1
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Chiou KL, Huang X, Bohlen MO, Tremblay S, DeCasien AR, O’Day DR, Spurrell CH, Gogate AA, Zintel TM, Andrews MG, Martínez MI, Starita LM, Montague MJ, Platt ML, Shendure J, Snyder-Mackler N. A single-cell multi-omic atlas spanning the adult rhesus macaque brain. SCIENCE ADVANCES 2023; 9:eadh1914. [PMID: 37824616 PMCID: PMC10569716 DOI: 10.1126/sciadv.adh1914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
Cataloging the diverse cellular architecture of the primate brain is crucial for understanding cognition, behavior, and disease in humans. Here, we generated a brain-wide single-cell multimodal molecular atlas of the rhesus macaque brain. Together, we profiled 2.58 M transcriptomes and 1.59 M epigenomes from single nuclei sampled from 30 regions across the adult brain. Cell composition differed extensively across the brain, revealing cellular signatures of region-specific functions. We also identified 1.19 M candidate regulatory elements, many previously unidentified, allowing us to explore the landscape of cis-regulatory grammar and neurological disease risk in a cell type-specific manner. Altogether, this multi-omic atlas provides an open resource for investigating the evolution of the human brain and identifying novel targets for disease interventions.
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Affiliation(s)
- Kenneth L. Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Martin O. Bohlen
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Sébastien Tremblay
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Alex R. DeCasien
- Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD, USA
| | - Diana R. O’Day
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Cailyn H. Spurrell
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Aishwarya A. Gogate
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Trisha M. Zintel
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Cayo Biobank Research Unit
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
- Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, PR, USA
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
- Marketing Department, University of Pennsylvania, Philadelphia, PA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Madeline G. Andrews
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Melween I. Martínez
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, PR, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Michael J. Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael L. Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
- Marketing Department, University of Pennsylvania, Philadelphia, PA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
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2
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Puls R, von Haefen C, Bührer C, Endesfelder S. Protective Effect of Dexmedetomidine against Hyperoxia-Damaged Cerebellar Neurodevelopment in the Juvenile Rat. Antioxidants (Basel) 2023; 12:antiox12040980. [PMID: 37107355 PMCID: PMC10136028 DOI: 10.3390/antiox12040980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Impaired cerebellar development of premature infants and the associated impairment of cerebellar functions in cognitive development could be crucial factors for neurodevelopmental disorders. Anesthetic- and hyperoxia-induced neurotoxicity of the immature brain can lead to learning and behavioral disorders. Dexmedetomidine (DEX), which is associated with neuroprotective properties, is increasingly being studied for off-label use in the NICU. For this purpose, six-day-old Wistar rats (P6) were exposed to hyperoxia (80% O2) or normoxia (21% O2) for 24 h after DEX (5 µg/kg, i.p.) or vehicle (0.9% NaCl) application. An initial detection in the immature rat cerebellum was performed after the termination of hyperoxia at P7 and then after recovery in room air at P9, P11, and P14. Hyperoxia reduced the proportion of Calb1+-Purkinje cells and affected the dendrite length at P7 and/or P9/P11. Proliferating Pax6+-granule progenitors remained reduced after hyperoxia and until P14. The expression of neurotrophins and neuronal transcription factors/markers of proliferation, migration, and survival were also reduced by oxidative stress in different manners. DEX demonstrated protective effects on hyperoxia-injured Purkinje cells, and DEX without hyperoxia modulated neuronal transcription in the short term without any effects at the cellular level. DEX protects hyperoxia-damaged Purkinje cells and appears to differentially affect cerebellar granular cell neurogenesis following oxidative stress.
