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Desiderio S, Schwaller F, Tartour K, Padmanabhan K, Lewin GR, Carroll P, Marmigere F. Touch receptor end-organ innervation and function require sensory neuron expression of the transcription factor Meis2. eLife 2024; 12:RP89287. [PMID: 38386003 PMCID: PMC10942617 DOI: 10.7554/elife.89287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024] Open
Abstract
Touch sensation is primarily encoded by mechanoreceptors, called low-threshold mechanoreceptors (LTMRs), with their cell bodies in the dorsal root ganglia. Because of their great diversity in terms of molecular signature, terminal endings morphology, and electrophysiological properties, mirroring the complexity of tactile experience, LTMRs are a model of choice to study the molecular cues differentially controlling neuronal diversification. While the transcriptional codes that define different LTMR subtypes have been extensively studied, the molecular players that participate in their late maturation and in particular in the striking diversity of their end-organ morphological specialization are largely unknown. Here we identified the TALE homeodomain transcription factor Meis2 as a key regulator of LTMRs target-field innervation in mice. Meis2 is specifically expressed in cutaneous LTMRs, and its expression depends on target-derived signals. While LTMRs lacking Meis2 survived and are normally specified, their end-organ innervations, electrophysiological properties, and transcriptome are differentially and markedly affected, resulting in impaired sensory-evoked behavioral responses. These data establish Meis2 as a major transcriptional regulator controlling the orderly formation of sensory neurons innervating peripheral end organs required for light touch.
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Affiliation(s)
- Simon Desiderio
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM U 1298MontpellierFrance
| | - Frederick Schwaller
- Department of Neuroscience, Max‐Delbrück Centre for Molecular MedicineBerlin‐BuchGermany
| | | | | | - Gary R Lewin
- Department of Neuroscience, Max‐Delbrück Centre for Molecular MedicineBerlin‐BuchGermany
| | - Patrick Carroll
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM U 1298MontpellierFrance
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2
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Fisher J, Verhagen M, Long Z, Moissidis M, Yan Y, He C, Wang J, Micoli E, Alastruey CM, Moors R, Marín O, Mi D, Lim L. Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories. Neuron 2024; 112:558-573.e8. [PMID: 38086373 DOI: 10.1016/j.neuron.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 08/22/2023] [Accepted: 11/10/2023] [Indexed: 02/24/2024]
Abstract
The mammalian cerebral cortex contains an extraordinary diversity of cell types that emerge by implementing different developmental programs. Delineating when and how cellular diversification occurs is particularly challenging for cortical inhibitory neurons because they represent a small proportion of all cortical cells and have a protracted development. Here, we combine single-cell RNA sequencing and spatial transcriptomics to characterize the emergence of neuronal diversity among somatostatin-expressing (SST+) cells in mice. We found that SST+ inhibitory neurons segregate during embryonic stages into long-range projection (LRP) neurons and two types of interneurons, Martinotti cells and non-Martinotti cells, following distinct developmental trajectories. Two main subtypes of LRP neurons and several subtypes of interneurons are readily distinguishable in the embryo, although interneuron diversity is likely refined during early postnatal life. Our results suggest that the timing for cellular diversification is unique for different subtypes of SST+ neurons and particularly divergent for LRP neurons and interneurons.
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Affiliation(s)
- Josephine Fisher
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK
| | - Marieke Verhagen
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Zhen Long
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Monika Moissidis
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK
| | - Yiming Yan
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chenyi He
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingyu Wang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Elia Micoli
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Clara Milían Alastruey
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Rani Moors
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE1 1UL London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, SE1 1UL, London, UK.
| | - Da Mi
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Lynette Lim
- VIB Center for Brain and Disease, 3000 Leuven, Belgium; Department of Neurosciences, Katholieke Universiteit (KU) Leuven, 3000 Leuven, Belgium.
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3
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Müller T, Reichlmeir M, Hau AC, Wittig I, Schulte D. The neuronal transcription factor MEIS2 is a calpain-2 protease target. J Cell Sci 2024; 137:jcs261482. [PMID: 38305737 PMCID: PMC10941658 DOI: 10.1242/jcs.261482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024] Open
Abstract
Tight control over transcription factor activity is necessary for a sensible balance between cellular proliferation and differentiation in the embryo and during tissue homeostasis by adult stem cells, but mechanistic details have remained incomplete. The homeodomain transcription factor MEIS2 is an important regulator of neurogenesis in the ventricular-subventricular zone (V-SVZ) adult stem cell niche in mice. We here identify MEIS2 as direct target of the intracellular protease calpain-2 (composed of the catalytic subunit CAPN2 and the regulatory subunit CAPNS1). Phosphorylation at conserved serine and/or threonine residues, or dimerization with PBX1, reduced the sensitivity of MEIS2 towards cleavage by calpain-2. In the adult V-SVZ, calpain-2 activity is high in stem and progenitor cells, but rapidly declines during neuronal differentiation, which is accompanied by increased stability of MEIS2 full-length protein. In accordance with this, blocking calpain-2 activity in stem and progenitor cells, or overexpression of a cleavage-insensitive form of MEIS2, increased the production of neurons, whereas overexpression of a catalytically active CAPN2 reduced it. Collectively, our results support a key role for calpain-2 in controlling the output of adult V-SVZ neural stem and progenitor cells through cleavage of the neuronal fate determinant MEIS2.
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Affiliation(s)
- Tanja Müller
- Goethe University, Faculty of Medicine, University Hospital Frankfurt, Institute of Neurology (Edinger Institute), 60528 Frankfurt, Germany
- Goethe University, University Hospital Frankfurt, Dr. Senckenberg Institute of Neurooncology and Institute of Neurology (Edinger Institute), Frankfurt Cancer Institute (FCI), University Cancer Center Frankfurt (UCT), MSNZ Junior Group Translational Neurooncology, 60528 Frankfurt, Germany
- Department of Cancer Research (DoCR), Luxembourg Institute of Health (LIH), Luxembourg Centre of Neuropathology (LCNP), 1445 Luxembourg, Luxembourg
| | - Marina Reichlmeir
- Goethe University, Faculty of Medicine, University Hospital Frankfurt, Institute of Neurology (Edinger Institute), 60528 Frankfurt, Germany
| | - Ann-Christin Hau
- Goethe University, University Hospital Frankfurt, Dr. Senckenberg Institute of Neurooncology and Institute of Neurology (Edinger Institute), Frankfurt Cancer Institute (FCI), University Cancer Center Frankfurt (UCT), MSNZ Junior Group Translational Neurooncology, 60528 Frankfurt, Germany
| | - Ilka Wittig
- Goethe University, Faculty of Medicine, Institute for Cardiovascular Physiology, Functional Proteomics, 60590, Frankfurt, Germany
| | - Dorothea Schulte
- Goethe University, Faculty of Medicine, University Hospital Frankfurt, Institute of Neurology (Edinger Institute), 60528 Frankfurt, Germany
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4
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Pavon N, Diep K, Yang F, Sebastian R, Martinez-Martin B, Ranjan R, Sun Y, Pak C. Patterning ganglionic eminences in developing human brain organoids using a morphogen-gradient-inducing device. CELL REPORTS METHODS 2024; 4:100689. [PMID: 38228151 PMCID: PMC10831957 DOI: 10.1016/j.crmeth.2023.100689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/21/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]
Abstract
In early neurodevelopment, the central nervous system is established through the coordination of various neural organizers directing tissue patterning and cell differentiation. Better recapitulation of morphogen gradient production and signaling will be crucial for establishing improved developmental models of the brain in vitro. Here, we developed a method by assembling polydimethylsiloxane devices capable of generating a sustained chemical gradient to produce patterned brain organoids, which we termed morphogen-gradient-induced brain organoids (MIBOs). At 3.5 weeks, MIBOs replicated dorsal-ventral patterning observed in the ganglionic eminences (GE). Analysis of mature MIBOs through single-cell RNA sequencing revealed distinct dorsal GE-derived CALB2+ interneurons, medium spiny neurons, and medial GE-derived cell types. Finally, we demonstrate long-term culturing capabilities with MIBOs maintaining stable neural activity in cultures grown up to 5.5 months. MIBOs demonstrate a versatile approach for generating spatially patterned brain organoids for embryonic development and disease modeling.
