS, Stein-O'Brien GL, Shiau F, Cannon GH, Davis-Marcisak E, Sherman T, Santiago CP, Hoang TV, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, Blackshaw S. Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification. Neuron 2019; 102:1111-1126.e5. [PMID: 31128945 PMCID: PMC6768831 DOI: 10.1016/j.neuron.2019.04.010] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/07/2019] [Accepted: 04/03/2019] [Indexed: 12/26/2022]
Abstract
Precise temporal control of gene expression in neuronal progenitors is necessary for correct regulation of neurogenesis and cell fate specification. However, the cellular heterogeneity of the developing CNS has posed a major obstacle to identifying the gene regulatory networks that control these processes. To address this, we used single-cell RNA sequencing to profile ten developmental stages encompassing the full course of retinal neurogenesis. This allowed us to comprehensively characterize changes in gene expression that occur during initiation of neurogenesis, changes in developmental competence, and specification and differentiation of each major retinal cell type. We identify the NFI transcription factors (Nfia, Nfib, and Nfix) as selectively expressed in late retinal progenitor cells and show that they control bipolar interneuron and Müller glia cell fate specification and promote proliferative quiescence.
Collapse
Affiliation(s)
- Brian S Clark
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Genevieve L Stein-O'Brien
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fion Shiau
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gabrielle H Cannon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emily Davis-Marcisak
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas Sherman
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clayton P Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thanh V Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fatemeh Rajaii
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rebecca E James-Esposito
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Elana J Fertig
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Computational Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Mathematical Institute for Data Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
36
|
Crow M, Gillis J. Single cell RNA-sequencing: replicability of cell types. Curr Opin Neurobiol 2019; 56:69-77. [PMID: 30654233 PMCID: PMC6551252 DOI: 10.1016/j.conb.2018.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/03/2018] [Accepted: 12/09/2018] [Indexed: 01/09/2023]
Abstract
Recent technical advances have enabled transcriptomics experiments at an unprecedented scale, and single-cell profiles from neural tissue are accumulating rapidly. There has been considerable effort to use these profiles to understand cell diversity, primarily through unsupervised clustering and differential expression analysis. However, current practices to validate these findings vary. In this review, we describe recent efforts to evaluate clusters from single-cell RNA-sequencing data, and provide a framework for considering current evidence and practices in terms of their capacity to establish principles of cell biology. Single-cell RNA-sequencing has already transformed neuroscience. By facilitating detailed comparative and genetic perturbation analyses, it may provide the tools to uncover fundamental mechanisms of neural diversity throughout the tree of life.
Collapse
Affiliation(s)
- Megan Crow
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
37
|
Tiong SYX, Oka Y, Sasaki T, Taniguchi M, Doi M, Akiyama H, Sato M. Kcnab1 Is Expressed in Subplate Neurons With Unilateral Long-Range Inter-Areal Projections. Front Neuroanat 2019; 13:39. [PMID: 31130851 PMCID: PMC6509479 DOI: 10.3389/fnana.2019.00039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/20/2019] [Indexed: 12/20/2022] Open
Abstract
Subplate (SP) neurons are among the earliest-born neurons in the cerebral cortex and heterogeneous in terms of gene expression. SP neurons consist mainly of projection neurons, which begin to extend their axons to specific target areas very early during development. However, the relationships between axon projection and gene expression patterns of the SP neurons, and their remnant layer 6b (L6b) neurons, are largely unknown. In this study, we analyzed the corticocortical projections of L6b/SP neurons in the mouse cortex and searched for a marker gene expressed in L6b/SP neurons that have ipsilateral inter-areal projections. Retrograde tracing experiments demonstrated that L6b/SP neurons in the primary somatosensory cortex (S1) projected to the primary motor cortex (M1) within the same cortical hemisphere at postnatal day (PD) 2 but did not show any callosal projection. This unilateral projection pattern persisted into adulthood. Our microarray analysis identified the gene encoding a β subunit of voltage-gated potassium channel (Kcnab1) as being expressed in L6b/SP. Double labeling with retrograde tracing and in situ hybridization demonstrated that Kcnab1 was expressed in the unilaterally-projecting neurons in L6b/SP. Embryonic expression was specifically detected in the SP as early as embryonic day (E) 14.5, shortly after the emergence of SP. Double immunostaining experiments revealed different degrees of co-expression of the protein product Kvβ1 with L6b/SP markers Ctgf (88%), Cplx3 (79%), and Nurr1 (58%), suggesting molecular subdivision of unilaterally-projecting L6b/SP neurons. In addition to expression in L6b/SP, scattered expression of Kcnab1 was observed during postnatal stages without layer specificity. Among splicing variants with three alternative first exons, the variant 1.1 explained all the cortical expression mentioned in this study. Together, our data suggest that L6b/SP neurons have corticocortical projections and Kcnab1 expression defines a subpopulation of L6b/SP neurons with a unilateral inter-areal projection.