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Affiliation(s)
- Robert Puls
- Department of Neonatology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Clarissa von Haefen
- Department of Anesthesiology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Christoph Bührer
- Department of Neonatology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefanie Endesfelder
- Department of Neonatology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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3
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Yan K, Bormuth I, Bormuth O, Tutukova S, Renner A, Bessa P, Schaub T, Rosário M, Tarabykin V. TrkB-dependent EphrinA reverse signaling regulates callosal axon fasciculate growth downstream of Neurod2/6. Cereb Cortex 2023; 33:1752-1767. [PMID: 35462405 DOI: 10.1093/cercor/bhac170] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/14/2022] Open
Abstract
Abnormal development of corpus callosum is relatively common and causes a broad spectrum of cognitive impairments in humans. We use acallosal Neurod2/6-deficient mice to study callosal axon guidance within the ipsilateral cerebral cortex. Initial callosal tracts form but fail to traverse the ipsilateral cingulum and are not attracted towards the midline in the absence of Neurod2/6. We show that the restoration of Ephrin-A4 (EfnA4) expression in the embryonic neocortex of Neurod2/6-deficient embryos is sufficient to partially rescue targeted callosal axon growth towards the midline. EfnA4 cannot directly mediate reverse signaling within outgrowing axons, but it forms co-receptor complexes with TrkB (Ntrk2). The ability of EfnA4 to rescue the guided growth of a subset of callosal axons in Neurod2/6-deficient mice is abolished by the co-expression of dominant negative TrkBK571N (kinase-dead) or TrkBY515F (SHC-binding deficient) variants, but not by TrkBY816F (PLCγ1-binding deficient). Additionally, EphA4 is repulsive to EfnA4-positive medially projecting axons in organotypic brain slice culture. Collectively, we suggest that EfnA4-mediated reverse signaling acts via TrkB-SHC and is required for ipsilateral callosal axon growth accuracy towards the midline downstream of Neurod family factors.
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Affiliation(s)
- Kuo Yan
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Ingo Bormuth
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Olga Bormuth
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany.,Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia
| | - Svetlana Tutukova
- Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia.,Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Ana Renner
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Paraskevi Bessa
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Theres Schaub
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Marta Rosário
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany
| | - Victor Tarabykin
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, D-10117, Berlin, Germany.,Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia.,Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
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Leung HW, Foo G, VanDongen A. Arc Regulates Transcription of Genes for Plasticity, Excitability and Alzheimer’s Disease. Biomedicines 2022; 10:biomedicines10081946. [PMID: 36009494 PMCID: PMC9405677 DOI: 10.3390/biomedicines10081946] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023] Open
Abstract
The immediate early gene Arc is a master regulator of synaptic function and a critical determinant of memory consolidation. Here, we show that Arc interacts with dynamic chromatin and closely associates with histone markers for active enhancers and transcription in cultured rat hippocampal neurons. Both these histone modifications, H3K27Ac and H3K9Ac, have recently been shown to be upregulated in late-onset Alzheimer’s disease (AD). When Arc induction by pharmacological network activation was prevented using a short hairpin RNA, the expression profile was altered for over 1900 genes, which included genes associated with synaptic function, neuronal plasticity, intrinsic excitability, and signalling pathways. Interestingly, about 100 Arc-dependent genes are associated with the pathophysiology of AD. When endogenous Arc expression was induced in HEK293T cells, the transcription of many neuronal genes was increased, suggesting that Arc can control expression in the absence of activated signalling pathways. Taken together, these data establish Arc as a master regulator of neuronal activity-dependent gene expression and suggest that it plays a significant role in the pathophysiology of AD.