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Affiliation(s)
- Narciso Pavon
- Graduate Program in Neuroscience and Behavior, UMass Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Karmen Diep
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Feiyu Yang
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA 01003, USA
| | - Rebecca Sebastian
- Graduate Program in Neuroscience and Behavior, UMass Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Beatriz Martinez-Martin
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA; Graduate Program in Molecular and Cellular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Ravi Ranjan
- Genomics Core, Institute of Applied Life Sciences, UMass Amherst, Amherst, MA 01003, USA
| | - Yubing Sun
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA 01003, USA.
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA.
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5
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Bonanno SL, Krantz DE. Transcriptional changes in specific subsets of Drosophila neurons following inhibition of the serotonin transporter. Transl Psychiatry 2023; 13:226. [PMID: 37355701 DOI: 10.1038/s41398-023-02521-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023] Open
Abstract
The transcriptional effects of SSRIs and other serotonergic drugs remain unclear, in part due to the heterogeneity of postsynaptic cells, which may respond differently to changes in serotonergic signaling. Relatively simple model systems such as Drosophila afford more tractable microcircuits in which to investigate these changes in specific cell types. Here, we focus on the mushroom body, an insect brain structure heavily innervated by serotonin and comprised of multiple different but related subtypes of Kenyon cells. We use fluorescence-activated cell sorting of Kenyon cells, followed by either bulk or single-cell RNA sequencing to explore the transcriptomic response of these cells to SERT inhibition. We compared the effects of two different Drosophila Serotonin Transporter (dSERT) mutant alleles as well as feeding the SSRI citalopram to adult flies. We find that the genetic architecture associated with one of the mutants contributed to significant artefactual changes in expression. Comparison of differential expression caused by loss of SERT during development versus aged, adult flies, suggests that changes in serotonergic signaling may have relatively stronger effects during development, consistent with behavioral studies in mice. Overall, our experiments revealed limited transcriptomic changes in Kenyon cells, but suggest that different subtypes may respond differently to SERT loss-of-function. Further work exploring the effects of SERT loss-of-function in other circuits may be used help to elucidate how SSRIs differentially affect a variety of different neuronal subtypes both during development and in adults.
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Affiliation(s)
- Shivan L Bonanno
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - David E Krantz
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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6
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Bonanno SL, Krantz DE. Transcriptional changes in specific subsets of Drosophila neurons following inhibition of the serotonin transporter. RESEARCH SQUARE 2023:rs.3.rs-2626506. [PMID: 36993644 PMCID: PMC10055553 DOI: 10.21203/rs.3.rs-2626506/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The transcriptional effects of SSRIs and other serotonergic drugs remain unclear, in part due to the heterogeneity of postsynaptic cells, which may respond differently to changes in serotonergic signaling. Relatively simple model systems such as Drosophila afford more tractable microcircuits in which to investigate these changes in specific cell types. Here, we focus on the mushroom body, an insect brain structure heavily innervated by serotonin and comprised of multiple different but related subtypes of Kenyon cells. We use fluorescence activated cell sorting of Kenyon cells, followed by either or bulk or single cell RNA sequencing to explore the transcriptomic response of these cells to SERT inhibition. We compared the effects of two different Drosophila Serotonin Transporter (dSERT) mutant alleles as well as feeding the SSRI citalapram to adult flies. We find that the genetic architecture associated with one of the mutants contributed to significant artefactual changes in expression. Comparison of differential expression caused by loss of SERT during development versus aged, adult flies, suggests that changes in serotonergic signaling may have relatively stronger effects during development, consistent with behavioral studies in mice. Overall, our experiments revealed limited transcriptomic changes in Kenyon cells, but suggest that different subtypes may respond differently to SERT loss-of-function. Further work exploring the effects of SERT loss-of-function in other Drosophila circuits may be used help to elucidate how SSRIs differentially affect a variety of different neuronal subtypes both during development and in adults.
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Affiliation(s)
- Shivan L. Bonanno
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - David E. Krantz
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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7
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Hunt CPJ, Moriarty N, van Deursen CBJ, Gantner CW, Thompson LH, Parish CL. Understanding and modeling regional specification of the human ganglionic eminence. Stem Cell Reports 2023; 18:654-671. [PMID: 36801004 PMCID: PMC10031306 DOI: 10.1016/j.stemcr.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
Inhibitory neurons originating from the ventral forebrain are associated with several neurological conditions. Distinct ventral forebrain subpopulations are generated from topographically defined zones; lateral-, medial- and caudal ganglionic eminences (LGE, MGE and CGE), yet key specification factors often span across developing zones contributing to difficulty in defining unique LGE, MGE or CGE profiles. Here we use human pluripotent stem cell (hPSC) reporter lines (NKX2.1-GFP and MEIS2-mCherry) and manipulation of morphogen gradients to gain greater insight into regional specification of these distinct zones. We identified Sonic hedgehog (SHH)-WNT crosstalk in regulating LGE and MGE fate and uncovered a role for retinoic acid signaling in CGE development. Unraveling the influence of these signaling pathways permitted development of fully defined protocols that favored generation of the three GE domains. These findings provide insight into the context-dependent role of morphogens in human GE specification and are of value for in vitro disease modeling and advancement of new therapies.
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Affiliation(s)
- Cameron P J Hunt
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia.
| | - Niamh Moriarty
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Coen B J van Deursen
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Carlos W Gantner
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Lachlan H Thompson
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Clare L Parish
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia.
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8
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Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nat Neurosci 2022; 25:1049-1058. [PMID: 35915179 PMCID: PMC9343253 DOI: 10.1038/s41593-022-01123-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/16/2022] [Indexed: 11/08/2022]
Abstract
Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex.