Collapse
Affiliation(s)
- Sheena Yin Xin Tiong
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan.,Division of Developmental Neuroscience, Department of Child Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan.,Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yuichiro Oka
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan.,Division of Developmental Neuroscience, Department of Child Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan.,Division of Cell Biology and Neuroscience, Department of Morphological and Physiological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui, Japan.,Research Center for Child Mental Development, University of Fukui, Fukui, Japan
| | - Tatsuya Sasaki
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Manabu Taniguchi
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Miyuki Doi
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hisanori Akiyama
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Makoto Sato
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan.,Division of Developmental Neuroscience, Department of Child Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan.,Division of Cell Biology and Neuroscience, Department of Morphological and Physiological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui, Japan.,Research Center for Child Mental Development, University of Fukui, Fukui, Japan
| |
Collapse
|
38
|
Kast RJ, Levitt P. Precision in the development of neocortical architecture: From progenitors to cortical networks. Prog Neurobiol 2019; 175:77-95. [PMID: 30677429 PMCID: PMC6402587 DOI: 10.1016/j.pneurobio.2019.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/02/2019] [Accepted: 01/21/2019] [Indexed: 02/07/2023]
Abstract
Of all brain regions, the 6-layered neocortex has undergone the most dramatic changes in size and complexity during mammalian brain evolution. These changes, occurring in the context of a conserved set of organizational features that emerge through stereotypical developmental processes, are considered responsible for the cognitive capacities and sensory specializations represented within the mammalian clade. The modern experimental era of developmental neurobiology, spanning 6 decades, has deciphered a number of mechanisms responsible for producing the diversity of cortical neuron types, their precise connectivity and the role of gene by environment interactions. Here, experiments providing insight into the development of cortical projection neuron differentiation and connectivity are reviewed. This current perspective integrates discussion of classic studies and new findings, based on recent technical advances, to highlight an improved understanding of the neuronal complexity and precise connectivity of cortical circuitry. These descriptive advances bring new opportunities for studies related to the developmental origins of cortical circuits that will, in turn, improve the prospects of identifying pathogenic targets of neurodevelopmental disorders.
Collapse
Affiliation(s)
- Ryan J Kast
- Department of Pediatrics and Program in Developmental Neuroscience and Developmental Neurogenetics, The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90027, USA
| | - Pat Levitt
- Department of Pediatrics and Program in Developmental Neuroscience and Developmental Neurogenetics, The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90027, USA.
| |
Collapse
|
39
|
Williamson RS, Polley DB. Parallel pathways for sound processing and functional connectivity among layer 5 and 6 auditory corticofugal neurons. eLife 2019; 8:e42974. [PMID: 30735128 PMCID: PMC6384027 DOI: 10.7554/elife.42974] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/06/2019] [Indexed: 11/27/2022] Open
Abstract
Cortical layers (L) 5 and 6 are populated by intermingled cell-types with distinct inputs and downstream targets. Here, we made optogenetically guided recordings from L5 corticofugal (CF) and L6 corticothalamic (CT) neurons in the auditory cortex of awake mice to discern differences in sensory processing and underlying patterns of functional connectivity. Whereas L5 CF neurons showed broad stimulus selectivity with sluggish response latencies and extended temporal non-linearities, L6 CTs exhibited sparse selectivity and rapid temporal processing. L5 CF spikes lagged behind neighboring units and imposed weak feedforward excitation within the local column. By contrast, L6 CT spikes drove robust and sustained activity, particularly in local fast-spiking interneurons. Our findings underscore a duality among sub-cortical projection neurons, where L5 CF units are canonical broadcast neurons that integrate sensory inputs for transmission to distributed downstream targets, while L6 CT neurons are positioned to regulate thalamocortical response gain and selectivity.
