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Puelles L, Stühmer T, Rubenstein JLR, Diaz C. Critical test of the assumption that the hypothalamic entopeduncular nucleus of rodents is homologous with the primate internal pallidum. J Comp Neurol 2023; 531:1715-1750. [PMID: 37695031 PMCID: PMC11418882 DOI: 10.1002/cne.25536] [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: 05/18/2023] [Revised: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 09/12/2023]
Abstract
The globus pallidus (GP) of primates is divided conventionally into distinct internal and external parts. The literature repeats since 1930 the opinion that the homolog of the primate internal pallidum in rodents is the hypothalamic entopeduncular nucleus (embedded within fiber tracts of the cerebral peduncle). To test this idea, we explored its historic fundaments, checked the development and genoarchitecture of mouse entopeduncular and pallidal neurons, and examined relevant comparative connectivity data. We found that the extratelencephalic mouse entopeduncular structure consists of four different components arrayed along a dorsoventral sequence in the alar hypothalamus. The ventral entopeduncular nucleus (EPV), with GABAergic neurons expressing Dlx5&6 and Nkx2-1, lies within the hypothalamic peduncular subparaventricular area. Three other formations-the dorsal entopeduncular nucleus (EPD), the prereticular entopeduncular nucleus (EPPRt ), and the preeminential entopeduncular nucleus (EPPEm )-lie within the overlying paraventricular area, under the subpallium. EPD contains glutamatergic neurons expressing Tbr1, Otp, and Pax6. The EPPRt has GABAergic cells expressing Isl1 and Meis2, whereas the EPPEm population expresses Foxg1 and may be glutamatergic. Genoarchitectonic observations on relevant areas of the mouse pallidal/diagonal subpallium suggest that the GP of rodents is constituted as in primates by two adjacent but molecularly and hodologically differentiable telencephalic portions (both expressing Foxg1). These and other reported data oppose the notion that the rodent extratelencephalic entopeduncular nucleus is homologous to the primate internal pallidum. We suggest instead that all mammals, including rodents, have dual subpallial GP components, whereas primates probably also have a comparable set of hypothalamic entopeduncular nuclei. Remarkably, there is close similarity in some gene expression properties of the telencephalic internal GP and the hypothalamic EPV. This apparently underlies their notable functional analogy, sharing GABAergic neurons and thalamopetal connectivity.
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Affiliation(s)
- Luis Puelles
- Department of Human Anatomy and Psychobiology and IMIB-Arrixaca Institute, University of Murcia, El Palmar (Murcia), 30120, Spain
| | - Thorsten Stühmer
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Medical School, San Francisco, California
| | - John L. R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Medical School, San Francisco, California
| | - Carmen Diaz
- School of Medicine and Institute for Research in Neurological Disabilities, University of Castilla-La Mancha, Albacete, 02006, Spain
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2
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Biswas S, Chan CS, Rubenstein JLR, Gan L. The transcription regulator Lmo3 is required for the development of medial ganglionic eminence derived neurons in the external globus pallidus. Dev Biol 2023; 503:10-24. [PMID: 37532091 PMCID: PMC10658356 DOI: 10.1016/j.ydbio.2023.07.007] [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: 02/13/2023] [Revised: 07/15/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
The external globus pallidus (GPe) is an essential component of the basal ganglia, a group of subcortical nuclei that are involved in control of action. Changes in the firing of GPe neurons are associated with both passive and active body movements. Aberrant activity of GPe neurons has been linked to motor symptoms of a variety of movement disorders, such as Parkinson's Disease, Huntington's disease and dystonia. Recent studies have helped delineate functionally distinct subtypes of GABAergic GPe projection neurons. However, not much is known about specific molecular mechanisms underlying the development of GPe neuronal subtypes. We show that the transcriptional regulator Lmo3 is required for the development of medial ganglionic eminence derived Nkx2.1+ and PV+ GPe neurons, but not lateral ganglionic eminence derived FoxP2+ neurons. As a consequence of the reduction in PV+ neurons, Lmo3-null mice have a reduced GPe input to the subthalamic nucleus.
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Affiliation(s)
- Shiona Biswas
- The Neuroscience Graduate Program, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14627, USA; Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14627, USA.
| | - C Savio Chan
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - John L R Rubenstein
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California at San Francisco, CA, 94143, USA
| | - Lin Gan
- Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14627, USA; Department of Ophthalmology and the Flaum Eye Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14627, USA
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3
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Ananth MR, Rajebhosale P, Kim R, Talmage DA, Role LW. Basal forebrain cholinergic signalling: development, connectivity and roles in cognition. Nat Rev Neurosci 2023; 24:233-251. [PMID: 36823458 PMCID: PMC10439770 DOI: 10.1038/s41583-023-00677-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 01/18/2023] [Indexed: 02/25/2023]
Abstract
Acetylcholine plays an essential role in fundamental aspects of cognition. Studies that have mapped the activity and functional connectivity of cholinergic neurons have shown that the axons of basal forebrain cholinergic neurons innervate the pallium with far more topographical and functional organization than was historically appreciated. Together with the results of studies using new probes that allow release of acetylcholine to be detected with high spatial and temporal resolution, these findings have implicated cholinergic networks in 'binding' diverse behaviours that contribute to cognition. Here, we review recent findings on the developmental origins, connectivity and function of cholinergic neurons, and explore the participation of cholinergic signalling in the encoding of cognition-related behaviours.
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Affiliation(s)
- Mala R Ananth
- Section on Circuits, Synapses, and Molecular Signalling, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Prithviraj Rajebhosale
- Section on Genetics of Neuronal Signalling, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ronald Kim
- Section on Genetics of Neuronal Signalling, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - David A Talmage
- Section on Genetics of Neuronal Signalling, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Lorna W Role
- Section on Circuits, Synapses, and Molecular Signalling, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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4
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Mispatterning and interneuron deficit in Tourette Syndrome basal ganglia organoids. Mol Psychiatry 2022; 27:5007-5019. [PMID: 36447010 PMCID: PMC9949887 DOI: 10.1038/s41380-022-01880-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022]
Abstract
Tourette Syndrome (TS) is a neuropsychiatric disorder thought to involve a reduction of basal ganglia (BG) interneurons and malfunctioning of the BG circuitry. However, whether interneurons fail to develop or are lost postnatally remains unknown. To investigate the pathophysiology of early development in TS, induced pluripotent stem cell (iPSC)-derived BG organoids from TS patients and healthy controls were compared on multiple levels of measurement and analysis. BG organoids from TS individuals manifested an impaired medial ganglionic eminence fate and a decreased differentiation of cholinergic and GABAergic interneurons. Transcriptome analyses revealed organoid mispatterning in TS, with a preference for dorsolateral at the expense of ventromedial fates. Our results point to altered expression of GLI transcription factors downstream of the Sonic Hedgehog signaling pathway with cilia disruption at the earliest stages of BG organoid differentiation as a potential mechanism for the BG mispatterning in TS. This study uncovers early neurodevelopmental underpinnings of TS neuropathological deficits using organoids as a model system.
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5
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Lu T, Ang CE, Zhuang X. Spatially resolved epigenomic profiling of single cells in complex tissues. Cell 2022; 185:4448-4464.e17. [PMID: 36272405 PMCID: PMC9691621 DOI: 10.1016/j.cell.2022.09.035] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 08/22/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
The recent development of spatial omics methods has enabled single-cell profiling of the transcriptome and 3D genome organization with high spatial resolution. Expanding the repertoire of spatial omics tools, a spatially resolved single-cell epigenomics method will accelerate understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved epigenomic profiling of single cells using in situ tagmentation and transcription followed by multiplexed imaging. We demonstrated the ability to profile histone modifications marking active promoters, putative enhancers, and silent promoters in individual cells, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results suggested putative promoter-enhancer pairs and enhancer hubs regulating developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.
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Affiliation(s)
- Tian Lu
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Cheen Euong Ang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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6
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Price JD, Lindtner S, Ypsilanti A, Binyameen F, Johnson JR, Newton BW, Krogan NJ, Rubenstein JLR. DLX1 and the NuRD complex cooperate in enhancer decommissioning and transcriptional repression. Development 2022; 149:dev199508. [PMID: 35695185 PMCID: PMC9245191 DOI: 10.1242/dev.199508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 03/17/2022] [Indexed: 09/27/2023]
Abstract
In the developing subpallium, the fate decision between neurons and glia is driven by expression of Dlx1/2 or Olig1/2, respectively, two sets of transcription factors with a mutually repressive relationship. The mechanism by which Dlx1/2 repress progenitor and oligodendrocyte fate, while promoting transcription of genes needed for differentiation, is not fully understood. We identified a motif within DLX1 that binds RBBP4, a NuRD complex subunit. ChIP-seq studies of genomic occupancy of DLX1 and six different members of the NuRD complex show that DLX1 and NuRD colocalize to putative regulatory elements enriched near other transcription factor genes. Loss of Dlx1/2 leads to dysregulation of genome accessibility at putative regulatory elements near genes repressed by Dlx1/2, including Olig2. Consequently, heterozygosity of Dlx1/2 and Rbbp4 leads to an increase in the production of OLIG2+ cells. These findings highlight the importance of the interplay between transcription factors and chromatin remodelers in regulating cell-fate decisions.