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9
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Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban AE, Leckman JF, Weinberger DR, Vaccarino FM, Abyzov A. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022; 377:511-517. [PMID: 35901164 PMCID: PMC9420557 DOI: 10.1126/science.abm6222] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable single-nucleotide mutations, but ~6% of brains harbored hundreds of somatic mutations. Hypermutability was associated with age and damaging mutations in genes implicated in cancers and, in some brains, reflected in vivo clonal expansions. Somatic duplications, likely arising during development, were found in ~5% of normal and diseased brains, reflecting background mutagenesis. Brains with autism were associated with mutations creating putative transcription factor binding motifs in enhancer-like regions in the developing brain. The top-ranked affected motifs corresponded to MEIS (myeloid ectopic viral integration site) transcription factors, suggesting a potential link between their involvement in gene regulation and autism.
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Affiliation(s)
- Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT 06520
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Milovan Suvakov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT 06520
| | - Caroline Dias
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | | | - Feinan Wu
- Child Study Center, Yale University, New Haven, CT 06520
| | - Arijit Panda
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Yasmine Chahine
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rebecca Yeh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rosalinda C. Roberts
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham Al, 35294
| | - Anita Huttner
- Department of Pathology, Yale University, New Haven, CT 06520
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Richard E. Straub
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD
| | - Flora M. Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520
- Department of Neuroscience, Yale University, New Haven, CT 06520
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
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10
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Llorca A, Deogracias R. Origin, Development, and Synaptogenesis of Cortical Interneurons. Front Neurosci 2022; 16:929469. [PMID: 35833090 PMCID: PMC9272671 DOI: 10.3389/fnins.2022.929469] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
The mammalian cerebral cortex represents one of the most recent and astonishing inventions of nature, responsible of a large diversity of functions that range from sensory processing to high-order cognitive abilities, such as logical reasoning or language. Decades of dedicated study have contributed to our current understanding of this structure, both at structural and functional levels. A key feature of the neocortex is its outstanding richness in cell diversity, composed by multiple types of long-range projecting neurons and locally connecting interneurons. In this review, we will describe the great diversity of interneurons that constitute local neocortical circuits and summarize the mechanisms underlying their development and their assembly into functional networks.
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Affiliation(s)
- Alfredo Llorca
- Visual Neuroscience Laboratory, Centre for Discovery Brain Sciences, School of Biomedical Sciences, University of Edinburgh, Edinburg, United Kingdom
- *Correspondence: Alfredo Llorca
| | - Ruben Deogracias
- Neuronal Circuits Formation and Brain Disorders Laboratory, Institute of Neurosciences of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain
- Institute of Biomedical Research of Salamanca, Salamanca, Spain
- Department of Cell Biology and Pathology, School of Medicine, University of Salamanca, Salamanca, Spain
- Ruben Deogracias
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11
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Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
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Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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12
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Schmitz MT, Sandoval K, Chen CP, Mostajo-Radji MA, Seeley WW, Nowakowski TJ, Ye CJ, Paredes MF, Pollen AA. The development and evolution of inhibitory neurons in primate cerebrum. Nature 2022; 603:871-877. [PMID: 35322231 PMCID: PMC8967711 DOI: 10.1038/s41586-022-04510-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 02/01/2022] [Indexed: 12/14/2022]
Abstract
Neuroanatomists have long speculated that expanded primate brains contain an increased morphological diversity of inhibitory neurons (INs)1, and recent studies have identified primate-specific neuronal populations at the molecular level2. However, we know little about the developmental mechanisms that specify evolutionarily novel cell types in the brain. Here, we reconstruct gene expression trajectories specifying INs generated throughout the neurogenic period in macaques and mice by analysing the transcriptomes of 250,181 cells. We find that the initial classes of INs generated prenatally are largely conserved among mammals. Nonetheless, we identify two contrasting developmental mechanisms for specifying evolutionarily novel cell types during prenatal development. First, we show that recently identified primate-specific TAC3 striatal INs are specified by a unique transcriptional programme in progenitors followed by induction of a distinct suite of neuropeptides and neurotransmitter receptors in new-born neurons. Second, we find that multiple classes of transcriptionally conserved olfactory bulb (OB)-bound precursors are redirected to expanded primate white matter and striatum. These classes include a novel peristriatal class of striatum laureatum neurons that resemble dopaminergic periglomerular cells of the OB. We propose an evolutionary model in which conserved initial classes of neurons supplying the smaller primate OB are reused in the enlarged striatum and cortex. Together, our results provide a unified developmental taxonomy of initial classes of mammalian INs and reveal multiple developmental mechanisms for neural cell type evolution. Evolutionary modelling shows that an initial set of inhibitory neurons serving olfactory bulbs may have been repurposed to diversify the taxonomy of interneurons found in the expanded striata and cortices in primates.
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Affiliation(s)
- Matthew T Schmitz
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Kadellyn Sandoval
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher P Chen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Mohammed A Mostajo-Radji
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - William W Seeley
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.,Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Chan Zuckerberg Biohub, 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.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Mercedes F Paredes
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Alex A Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA. .,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA. .,Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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13
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Franjic D, Skarica M, Ma S, Arellano JI, Tebbenkamp ATN, Choi J, Xu C, Li Q, Morozov YM, Andrijevic D, Vrselja Z, Spajic A, Santpere G, Li M, Zhang S, Liu Y, Spurrier J, Zhang L, Gudelj I, Rapan L, Takahashi H, Huttner A, Fan R, Strittmatter SM, Sousa AMM, Rakic P, Sestan N. Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells. Neuron 2022; 110:452-469.e14. [PMID: 34798047 PMCID: PMC8813897 DOI: 10.1016/j.neuron.2021.10.036] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 10/17/2021] [Accepted: 10/26/2021] [Indexed: 02/04/2023]
Abstract
The hippocampal-entorhinal system supports cognitive functions, has lifelong neurogenic capabilities in many species, and is selectively vulnerable to Alzheimer's disease. To investigate neurogenic potential and cellular diversity, we profiled single-nucleus transcriptomes in five hippocampal-entorhinal subregions in humans, macaques, and pigs. Integrated cross-species analysis revealed robust transcriptomic and histologic signatures of neurogenesis in the adult mouse, pig, and macaque but not humans. Doublecortin (DCX), a widely accepted marker of newly generated granule cells, was detected in diverse human neurons, but it did not define immature neuron populations. To explore species differences in cellular diversity and implications for disease, we characterized subregion-specific, transcriptomically defined cell types and transitional changes from the three-layered archicortex to the six-layered neocortex. Notably, METTL7B defined subregion-specific excitatory neurons and astrocytes in primates, associated with endoplasmic reticulum and lipid droplet proteins, including Alzheimer's disease-related proteins. This resource reveals cell-type- and species-specific properties shaping hippocampal-entorhinal neurogenesis and function.