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Affiliation(s)
| | - Gabriel Foo
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Antonius VanDongen
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
- Correspondence:
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5
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Dendritic Inhibition by Shh Signaling-Dependent Stellate Cell Pool Is Critical for Motor Learning. J Neurosci 2022; 42:5130-5143. [PMID: 35589396 PMCID: PMC9236294 DOI: 10.1523/jneurosci.2073-21.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/14/2022] [Accepted: 04/11/2022] [Indexed: 12/31/2022] Open
Abstract
Cerebellar inhibitory interneurons are important regulators of neural circuit activity for diverse motor and nonmotor functions. The molecular layer interneurons (MLIs), consisting of basket cells (BCs) and stellate cells (SCs), provide dendritic and somatic inhibitory synapses onto Purkinje cells, respectively. They are sequentially generated in an inside-out pattern from Pax2+ immature interneurons, which migrate from the prospective white matter to the ML of the cortex. However, little is known about how MLI subtype identities and pool sizes are determined, nor are their contributions to motor learning well understood. Here, we show that GABAergic progenitors fated to generate both BCs and SCs respond to the Sonic hedgehog (Shh) signal. Conditional abrogation of Shh signaling of either sex inhibited proliferation of GABAergic progenitors and reduced the number of Pax2+ cells, whereas persistent Shh pathway activation increased their numbers. These changes, however, did not affect early born BC numbers but selectively altered the SC pool size. Moreover, genetic depletion of GABAergic progenitors when BCs are actively generated also resulted in a specific reduction of SCs, suggesting that the specification of MLI subtypes is independent of Shh signaling and their birth order and likely occurs after Pax2+ cells settle into their laminar positions in an inside-out sequence. Mutant mice with reduced SC numbers displayed decreased dendritic inhibitory synapses and neurotransmission onto Purkinje cells, resulting in an impaired acquisition of eyeblink conditioning. These findings also reveal an essential role of Shh signaling-dependent SCs in regulating inhibitory dendritic synapses and motor learning.SIGNIFICANCE STATEMENT The cerebellar circuit that enables fine motor learning involves MLIs of BCs and SCs, which provide dendritic and somatic inhibitory synapses onto Purkinje cells. Little is known about how their identities and numbers are determined, nor are their specific contributions to motor learning well understood. We show that MLI subtypes are specified independent of Shh signaling and their birth orders but appear to occur in their terminal laminar positions according to the inside-out sequence. This finding challenges the current view that MLI subtypes are specified sequentially at the progenitor level. We also demonstrate that dendritic inhibition by Shh signaling-dependent SC pool is necessary for motor learning.
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6
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Morphological pseudotime ordering and fate mapping reveal diversification of cerebellar inhibitory interneurons. Nat Commun 2022; 13:3433. [PMID: 35701402 PMCID: PMC9197879 DOI: 10.1038/s41467-022-30977-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/20/2022] [Indexed: 12/15/2022] Open
Abstract
Understanding how diverse neurons are assembled into circuits requires a framework for describing cell types and their developmental trajectories. Here we combine genetic fate-mapping, pseudotemporal profiling of morphogenesis, and dual morphology and RNA labeling to resolve the diversification of mouse cerebellar inhibitory interneurons. Molecular layer interneurons (MLIs) derive from a common progenitor population but comprise diverse dendritic-, somatic-, and axon initial segment-targeting interneurons. Using quantitative morphology from 79 mature MLIs, we identify two discrete morphological types and presence of extensive within-class heterogeneity. Pseudotime trajectory inference using 732 developmental morphologies indicate the emergence of distinct MLI types during migration, before reaching their final positions. By comparing MLI identities from morphological and transcriptomic signatures, we demonstrate the dissociation between these modalities and that subtype divergence can be resolved from axonal morphogenesis prior to marker gene expression. Our study illustrates the utility of applying single-cell methods to quantify morphology for defining neuronal diversification.
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7
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The Conflicting Role of Caffeine Supplementation on Hyperoxia-Induced Injury on the Cerebellar Granular Cell Neurogenesis of Newborn Rats. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5769784. [PMID: 35693697 PMCID: PMC9175096 DOI: 10.1155/2022/5769784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/04/2022] [Accepted: 04/28/2022] [Indexed: 11/28/2022]
Abstract
Preterm birth disrupts cerebellar development, which may be mediated by systemic oxidative stress that damages neuronal developmental stages. Impaired cerebellar neurogenesis affects several downstream targets important for cognition, emotion, and speech. In this study, we demonstrate that oxidative stress induced with high oxygen (80%) for three or five postnatal days (P3/P5) could significantly damage neurogenesis and proliferative capacity of granular cell precursor and Purkinje cells in rat pups. Reversal of cellular neuronal damage after recovery to room air (P15) was augmented by treatment with caffeine. However, downstream transcripts important for migration and differentiation of postmitotic granular cells were irreversibly reduced by hyperoxia, without rescue by caffeine. Protective effects of caffeine in the cerebellum were limited to neuronal survival but failed to restore important transcript signatures.