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Affiliation(s)
- James D. Price
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA 94143, USA
| | - Susan Lindtner
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Athena Ypsilanti
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Fadya Binyameen
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jeffrey R. Johnson
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institute of Data Science and Biosciences, J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Billy W. Newton
- Gladstone Institute of Data Science and Biosciences, J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institute of Data Science and Biosciences, J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John L. R. Rubenstein
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
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7
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Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia. Proc Natl Acad Sci U S A 2022; 119:e2108760119. [PMID: 35377797 PMCID: PMC9169651 DOI: 10.1073/pnas.2108760119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
During brain development, neurons are generated by spatially and temporally distinct processes that remain to be fully characterized. The ganglionic eminences (GEs) in the embryonic subpallium give rise to GABAergic and cholinergic neuron lineages that form the basal ganglia or migrate to the cerebral cortex. Beyond a limited set of canonical RNA markers, the transcriptional states of GE progenitors and immature neurons cells remain poorly defined. We combine enhancer labeling, single-cell transcriptomics using transcription factor-anchored clustering, and integration with in situ hybridization data to distinguish emerging neuronal populations in embryonic mouse basal ganglia. Our results demonstrate the specificity of enhancer-based labeling at single-cell resolution and reveal developmental origins and specification processes of critical neuronal lineages. Enhancers integrate transcription factor signaling pathways that drive cell fate specification in the developing brain. We paired enhancer labeling and single-cell RNA-sequencing (scRNA-seq) to delineate and distinguish specification of neuronal lineages in mouse medial, lateral, and caudal ganglionic eminences (MGE, LGE, and CGE) at embryonic day (E)11.5. We show that scRNA-seq clustering using transcription factors improves resolution of regional and developmental populations, and that enhancer activities identify specific and overlapping GE-derived neuronal populations. First, we mapped the activities of seven evolutionarily conserved brain enhancers at single-cell resolution in vivo, finding that the selected enhancers had diverse activities in specific progenitor and neuronal populations across the GEs. We then applied enhancer-based labeling, scRNA-seq, and analysis of in situ hybridization data to distinguish transcriptionally distinct and spatially defined subtypes of MGE-derived GABAergic and cholinergic projection neurons and interneurons. Our results map developmental origins and specification paths underlying neurogenesis in the embryonic basal ganglia and showcase the power of scRNA-seq combined with enhancer-based labeling to resolve the complex paths of neuronal specification underlying mouse brain development.
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8
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Su Z, Wang Z, Lindtner S, Yang L, Shang Z, Tian Y, Guo R, You Y, Zhou W, Rubenstein JL, Yang Z, Zhang Z. Dlx1/2-dependent expression of Meis2 promotes neuronal fate determination in the mammalian striatum. Development 2022; 149:dev200035. [PMID: 35156680 PMCID: PMC8918808 DOI: 10.1242/dev.200035] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/04/2022] [Indexed: 12/16/2022]
Abstract
The striatum is a central regulator of behavior and motor function through the actions of D1 and D2 medium-sized spiny neurons (MSNs), which arise from a common lateral ganglionic eminence (LGE) progenitor. The molecular mechanisms of cell fate specification of these two neuronal subtypes are incompletely understood. Here, we found that deletion of murine Meis2, which is highly expressed in the LGE and derivatives, led to a large reduction in striatal MSNs due to a block in their differentiation. Meis2 directly binds to the Zfp503 and Six3 promoters and is required for their expression and specification of D1 and D2 MSNs, respectively. Finally, Meis2 expression is regulated by Dlx1/2 at least partially through the enhancer hs599 in the LGE subventricular zone. Overall, our findings define a pathway in the LGE whereby Dlx1/2 drives expression of Meis2, which subsequently promotes the fate determination of striatal D1 and D2 MSNs via Zfp503 and Six3.
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Affiliation(s)
- Zihao Su
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Ziwu Wang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Susan Lindtner
- Department of Psychiatry, Nina Ireland Laboratory of Developmental Neurobiology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Lin Yang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Zicong Shang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Yu Tian
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Rongliang Guo
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Yan You
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Wenhao Zhou
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - John L. Rubenstein
- Department of Psychiatry, Nina Ireland Laboratory of Developmental Neurobiology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Zhengang Yang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
| | - Zhuangzhi Zhang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, China
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9
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Emerging strategies for the genetic dissection of gene functions, cell types, and neural circuits in the mammalian brain. Mol Psychiatry 2022; 27:422-435. [PMID: 34561609 DOI: 10.1038/s41380-021-01292-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
The mammalian brain is composed of a large number of highly diverse cell types with different molecular, anatomical, and functional features. Distinct cellular identities are generated during development under the regulation of intricate genetic programs and manifested through unique combinations of gene expression. Recent advancements in our understanding of the molecular and cellular mechanisms underlying the assembly, function, and pathology of the brain circuitry depend on the invention and application of genetic strategies that engage intrinsic gene regulatory mechanisms. Here we review the strategies for gene regulation on DNA, RNA, and protein levels and their applications in cell type targeting and neural circuit dissection. We highlight newly emerged strategies and emphasize the importance of combinatorial approaches. We also discuss the potential caveats and pitfalls in current methods and suggest future prospects to improve their comprehensiveness and versatility.
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10
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Yu Y, Zeng Z, Xie D, Chen R, Sha Y, Huang S, Cai W, Chen W, Li W, Ke R, Sun T. Interneuron origin and molecular diversity in the human fetal brain. Nat Neurosci 2021; 24:1745-1756. [PMID: 34737447 DOI: 10.1038/s41593-021-00940-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
Precise generation of excitatory neurons and inhibitory interneurons is crucial for proper formation and function of neural circuits in the mammalian brain. Because of the size and complexity of the human brain, it is a challenge to reveal the rich diversity of interneurons. To decipher origin and diversity of interneurons in the human fetal subpallium, here we show molecular features of diverse subtypes of interneuron progenitors and precursors by conducting single-cell RNA sequencing and in situ sequencing. Interneuron precursors in the medial and lateral ganglionic eminence simultaneously procure temporal and spatial identity through expressing a combination of specific sets of RNA transcripts. Acquisition of various interneuron subtypes in adult human brains occurs even at fetal stages. Our study uncovers complex molecular signatures of interneuron progenitors and precursors in the human fetal subpallium and highlights the logic and programs in the origin and lineage specification of various interneurons.
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Affiliation(s)
- Yuan Yu
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Zhiwei Zeng
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Danlin Xie
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Renliang Chen
- Taokang Institute of Neuro Medicine, Xiamen, Fujian, China
| | - Yongqiang Sha
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China.,School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Shiying Huang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Wenjie Cai
- Department of Radiation Oncology, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Wanhua Chen
- Department of Clinical Laboratory, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, Fujian, China
| | - Wenjun Li
- Fujian University of Traditional Chinese Medicine Jinjiang Affliated Hospital, Quanzhou, Fujian, China
| | - Rongqin Ke
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China.,School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Tao Sun
- Center for Precision Medicine, Huaqiao University, Xiamen, Fujian, China. .,School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China.
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11
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Knowles R, Dehorter N, Ellender T. From Progenitors to Progeny: Shaping Striatal Circuit Development and Function. J Neurosci 2021; 41:9483-9502. [PMID: 34789560 PMCID: PMC8612473 DOI: 10.1523/jneurosci.0620-21.2021] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 12/29/2022] Open
Abstract
Understanding how neurons of the striatum are formed and integrate into complex synaptic circuits is essential to provide insight into striatal function in health and disease. In this review, we summarize our current understanding of the development of striatal neurons and associated circuits with a focus on their embryonic origin. Specifically, we address the role of distinct types of embryonic progenitors, found in the proliferative zones of the ganglionic eminences in the ventral telencephalon, in the generation of diverse striatal interneurons and projection neurons. Indeed, recent evidence would suggest that embryonic progenitor origin dictates key characteristics of postnatal cells, including their neurochemical content, their location within striatum, and their long-range synaptic inputs. We also integrate recent observations regarding embryonic progenitors in cortical and other regions and discuss how this might inform future research on the ganglionic eminences. Last, we examine how embryonic progenitor dysfunction can alter striatal formation, as exemplified in Huntington's disease and autism spectrum disorder, and how increased understanding of embryonic progenitors can have significant implications for future research directions and the development of improved therapeutic options.SIGNIFICANCE STATEMENT This review highlights recently defined novel roles for embryonic progenitor cells in shaping the functional properties of both projection neurons and interneurons of the striatum. It outlines the developmental mechanisms that guide neuronal development from progenitors in the embryonic ganglionic eminences to progeny in the striatum. Where questions remain open, we integrate observations from cortex and other regions to present possible avenues for future research. Last, we provide a progenitor-centric perspective onto both Huntington's disease and autism spectrum disorder. We suggest that future investigations and manipulations of embryonic progenitor cells in both research and clinical settings will likely require careful consideration of their great intrinsic diversity and neurogenic potential.
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Affiliation(s)
- Rhys Knowles
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Nathalie Dehorter
- The John Curtin School of Medical Research, The Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Tommas Ellender
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
- Department of Biomedical Sciences, University of Antwerp, 2610 Wilrijk, Belgium
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12
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Cui Q, Pamukcu A, Cherian S, Chang IYM, Berceau BL, Xenias HS, Higgs MH, Rajamanickam S, Chen Y, Du X, Zhang Y, McMorrow H, Abecassis ZA, Boca SM, Justice NJ, Wilson CJ, Chan CS. Dissociable Roles of Pallidal Neuron Subtypes in Regulating Motor Patterns. J Neurosci 2021; 41:4036-4059. [PMID: 33731450 PMCID: PMC8176746 DOI: 10.1523/jneurosci.2210-20.2021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 01/21/2021] [Accepted: 02/20/2021] [Indexed: 01/27/2023] Open
Abstract
We have previously established that PV+ neurons and Npas1+ neurons are distinct neuron classes in the external globus pallidus (GPe): they have different topographical, electrophysiological, circuit, and functional properties. Aside from Foxp2+ neurons, which are a unique subclass within the Npas1+ class, we lack driver lines that effectively capture other GPe neuron subclasses. In this study, we examined the utility of Kcng4-Cre, Npr3-Cre, and Npy2r-Cre mouse lines (both males and females) for the delineation of GPe neuron subtypes. By using these novel driver lines, we have provided the most exhaustive investigation of electrophysiological studies of GPe neuron subtypes to date. Corroborating our prior studies, GPe neurons can be divided into two statistically distinct clusters that map onto PV+ and Npas1+ classes. By combining optogenetics and machine learning-based tracking, we showed that optogenetic perturbation of GPe neuron subtypes generated unique behavioral structures. Our findings further highlighted the dissociable roles of GPe neurons in regulating movement and anxiety-like behavior. We concluded that Npr3+ neurons and Kcng4+ neurons are distinct subclasses of Npas1+ neurons and PV+ neurons, respectively. Finally, by examining local collateral connectivity, we inferred the circuit mechanisms involved in the motor patterns observed with optogenetic perturbations. In summary, by identifying mouse lines that allow for manipulations of GPe neuron subtypes, we created new opportunities for interrogations of cellular and circuit substrates that can be important for motor function and dysfunction.SIGNIFICANCE STATEMENT Within the basal ganglia, the external globus pallidus (GPe) has long been recognized for its involvement in motor control. However, we lacked an understanding of precisely how movement is controlled at the GPe level as a result of its cellular complexity. In this study, by using transgenic and cell-specific approaches, we showed that genetically-defined GPe neuron subtypes have distinct roles in regulating motor patterns. In addition, the in vivo contributions of these neuron subtypes are in part shaped by the local, inhibitory connections within the GPe. In sum, we have established the foundation for future investigations of motor function and disease pathophysiology.