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Affiliation(s)
- Daniel Franjic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mario Skarica
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jon I Arellano
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Jinmyung Choi
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Chuan Xu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Qian Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yury M Morozov
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - David Andrijevic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Zvonimir Vrselja
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ana Spajic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), DCEXS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Mingfeng Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shupei Zhang
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yang Liu
- Department of Biomedical Engineering, Yale Stem Cell Center and Yale Cancer Center, and Human and Translational Immunology Program, Yale University, New Haven, CT 06520, USA
| | - Joshua Spurrier
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neurology and of Neuroscience, Yale School of Medicine, New Haven, CT 06536, USA
| | - Le Zhang
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neurology and of Neuroscience, Yale School of Medicine, New Haven, CT 06536, USA
| | - Ivan Gudelj
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Lucija Rapan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Hideyuki Takahashi
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neurology and of Neuroscience, Yale School of Medicine, New Haven, CT 06536, USA
| | - Anita Huttner
- Department of Pathology, Brady Memorial Laboratory, Yale School of Medicine, New Haven, CT 06510, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale Stem Cell Center and Yale Cancer Center, and Human and Translational Immunology Program, Yale University, New Haven, CT 06520, USA
| | - Stephen M Strittmatter
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Departments of Neurology and of Neuroscience, Yale School of Medicine, New Haven, CT 06536, USA
| | - Andre M M Sousa
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Waisman Center and Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Pasko Rakic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Departments of Psychiatry and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA.
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14
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Di Bella DJ, Habibi E, Stickels RR, Scalia G, Brown J, Yadollahpour P, Yang SM, Abbate C, Biancalani T, Macosko EZ, Chen F, Regev A, Arlotta P. Molecular logic of cellular diversification in the mouse cerebral cortex. Nature 2021; 595:554-559. [PMID: 34163074 PMCID: PMC9006333 DOI: 10.1038/s41586-021-03670-5] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 05/24/2021] [Indexed: 02/06/2023]
Abstract
The mammalian cerebral cortex has an unparalleled diversity of cell types, which are generated during development through a series of temporally orchestrated events that are under tight evolutionary constraint and are critical for proper cortical assembly and function1,2. However, the molecular logic that governs the establishment and organization of cortical cell types remains unknown, largely due to the large number of cell classes that undergo dynamic cell-state transitions over extended developmental timelines. Here we generate a comprehensive atlas of the developing mouse neocortex, using single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin using sequencing. We sampled the neocortex every day throughout embryonic corticogenesis and at early postnatal ages, and complemented the sequencing data with a spatial transcriptomics time course. We computationally reconstruct developmental trajectories across the diversity of cortical cell classes, and infer their spatial organization and the gene regulatory programs that accompany their lineage bifurcation decisions and differentiation trajectories. Finally, we demonstrate how this developmental map pinpoints the origin of lineage-specific developmental abnormalities that are linked to aberrant corticogenesis in mutant mice. The data provide a global picture of the regulatory mechanisms that govern cellular diversification in the neocortex.
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Affiliation(s)
- Daniela J. Di Bella
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ehsan Habibi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Gabriele Scalia
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Current address: Genentech, South San Francisco, CA, USA
| | - Juliana Brown
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Payman Yadollahpour
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sung Min Yang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine Abbate
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tommasso Biancalani
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Current address: Genentech, South San Francisco, CA, USA
| | - Evan Z. Macosko
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Fei Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Current address: Genentech, South San Francisco, CA, USA,Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA,Correspondence should be addressed to and
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Correspondence should be addressed to and
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15
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Yao Z, van Velthoven CTJ, Nguyen TN, Goldy J, Sedeno-Cortes AE, Baftizadeh F, Bertagnolli D, Casper T, Chiang M, Crichton K, Ding SL, Fong O, Garren E, Glandon A, Gouwens NW, Gray J, Graybuck LT, Hawrylycz MJ, Hirschstein D, Kroll M, Lathia K, Lee C, Levi B, McMillen D, Mok S, Pham T, Ren Q, Rimorin C, Shapovalova N, Sulc J, Sunkin SM, Tieu M, Torkelson A, Tung H, Ward K, Dee N, Smith KA, Tasic B, Zeng H. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. Cell 2021; 184:3222-3241.e26. [PMID: 34004146 PMCID: PMC8195859 DOI: 10.1016/j.cell.2021.04.021] [Citation(s) in RCA: 388] [Impact Index Per Article: 129.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 02/09/2021] [Accepted: 04/14/2021] [Indexed: 12/23/2022]
Abstract
The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion, and learning. We profiled ∼1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic cell-type taxonomy revealing a comprehensive repertoire of glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and the isocortex share a common circuit organization. We also identify large-scale continuous and graded variations of cell types along isocortical depth, across the isocortical sheet, and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of the mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity, and function of these two brain structures.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Megan Chiang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Matthew Kroll
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Stephanie Mok
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Qingzhong Ren
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
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16
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White Matter Interstitial Neurons in the Adult Human Brain: 3% of Cortical Neurons in Quest for Recognition. Cells 2021; 10:cells10010190. [PMID: 33477896 PMCID: PMC7833373 DOI: 10.3390/cells10010190] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 02/03/2023] Open
Abstract
White matter interstitial neurons (WMIN) are a subset of cortical neurons located in the subcortical white matter. Although they were fist described over 150 years ago, they are still largely unexplored and often considered a small, functionally insignificant neuronal population. WMIN are adult remnants of neurons located in the transient fetal subplate zone (SP). Following development, some of the SP neurons undergo apoptosis, and the remaining neurons are incorporated in the adult white matter as WMIN. In the adult human brain, WMIN are quite a large population of neurons comprising at least 3% of all cortical neurons (between 600 and 1100 million neurons). They include many of the morphological neuronal types that can be found in the overlying cerebral cortex. Furthermore, the phenotypic and molecular diversity of WMIN is similar to that of the overlying cortical neurons, expressing many glutamatergic and GABAergic biomarkers. WMIN are often considered a functionally unimportant subset of neurons. However, upon closer inspection of the scientific literature, it has been shown that WMIN are integrated in the cortical circuitry and that they exhibit diverse electrophysiological properties, send and receive axons from the cortex, and have active synaptic contacts. Based on these data, we are able to enumerate some of the potential WMIN roles, such as the control of the cerebral blood flow, sleep regulation, and the control of information flow through the cerebral cortex. Also, there is a number of studies indicating the involvement of WMIN in the pathophysiology of many brain disorders such as epilepsy, schizophrenia, Alzheimer’s disease, etc. All of these data indicate that WMIN are a large population with an important function in the adult brain. Further investigation of WMIN could provide us with novel data crucial for an improved elucidation of the pathophysiology of many brain disorders. In this review, we provide an overview of the current WMIN literature, with an emphasis on studies conducted on the human brain.