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8
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Jiao S, Johnson K, Moreno C, Yano S, Holmgren M. Comparative description of the mRNA expression profile of Na + /K + -ATPase isoforms in adult mouse nervous system. J Comp Neurol 2021; 530:627-647. [PMID: 34415061 PMCID: PMC8716420 DOI: 10.1002/cne.25234] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/16/2021] [Accepted: 08/16/2021] [Indexed: 11/09/2022]
Abstract
Mutations in genes encoding Na+ /K+ -ATPase α1, α2, and α3 subunits cause a wide range of disabling neurological disorders, and dysfunction of Na+ /K+ -ATPase may contribute to neuronal injury in stroke and dementia. To better understand the pathogenesis of these diseases, it is important to determine the expression patterns of the different Na+ /K+ -ATPase subunits within the brain and among specific cell types. Using two available scRNA-Seq databases from the adult mouse nervous system, we examined the mRNA expression patterns of the different isoforms of the Na+ /K+ -ATPase α, β and Fxyd subunits at the single-cell level among brain regions and various neuronal populations. We subsequently identified specific types of neurons enriched with transcripts for α1 and α3 isoforms and elaborated how α3-expressing neuronal populations govern cerebellar neuronal circuits. We further analyzed the co-expression network for α1 and α3 isoforms, highlighting the genes that positively correlated with α1 and α3 expression. The top 10 genes for α1 were Chn2, Hpcal1, Nrgn, Neurod1, Selm, Kcnc1, Snrk, Snap25, Ckb and Ccndbp1 and for α3 were Sorcs3, Eml5, Neurod2, Ckb, Tbc1d4, Ptprz1, Pvrl1, Kirrel3, Pvalb, and Asic2.
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Affiliation(s)
- Song Jiao
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Kory Johnson
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Cristina Moreno
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Sho Yano
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Miguel Holmgren
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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9
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Tutukova S, Tarabykin V, Hernandez-Miranda LR. The Role of Neurod Genes in Brain Development, Function, and Disease. Front Mol Neurosci 2021; 14:662774. [PMID: 34177462 PMCID: PMC8221396 DOI: 10.3389/fnmol.2021.662774] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 01/14/2023] Open
Abstract
Transcriptional regulation is essential for the correct functioning of cells during development and in postnatal life. The basic Helix-loop-Helix (bHLH) superfamily of transcription factors is well conserved throughout evolution and plays critical roles in tissue development and tissue maintenance. A subgroup of this family, called neural lineage bHLH factors, is critical in the development and function of the central nervous system. In this review, we will focus on the function of one subgroup of neural lineage bHLH factors, the Neurod family. The Neurod family has four members: Neurod1, Neurod2, Neurod4, and Neurod6. Available evidence shows that these four factors are key during the development of the cerebral cortex but also in other regions of the central nervous system, such as the cerebellum, the brainstem, and the spinal cord. We will also discuss recent reports that link the dysfunction of these transcription factors to neurological disorders in humans.
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Affiliation(s)
- Svetlana Tutukova
- Institute of Neuroscience, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
| | - Victor Tarabykin
- Institute of Neuroscience, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
| | - Luis R Hernandez-Miranda
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
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Cadilhac C, Bachy I, Forget A, Hodson DJ, Jahannault-Talignani C, Furley AJ, Ayrault O, Mollard P, Sotelo C, Ango F. Excitatory granule neuron precursors orchestrate laminar localization and differentiation of cerebellar inhibitory interneuron subtypes. Cell Rep 2021; 34:108904. [PMID: 33789110 DOI: 10.1016/j.celrep.2021.108904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 12/19/2020] [Accepted: 03/03/2021] [Indexed: 12/18/2022] Open
Abstract
GABAergic interneurons migrate long distances through stereotyped migration programs toward specific laminar positions. During their migration, GABAergic interneurons are morphologically alike but then differentiate into a rich array of interneuron subtypes critical for brain function. How interneuron subtypes acquire their final phenotypic traits remains largely unknown. Here, we show that cerebellar molecular layer GABAergic interneurons, derived from the same progenitor pool, use separate migration paths to reach their laminar position and differentiate into distinct basket cell (BC) and stellate cell (SC) GABAergic interneuron subtypes. Using two-photon live imaging, we find that SC final laminar position requires an extra step of tangential migration supported by a subpopulation of glutamatergic granule cells (GCs). Conditional depletion of GCs affects SC differentiation but does not affect BCs. Our results reveal how timely feedforward control of inhibitory interneuron migration path regulates their terminal differentiation and, thus, establishment of the local inhibitory circuit assembly.