Collapse
Affiliation(s)
- Ross S Williamson
- Eaton-Peabody LaboratoriesMassachusetts Eye and Ear InfirmaryBostonUnited States
- Department of OtolaryngologyHarvard Medical SchoolBostonUnited States
| | - Daniel B Polley
- Eaton-Peabody LaboratoriesMassachusetts Eye and Ear InfirmaryBostonUnited States
- Department of OtolaryngologyHarvard Medical SchoolBostonUnited States
| |
Collapse
|
40
|
Klingler E, De la Rossa A, Fièvre S, Devaraju K, Abe P, Jabaudon D. A Translaminar Genetic Logic for the Circuit Identity of Intracortically Projecting Neurons. Curr Biol 2019; 29:332-339.e5. [DOI: 10.1016/j.cub.2018.11.071] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/11/2018] [Accepted: 11/29/2018] [Indexed: 11/26/2022]
|
41
|
Soiza-Reilly M, Meye FJ, Olusakin J, Telley L, Petit E, Chen X, Mameli M, Jabaudon D, Sze JY, Gaspar P. SSRIs target prefrontal to raphe circuits during development modulating synaptic connectivity and emotional behavior. Mol Psychiatry 2019; 24:726-745. [PMID: 30279456 PMCID: PMC6445781 DOI: 10.1038/s41380-018-0260-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/08/2018] [Accepted: 09/06/2018] [Indexed: 12/24/2022]
Abstract
Antidepressants that block the serotonin transporter, (Slc6a4/SERT), selective serotonin reuptake inhibitors (SSRIs) improve mood in adults but have paradoxical long-term effects when administered during perinatal periods, increasing the risk to develop anxiety and depression. The basis for this developmental effect is not known. Here, we show that during an early postnatal period in mice (P0-P10), Slc6a4/SERT is transiently expressed in a subset of layer 5-6 pyramidal neurons of the prefrontal cortex (PFC). PFC-SERT+ neurons establish glutamatergic synapses with subcortical targets, including the serotonin (5-HT) and GABA neurons of the dorsal raphe nucleus (DRN). PFC-to-DRN circuits develop postnatally, coinciding with the period of PFC Slc6a4/SERT expression. Complete or cortex-specific ablation of SERT increases the number of functional PFC glutamate synapses on both 5-HT and GABA neurons in the DRN. This PFC-to-DRN hyperinnervation is replicated by early-life exposure to the SSRI, fluoxetine (from P2 to P14), that also causes anxiety/depressive-like symptoms. We show that pharmacogenetic manipulation of PFC-SERT+ neuron activity bidirectionally modulates these symptoms, suggesting that PFC hypofunctionality has a causal role in these altered responses to stress. Overall, our data identify specific PFC descending circuits that are targets of antidepressant drugs during development. We demonstrate that developmental expression of SERT in this subset of PFC neurons controls synaptic maturation of PFC-to-DRN circuits, and that remodeling of these circuits in early life modulates behavioral responses to stress in adulthood.