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17
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Abstract
The mammalian cerebral cortex is the pinnacle of brain evolution, reaching its maximum complexity in terms of neuron number, diversity and functional circuitry. The emergence of this outstanding complexity begins during embryonic development, when a limited number of neural stem and progenitor cells manage to generate myriads of neurons in the appropriate numbers, types and proportions, in a process called neurogenesis. Here we review the current knowledge on the regulation of cortical neurogenesis, beginning with a description of the types of progenitor cells and their lineage relationships. This is followed by a review of the determinants of neuron fate, the molecular and genetic regulatory mechanisms, and considerations on the evolution of cortical neurogenesis in vertebrates leading to humans. We finish with an overview on how dysregulation of neurogenesis is a leading cause of human brain malformations and functional disabilities.
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Affiliation(s)
- Ana Villalba
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Zentrum München & Biomedical Center, Ludwig-Maximilians Universitaet, Planegg-Martinsried, Germany
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain.
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18
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Genescu I, Garel S. Being superficial: a developmental viewpoint on cortical layer 1 wiring. Curr Opin Neurobiol 2020; 66:125-134. [PMID: 33186879 DOI: 10.1016/j.conb.2020.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/03/2020] [Accepted: 10/04/2020] [Indexed: 01/01/2023]
Abstract
Functioning of the neocortex relies on a complex architecture of circuits, as illustrated by the causal link between neocortical excitation/inhibition imbalance and the etiology of several neurodevelopmental disorders. An important entry point to cortical circuits is located in the superficial layer 1 (L1), which contains mostly local and long-range inputs and sparse inhibitory interneurons that collectively regulate cerebral functions. While increasing evidence indicates that L1 has important physiological roles, our understanding of how it wires up during development remains limited. Here, we provide an integrated overview of L1 anatomy, function and development, with a focus on transient early born Cajal-Retzius neurons, and highlight open questions key for progressing our understanding of this essential yet understudied layer of the cerebral cortex.
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Affiliation(s)
- Ioana Genescu
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Sonia Garel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France; Collège de France, Paris, France.
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19
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Gesuita L, Karayannis T. A 'Marginal' tale: the development of the neocortical layer 1. Curr Opin Neurobiol 2020; 66:37-47. [PMID: 33069991 DOI: 10.1016/j.conb.2020.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/03/2020] [Accepted: 09/02/2020] [Indexed: 01/06/2023]
Abstract
The development of neocortical layer 1 is a very dynamic process and the scene of multiple transient events, with Cajal-Retzius cell death being one of the most characteristic ones. Layer 1 is also the route of migration for a substantial number of GABAergic interneurons during embryogenesis and where some of which will ultimately remain in the adult. The two cell types, together with a diverse set of incoming axons and dendrites, create an early circuit that will dramatically change in structure and function in the adult cortex to give prominence to inhibition. Through the engagement of a diverse set of GABAergic inhibitory cells by bottom-up and top-down inputs, adult layer 1 becomes a powerful computational platform for the neocortex.
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Affiliation(s)
- Lorenzo Gesuita
- Laboratory of Neural Circuit Assembly, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland
| | - Theofanis Karayannis
- Laboratory of Neural Circuit Assembly, Brain Research Institute, University of Zurich, 8057 Zurich, Switzerland.
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20
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Du R, Carey V, Weiss ST. deconvSeq: deconvolution of cell mixture distribution in sequencing data. Bioinformatics 2020; 35:5095-5102. [PMID: 31147676 DOI: 10.1093/bioinformatics/btz444] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 05/17/2019] [Accepted: 05/27/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Although single-cell sequencing is becoming more widely available, many tissue samples such as intracranial aneurysms are both fibrous and minute, and therefore not easily dissociated into single cells. To account for the cell type heterogeneity in such tissues therefore requires a computational method. We present a computational deconvolution method, deconvSeq, for sequencing data (RNA and bisulfite) obtained from bulk tissue. This method can also be applied to single-cell RNA sequencing data. RESULTS DeconvSeq utilizes a generalized linear model to model effects of tissue type on feature quantification, which is specific to the data structure of the sequencing type used. Estimated model coefficients can then be used to predict the cell type mixture within a tissue. Predicted cell type mixtures were validated against actual cell counts in whole blood samples. Using this method, we obtained a mean correlation of 0.998 (95% CI 0.995-0.999) from the RNA sequencing data of 35 whole blood samples and 0.95 (95% CI 0.91-0.98) from the reduced representation bisulfite sequencing data from 35 whole blood samples. Using symmetric balances to obtain the correlation between compositional parts, we found that the lowest correlation occurred for monocytes for both RNA and bisulfite sequencing. Comparison with other methods of decomposition such as deconRNAseq, CIBERSORT, MuSiC and EpiDISH showed that deconvSeq is able to achieve good prediction using mean correlation with far fewer genes or CpG sites in the signature set. AVAILABILITY AND IMPLEMENTATION Software implementing deconvSeq is available at https://github.com/rosedu1/deconvSeq. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rose Du
- Department of Neurosurgery, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vince Carey
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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21
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Gulati GS, Sikandar SS, Wesche DJ, Manjunath A, Bharadwaj A, Berger MJ, Ilagan F, Kuo AH, Hsieh RW, Cai S, Zabala M, Scheeren FA, Lobo NA, Qian D, Yu FB, Dirbas FM, Clarke MF, Newman AM. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 2020; 367:405-411. [PMID: 31974247 PMCID: PMC7694873 DOI: 10.1126/science.aax0249] [Citation(s) in RCA: 405] [Impact Index Per Article: 101.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/03/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful approach for reconstructing cellular differentiation trajectories. However, inferring both the state and direction of differentiation is challenging. Here, we demonstrate a simple, yet robust, determinant of developmental potential-the number of expressed genes per cell-and leverage this measure of transcriptional diversity to develop a computational framework (CytoTRACE) for predicting differentiation states from scRNA-seq data. When applied to diverse tissue types and organisms, CytoTRACE outperformed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally determined developmental trajectories. Additionally, it facilitated the identification of quiescent stem cells and revealed genes that contribute to breast tumorigenesis. This study thus establishes a key RNA-based feature of developmental potential and a platform for delineation of cellular hierarchies.