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Affiliation(s)
- Qiaoling Cui
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Arin Pamukcu
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Suraj Cherian
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Isaac Y M Chang
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Brianna L Berceau
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Harry S Xenias
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Matthew H Higgs
- Department of Biology, University of Texas at San Antonio, San Antonio 78249, Texas
| | - Shivakumar Rajamanickam
- Center for Metabolic and degenerative disease, Institute of Molecular Medicine, University of Texas, Houston 77030, Texas
- Department of Integrative Pharmacology, University of Texas, Houston 77030, Texas
| | - Yi Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison 53706, Wisconsin
| | - Xixun Du
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Yu Zhang
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Hayley McMorrow
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Zachary A Abecassis
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
| | - Simina M Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington 20057, DC
| | - Nicholas J Justice
- Center for Metabolic and degenerative disease, Institute of Molecular Medicine, University of Texas, Houston 77030, Texas
- Department of Integrative Pharmacology, University of Texas, Houston 77030, Texas
| | - Charles J Wilson
- Department of Biology, University of Texas at San Antonio, San Antonio 78249, Texas
| | - C Savio Chan
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago 60611, Illinois
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13
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Mich JK, Graybuck LT, Hess EE, Mahoney JT, Kojima Y, Ding Y, Somasundaram S, Miller JA, Kalmbach BE, Radaelli C, Gore BB, Weed N, Omstead V, Bishaw Y, Shapovalova NV, Martinez RA, Fong O, Yao S, Mortrud M, Chong P, Loftus L, Bertagnolli D, Goldy J, Casper T, Dee N, Opitz-Araya X, Cetin A, Smith KA, Gwinn RP, Cobbs C, Ko AL, Ojemann JG, Keene CD, Silbergeld DL, Sunkin SM, Gradinaru V, Horwitz GD, Zeng H, Tasic B, Lein ES, Ting JT, Levi BP. Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex. Cell Rep 2021; 34:108754. [PMID: 33789096 PMCID: PMC8163032 DOI: 10.1016/j.celrep.2021.108754] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/07/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Viral genetic tools that target specific brain cell types could transform basic neuroscience and targeted gene therapy. Here, we use comparative open chromatin analysis to identify thousands of human-neocortical-subclass-specific putative enhancers from across the genome to control gene expression in adeno-associated virus (AAV) vectors. The cellular specificity of reporter expression from enhancer-AAVs is established by molecular profiling after systemic AAV delivery in mouse. Over 30% of enhancer-AAVs produce specific expression in the targeted subclass, including both excitatory and inhibitory subclasses. We present a collection of Parvalbumin (PVALB) enhancer-AAVs that show highly enriched expression not only in cortical PVALB cells but also in some subcortical PVALB populations. Five vectors maintain PVALB-enriched expression in primate neocortex. These results demonstrate how genome-wide open chromatin data mining and cross-species AAV validation can be used to create the next generation of non-species-restricted viral genetic tools.
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Affiliation(s)
- John K Mich
- Allen Institute for Brain Science, Seattle, WA, USA.
| | | | - Erik E Hess
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Yoshiko Kojima
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Yi Ding
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Brian E Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | - Bryan B Gore
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Luke Loftus
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ali Cetin
- Department of Biology and Applied Physics, Stanford University, Stanford, CA, USA
| | | | - Ryder P Gwinn
- Epilepsy Surgery and Functional Neurosurgery, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Charles Cobbs
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery and Alvord Brain Tumor Center, University of Washington, Seattle, WA, USA
| | | | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gregory D Horwitz
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA; Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA; Washington National Primate Research Center, University of Washington, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA.
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14
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Puelles L, Diaz C, Stühmer T, Ferran JL, Martínez‐de la Torre M, Rubenstein JLR. LacZ-reporter mapping of Dlx5/6 expression and genoarchitectural analysis of the postnatal mouse prethalamus. J Comp Neurol 2021; 529:367-420. [PMID: 32420617 PMCID: PMC7671952 DOI: 10.1002/cne.24952] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022]
Abstract
We present here a thorough and complete analysis of mouse P0-P140 prethalamic histogenetic subdivisions and corresponding nuclear derivatives, in the context of local tract landmarks. The study used as fundamental material brains from a transgenic mouse line that expresses LacZ under the control of an intragenic enhancer of Dlx5 and Dlx6 (Dlx5/6-LacZ). Subtle shadings of LacZ signal, jointly with pan-DLX immunoreaction, and several other ancillary protein or RNA markers, including Calb2 and Nkx2.2 ISH (for the prethalamic eminence, and derivatives of the rostral zona limitans shell domain, respectively) were mapped across the prethalamus. The resulting model of the prethalamic region postulates tetrapartite rostrocaudal and dorsoventral subdivisions, as well as a tripartite radial stratification, each cell population showing a characteristic molecular profile. Some novel nuclei are proposed, and some instances of potential tangential cell migration were noted.
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Affiliation(s)
- Luis Puelles
- Department of Human Anatomy and Psychobiology and IMIB‐Arrixaca InstituteUniversity of MurciaMurciaSpain
| | - Carmen Diaz
- Department of Medical Sciences, School of Medicine and Institute for Research in Neurological DisabilitiesUniversity of Castilla‐La ManchaAlbaceteSpain
| | - Thorsten Stühmer
- Nina Ireland Laboratory of Developmental Neurobiology, Department of PsychiatryUCSF Medical SchoolSan FranciscoCaliforniaUSA
| | - José L. Ferran
- Department of Human Anatomy and Psychobiology and IMIB‐Arrixaca InstituteUniversity of MurciaMurciaSpain
| | | | - John L. R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of PsychiatryUCSF Medical SchoolSan FranciscoCaliforniaUSA
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15
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Lambert JT, Su-Feher L, Cichewicz K, Warren TL, Zdilar I, Wang Y, Lim KJ, Haigh JL, Morse SJ, Canales CP, Stradleigh TW, Castillo Palacios E, Haghani V, Moss SD, Parolini H, Quintero D, Shrestha D, Vogt D, Byrne LC, Nord AS. Parallel functional testing identifies enhancers active in early postnatal mouse brain. eLife 2021; 10:69479. [PMID: 34605404 PMCID: PMC8577842 DOI: 10.7554/elife.69479] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/02/2021] [Indexed: 01/07/2023] Open
Abstract
Enhancers are cis-regulatory elements that play critical regulatory roles in modulating developmental transcription programs and driving cell-type-specific and context-dependent gene expression in the brain. The development of massively parallel reporter assays (MPRAs) has enabled high-throughput functional screening of candidate DNA sequences for enhancer activity. Tissue-specific screening of in vivo enhancer function at scale has the potential to greatly expand our understanding of the role of non-coding sequences in development, evolution, and disease. Here, we adapted a self-transcribing regulatory element MPRA strategy for delivery to early postnatal mouse brain via recombinant adeno-associated virus (rAAV). We identified and validated putative enhancers capable of driving reporter gene expression in mouse forebrain, including regulatory elements within an intronic CACNA1C linkage disequilibrium block associated with risk in neuropsychiatric disorder genetic studies. Paired screening and single enhancer in vivo functional testing, as we show here, represents a powerful approach towards characterizing regulatory activity of enhancers and understanding how enhancer sequences organize gene expression in the brain.
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Affiliation(s)
- Jason T Lambert
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Linda Su-Feher
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Karol Cichewicz
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Tracy L Warren
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Iva Zdilar
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Yurong Wang
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Kenneth J Lim
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Jessica L Haigh
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Sarah J Morse
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Cesar P Canales
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Tyler W Stradleigh
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Erika Castillo Palacios
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Viktoria Haghani
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Spencer D Moss
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Hannah Parolini
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Diana Quintero
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Diwash Shrestha
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Grand Rapids Research Center, Michigan State UniversityGrand RapidsUnited States
| | - Leah C Byrne
- Helen Wills Neuroscience Institute, University of California, BerkeleyBerkeleyUnited States,Departments of Ophthalmology and Neurobiology, University of PittsburghPittsburghUnited States
| | - Alex S Nord
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
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16
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Regulatory Elements Inserted into AAVs Confer Preferential Activity in Cortical Interneurons. eNeuro 2020; 7:ENEURO.0211-20.2020. [PMID: 33199411 PMCID: PMC7768279 DOI: 10.1523/eneuro.0211-20.2020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 11/21/2022] Open
Abstract
Cortical interneuron (CIN) dysfunction is thought to play a major role in neuropsychiatric conditions like epilepsy, schizophrenia and autism. It is therefore essential to understand how the development, physiology, and functions of CINs influence cortical circuit activity and behavior in model organisms such as mice and primates. While transgenic driver lines are powerful tools for studying CINs in mice, this technology is limited in other species. An alternative approach is to use viral vectors such as AAV, which can be used in multiple species including primates and also have potential for therapeutic use in humans. Thus, we sought to discover gene regulatory enhancer elements (REs) that can be used in viral vectors to drive expression in specific cell types. The present study describes the systematic genome-wide identification of putative REs (pREs) that are preferentially active in immature CINs by histone modification chromatin immunoprecipitation and sequencing (ChIP-seq). We evaluated two novel pREs in AAV vectors, alongside the well-established Dlx I12b enhancer, and found that they drove CIN-specific reporter expression in adult mice. We also showed that the identified Arl4d pRE could drive sufficient expression of channelrhodopsin for optogenetic rescue of behavioral deficits in the Dlx5/6+/- mouse model of fast-spiking CIN dysfunction.