Collapse
Affiliation(s)
- M. Soiza-Reilly
- 0000 0004 0520 8345grid.462192.aInstitut du Fer à Moulin, Paris, France ,0000000121866389grid.7429.8Inserm, UMR-S 839, Paris, France ,0000 0001 2308 1657grid.462844.8Sorbonne Universités, Paris, France
| | - F. J. Meye
- 0000 0004 0520 8345grid.462192.aInstitut du Fer à Moulin, Paris, France ,0000000121866389grid.7429.8Inserm, UMR-S 839, Paris, France ,0000 0001 2308 1657grid.462844.8Sorbonne Universités, Paris, France
| | - J. Olusakin
- 0000 0004 0520 8345grid.462192.aInstitut du Fer à Moulin, Paris, France ,0000000121866389grid.7429.8Inserm, UMR-S 839, Paris, France ,0000 0001 2308 1657grid.462844.8Sorbonne Universités, Paris, France
| | - L. Telley
- 0000 0001 2322 4988grid.8591.5Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - E. Petit
- 0000000121791997grid.251993.5Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York USA
| | - X. Chen
- 0000000121791997grid.251993.5Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York USA
| | - M. Mameli
- 0000 0004 0520 8345grid.462192.aInstitut du Fer à Moulin, Paris, France ,0000000121866389grid.7429.8Inserm, UMR-S 839, Paris, France ,0000 0001 2308 1657grid.462844.8Sorbonne Universités, Paris, France
| | - D. Jabaudon
- 0000 0001 2322 4988grid.8591.5Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - J.-Y. Sze
- 0000000121791997grid.251993.5Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York USA
| | - P. Gaspar
- 0000 0004 0520 8345grid.462192.aInstitut du Fer à Moulin, Paris, France ,0000000121866389grid.7429.8Inserm, UMR-S 839, Paris, France ,0000 0001 2308 1657grid.462844.8Sorbonne Universités, Paris, France
| |
Collapse
|
42
|
Mancinelli S, Lodato S. Decoding neuronal diversity in the developing cerebral cortex: from single cells to functional networks. Curr Opin Neurobiol 2018; 53:146-155. [DOI: 10.1016/j.conb.2018.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/13/2018] [Accepted: 08/03/2018] [Indexed: 12/14/2022]
|
43
|
Simi A, Studer M. Developmental genetic programs and activity-dependent mechanisms instruct neocortical area mapping. Curr Opin Neurobiol 2018; 53:96-102. [DOI: 10.1016/j.conb.2018.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/07/2018] [Accepted: 06/14/2018] [Indexed: 12/18/2022]
|
44
|
Fazel Darbandi S, Robinson Schwartz SE, Qi Q, Catta-Preta R, Pai ELL, Mandell JD, Everitt A, Rubin A, Krasnoff RA, Katzman S, Tastad D, Nord AS, Willsey AJ, Chen B, State MW, Sohal VS, Rubenstein JLR. Neonatal Tbr1 Dosage Controls Cortical Layer 6 Connectivity. Neuron 2018; 100:831-845.e7. [PMID: 30318412 PMCID: PMC6250594 DOI: 10.1016/j.neuron.2018.09.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 12/27/2022]
Abstract
An understanding of how heterozygous loss-of-function mutations in autism spectrum disorder (ASD) risk genes, such as TBR1, contribute to ASD remains elusive. Conditional Tbr1 deletion during late mouse gestation in cortical layer 6 neurons (Tbr1layer6 mutants) provides novel insights into its function, including dendritic patterning, synaptogenesis, and cell-intrinsic physiology. These phenotypes occur in heterozygotes, providing insights into mechanisms that may underlie ASD pathophysiology. Restoring expression of Wnt7b largely rescues the synaptic deficit in Tbr1layer6 mutant neurons. Furthermore, Tbr1layer6 heterozygotes have increased anxiety-like behavior, a phenotype seen ASD. Integrating TBR1 chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) data from layer 6 neurons and activity of TBR1-bound candidate enhancers provides evidence for how TBR1 regulates layer 6 properties. Moreover, several putative TBR1 targets are ASD risk genes, placing TBR1 in a central position both for ASD risk and for regulating transcriptional circuits that control multiple steps in layer 6 development essential for the assembly of neural circuits.