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Affiliation(s)
- Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Shaheen S Sikandar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel J Wesche
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Anoop Manjunath
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Anjan Bharadwaj
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark J Berger
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Francisco Ilagan
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angera H Kuo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Robert W Hsieh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Shang Cai
- School of Life Sciences, Westlake University, Zhejiang Province, China
| | - Maider Zabala
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ferenc A Scheeren
- Department of Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
| | - Neethan A Lobo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dalong Qian
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94305, USA
| | - Frederick M Dirbas
- Department of Surgery, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Michael F Clarke
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.,Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA. .,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
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22
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Borra E, Luppino G, Gerbella M, Rozzi S, Rockland KS. Projections to the putamen from neurons located in the white matter and the claustrum in the macaque. J Comp Neurol 2019; 528:453-467. [PMID: 31483857 DOI: 10.1002/cne.24768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/24/2019] [Accepted: 08/26/2019] [Indexed: 12/21/2022]
Abstract
Continuing investigations of corticostriatal connections in rodents emphasize an intricate architecture where striatal projections originate from different combinations of cortical layers, include an inhibitory component, and form terminal arborizations which are cell-type dependent, extensive, or compact. Here, we report that in macaque monkeys, deep and superficial cortical white matter neurons (WMNs), peri-claustral WMNs, and the claustrum proper project to the putamen. WMNs retrogradely labeled by injections in the putamen (four injections in three macaques) were widely distributed, up to 10 mm antero-posterior from the injection site, mainly dorsal to the putamen in the external capsule, and below the premotor cortex. Striatally projecting labeled WMNs (WMNsST) were heterogeneous in size and shape, including a small GABAergic component. We compared the number of WMNsST with labeled claustral and cortical neurons and also estimated their proportion in relation to total WMNs. Since some WMNsST were located adjoining the claustrum, we wanted to compare results for density and distribution of striatally projecting claustral neurons (ClaST). ClaST neurons were morphologically heterogeneous and mainly located in the dorsal and anterior claustrum, in regions known to project to frontal, motor, and cingulate cortical areas. The ratio of ClaST to WMNsST was about 4:1 averaged across the four injections. These results provide new specifics on the connectional networks of WMNs in nonhuman primates, and delineate additional loops in the corticostriatal architecture, consisting of interconnections across cortex, claustralstriatal and striatally projecting WMNs.
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Affiliation(s)
- Elena Borra
- Department of Medicine and Surgery, Neuroscience Unit, University of Parma, Parma, Italy
| | - Giuseppe Luppino
- Department of Medicine and Surgery, Neuroscience Unit, University of Parma, Parma, Italy
| | - Marzio Gerbella
- Department of Medicine and Surgery, Neuroscience Unit, University of Parma, Parma, Italy
| | - Stefano Rozzi
- Department of Medicine and Surgery, Neuroscience Unit, University of Parma, Parma, Italy
| | - Kathleen S Rockland
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA
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23
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Donega V, Marcy G, Lo Giudice Q, Zweifel S, Angonin D, Fiorelli R, Abrous DN, Rival-Gervier S, Koehl M, Jabaudon D, Raineteau O. Transcriptional Dysregulation in Postnatal Glutamatergic Progenitors Contributes to Closure of the Cortical Neurogenic Period. Cell Rep 2019. [PMID: 29514086 DOI: 10.1016/j.celrep.2018.02.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Progenitors of cortical glutamatergic neurons (Glu progenitors) are usually thought to switch fate before birth to produce astrocytes. We used fate-mapping approaches to show that a large fraction of Glu progenitors persist in the postnatal forebrain after closure of the cortical neurogenesis period. Postnatal Glu progenitors do not accumulate during embryonal development but are produced by embryonal radial glial cells that persist after birth in the dorsal subventricular zone and continue to give rise to cortical neurons, although with low efficiency. Single-cell RNA sequencing reveals a dysregulation of transcriptional programs, which parallels changes in m6A methylation and correlates with the gradual decline in cortical neurogenesis observed in vivo. Rescuing experiments show that postnatal progenitors are partially permissive to genetic and pharmacological manipulations. Our study provides an in-depth characterization of postnatal Glu progenitors and identifies potential therapeutic targets for promoting brain repair.
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Affiliation(s)
- Vanessa Donega
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France.
| | - Guillaume Marcy
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France; Neurogenetics Department, Ecole Pratique des Hautes Etudes, PSL Research University, 75014 Paris, France
| | - Quentin Lo Giudice
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Stefan Zweifel
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Diane Angonin
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Roberto Fiorelli
- Brain Research Institute, University of Zürich/ETHZ, Zürich, Switzerland
| | - Djoher Nora Abrous
- Neurocentre Magendie, Neurogenesis and Physiopathology Group, Inserm, U1215, 33077 Bordeaux, France; Université de Bordeaux, 33077 Bordeaux, France
| | - Sylvie Rival-Gervier
- Stem Cell and Brain Research Institute U1208, Université Claude Bernard Lyon 1, Inserm, INRA, USC1361, 69500 Bron, France
| | - Muriel Koehl
- Neurocentre Magendie, Neurogenesis and Physiopathology Group, Inserm, U1215, 33077 Bordeaux, France; Université de Bordeaux, 33077 Bordeaux, France
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Olivier Raineteau
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France; Brain Research Institute, University of Zürich/ETHZ, Zürich, Switzerland.
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24
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Sedmak G, Judaš M. The total number of white matter interstitial neurons in the human brain. J Anat 2019; 235:626-636. [PMID: 31173356 DOI: 10.1111/joa.13018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2019] [Indexed: 02/06/2023] Open
Abstract
In the adult human brain, the interstitial neurons (WMIN) of the subcortical white matter are the surviving remnants of the fetal subplate zone. It has been suggested that they perform certain important functions and may be involved in the pathogenesis of several neurological and psychiatric disorders. However, many important features of this class of human cortical neurons remain insufficiently explored. In this study, we analyzed the total number, and regional and topological distribution of WMIN in the adult human subcortical white matter, using a combined immunocytochemical (NeuN) and stereological approaches. We found that the average number of WMIN in 1 mm3 of the subcortical white matter is 1.230 ± 549, which translates to the average total number of 593 811 183.6 ± 264 849 443.35 of WMIN in the entire subcortical telencephalic white matter. While there were no significant differences in their regional distribution, the lowest number of WMIN has been consistently observed in the limbic cortex, and the highest number in the frontal cortex. With respect to their topological distribution, the WMIN were consistently more numerous within gyral crowns, less numerous along gyral walls and least numerous at the bottom of cortical sulci (where they occupy a narrow and compact zone below the cortical-white matter border). The topological location of WMIN is also significantly correlated with their morphology: pyramidal and multipolar forms are the most numerous within gyral crowns, whereas bipolar forms predominate at the bottom of cortical sulci. Our results indicate that WMIN represent substantial neuronal population in the adult human cerebral cortex (e.g. more numerous than thalamic or basal ganglia neurons) and thus deserve more detailed morphological and functional investigations in the future.