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17
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Miura Y, Li MY, Birey F, Ikeda K, Revah O, Thete MV, Park JY, Puno A, Lee SH, Porteus MH, Pașca SP. Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells. Nat Biotechnol 2020; 38:1421-1430. [PMID: 33273741 PMCID: PMC9042317 DOI: 10.1038/s41587-020-00763-w] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022]
Abstract
Cortico-striatal projections are critical components of forebrain circuitry that regulate motivated behaviors. To enable the study of the human cortico-striatal pathway and how its dysfunction leads to neuropsychiatric disease, we developed a method to convert human pluripotent stem cells into region-specific brain organoids that resemble the developing human striatum and include electrically active medium spiny neurons. We then assembled these organoids with cerebral cortical organoids in three-dimensional cultures to form cortico-striatal assembloids. Using viral tracing and functional assays in intact or sliced assembloids, we show that cortical neurons send axonal projections into striatal organoids and form synaptic connections. Medium spiny neurons mature electrophysiologically following assembly and display calcium activity after optogenetic stimulation of cortical neurons. Moreover, we derive cortico-striatal assembloids from patients with a neurodevelopmental disorder caused by a deletion on chromosome 22q13.3 and capture disease-associated defects in calcium activity, showing that this approach will allow investigation of the development and functional assembly of cortico-striatal connectivity using patient-derived cells.
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Affiliation(s)
- Yuki Miura
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
| | - Min-Yin Li
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
| | - Fikri Birey
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
| | - Kazuya Ikeda
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Omer Revah
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
| | - Mayuri Vijay Thete
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
| | - Jin-Young Park
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
| | - Alyssa Puno
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Samuel H Lee
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | | | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA.
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18
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Garcia-Calero E, Puelles L. Histogenetic Radial Models as Aids to Understanding Complex Brain Structures: The Amygdalar Radial Model as a Recent Example. Front Neuroanat 2020; 14:590011. [PMID: 33240050 PMCID: PMC7683391 DOI: 10.3389/fnana.2020.590011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/05/2020] [Indexed: 01/17/2023] Open
Abstract
The radial dimension expands during central nervous system development after the proliferative neuroepithelium is molecularly patterned. The process is associated with neurogenesis, radial glia scaffolding, and migration of immature neurons into the developing mantle stratum. Radial histogenetic units, defined as a delimited neural polyclone whose cells share the same molecular profile, are molded during these processes, and usually become roughly stratified into periventricular, intermediate, and superficial (subpial) strata wherein neuronal cell types may differ and be distributed in various patterns. Cell-cell adhesion or repulsion phenomena together with interaction with local intercellular matrix cues regulate the acquisition of nuclear, reticular, or layer histogenetic forms in such strata. Finally, the progressive addition of inputs and outputs soon follows the purely neurogenetic and radial migratory phase. Frequently there is heterochrony in the radial development of adjacent histogenetic units, apart of peculiarities in differentiation due to non-shared aspects of the respective molecular profiles. Tangential migrations may add complexity to radial unit cytoarchitecture and function. The study of the contributions of such genetically controlled radial histogenetic units to the emerging complex neural structure is a key instrument to understand central nervous system morphology and function. One recent example in this scenario is the recently proposed radial model of the mouse pallial amygdala. This is theoretically valid generally in mammals (Garcia-Calero et al., 2020), and subdivides the nuclear complex of the pallial amygdala into five main radial units. The approach applies a novel ad hoc amygdalar section plane, given the observed obliquity of the amygdalar radial glial framework. The general relevance of radial unit studies for clarifying structural analysis of all complex brain regions such as the pallial amygdala is discussed, with additional examples.
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Affiliation(s)
- Elena Garcia-Calero
- Department of Human Anatomy, School of Medicine and IMIB-Arrixaca Institute, University of Murcia, Murcia, Spain
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19
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Liu Z, Zhang Z, Lindtner S, Li Z, Xu Z, Wei S, Liang Q, Wen Y, Tao G, You Y, Chen B, Wang Y, Rubenstein JL, Yang Z. Sp9 Regulates Medial Ganglionic Eminence-Derived Cortical Interneuron Development. Cereb Cortex 2020; 29:2653-2667. [PMID: 29878134 DOI: 10.1093/cercor/bhy133] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/06/2018] [Indexed: 11/12/2022] Open
Abstract
Immature neurons generated by the subpallial MGE tangentially migrate to the cortex where they become parvalbumin-expressing (PV+) and somatostatin (SST+) interneurons. Here, we show that the Sp9 transcription factor controls the development of MGE-derived cortical interneurons. SP9 is expressed in the MGE subventricular zone and in MGE-derived migrating interneurons. Sp9 null and conditional mutant mice have approximately 50% reduction of MGE-derived cortical interneurons, an ectopic aggregation of MGE-derived neurons in the embryonic ventral telencephalon, and an increased ratio of SST+/PV+ cortical interneurons. RNA-Seq and SP9 ChIP-Seq reveal that SP9 regulates MGE-derived cortical interneuron development through controlling the expression of key transcription factors Arx, Lhx6, Lhx8, Nkx2-1, and Zeb2 involved in interneuron development, as well as genes implicated in regulating interneuron migration Ackr3, Epha3, and St18. Thus, Sp9 has a central transcriptional role in MGE-derived cortical interneuron development.
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Affiliation(s)
- Zhidong Liu
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhuangzhi Zhang
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Zhenmeiyu Li
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhejun Xu
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Song Wei
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qifei Liang
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yan Wen
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guangxu Tao
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yan You
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bin Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yanling Wang
- Department of Neurological Sciences, Rush University Medical Center, Rush University, Chicago, IL, USA
| | - John L Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Zhengang Yang
- State Key Laboratory of Medical Neurobiology, Department of Neurology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
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20
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Lindtner S, Catta-Preta R, Tian H, Su-Feher L, Price JD, Dickel DE, Greiner V, Silberberg SN, McKinsey GL, McManus MT, Pennacchio LA, Visel A, Nord AS, Rubenstein JLR. Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons. Cell Rep 2020; 28:2048-2063.e8. [PMID: 31433982 PMCID: PMC6750766 DOI: 10.1016/j.celrep.2019.07.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/29/2019] [Accepted: 07/08/2019] [Indexed: 11/24/2022] Open
Abstract
DLX transcription factors (TFs) are master regulators of the developing vertebrate brain, driving forebrain GABAergic neuronal differentiation. Ablation of Dlx1&2 alters expression of genes that are critical for forebrain GABAergic development. We integrated epigenomic and transcriptomic analyses, complemented with in situ hybridization (ISH), and in vivo and in vitro studies of regulatory element (RE) function. This revealed the DLX-organized gene regulatory network at genomic, cellular, and spatial levels in mouse embryonic basal ganglia. DLX TFs perform dual activating and repressing functions; the consequences of their binding were determined by the sequence and genomic context of target loci. Our results reveal and, in part, explain the paradox of widespread DLX binding contrasted with a limited subset of target loci that are sensitive at the epigenomic and transcriptomic level to Dlx1&2 ablation. The regulatory properties identified here for DLX TFs suggest general mechanisms by which TFs orchestrate dynamic expression programs underlying neurodevelopment. Lindtner et al. reveal the regulatory wiring organized by DLX transcription factors in forebrain GABAergic neuronal specification, by integrating functional genomic, epigenomic, and genetic data on a transgenic mouse model. This network determines key sequence-encoded regulatory elements and implicates a combination of histone modifications and biophysical interactions.
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Affiliation(s)
- Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rinaldo Catta-Preta
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - Hua Tian
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Linda Su-Feher
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA
| | - James D Price
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Development and Stem Cell Biology Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vanille Greiner
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shanni N Silberberg
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gabriel L McKinsey
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Comparative Biochemistry Program, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA.
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Development and Stem Cell Biology Program, University of California, San Francisco, San Francisco, CA 94158, USA.
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21
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Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL. A Chromatin Accessibility Atlas of the Developing Human Telencephalon. Cell 2020; 182:754-769.e18. [PMID: 32610082 PMCID: PMC7415678 DOI: 10.1016/j.cell.2020.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/16/2020] [Accepted: 05/29/2020] [Indexed: 12/26/2022]
Abstract
To discover regulatory elements driving the specificity of gene expression in different cell types and regions of the developing human brain, we generated an atlas of open chromatin from nine dissected regions of the mid-gestation human telencephalon, as well as microdissected upper and deep layers of the prefrontal cortex. We identified a subset of open chromatin regions (OCRs), termed predicted regulatory elements (pREs), that are likely to function as developmental brain enhancers. pREs showed temporal, regional, and laminar differences in chromatin accessibility and were correlated with gene expression differences across regions and gestational ages. We identified two functional de novo variants in a pRE for autism risk gene SLC6A1, and using CRISPRa, demonstrated that this pRE regulates SCL6A1. Additionally, mouse transgenic experiments validated enhancer activity for pREs proximal to FEZF2 and BCL11A. Thus, this atlas serves as a resource for decoding neurodevelopmental gene regulation in health and disease.