Collapse
Affiliation(s)
- Siavash Fazel Darbandi
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sarah E Robinson Schwartz
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Qihao Qi
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rinaldo Catta-Preta
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - Emily Ling-Lin Pai
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey D Mandell
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amanda Everitt
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anna Rubin
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rebecca A Krasnoff
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sol Katzman
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Tastad
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew W State
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Vikaas S Sohal
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience and Sloan-Swartz Center for Theoretical Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
45
|
Hackett TA. Adenosine A 1 Receptor mRNA Expression by Neurons and Glia in the Auditory Forebrain. Anat Rec (Hoboken) 2018; 301:1882-1905. [PMID: 30315630 PMCID: PMC6282551 DOI: 10.1002/ar.23907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/05/2017] [Accepted: 01/10/2018] [Indexed: 12/30/2022]
Abstract
In the brain, purines such as ATP and adenosine can function as neurotransmitters and co‐transmitters, or serve as signals in neuron–glial interactions. In thalamocortical (TC) projections to sensory cortex, adenosine functions as a negative regulator of glutamate release via activation of the presynaptic adenosine A1 receptor (A1R). In the auditory forebrain, restriction of A1R‐adenosine signaling in medial geniculate (MG) neurons is sufficient to extend LTP, LTD, and tonotopic map plasticity in adult mice for months beyond the critical period. Interfering with adenosine signaling in primary auditory cortex (A1) does not contribute to these forms of plasticity, suggesting regional differences in the roles of A1R‐mediated adenosine signaling in the forebrain. To advance understanding of the circuitry, in situ hybridization was used to localize neuronal and glial cell types in the auditory forebrain that express A1R transcripts (Adora1), based on co‐expression with cell‐specific markers for neuronal and glial subtypes. In A1, Adora1 transcripts were concentrated in L3/4 and L6 of glutamatergic neurons. Subpopulations of GABAergic neurons, astrocytes, oligodendrocytes, and microglia expressed lower levels of Adora1. In MG, Adora1 was expressed by glutamatergic neurons in all divisions, and subpopulations of all glial classes. The collective findings imply that A1R‐mediated signaling broadly extends to all subdivisions of auditory cortex and MG. Selective expression by neuronal and glial subpopulations suggests that experimental manipulations of A1R‐adenosine signaling could impact several cell types, depending on their location. Strategies to target Adora1 in specific cell types can be developed from the data generated here. Anat Rec, 301:1882–1905, 2018. © 2018 The Authors. The Anatomical Record published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.
Collapse
Affiliation(s)
- Troy A Hackett
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Psychology, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee, USA
| |
Collapse
|
46
|
Xu SJ, Heller EA. Single sample sequencing (S3EQ) of epigenome and transcriptome in nucleus accumbens. J Neurosci Methods 2018; 308:62-73. [PMID: 30031009 PMCID: PMC6296235 DOI: 10.1016/j.jneumeth.2018.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/19/2018] [Accepted: 07/06/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND High-throughput sequencing has been widely applied to uncover the molecular mechanisms underlying neurological and psychiatric disorders. The large body of data support the role of epigenetic mechanisms in neurological function of both human and animals. Yet, the existing data is limited by the fact that epigenetic and transcriptomic changes have only been measured in separate cohorts. This has limited precise correlation of epigenetic changes in gene expression. NEW METHOD Single Sample Sequencing (S3EQ) is an innovative approach to analyze both epigenetic and transcriptomic regulation within a single neuronal sample. Using this method, we analyzed chromatin immunoprecipitation (ChIP)- and RNA-sequencing data from the nucleus accumbens (NAc) of the same animal. RESULTS ChIP-S3EQ of neuronal nuclei reliably identified hPTM enrichment in the adult mouse NAc with high precision. Comparing cellular compartments, we found that the spliceosome of whole cell RNA-seq was more closely recapitulated by cytosolic RNA-S3EQ than nuclear RNA-seq. Finally, S3EQ showed increased sensitivity for correlating chromatin modifications with gene expression, especially for lowly expressed transcripts. COMPARISON WITH EXISTING METHODS S3EQ accurately generates both RNA- and ChIP-seq from a single sample, providing a clear advantage over existing methods which require two samples. ChIP-S3EQ performance was comparable to ChIP-seq, while RNA-S3EQ generated an almost identical expression profile to nuclear-enriched and whole cell RNA-seq. Finally, we directly compared RNA-seq by cellular compartments, addressing a limitation of RNA-seq studies limited to neuronal nuclei. CONCLUSION The S3EQ method can be applied to improve the correlative power of transcriptomic and epigenomic studies in neuronal tissue.