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Affiliation(s)
- Goran Sedmak
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia.,Center for Excellence in Basic, Clinical and Translational Neuroscience, Zagreb, Croatia
| | - Miloš Judaš
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia.,Center for Excellence in Basic, Clinical and Translational Neuroscience, Zagreb, Croatia
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25
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Tasic B, Yao Z, Graybuck LT, Smith KA, Nguyen TN, Bertagnolli D, Goldy J, Garren E, Economo MN, Viswanathan S, Penn O, Bakken T, Menon V, Miller J, Fong O, Hirokawa KE, Lathia K, Rimorin C, Tieu M, Larsen R, Casper T, Barkan E, Kroll M, Parry S, Shapovalova NV, Hirschstein D, Pendergraft J, Sullivan HA, Kim TK, Szafer A, Dee N, Groblewski P, Wickersham I, Cetin A, Harris JA, Levi BP, Sunkin SM, Madisen L, Daigle TL, Looger L, Bernard A, Phillips J, Lein E, Hawrylycz M, Svoboda K, Jones AR, Koch C, Zeng H. Shared and distinct transcriptomic cell types across neocortical areas. Nature 2018; 563:72-78. [PMID: 30382198 DOI: 10.1038/s41586-018-0654-5] [Citation(s) in RCA: 946] [Impact Index Per Article: 157.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 09/24/2018] [Indexed: 12/11/2022]
Abstract
The neocortex contains a multitude of cell types that are segregated into layers and functionally distinct areas. To investigate the diversity of cell types across the mouse neocortex, here we analysed 23,822 cells from two areas at distant poles of the mouse neocortex: the primary visual cortex and the anterior lateral motor cortex. We define 133 transcriptomic cell types by deep, single-cell RNA sequencing. Nearly all types of GABA (γ-aminobutyric acid)-containing neurons are shared across both areas, whereas most types of glutamatergic neurons were found in one of the two areas. By combining single-cell RNA sequencing and retrograde labelling, we match transcriptomic types of glutamatergic neurons to their long-range projection specificity. Our study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct areas of the adult mouse cortex.
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Affiliation(s)
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael N Economo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sarada Viswanathan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Osnat Penn
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Vilas Menon
- Allen Institute for Brain Science, Seattle, WA, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Sheana Parry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ian Wickersham
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ali Cetin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Loren Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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26
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Swiegers J, Bhagwandin A, Sherwood CC, Bertelsen MF, Maseko BC, Hemingway J, Rockland KS, Molnár Z, Manger PR. The distribution, number, and certain neurochemical identities of infracortical white matter neurons in a lar gibbon (Hylobates lar) brain. J Comp Neurol 2018; 527:1633-1653. [PMID: 30378128 DOI: 10.1002/cne.24545] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/04/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023]
Abstract
We examined the number, distribution, and immunoreactivity of the infracortical white matter neuronal population, also termed white matter interstitial cells (WMICs), in the brain of a lesser ape, the lar gibbon. Staining for neuronal nuclear marker (NeuN) revealed WMICs throughout the infracortical white matter, these cells being most numerous and dense close to cortical layer VI, decreasing significantly in density with depth in the white matter. Stereological analysis of NeuN-immunopositive cells revealed a global estimate of ~67.5 million WMICs within the infracortical white matter of the gibbon brain, indicating that the WMICs are a numerically significant population, ~2.5% of the total cortical gray matter neurons that would be estimated for a primate brain the mass of that of the lar gibbon. Immunostaining revealed subpopulations of WMICs containing neuronal nitric oxide synthase (nNOS, ~7 million in number, with both small and large soma volumes), calretinin (~8.6 million in number, all of similar soma volume), very few WMICs containing parvalbumin, and no calbindin-immunopositive neurons. These nNOS, calretinin, and parvalbumin immunopositive WMICs, presumably all inhibitory neurons, represent ~23.1% of the total WMIC population. As the white matter is affected in many cognitive conditions, such as schizophrenia, autism and also in neurodegenerative diseases, understanding these neurons across species is important for the translation of findings of neural dysfunction in animal models to humans. Furthermore, studies of WMICs in species such as apes provide a crucial phylogenetic context for understanding the evolution of these cell types in the human brain.
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Affiliation(s)
- Jordan Swiegers
- Faculty of Health Sciences, School of Anatomical Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Adhil Bhagwandin
- Faculty of Health Sciences, School of Anatomical Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia
| | - Mads F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Busisiwe C Maseko
- Faculty of Health Sciences, School of Anatomical Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Jason Hemingway
- Faculty of Health Sciences, School of Anatomical Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Kathleen S Rockland
- Department of Anatomy and Neurobiology, School of Medicine, Boston University, Boston, Massachusetts
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, England
| | - Paul R Manger
- Faculty of Health Sciences, School of Anatomical Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
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27
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Lim L, Mi D, Llorca A, Marín O. Development and Functional Diversification of Cortical Interneurons. Neuron 2018; 100:294-313. [PMID: 30359598 PMCID: PMC6290988 DOI: 10.1016/j.neuron.2018.10.009] [Citation(s) in RCA: 364] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 12/18/2022]
Abstract
In the cerebral cortex, GABAergic interneurons have evolved as a highly heterogeneous collection of cell types that are characterized by their unique spatial and temporal capabilities to influence neuronal circuits. Current estimates suggest that up to 50 different types of GABAergic neurons may populate the cerebral cortex, all derived from progenitor cells in the subpallium, the ventral aspect of the embryonic telencephalon. In this review, we provide an overview of the mechanisms underlying the generation of the distinct types of interneurons and their integration in cortical circuits. Interneuron diversity seems to emerge through the implementation of cell-intrinsic genetic programs in progenitor cells, which unfold over a protracted period of time until interneurons acquire mature characteristics. The developmental trajectory of interneurons is also modulated by activity-dependent, non-cell-autonomous mechanisms that influence their ability to integrate in nascent circuits and sculpt their final distribution in the adult 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 SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Da Mi
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Alfredo Llorca
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, UK.
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28
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Elucidating the developmental trajectories of GABAergic cortical interneuron subtypes. Neurosci Res 2018; 138:26-32. [PMID: 30227162 DOI: 10.1016/j.neures.2018.09.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022]
Abstract
GABAergic interneurons in the neocortex play pivotal roles in the feedforward and feedback inhibition that control higher order information processing and thus, malfunction in the inhibitory circuits often leads to neurodevelopmental disorders. Very interestingly, a large diversity of morphology, synaptic targeting specificity, electrophysiological properties and molecular expression profiles are found in cortical interneurons, which originate within the distantly located embryonic ganglionic eminences. Here, I will review the still ongoing effort to understand the developmental trajectories of GABAergic cortical interneuron subtypes.
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29
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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: 53] [Impact Index Per Article: 8.8] [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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30
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Harris KD, Hochgerner H, Skene NG, Magno L, Katona L, Bengtsson Gonzales C, Somogyi P, Kessaris N, Linnarsson S, Hjerling-Leffler J. Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics. PLoS Biol 2018; 16:e2006387. [PMID: 29912866 PMCID: PMC6029811 DOI: 10.1371/journal.pbio.2006387] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/03/2018] [Accepted: 05/22/2018] [Indexed: 01/19/2023] Open
Abstract
Understanding any brain circuit will require a categorization of its constituent neurons. In hippocampal area CA1, at least 23 classes of GABAergic neuron have been proposed to date. However, this list may be incomplete; additionally, it is unclear whether discrete classes are sufficient to describe the diversity of cortical inhibitory neurons or whether continuous modes of variability are also required. We studied the transcriptomes of 3,663 CA1 inhibitory cells, revealing 10 major GABAergic groups that divided into 49 fine-scale clusters. All previously described and several novel cell classes were identified, with three previously described classes unexpectedly found to be identical. A division into discrete classes, however, was not sufficient to describe the diversity of these cells, as continuous variation also occurred between and within classes. Latent factor analysis revealed that a single continuous variable could predict the expression levels of several genes, which correlated similarly with it across multiple cell types. Analysis of the genes correlating with this variable suggested it reflects a range from metabolically highly active faster-spiking cells that proximally target pyramidal cells to slower-spiking cells targeting distal dendrites or interneurons. These results elucidate the complexity of inhibitory neurons in one of the simplest cortical structures and show that characterizing these cells requires continuous modes of variation as well as discrete cell classes.