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Affiliation(s)
- Eirene Markenscoff-Papadimitriou
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institutes, San Francisco, CA, USA
| | | | | | - Fadya Binyameen
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Arnold R Kriegstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Stephan J Sanders
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew W State
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - John L Rubenstein
- Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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22
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Abstract
Cortical interneurons display striking differences in shape, physiology, and other attributes, challenging us to appropriately classify them. We previously suggested that interneuron types should be defined by their role in cortical processing. Here, we revisit the question of how to codify their diversity based upon their division of labor and function as controllers of cortical information flow. We suggest that developmental trajectories provide a guide for appreciating interneuron diversity and argue that subtype identity is generated using a configurational (rather than combinatorial) code of transcription factors that produce attractor states in the underlying gene regulatory network. We present our updated three-stage model for interneuron specification: an initial cardinal step, allocating interneurons into a few major classes, followed by definitive refinement, creating subclasses upon settling within the cortex, and lastly, state determination, reflecting the incorporation of interneurons into functional circuit ensembles. We close by discussing findings indicating that major interneuron classes are both evolutionarily ancient and conserved. We propose that the complexity of cortical circuits is generated by phylogenetically old interneuron types, complemented by an evolutionary increase in principal neuron diversity. This suggests that a natural neurobiological definition of interneuron types might be derived from a match between their developmental origin and computational function.
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Affiliation(s)
- Gord Fishell
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA;
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts 02142, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Adam Kepecs
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Department of Neuroscience, Washington University in St. Louis, St. Louis, Missouri 63130, USA;
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23
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Garcia-Calero E, Martínez-de-la-Torre M, Puelles L. A radial histogenetic model of the mouse pallial amygdala. Brain Struct Funct 2020; 225:1921-1956. [PMID: 32583144 PMCID: PMC7473974 DOI: 10.1007/s00429-020-02097-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/05/2020] [Indexed: 12/14/2022]
Abstract
Conventional anatomic models of the rodent (mammalian) amygdala are based on section planes oblique to its intrinsic radial glial organization. As a result, we still lack a model of amygdalar histogenesis in terms of radial units (progenitor domains and related radial migration and layering patterns). A radial model of the mouse pallial amygdala is first offered here, based on three logical steps: (1) analysis of amygdalar radial structure in variously discriminative genoarchitectonic material, using an optimal ad hoc section plane; (2) testing preliminary models with experiments labelling at the brain surface single packets of radial glia processes, to be followed into the ventricular surface across intervening predicted elements; (3) selection of 81 differential amygdalar gene markers and checking planar and radial aspects of their distribution across the model elements. This approach shows that subtle changes to the conventional schema of the amygdala allow a radial histogenetic model to be recognized, which is consistent with molecularly coded differential identities of its units and strata. It is expected that this model will help both causal studies of amygdalar developmental patterning and comparative evolutionary studies. It also may have potential impact on hodological and functional studies.
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Affiliation(s)
- Elena Garcia-Calero
- Department of Human Anatomy, School of Medicine and IMIB-Arrixaca Institute, University of Murcia, 30120, Murcia, Spain.
| | - Margaret Martínez-de-la-Torre
- Department of Human Anatomy, School of Medicine and IMIB-Arrixaca Institute, University of Murcia, 30120, Murcia, Spain
| | - Luis Puelles
- Department of Human Anatomy, School of Medicine and IMIB-Arrixaca Institute, University of Murcia, 30120, Murcia, Spain
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24
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Luo L, Ambrozkiewicz MC, Benseler F, Chen C, Dumontier E, Falkner S, Furlanis E, Gomez AM, Hoshina N, Huang WH, Hutchison MA, Itoh-Maruoka Y, Lavery LA, Li W, Maruo T, Motohashi J, Pai ELL, Pelkey KA, Pereira A, Philips T, Sinclair JL, Stogsdill JA, Traunmüller L, Wang J, Wortel J, You W, Abumaria N, Beier KT, Brose N, Burgess HA, Cepko CL, Cloutier JF, Eroglu C, Goebbels S, Kaeser PS, Kay JN, Lu W, Luo L, Mandai K, McBain CJ, Nave KA, Prado MA, Prado VF, Rothstein J, Rubenstein JL, Saher G, Sakimura K, Sanes JR, Scheiffele P, Takai Y, Umemori H, Verhage M, Yuzaki M, Zoghbi HY, Kawabe H, Craig AM. Optimizing Nervous System-Specific Gene Targeting with Cre Driver Lines: Prevalence of Germline Recombination and Influencing Factors. Neuron 2020; 106:37-65.e5. [PMID: 32027825 PMCID: PMC7377387 DOI: 10.1016/j.neuron.2020.01.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/12/2019] [Accepted: 01/10/2020] [Indexed: 12/17/2022]
Abstract
The Cre-loxP system is invaluable for spatial and temporal control of gene knockout, knockin, and reporter expression in the mouse nervous system. However, we report varying probabilities of unexpected germline recombination in distinct Cre driver lines designed for nervous system-specific recombination. Selective maternal or paternal germline recombination is showcased with sample Cre lines. Collated data reveal germline recombination in over half of 64 commonly used Cre driver lines, in most cases with a parental sex bias related to Cre expression in sperm or oocytes. Slight differences among Cre driver lines utilizing common transcriptional control elements affect germline recombination rates. Specific target loci demonstrated differential recombination; thus, reporters are not reliable proxies for another locus of interest. Similar principles apply to other recombinase systems and other genetically targeted organisms. We hereby draw attention to the prevalence of germline recombination and provide guidelines to inform future research for the neuroscience and broader molecular genetics communities.
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Affiliation(s)
- Lin Luo
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Mateusz C. Ambrozkiewicz
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany,Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Fritz Benseler
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Cui Chen
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Emilie Dumontier
- Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | | | - Naosuke Hoshina
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei-Hsiang Huang
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA,Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montreal, QC H3G 1A4, Canada
| | - Mary Anne Hutchison
- Synapse and Neural Circuit Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yu Itoh-Maruoka
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Laura A. Lavery
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77003, USA,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wei Li
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Tomohiko Maruo
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan,Department of Biochemistry, Tokushima University Graduate School of Medical Sciences, 3-18-15, Kuramoto-cho, Tokushima 770-8503, Japan,Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Junko Motohashi
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Emily Ling-Lin Pai
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kenneth A. Pelkey
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ariane Pereira
- Department of Neurobiology and Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas Philips
- Department of Neurology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jennifer L. Sinclair
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Jeff A. Stogsdill
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02139, USA
| | | | - Jiexin Wang
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Joke Wortel
- Department of Functional Genomics and Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and University Medical Center Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Wenjia You
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA,Departments of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nashat Abumaria
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China,Department of Laboratory Animal Science, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Kevin T. Beier
- Department of Physiology and Biophysics, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92697, USA
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Harold A. Burgess
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Constance L. Cepko
- Departments of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jean-François Cloutier
- Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Cagla Eroglu
- Department of Cell Biology, Department of Neurobiology, and Duke Institute for Brain Sciences, Regeneration Next Initiative, Duke University Medical Center, Durham, NC 27710, USA
| | - Sandra Goebbels
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Pascal S. Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeremy N. Kay
- Department of Neurobiology and Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wei Lu
- Synapse and Neural Circuit Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Kenji Mandai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan,Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Chris J. McBain
- Section on Cellular and Synaptic Physiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Klaus-Armin Nave
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Marco A.M. Prado
- Robarts Research Institute, Department of Anatomy and Cell Biology, and Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada,Brain and Mind Institute, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Vania F. Prado
- Robarts Research Institute, Department of Anatomy and Cell Biology, and Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON N6A 5B7, Canada,Brain and Mind Institute, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Jeffrey Rothstein
- Department of Neurology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - John L.R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA,Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gesine Saher
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Yoshimi Takai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hisashi Umemori
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthijs Verhage
- Department of Functional Genomics and Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and University Medical Center Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Michisuke Yuzaki
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Huda Yahya Zoghbi
- Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77003, USA,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hiroshi Kawabe
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany; Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Gerontology, Laboratory of Molecular Life Science, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, 2-2 Minatojima-minamimachi Chuo-ku, Kobe, Hyogo 650-0047, Japan.
| | - Ann Marie Craig
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada.
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25
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Angara K, Pai ELL, Bilinovich SM, Stafford AM, Nguyen JT, Li KX, Paul A, Rubenstein JL, Vogt D. Nf1 deletion results in depletion of the Lhx6 transcription factor and a specific loss of parvalbumin + cortical interneurons. Proc Natl Acad Sci U S A 2020; 117:6189-6195. [PMID: 32123116 PMCID: PMC7084085 DOI: 10.1073/pnas.1915458117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Neurofibromatosis 1 (NF1) is caused by mutations in the NF1 gene, which encodes the protein, neurofibromin, an inhibitor of Ras activity. Cortical GABAergic interneurons (CINs) are implicated in NF1 pathology, but the cellular and molecular changes to CINs are unknown. We deleted mouse Nf1 from the medial ganglionic eminence, which gives rise to both oligodendrocytes and CINs that express somatostatin and parvalbumin. Nf1 loss led to a persistence of immature oligodendrocytes that prevented later-generated oligodendrocytes from occupying the cortex. Moreover, molecular and cellular properties of parvalbumin (PV)-positive CINs were altered by the loss of Nf1, without changes in somatostatin (SST)-positive CINs. We discovered that loss of Nf1 results in a dose-dependent decrease in Lhx6 expression, the transcription factor necessary to establish SST+ and PV+ CINs, which was rescued by the MEK inhibitor SL327, revealing a mechanism whereby a neurofibromin/Ras/MEK pathway regulates a critical CIN developmental milestone.