Collapse
Affiliation(s)
- S J Xu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - E A Heller
- Department of Systems Pharmacology and Translational Therapeutics and Penn Epigenetics Institute, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
47
|
Seeman SC, Campagnola L, Davoudian PA, Hoggarth A, Hage TA, Bosma-Moody A, Baker CA, Lee JH, Mihalas S, Teeter C, Ko AL, Ojemann JG, Gwinn RP, Silbergeld DL, Cobbs C, Phillips J, Lein E, Murphy G, Koch C, Zeng H, Jarsky T. Sparse recurrent excitatory connectivity in the microcircuit of the adult mouse and human cortex. eLife 2018; 7:e37349. [PMID: 30256194 PMCID: PMC6158007 DOI: 10.7554/elife.37349] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 08/21/2018] [Indexed: 01/09/2023] Open
Abstract
Generating a comprehensive description of cortical networks requires a large-scale, systematic approach. To that end, we have begun a pipeline project using multipatch electrophysiology, supplemented with two-photon optogenetics, to characterize connectivity and synaptic signaling between classes of neurons in adult mouse primary visual cortex (V1) and human cortex. We focus on producing results detailed enough for the generation of computational models and enabling comparison with future studies. Here, we report our examination of intralaminar connectivity within each of several classes of excitatory neurons. We find that connections are sparse but present among all excitatory cell classes and layers we sampled, and that most mouse synapses exhibited short-term depression with similar dynamics. Synaptic signaling between a subset of layer 2/3 neurons, however, exhibited facilitation. These results contribute to a body of evidence describing recurrent excitatory connectivity as a conserved feature of cortical microcircuits.
Collapse
Affiliation(s)
| | | | | | - Alex Hoggarth
- Allen Institute for Brain ScienceSeattleUnited States
| | - Travis A Hage
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Jung Hoon Lee
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Andrew L Ko
- Regional Epilepsy Center at Harborview Medical CenterSeattleUnited States
- Department of Neurological SurgeryUniversity of Washington School of MedicineSeattleUnited States
| | - Jeffrey G Ojemann
- Regional Epilepsy Center at Harborview Medical CenterSeattleUnited States
- Department of Neurological SurgeryUniversity of Washington School of MedicineSeattleUnited States
| | - Ryder P Gwinn
- Epilepsy Surgery and Functional NeurosurgerySwedish Neuroscience InstituteSeattleUnited States
| | - Daniel L Silbergeld
- Department of Neurological SurgeryUniversity of Washington School of MedicineSeattleUnited States
| | - Charles Cobbs
- The Ben and Catherine Ivy Center for Advanced Brain Tumor TreatmentSwedish Neuroscience InstituteSeattleUnited States
| | - John Phillips
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Gabe Murphy
- Allen Institute for Brain ScienceSeattleUnited States
| | - Christof Koch
- Allen Institute for Brain ScienceSeattleUnited States
| | - Hongkui Zeng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Tim Jarsky
- Allen Institute for Brain ScienceSeattleUnited States
| |
Collapse
|
48
|
Chang M, Kawai HD. A characterization of laminar architecture in mouse primary auditory cortex. Brain Struct Funct 2018; 223:4187-4209. [PMID: 30187193 DOI: 10.1007/s00429-018-1744-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/29/2018] [Indexed: 12/19/2022]
Abstract
Laminar architecture of primary auditory cortex (A1) has long been investigated by traditional histochemical techniques such as Nissl staining, retrograde and anterograde tracings. Uncertainty still remains, however, about laminar boundaries in mice. Here we investigated the cortical lamina structure by combining neuronal tracing and immunofluorochemistry for laminar specific markers. Most retrogradely labeled corticothalamic neurons expressed Forkhead box protein P2 (Foxp2) and distributed within the laminar band of Foxp2-expressing cells, identifying layer 6. Cut-like homeobox 1 (Cux1) expression in layer 2-4 neurons divided the upper layers into low expression layers 2/3 and high expression layers 3/4, which overlapped with the dense terminals of vesicular glutamate transporter 2 (vGluT2) and anterogradely labeled lemniscal thalamocortical