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Affiliation(s)
| | - Isabelle Bachy
- IGF, University Montpellier, CNRS, INSERM, Montpellier, France
| | - Antoine Forget
- Institut Curie, Université PSL, CNRS UMR3347, INSERM U1021, Signaling Radiobiology and Cancer, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3347, INSERM U1021, Signaling Radiobiology and Cancer, 91400 Orsay, France
| | - David J Hodson
- Institute of Metabolism and Systems Research and Centre of Membrane Proteins and Receptors, University of Birmingham, Edgbaston B15 2TT, UK
| | | | - Andrew J Furley
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Olivier Ayrault
- Institut Curie, Université PSL, CNRS UMR3347, INSERM U1021, Signaling Radiobiology and Cancer, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3347, INSERM U1021, Signaling Radiobiology and Cancer, 91400 Orsay, France
| | - Patrice Mollard
- IGF, University Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Fabrice Ango
- IGF, University Montpellier, CNRS, INSERM, Montpellier, France; INM, University Montpellier, INSERM, CNRS, Montpellier, France.
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11
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Safari MS, Obexer D, Baier-Bitterlich G, Zur Nedden S. PKN1 Is a Novel Regulator of Hippocampal GluA1 Levels. Front Synaptic Neurosci 2021; 13:640495. [PMID: 33613259 PMCID: PMC7892898 DOI: 10.3389/fnsyn.2021.640495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
Alterations in the processes that control α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) expression, assembly and trafficking are closely linked to psychiatric and neurodegenerative disorders. We have recently shown that the serine/threonine kinase Protein kinase N1 (PKN1) is a developmentally active regulator of cerebellar synaptic maturation by inhibiting AKT and the neurogenic transcription factor neurogenic differentiation factor-2 (NeuroD2). NeuroD2 is involved in glutamatergic synaptic maturation by regulating expression levels of various synaptic proteins. Here we aimed to study the effect of Pkn1 knockout on AKT phosphorylation and NeuroD2 levels in the hippocampus and the subsequent expression levels of the NeuroD2 targets and AMPAR subunits: glutamate receptor 1 (GluA1) and GluA2/3. We show that PKN1 is expressed throughout the hippocampus. Interestingly, not only postnatal but also adult hippocampal phospho-AKT and NeuroD2 levels were significantly elevated upon Pkn1 knockout. Postnatal and adult Pkn1 -/- hippocampi showed enhanced expression of the AMPAR subunit GluA1, particularly in area CA1. Surprisingly, GluA2/3 levels were not different between both genotypes. In addition to higher protein levels, we also found an enhanced GluA1 content in the membrane fraction of postnatal and adult Pkn1 -/- animals, while GluA2/3 levels remained unchanged. This points toward a very specific regulation of GluA1 expression and/or trafficking by the novel PKN1-AKT-NeuroD2 axis. Considering the important role of GluA1 in hippocampal development as well as the pathophysiology of several disorders, ranging from Alzheimer's, to depression and schizophrenia, our results validate PKN1 for future studies into neurological disorders related to altered AMPAR subunit expression in the hippocampus.
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Affiliation(s)
- Motahareh Solina Safari
- CCB-Biocenter, Institute of Neurobiochemistry, Medical University of Innsbruck, Innsbruck, Austria
| | - Dido Obexer
- CCB-Biocenter, Institute of Neurobiochemistry, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Stephanie Zur Nedden
- CCB-Biocenter, Institute of Neurobiochemistry, Medical University of Innsbruck, Innsbruck, Austria
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12
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Consalez GG, Goldowitz D, Casoni F, Hawkes R. Origins, Development, and Compartmentation of the Granule Cells of the Cerebellum. Front Neural Circuits 2021; 14:611841. [PMID: 33519389 PMCID: PMC7843939 DOI: 10.3389/fncir.2020.611841] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/17/2020] [Indexed: 12/21/2022] Open
Abstract
Granule cells (GCs) are the most numerous cell type in the cerebellum and indeed, in the brain: at least 99% of all cerebellar neurons are granule cells. In this review article, we first consider the formation of the upper rhombic lip, from which all granule cell precursors arise, and the way by which the upper rhombic lip generates the external granular layer, a secondary germinal epithelium that serves to amplify the upper rhombic lip precursors. Next, we review the mechanisms by which postmitotic granule cells are generated in the external granular layer and migrate radially to settle in the granular layer. In addition, we review the evidence that far from being a homogeneous population, granule cells come in multiple phenotypes with distinct topographical distributions and consider ways in which the heterogeneity of granule cells might arise during development.