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Affiliation(s)
- Kartik Angara
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Emily Ling-Lin Pai
- Department of Psychiatry, University of California, San Francisco, CA 94158
- Neuroscience Program, University of California, San Francisco, CA 94158
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158
| | - Stephanie M Bilinovich
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - April M Stafford
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Julie T Nguyen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Katie X Li
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503
| | - Anirban Paul
- Department of Neural and Behavioral Sciences, PennState University, Hershey, PA 17033
| | - John L Rubenstein
- Department of Psychiatry, University of California, San Francisco, CA 94158
- Neuroscience Program, University of California, San Francisco, CA 94158
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503;
- Neuroscience Program, Michigan State University, Grand Rapids, MI 49503
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26
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Pai ELL, Vogt D, Clemente-Perez A, McKinsey GL, Cho FS, Hu JS, Wimer M, Paul A, Fazel Darbandi S, Pla R, Nowakowski TJ, Goodrich LV, Paz JT, Rubenstein JLR. Mafb and c-Maf Have Prenatal Compensatory and Postnatal Antagonistic Roles in Cortical Interneuron Fate and Function. Cell Rep 2020; 26:1157-1173.e5. [PMID: 30699346 PMCID: PMC6602795 DOI: 10.1016/j.celrep.2019.01.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 11/17/2018] [Accepted: 01/08/2019] [Indexed: 10/27/2022] Open
Abstract
Mafb and c-Maf transcription factor (TF) expression is enriched in medial ganglionic eminence (MGE) lineages, beginning in late-secondary progenitors and continuing into mature parvalbumin (PV+) and somatostatin (SST+) interneurons. However, the functions of Maf TFs in MGE development remain to be elucidated. Herein, Mafb and c-Maf were conditionally deleted, alone and together, in the MGE and its lineages. Analyses of Maf mutant mice revealed redundant functions of Mafb and c-Maf in secondary MGE progenitors, where they repress the generation of SST+ cortical and hippocampal interneurons. By contrast, Mafb and c-Maf have distinct roles in postnatal cortical interneuron (CIN) morphological maturation, synaptogenesis, and cortical circuit integration. Thus, Mafb and c-Maf have redundant and opposing functions at different steps in CIN development.
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Affiliation(s)
- Emily Ling-Lin Pai
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel Vogt
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Alexandra Clemente-Perez
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Gabriel L McKinsey
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Frances S Cho
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Jia Sheng Hu
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matt Wimer
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Anirban Paul
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Siavash Fazel Darbandi
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ramon Pla
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lisa V Goodrich
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeanne T Paz
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.
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Abecassis ZA, Berceau BL, Win PH, García D, Xenias HS, Cui Q, Pamukcu A, Cherian S, Hernández VM, Chon U, Lim BK, Kim Y, Justice NJ, Awatramani R, Hooks BM, Gerfen CR, Boca SM, Chan CS. Npas1 +-Nkx2.1 + Neurons Are an Integral Part of the Cortico-pallido-cortical Loop. J Neurosci 2020; 40:743-768. [PMID: 31811030 PMCID: PMC6975296 DOI: 10.1523/jneurosci.1199-19.2019] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 11/21/2022] Open
Abstract
Within the basal ganglia circuit, the external globus pallidus (GPe) is critically involved in motor control. Aside from Foxp2+ neurons and ChAT+ neurons that have been established as unique neuron types, there is little consensus on the classification of GPe neurons. Properties of the remaining neuron types are poorly defined. In this study, we leverage new mouse lines, viral tools, and molecular markers to better define GPe neuron subtypes. We found that Sox6 represents a novel, defining marker for GPe neuron subtypes. Lhx6+ neurons that lack the expression of Sox6 were devoid of both parvalbumin and Npas1. This result confirms previous assertions of the existence of a unique Lhx6+ population. Neurons that arise from the Dbx1+ lineage were similarly abundant in the GPe and displayed a heterogeneous makeup. Importantly, tracing experiments revealed that Npas1+-Nkx2.1+ neurons represent the principal noncholinergic, cortically-projecting neurons. In other words, they form the pallido-cortical arm of the cortico-pallido-cortical loop. Our data further show that pyramidal-tract neurons in the cortex collateralized within the GPe, forming a closed-loop system between the two brain structures. Overall, our findings reconcile some of the discrepancies that arose from differences in techniques or the reliance on preexisting tools. Although spatial distribution and electrophysiological properties of GPe neurons reaffirm the diversification of GPe subtypes, statistical analyses strongly support the notion that these neuron subtypes can be categorized under the two principal neuron classes: PV+ neurons and Npas1+ neurons.SIGNIFICANCE STATEMENT The poor understanding of the neuronal composition in the external globus pallidus (GPe) undermines our ability to interrogate its precise behavioral and disease involvements. In this study, 12 different genetic crosses were used, hundreds of neurons were electrophysiologically characterized, and >100,000 neurons were histologically- and/or anatomically-profiled. Our current study further establishes the segregation of GPe neuron classes and illustrates the complexity of GPe neurons in adult mice. Our results support the idea that Npas1+-Nkx2.1+ neurons are a distinct GPe neuron subclass. By providing a detailed analysis of the organization of the cortico-pallidal-cortical projection, our findings establish the cellular and circuit substrates that can be important for motor function and dysfunction.
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Affiliation(s)
- Zachary A Abecassis
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Brianna L Berceau
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Phyo H Win
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Daniela García
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Harry S Xenias
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Qiaoling Cui
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Arin Pamukcu
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Suraj Cherian
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Vivian M Hernández
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Uree Chon
- Department of Neural and Behavioral Sciences, College of Medicine, Pennsylvania State University, Hershey, Pennsylvania
| | - Byung Kook Lim
- Neurobiology Section, Biological Sciences Division, University of California San Diego, La Jolla, California
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, College of Medicine, Pennsylvania State University, Hershey, Pennsylvania
| | - Nicholas J Justice
- Center for Metabolic and degenerative disease, Institute of Molecular Medicine, University of Texas, Houston, Texas
- Department of Integrative Pharmacology, University of Texas, Houston, Texas
| | - Raj Awatramani
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Bryan M Hooks
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Charles R Gerfen
- Laboratory of Systems Neuroscience, National Institute of Mental Health, Bethesda, Maryland, and
| | - Simina M Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, District of Columbia
| | - C Savio Chan
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois,
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28
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Longitudinal developmental analysis of prethalamic eminence derivatives in the chick by mapping of Tbr1 in situ expression. Brain Struct Funct 2020; 225:481-510. [DOI: 10.1007/s00429-019-02015-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023]
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29
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McGregor MM, McKinsey GL, Girasole AE, Bair-Marshall CJ, Rubenstein JLR, Nelson AB. Functionally Distinct Connectivity of Developmentally Targeted Striosome Neurons. Cell Rep 2019; 29:1419-1428.e5. [PMID: 31693884 PMCID: PMC6866662 DOI: 10.1016/j.celrep.2019.09.076] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 11/30/2022] Open
Abstract
One long-standing model of striatal function divides the striatum into compartments called striosome and matrix. While some anatomical evidence suggests that these populations represent distinct striatal pathways with differing inputs and outputs, functional investigation has been limited by the methods for identifying and manipulating these populations. Here, we utilize hs599CreER mice as a new tool for targeting striosome projection neurons and testing their functional connectivity. Extending anatomical work, we demonstrate that striosome neurons receive greater synaptic input from prelimbic cortex, whereas matrix neurons receive greater input from primary motor cortex. We also identify functional differences in how striosome and matrix neurons process excitatory input, providing the first electrophysiological method for delineating striatal output neuron subtypes. Lastly, we provide the first functional demonstration that striosome neurons are the predominant striatal output to substantia nigra pars compacta dopamine neurons. These results identify striosome and matrix as functionally distinct striatal pathways.
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Affiliation(s)
- Matthew M McGregor
- Neuroscience Graduate Program, UCSF, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, UCSF, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience, UCSF, San Francisco, CA 94158, USA
| | - Gabriel L McKinsey
- Neuroscience Graduate Program, UCSF, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, UCSF, San Francisco, CA 94158, USA; Department of Psychiatry, UCSF, San Francisco, CA, 94158, USA
| | - Allison E Girasole
- Neuroscience Graduate Program, UCSF, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, UCSF, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience, UCSF, San Francisco, CA 94158, USA
| | | | - John L R Rubenstein
- Weill Institute for Neurosciences, UCSF, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience, UCSF, San Francisco, CA 94158, USA; Department of Psychiatry, UCSF, San Francisco, CA, 94158, USA
| | - Alexandra B Nelson
- Neuroscience Graduate Program, UCSF, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, UCSF, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience, UCSF, San Francisco, CA 94158, USA; Department of Neurology, UCSF, San Francisco, CA 94158, USA.
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Abstract
Nobel laureate Nikolaas Tinbergen provided clear criteria for declaring a neuroscience problem solved, criteria which despite the passage of more than 50 years and vastly expanded neuroscience tool kits remain applicable today. Tinbergen said for neuroscientists to claim that a behavior is understood, they must correspondingly understand its (i) development and its (ii) mechanisms and its (iii) function and its (iv) evolution. Now, all four of these domains represent hotbeds of current experimental work, each using arrays of new techniques which overlap only partly. Thus, as new methodologies come online, from single-nerve-cell RNA sequencing, for example, to smart FISH, large-scale calcium imaging from cortex and deep brain structures, computational ethology, and so on, one person, however smart, cannot master everything. Our response to the likely “fracturing” of neuroscience recognizes the value of ever larger consortia. This response suggests new kinds of problems for (i) funding and (ii) the fair distribution of credit, especially for younger scientists.
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Puelles L, Alonso A, García-Calero E, Martínez-de-la-Torre M. Concentric ring topology of mammalian cortical sectors and relevance for patterning studies. J Comp Neurol 2019; 527:1731-1752. [PMID: 30737959 DOI: 10.1002/cne.24650] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/05/2019] [Accepted: 01/28/2019] [Indexed: 01/07/2023]
Abstract
Models aiming to explain causally the evolutionary or ontogenetic emergence of the pallial isocortex and its regional/areal heterogeneity in mammals use simple or complex assumptions about the pallial structure present in basal mammals and nonmammals. The question arises: how complex is the pattern that needs to be accounted for in causal models? This topic is also paramount for comparative purposes, since some topological relationships may be explained as being ancestral, rather than newly emerged. The mouse pallium is apt to be reexamined in this context, due to the breadth of available molecular markers and correlative experimental patterning results. We center the present essay on a recapitulative glance at the classic theory of concentric mammalian allo-, meso-, and neocortex domains. In its simplest terms, this theory postulates a central neocortical island (6 layers) separated by a surrounding mesocortical ring (4-5 layers) from a peripheral allocortical ring (3 layers). These territories show additional partition into regional or areal subdivisions. There are also borderline amygdalar, claustral, and septal areas of the pallium, nuclear in structure. There has been little effort so far to contemplate the full concentric ring model in current "cortex patterning" models. In this essay, we recapitulate the ring idea in mammals (mouse) and consider a potential causal patterning scenario using topologic models. Finally, we briefly explore how far this theory may apply to pallium models proposed recently for sauropsids.