axons. In layer 5, between Cux1-expressing layers 2-4 and Foxp2-defined layer 6, retrogradely labeled corticocollicular projection neurons mostly expressed COUP-TF interacting protein 2 (Ctip2). Ctip2-expressing neurons formed a laminar band in the middle of layer 5 distant from layer 6, creating a laminar gap between the two laminas. This gap contained a high population of commissural neurons projecting to contralateral A1 compared to other layers and received vGluT2-immunopositive, presumptive thalamocortical axon collateral inputs. Our study shows that layer 5 is much wider than layer 6, and layer 5 can be divided into at least three sublayers. The thalamorecipient layers 3/4 may be separated from layers 2/3 using Cux1 and can be also divided into layer 4 and layer 3 based on the neuronal soma size. These data provide a new insight for the laminar structure of mouse A1.
Collapse
Affiliation(s)
- Minzi Chang
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo, 192-8577, Japan
| | - Hideki Derek Kawai
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo, 192-8577, Japan. .,Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, Hachioji, Tokyo, 192-8577, Japan.
| |
Collapse
|
49
|
Harris KD, Hochgerner H, Skene NG, Magno L, Katona L, Bengtsson Gonzales C, Somogyi P, Kessaris N, Linnarsson S, Hjerling-Leffler J. Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics. PLoS Biol 2018; 16:e2006387. [PMID: 29912866 PMCID: PMC6029811 DOI: 10.1371/journal.pbio.2006387] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/03/2018] [Accepted: 05/22/2018] [Indexed: 01/19/2023] Open
Abstract
Understanding any brain circuit will require a categorization of its constituent neurons. In hippocampal area CA1, at least 23 classes of GABAergic neuron have been proposed to date. However, this list may be incomplete; additionally, it is unclear whether discrete classes are sufficient to describe the diversity of cortical inhibitory neurons or whether continuous modes of variability are also required. We studied the transcriptomes of 3,663 CA1 inhibitory cells, revealing 10 major GABAergic groups that divided into 49 fine-scale clusters. All previously described and several novel cell classes were identified, with three previously described classes unexpectedly found to be identical. A division into discrete classes, however, was not sufficient to describe the diversity of these cells, as continuous variation also occurred between and within classes. Latent factor analysis revealed that a single continuous variable could predict the expression levels of several genes, which correlated similarly with it across multiple cell types. Analysis of the genes correlating with this variable suggested it reflects a range from metabolically highly active faster-spiking cells that proximally target pyramidal cells to slower-spiking cells targeting distal dendrites or interneurons. These results elucidate the complexity of inhibitory neurons in one of the simplest cortical structures and show that characterizing these cells requires continuous modes of variation as well as discrete cell classes.
Collapse
Affiliation(s)
- Kenneth D. Harris
- University College London Institute of Neurology, London, United Kingdom
- University College London Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Hannah Hochgerner
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nathan G. Skene
- University College London Institute of Neurology, London, United Kingdom
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Lorenza Magno
- University College London Wolfson Institute for Biomedical Research, London, United Kingdom
| | - Linda Katona
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Carolina Bengtsson Gonzales
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Somogyi
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Nicoletta Kessaris
- University College London Wolfson Institute for Biomedical Research, London, United Kingdom
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jens Hjerling-Leffler
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
50
|
Tasic B. Single cell transcriptomics in neuroscience: cell classification and beyond. Curr Opin Neurobiol 2018; 50:242-249. [DOI: 10.1016/j.conb.2018.04.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 12/15/2022]
|