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Affiliation(s)
- G Giacomo Consalez
- Division of Neuroscience, San Raffaele Scientific Institute, San Raffaele University, Milan, Italy
| | - Daniel Goldowitz
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Filippo Casoni
- Division of Neuroscience, San Raffaele Scientific Institute, San Raffaele University, Milan, Italy
| | - Richard Hawkes
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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13
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Mis EK, Sega AG, Signer RH, Cartwright T, Ji W, Martinez-Agosto JA, Nelson SF, Palmer CGS, Lee H, Mitzelfelt T, Konstantino M, Jeffries L, Khokha MK, Marco E, Martin MG, Lakhani SA. Expansion of NEUROD2 phenotypes to include developmental delay without seizures. Am J Med Genet A 2021; 185:1076-1080. [PMID: 33438828 DOI: 10.1002/ajmg.a.62064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/29/2020] [Accepted: 12/09/2020] [Indexed: 01/23/2023]
Abstract
De novo heterozygous variants in the brain-specific transcription factor Neuronal Differentiation Factor 2 (NEUROD2) have been recently associated with early-onset epileptic encephalopathy and developmental delay. Here, we report an adolescent with developmental delay without seizures who was found to have a novel de novo heterozygous NEUROD2 missense variant, p.(Leu163Pro). Functional testing using an in vivo assay of neuronal differentiation in Xenopus laevis tadpoles demonstrated that the patient variant of NEUROD2 displays minimal protein activity, strongly suggesting a loss of function effect. In contrast, a second rare NEUROD2 variant, p.(Ala235Thr), identified in an adolescent with developmental delay but lacking parental studies for inheritance, showed normal in vivo NEUROD2 activity. We thus provide clinical, genetic, and functional evidence that NEUROD2 variants can lead to developmental delay without accompanying early-onset seizures, and demonstrate how functional testing can complement genetic data when determining variant pathogenicity.
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Affiliation(s)
- Emily K Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Annalisa G Sega
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Rebecca H Signer
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, USA
| | | | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Julian A Martinez-Agosto
- Deparment of Pediatrics, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Stanley F Nelson
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, USA.,Deparment of Pediatrics, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Christina G S Palmer
- Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.,Institute for Society and Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Hane Lee
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Thomas Mitzelfelt
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Elysa Marco
- Cortica, San Rafael, California, USA.,Pediatric Brain Center, University of California San Francisco, San Francisco, California, USA
| | - Martin G Martin
- Deparment of Pediatrics, University of California Los Angeles, Los Angeles, California, USA
| | - Saquib A Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
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14
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Disruption of NEUROD2 causes a neurodevelopmental syndrome with autistic features via cell-autonomous defects in forebrain glutamatergic neurons. Mol Psychiatry 2021; 26:6125-6148. [PMID: 34188164 PMCID: PMC8760061 DOI: 10.1038/s41380-021-01179-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023]
Abstract
While the transcription factor NEUROD2 has recently been associated with epilepsy, its precise role during nervous system development remains unclear. Using a multi-scale approach, we set out to understand how Neurod2 deletion affects the development of the cerebral cortex in mice. In Neurod2 KO embryos, cortical projection neurons over-migrated, thereby altering the final size and position of layers. In juvenile and adults, spine density and turnover were dysregulated in apical but not basal compartments in layer 5 neurons. Patch-clamp recordings in layer 5 neurons of juvenile mice revealed increased intrinsic excitability. Bulk RNA sequencing showed dysregulated expression of many genes associated with neuronal excitability and synaptic function, whose human orthologs were strongly associated with autism spectrum disorders (ASD). At the behavior level, Neurod2 KO mice displayed social interaction deficits, stereotypies, hyperactivity, and occasionally spontaneous seizures. Mice heterozygous for Neurod2 had similar defects, indicating that Neurod2 is haploinsufficient. Finally, specific deletion of Neurod2 in forebrain excitatory neurons recapitulated cellular and behavioral phenotypes found in constitutive KO mice, revealing the region-specific contribution of dysfunctional Neurod2 in symptoms. Informed by these neurobehavioral features in mouse mutants, we identified eleven patients from eight families with a neurodevelopmental disorder including intellectual disability and ASD associated with NEUROD2 pathogenic mutations. Our findings demonstrate crucial roles for Neurod2 in neocortical development, whose alterations can cause neurodevelopmental disorders including intellectual disability and ASD.