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Affiliation(s)
- Luis Puelles
- Department of Human Anatomy and IMIB-Arrixaca Institute, School of Medicine, University of Murcia, Murcia, Spain
| | - Antonia Alonso
- Department of Human Anatomy and IMIB-Arrixaca Institute, School of Medicine, University of Murcia, Murcia, Spain
| | - Elena García-Calero
- Department of Human Anatomy and IMIB-Arrixaca Institute, School of Medicine, University of Murcia, Murcia, Spain
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Genomic analysis of transcriptional networks directing progression of cell states during MGE development. Neural Dev 2018; 13:21. [PMID: 30217225 PMCID: PMC6138899 DOI: 10.1186/s13064-018-0119-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/27/2018] [Indexed: 01/01/2023] Open
Abstract
Background Homeodomain (HD) transcription factor (TF) NKX2–1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. NKX2–1 defines MGE regional identity in large part through transcriptional repression, while specification and maturation of GABAergic and cholinergic fates is mediated in part by transcriptional activation via TFs such as LHX6 and LHX8. Here we analyze the signaling and TF pathways, downstream of NKX2–1, required for GABAergic and cholinergic neuron fate maturation. Methods Differential ChIP-seq analysis was used to identify regulatory elements (REs) where chromatin state was sensitive to change in the Nkx2–1cKO MGE at embryonic day (E) 13.5. TF motifs in the REs were identified using RSAT. CRISPR-mediated genome editing was used to generate enhancer knockouts. Differential gene expression in these knockouts was analyzed through RT-qPCR and in situ hybridization. Functional analysis of motifs within hs623 was analyzed via site directed mutagenesis and reporter assays in primary MGE cultures. Results We identified 4782 activating REs (aREs) and 6391 repressing REs (rREs) in the Nkx2–1 conditional knockout (Nkx2–1cKO) MGE. aREs are associated with basic-Helix-Loop-Helix (bHLH) TFs. Deletion of hs623, an intragenic Tcf12 aRE, caused a reduction of Tcf12 expression in the sub-ventricular zone (SVZ) and mantle zone (MZ) of the MGE. Mutation of LHX, SOX and octamers, within hs623, caused a reduction of hs623 activity in MGE primary cultures. Conclusions Tcf12 expression in the SVZ of the MGE is mediated through aRE hs623. The activity of hs623 is dependent on LHX6, SOX and octamers. Thus, maintaining the expression of Tcf12 in the SVZ involves on TF pathways parallel and genetically downstream of NKX2–1. Electronic supplementary material The online version of this article (10.1186/s13064-018-0119-4) contains supplementary material, which is available to authorized users.
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Xu Z, Liang Q, Song X, Zhang Z, Lindtner S, Li Z, Wen Y, Liu G, Guo T, Qi D, Wang M, Wang C, Li H, You Y, Wang X, Chen B, Feng H, Rubenstein JL, Yang Z. SP8 and SP9 coordinately promote D2-type medium spiny neuron production by activating Six3 expression. Development 2018; 145:dev165456. [PMID: 29967281 PMCID: PMC6078334 DOI: 10.1242/dev.165456] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 06/18/2018] [Indexed: 12/21/2022]
Abstract
Dopamine receptor DRD1-expressing medium spiny neurons (D1 MSNs) and dopamine receptor DRD2-expressing medium spiny neurons (D2 MSNs) are the principal projection neurons in the striatum, which is divided into dorsal striatum (caudate nucleus and putamen) and ventral striatum (nucleus accumbens and olfactory tubercle). Progenitors of these neurons arise in the lateral ganglionic eminence (LGE). Using conditional deletion, we show that mice lacking the transcription factor genes Sp8 and Sp9 lose virtually all D2 MSNs as a result of reduced neurogenesis in the LGE, whereas D1 MSNs are largely unaffected. SP8 and SP9 together drive expression of the transcription factor Six3 in a spatially restricted domain of the LGE subventricular zone. Conditional deletion of Six3 also prevents the formation of most D2 MSNs, phenocopying the Sp8/9 mutants. Finally, ChIP-Seq reveals that SP9 directly binds to the promoter and a putative enhancer of Six3 Thus, this study defines components of a transcription pathway in a regionally restricted LGE progenitor domain that selectively drives the generation of D2 MSNs.
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Affiliation(s)
- Zhejun Xu
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qifei Liang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xiaolei Song
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhuangzhi Zhang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Susan Lindtner
- Department of Psychiatry, Nina Ireland Laboratory of Developmental Neurobiology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Zhenmeiyu Li
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yan Wen
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guoping Liu
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Teng Guo
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Dashi Qi
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Min Wang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chunyang Wang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Hao Li
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yan You
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xin Wang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bin Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Hua Feng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - John L Rubenstein
- Department of Psychiatry, Nina Ireland Laboratory of Developmental Neurobiology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Zhengang Yang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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Lim L, Pakan JMP, Selten MM, Marques-Smith A, Llorca A, Bae SE, Rochefort NL, Marín O. Optimization of interneuron function by direct coupling of cell migration and axonal targeting. Nat Neurosci 2018; 21:920-931. [PMID: 29915195 PMCID: PMC6061935 DOI: 10.1038/s41593-018-0162-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/13/2018] [Indexed: 12/31/2022]
Abstract
Neural circuit assembly relies on the precise synchronization of developmental processes, such as cell migration and axon targeting, but the cell-autonomous mechanisms coordinating these events remain largely unknown. Here we found that different classes of interneurons use distinct routes of migration to reach the embryonic cerebral cortex. Somatostatin-expressing interneurons that migrate through the marginal zone develop into Martinotti cells, one of the most distinctive classes of cortical interneurons. For these cells, migration through the marginal zone is linked to the development of their characteristic layer 1 axonal arborization. Altering the normal migratory route of Martinotti cells by conditional deletion of Mafb-a gene that is preferentially expressed by these cells-cell-autonomously disrupts axonal development and impairs the function of these cells in vivo. Our results suggest that migration and axon targeting programs are coupled to optimize the assembly of inhibitory circuits in the cerebral cortex.
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Affiliation(s)
- Lynette Lim
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Janelle M P Pakan
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
- Center for Behavioral Brain Sciences, Institute of Cognitive Neurology and Dementia Research, German Center for Neurodegenerative Diseases, Otto-von-Guericke University, Magdeburg, Germany
| | - Martijn M Selten
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - André Marques-Smith
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Alfredo Llorca
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Sung Eun Bae
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Nathalie L Rochefort
- Centre for Integrative Physiology, School of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain.
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Blankvoort S, Witter MP, Noonan J, Cotney J, Kentros C. Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression. Curr Biol 2018; 28:2103-2114.e5. [PMID: 30008330 DOI: 10.1016/j.cub.2018.05.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 04/27/2018] [Accepted: 05/04/2018] [Indexed: 10/28/2022]
Abstract
Understanding neural circuit function requires individually addressing their component parts: specific neuronal cell types. However, not only do the precise genetic mechanisms specifying neuronal cell types remain obscure, access to these neuronal cell types by transgenic techniques also remains elusive. Whereas most genes are expressed in the brain, the vast majority are expressed in many different kinds of neurons, suggesting that promoters alone are not sufficiently specific to distinguish cell types. However, there are orders of magnitude more distal genetic cis-regulatory elements controlling transcription (i.e., enhancers), so we screened for enhancer activity in microdissected samples of mouse cortical subregions. This identified thousands of novel putative enhancers, many unique to particular cortical subregions. Pronuclear injection of expression constructs containing such region-specific enhancers resulted in transgenic lines driving expression in distinct sets of cells specifically in the targeted cortical subregions, even though the parent gene's promoter was relatively non-specific. These data showcase the promise of utilizing the genetic mechanisms underlying the specification of diverse neuronal cell types for the development of genetic tools potentially capable of targeting any neuronal circuit of interest, an approach we call enhancer-driven gene expression (EDGE).
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Affiliation(s)
- Stefan Blankvoort
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - Menno P Witter
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway
| | - James Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Kavli Institute for Neuroscience, Yale University, New Haven, CT, USA
| | - Justin Cotney
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Centre, Farmington, CT, USA.
| | - Cliff Kentros
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, NTNU, Trondheim, Norway; Institute of Neuroscience, University of Oregon, Eugene, OR, USA.
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36
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He M, Huang ZJ. Genetic approaches to access cell types in mammalian nervous systems. Curr Opin Neurobiol 2018; 50:109-118. [PMID: 29471215 PMCID: PMC5984678 DOI: 10.1016/j.conb.2018.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/19/2018] [Accepted: 02/04/2018] [Indexed: 12/11/2022]
Abstract
Understanding brain circuit organization and function requires systematic dissection of its cellular components. With vast cell number and diversity, mammalian nervous systems present a daunting challenge for achieving specific and comprehensive cell type access-prerequisite to circuit analysis. Genetic approaches in the mouse have relied on germline engineering to access marker-defined cell populations. Combinatorial strategies that engage marker intersection, anatomy and projection pattern (e.g. antero-grade and retro-grade viral vectors), and developmental lineage substantially increase the specificity of cell type targeting. While increasing number of mouse cell types are becoming experimentally accessible, comprehensive coverage requires larger coordinated efforts with strategic infrastructural and fiscal planning. CRISPR-based genome editing may enable cell type access in other species, but issues of time, cost and ethics remain, especially for primates. Novel approaches that bypass the germline, such as somatic cell engineering and cell surface-based gene delivery, may reduce the barrier of genetic access to mammalian cell types.