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Affiliation(s)
- Kenneth D. Harris
- University College London Institute of Neurology, London, United Kingdom
- University College London Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Hannah Hochgerner
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nathan G. Skene
- University College London Institute of Neurology, London, United Kingdom
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Lorenza Magno
- University College London Wolfson Institute for Biomedical Research, London, United Kingdom
| | - Linda Katona
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Carolina Bengtsson Gonzales
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Somogyi
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Nicoletta Kessaris
- University College London Wolfson Institute for Biomedical Research, London, United Kingdom
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jens Hjerling-Leffler
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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Tasic B. Single cell transcriptomics in neuroscience: cell classification and beyond. Curr Opin Neurobiol 2018; 50:242-249. [DOI: 10.1016/j.conb.2018.04.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 12/15/2022]
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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: 146] [Impact Index Per Article: 24.3] [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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Mayer C, Hafemeister C, Bandler RC, Machold R, Brito RB, Jaglin X, Allaway K, Butler A, Fishell G, Satija R. Developmental diversification of cortical inhibitory interneurons. Nature 2018; 555:457-462. [PMID: 29513653 PMCID: PMC6052457 DOI: 10.1038/nature25999] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 02/12/2018] [Indexed: 12/28/2022]
Abstract
Diverse subsets of cortical interneurons have vital roles in higher-order brain functions. To investigate how this diversity is generated, here we used single-cell RNA sequencing to profile the transcriptomes of mouse cells collected along a developmental time course. Heterogeneity within mitotic progenitors in the ganglionic eminences is driven by a highly conserved maturation trajectory, alongside eminence-specific transcription factor expression that seeds the emergence of later diversity. Upon becoming postmitotic, progenitors diverge and differentiate into transcriptionally distinct states, including an interneuron precursor state. By integrating datasets across developmental time points, we identified shared sources of transcriptomic heterogeneity between adult interneurons and their precursors, and uncovered the embryonic emergence of cardinal interneuron subtypes. Our analysis revealed that the transcription factor Mef2c, which is linked to various neuropsychiatric and neurodevelopmental disorders, delineates early precursors of parvalbumin-expressing neurons, and is essential for their development. These findings shed new light on the molecular diversification of early inhibitory precursors, and identify gene modules that may influence the specification of human interneuron subtypes.
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Affiliation(s)
- Christian Mayer
- NYU Neuroscience Institute, Langone Medical Center, New York, NY,
USA
- New York Genome Center, New York, NY, USA
- Harvard Medical School, Department of Neurobiology, Boston MA,
USA
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge
MA, USA
| | | | - Rachel C. Bandler
- NYU Neuroscience Institute, Langone Medical Center, New York, NY,
USA
| | - Robert Machold
- NYU Neuroscience Institute, Langone Medical Center, New York, NY,
USA
| | - Renata Batista Brito
- NYU Neuroscience Institute, Langone Medical Center, New York, NY,
USA
- Dominick P Purpura Department of Neuroscience, Albert Einstein
College of Medicine, Bronx, New York, USA
| | - Xavier Jaglin
- NYU Neuroscience Institute, Langone Medical Center, New York, NY,
USA
- Harvard Medical School, Department of Neurobiology, Boston MA,
USA
| | - Kathryn Allaway
- NYU Neuroscience Institute, Langone Medical Center, New York, NY,
USA
- Harvard Medical School, Department of Neurobiology, Boston MA,
USA
| | - Andrew Butler
- New York Genome Center, New York, NY, USA
- New York University, Center for Genomics and Systems Biology, New
York NY, USA
| | - Gord Fishell
- NYU Neuroscience Institute, Langone Medical Center, New York, NY,
USA
- Harvard Medical School, Department of Neurobiology, Boston MA,
USA
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge
MA, USA
| | - Rahul Satija
- New York Genome Center, New York, NY, USA
- New York University, Center for Genomics and Systems Biology, New
York NY, USA
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Castrillo JI, Lista S, Hampel H, Ritchie CW. Systems Biology Methods for Alzheimer’s Disease Research Toward Molecular Signatures, Subtypes, and Stages and Precision Medicine: Application in Cohort Studies and Trials. Methods Mol Biol 2018; 1750:31-66. [PMID: 29512064 DOI: 10.1007/978-1-4939-7704-8_3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juan I Castrillo
- Genetadi Biotech S.L. Parque Tecnológico de Bizkaia, Derio, Bizkaia, Spain.
| | - Simone Lista
- AXA Research Fund & UPMC Chair, F-75013, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l'hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l'hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l'hôpital, F-75013, Paris, France
| | - Harald Hampel
- AXA Research Fund & UPMC Chair, F-75013, Paris, France
- Sorbonne Université, AP-HP, GRC n° 21, Alzheimer Precision Medicine (APM), Hôpital de la Pitié-Salpêtrière, Boulevard de l'hôpital, F-75013, Paris, France
- Institut du Cerveau et de la Moelle Épinière (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l'hôpital, F-75013, Paris, France
- Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Boulevard de l'hôpital, F-75013, Paris, France
| | - Craig W Ritchie
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
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Ruiz-Reig N, Studer M. Rostro-Caudal and Caudo-Rostral Migrations in the Telencephalon: Going Forward or Backward? Front Neurosci 2017; 11:692. [PMID: 29311773 PMCID: PMC5742585 DOI: 10.3389/fnins.2017.00692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/23/2017] [Indexed: 11/13/2022] Open
Abstract
The generation and differentiation of an appropriate number of neurons, as well as its distribution in different parts of the brain, is crucial for the proper establishment, maintenance and plasticity of neural circuitries. Newborn neurons travel along the brain in a process known as neuronal migration, to finalize their correct position in the nervous system. Defects in neuronal migration produce abnormalities in the brain that can generate neurodevelopmental pathologies, such as autism, schizophrenia and intellectual disability. In this review, we present an overview of the developmental origin of the different telencephalic subdivisions and a description of migratory pathways taken by distinct neural populations traveling long distances before reaching their target position in the brain. In addition, we discuss some of the molecules implicated in the guidance of these migratory paths and transcription factors that contribute to the correct migration and integration of these neurons.
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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: 163] [Impact Index Per Article: 23.3] [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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