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15
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Badea L, Stănescu E. Identifying transcriptomic correlates of histology using deep learning. PLoS One 2020; 15:e0242858. [PMID: 33237966 PMCID: PMC7688140 DOI: 10.1371/journal.pone.0242858] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/11/2020] [Indexed: 12/18/2022] Open
Abstract
Linking phenotypes to specific gene expression profiles is an extremely important problem in biology, which has been approached mainly by correlation methods or, more fundamentally, by studying the effects of gene perturbations. However, genome-wide perturbations involve extensive experimental efforts, which may be prohibitive for certain organisms. On the other hand, the characterization of the various phenotypes frequently requires an expert's subjective interpretation, such as a histopathologist's description of tissue slide images in terms of complex visual features (e.g. 'acinar structures'). In this paper, we use Deep Learning to eliminate the inherent subjective nature of these visual histological features and link them to genomic data, thus establishing a more precisely quantifiable correlation between transcriptomes and phenotypes. Using a dataset of whole slide images with matching gene expression data from 39 normal tissue types, we first developed a Deep Learning tissue classifier with an accuracy of 94%. Then we searched for genes whose expression correlates with features inferred by the classifier and demonstrate that Deep Learning can automatically derive visual (phenotypical) features that are well correlated with the transcriptome and therefore biologically interpretable. As we are particularly concerned with interpretability and explainability of the inferred histological models, we also develop visualizations of the inferred features and compare them with gene expression patterns determined by immunohistochemistry. This can be viewed as a first step toward bridging the gap between the level of genes and the cellular organization of tissues.
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Affiliation(s)
- Liviu Badea
- Artificial Intelligence and Bioinformatics Group, National Institute for Research and Development in Informatics, Bucharest, Romania
| | - Emil Stănescu
- Artificial Intelligence and Bioinformatics Group, National Institute for Research and Development in Informatics, Bucharest, Romania
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16
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Inglis GAS, Zhou Y, Patterson DG, Scharer CD, Han Y, Boss JM, Wen Z, Escayg A. Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons. Hum Mol Genet 2020; 29:2579-2595. [PMID: 32794569 PMCID: PMC7471504 DOI: 10.1093/hmg/ddaa150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/09/2020] [Accepted: 07/11/2020] [Indexed: 12/13/2022] Open
Abstract
GABAergic interneurons (GINs) are a heterogeneous population of inhibitory neurons that collectively contribute to the maintenance of normal neuronal excitability and network activity. Identification of the genetic regulatory elements and transcription factors that contribute toward GIN function may provide new insight into the pathways underlying proper GIN activity while also indicating potential therapeutic targets for GIN-associated disorders, such as schizophrenia and epilepsy. In this study, we examined the temporal changes in gene expression and chromatin accessibility during GIN development by performing transcriptomic and epigenomic analyses on human induced pluripotent stem cell-derived neurons at 22, 50 and 78 days (D) post-differentiation. We observed 13 221 differentially accessible regions (DARs) of chromatin that associate with temporal changes in gene expression at D78 and D50, relative to D22. We also classified families of transcription factors that are increasingly enriched at DARs during differentiation, indicating regulatory networks that likely drive GIN development. Collectively, these data provide a resource for examining the molecular networks regulating GIN functionality.
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Affiliation(s)
- George Andrew S Inglis
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ying Zhou
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dillon G Patterson
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yanfei Han
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew Escayg
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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