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Affiliation(s)
- Miao He
- Department of Neurology, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Mi D, Li Z, Lim L, Li M, Moissidis M, Yang Y, Gao T, Hu TX, Pratt T, Price DJ, Sestan N, Marín O. Early emergence of cortical interneuron diversity in the mouse embryo. Science 2018; 360:81-85. [PMID: 29472441 PMCID: PMC6195193 DOI: 10.1126/science.aar6821] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/14/2018] [Indexed: 12/18/2022]
Abstract
GABAergic interneurons (GABA, γ-aminobutyric acid) regulate neural-circuit activity in the mammalian cerebral cortex. These cortical interneurons are structurally and functionally diverse. Here, we use single-cell transcriptomics to study the origins of this diversity in the mouse. We identify distinct types of progenitor cells and newborn neurons in the ganglionic eminences, the embryonic proliferative regions that give rise to cortical interneurons. These embryonic precursors show temporally and spatially restricted transcriptional patterns that lead to different classes of interneurons in the adult cerebral cortex. Our findings suggest that shortly after the interneurons become postmitotic, their diversity is already patent in their diverse transcriptional programs, which subsequently guide further differentiation in the developing cortex.
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Affiliation(s)
- Da Mi
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE1 1UL, UK
- Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Zhen Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Lynette Lim
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE1 1UL, UK
- Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Monika Moissidis
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE1 1UL, UK
- Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Yifei Yang
- Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Tianliuyun Gao
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tim Xiaoming Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02446, USA
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, UK
| | - Thomas Pratt
- Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - David J Price
- Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE1 1UL, UK.
- Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
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38
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Sultan KT, Shi SH. Generation of diverse cortical inhibitory interneurons. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.306. [PMID: 29115042 PMCID: PMC5814332 DOI: 10.1002/wdev.306] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/14/2017] [Accepted: 09/19/2017] [Indexed: 12/16/2022]
Abstract
First described by Ramon y Cajal as 'short-axon' cells over a century ago, inhibitory interneurons in the cerebral cortex make up ~20-30% of the neuronal milieu. A key feature of these interneurons is the striking structural and functional diversity, which allows them to modulate neural activity in diverse ways and ultimately endow neural circuits with remarkable computational power. Here, we review our current understanding of the generation of cortical interneurons, with a focus on recent efforts to bridge the gap between progenitor behavior and interneuron production, and how these aspects influence interneuron diversity and organization. WIREs Dev Biol 2018, 7:e306. doi: 10.1002/wdev.306 This article is categorized under: Nervous System Development > Vertebrates: General Principles.
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Affiliation(s)
- Khadeejah T Sultan
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Neuroscience Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Song-Hai Shi
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Neuroscience Graduate Program, Weill Cornell Medical College, New York, NY, USA
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39
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Kaneko R, Takatsuru Y, Morita A, Amano I, Haijima A, Imayoshi I, Tamamaki N, Koibuchi N, Watanabe M, Yanagawa Y. Inhibitory neuron-specific Cre-dependent red fluorescent labeling using VGAT BAC-based transgenic mouse lines with identified transgene integration sites. J Comp Neurol 2018; 526:373-396. [PMID: 29063602 DOI: 10.1002/cne.24343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/30/2017] [Accepted: 10/17/2017] [Indexed: 01/15/2023]
Abstract
Inhibitory neurons are crucial for shaping and regulating the dynamics of the entire network, and disturbances in these neurons contribute to brain disorders. Despite the recent progress in genetic labeling techniques, the heterogeneity of inhibitory neurons requires the development of highly characterized tools that allow accurate, convenient, and versatile visualization of inhibitory neurons in the mouse brain. Here, we report a novel genetic technique to visualize the vast majority and/or sparse subsets of inhibitory neurons in the mouse brain without using techniques that require advanced skills. We developed several lines of Cre-dependent tdTomato reporter mice based on the vesicular GABA transporter (VGAT)-BAC, named VGAT-stop-tdTomato mice. The most useful line (line #54) was selected for further analysis based on two characteristics: the inhibitory neuron-specificity of tdTomato expression and the transgene integration site, which confers efficient breeding and fewer adverse effects resulting from transgene integration-related genomic disruption. Robust and inhibitory neuron-specific expression of tdTomato was observed in a wide range of developmental and cellular contexts. By breeding the VGAT-stop-tdTomato mouse (line #54) with a novel Cre driver mouse line, Galntl4-CreER, sparse labeling of inhibitory neurons was achieved following tamoxifen administration. Furthermore, another interesting line (line #58) was generated through the unexpected integration of the transgene into the X-chromosome and will be used to map X-chromosome inactivation of inhibitory neurons. Taken together, our studies provide new, well-characterized tools with which multiple aspects of inhibitory neurons can be studied in the mouse.
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Affiliation(s)
- Ryosuke Kaneko
- Bioresource Center, Gunma University Graduate School of Medicine, Gunma, Japan
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yusuke Takatsuru
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma, Japan
- Department of Medicine, Johmoh Hospital, Gunma, Japan
| | - Ayako Morita
- Bioresource Center, Gunma University Graduate School of Medicine, Gunma, Japan
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Izuki Amano
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Asahi Haijima
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Itaru Imayoshi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nobuaki Tamamaki
- Department of Morphological Neural Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Noriyuki Koibuchi
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yuchio Yanagawa
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Gunma, Japan
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40
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Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat Neurosci 2018; 21:432-439. [PMID: 29434377 DOI: 10.1038/s41593-018-0079-3] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/27/2017] [Indexed: 01/23/2023]
Abstract
Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.
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41
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de Juan Romero C, Borrell V. Genetic maps and patterns of cerebral cortex folding. Curr Opin Cell Biol 2017; 49:31-37. [PMID: 29227862 DOI: 10.1016/j.ceb.2017.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/17/2017] [Accepted: 11/26/2017] [Indexed: 01/24/2023]
Abstract
Folding of the cerebral cortex during brain development is a complex process that depends on the orchestrated action of a number of factors, including generation and proliferation of basal progenitor cells, and the radial migration of neurons. Patterns of primary cortical folding are stereotyped between individuals and across phylogeny, reflecting a strong genetic regulation of the underlying cellular mechanisms. Here we summarize recent findings on cellular and genetic mechanisms regulating this fascinating process that underlies expansion and functional complexification of the mammalian cerebral cortex.
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Affiliation(s)
- Camino de Juan Romero
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain
| | - Víctor Borrell
- Instituto de Neurociencias, Agencia Estatal Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain.
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42
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Hu JS, Vogt D, Sandberg M, Rubenstein JL. Cortical interneuron development: a tale of time and space. Development 2017; 144:3867-3878. [PMID: 29089360 DOI: 10.1242/dev.132852] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cortical interneurons are a diverse group of neurons that project locally and are crucial for regulating information processing and flow throughout the cortex. Recent studies in mice have advanced our understanding of how these neurons are specified, migrate and mature. Here, we evaluate new findings that provide insights into the development of cortical interneurons and that shed light on when their fate is determined, on the influence that regional domains have on their development, and on the role that key transcription factors and other crucial regulatory genes play in these events. We focus on cortical interneurons that are derived from the medial ganglionic eminence, as most studies have examined this interneuron population. We also assess how these data inform our understanding of neuropsychiatric disease and discuss the potential role of cortical interneurons in cell-based therapies.
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Affiliation(s)
- Jia Sheng Hu
- Department of Psychiatry, University of California, San Francisco, CA 94158, USA.,Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158, USA
| | - Daniel Vogt
- Department of Psychiatry, University of California, San Francisco, CA 94158, USA.,Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158, USA
| | - Magnus Sandberg
- Department of Psychiatry, University of California, San Francisco, CA 94158, USA.,Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158, USA
| | - John L Rubenstein
- Department of Psychiatry, University of California, San Francisco, CA 94158, USA .,Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158, USA
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43
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Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron 2017; 96:542-557. [PMID: 29096072 PMCID: PMC5689454 DOI: 10.1016/j.neuron.2017.10.007] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 10/25/2022]
Abstract
A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans.
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Affiliation(s)
- Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Ngai
- Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Damon Polioudakis
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Department of Biology, Koch Institute of Integrative Cancer Research, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nenad Sestan
- Departments of Neuroscience, Genetics, Psychiatry and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Child Study Center, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ian R Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
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44
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Hu JS, Vogt D, Lindtner S, Sandberg M, Silberberg SN, Rubenstein JLR. Coup-TF1 and Coup-TF2 control subtype and laminar identity of MGE-derived neocortical interneurons. Development 2017; 144:2837-2851. [PMID: 28694260 DOI: 10.1242/dev.150664] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/29/2017] [Indexed: 12/23/2022]
Abstract
Distinct cortical interneuron (CIN) subtypes have unique circuit functions; dysfunction in specific subtypes is implicated in neuropsychiatric disorders. Somatostatin- and parvalbumin-expressing (SST+ and PV+) interneurons are the two major subtypes generated by medial ganglionic eminence (MGE) progenitors. Spatial and temporal mechanisms governing their cell-fate specification and differential integration into cortical layers are largely unknown. We provide evidence that Coup-TF1 and Coup-TF2 (Nr2f1 and Nr2f2) transcription factor expression in an arc-shaped progenitor domain within the MGE promotes time-dependent survival of this neuroepithelium and the time-dependent specification of layer V SST+ CINs. Coup-TF1 and Coup-TF2 autonomously repress PV+ fate in MGE progenitors, in part through directly driving Sox6 expression. These results have identified, in mouse, a transcriptional pathway that controls SST-PV fate.
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Affiliation(s)
- Jia Sheng Hu
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daniel Vogt
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Susan Lindtner
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Magnus Sandberg
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Shanni N Silberberg
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - John L R Rubenstein
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94158, USA
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