1
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Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J. Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches. Genome Res 2024; 34:484-497. [PMID: 38580401 PMCID: PMC11067882 DOI: 10.1101/gr.277926.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/21/2024] [Indexed: 04/07/2024]
Abstract
Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.
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Affiliation(s)
- Muyoung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingqing Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Joonhyuk Choi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alia Segura
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alper Genceroglu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Nereida Ramirez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yeejin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA;
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2
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Rakotobe M, Fjerdingstad N, Ruiz-Reig N, Lamonerie T, D'Autréaux F. Central role of the habenulo-interpeduncular system in the neurodevelopmental basis of susceptibility and resilience to anxiety in mice. Neurobiol Dis 2024; 191:106392. [PMID: 38145853 DOI: 10.1016/j.nbd.2023.106392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/27/2023] Open
Abstract
Having experienced stress during sensitive periods of brain development strongly influences how individuals cope with later stress. Some are prone to develop anxiety or depression, while others appear resilient. The as-yet-unknown mechanisms underlying these differences may lie in how genes and environmental stress interact to shape the circuits that control emotions. Here, we investigated the role of the habenulo-interpeduncular system (HIPS), a critical node in reward circuits, in early stress-induced anxiety in mice. We found that habenular and IPN components characterized by the expression of Otx2 are synaptically connected and particularly sensitive to chronic stress (CS) during the peripubertal period. Stress-induced peripubertal activation of this HIPS subcircuit elicits both HIPS hypersensitivity to later stress and susceptibility to develop anxiety. We also show that HIPS silencing through conditional Otx2 knockout counteracts these effects of stress. Together, these results demonstrate that a genetic factor, Otx2, and stress interact during the peripubertal period to shape the stress sensitivity of the HIPS, which is shown to be a key modulator of susceptibility or resilience to develop anxiety.
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Affiliation(s)
- Malalaniaina Rakotobe
- Université Côte d'Azur, CNRS, Inserm, iBV, Institut de Biologie Valrose, 06108 Nice, France
| | - Niels Fjerdingstad
- Université Côte d'Azur, CNRS, Inserm, iBV, Institut de Biologie Valrose, 06108 Nice, France
| | - Nuria Ruiz-Reig
- Université Côte d'Azur, CNRS, Inserm, iBV, Institut de Biologie Valrose, 06108 Nice, France
| | - Thomas Lamonerie
- Université Côte d'Azur, CNRS, Inserm, iBV, Institut de Biologie Valrose, 06108 Nice, France.
| | - Fabien D'Autréaux
- Université Côte d'Azur, CNRS, Inserm, iBV, Institut de Biologie Valrose, 06108 Nice, France. Fabien.D'
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3
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van de Haar LL, Riga D, Boer JE, Garritsen O, Adolfs Y, Sieburgh TE, van Dijk RE, Watanabe K, van Kronenburg NCH, Broekhoven MH, Posthuma D, Meye FJ, Basak O, Pasterkamp RJ. Molecular signatures and cellular diversity during mouse habenula development. Cell Rep 2022; 40:111029. [PMID: 35793630 DOI: 10.1016/j.celrep.2022.111029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/18/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022] Open
Abstract
The habenula plays a key role in various motivated and pathological behaviors and is composed of molecularly distinct neuron subtypes. Despite progress in identifying mature habenula neuron subtypes, how these subtypes develop and organize into functional brain circuits remains largely unknown. Here, we performed single-cell transcriptional profiling of mouse habenular neurons at critical developmental stages, instructed by detailed three-dimensional anatomical data. Our data reveal cellular and molecular trajectories during embryonic and postnatal development, leading to different habenular subtypes. Further, based on this analysis, our work establishes the distinctive functional properties and projection target of a subtype of Cartpt+ habenula neurons. Finally, we show how comparison of single-cell transcriptional profiles and GWAS data links specific developing habenular subtypes to psychiatric disease. Together, our study begins to dissect the mechanisms underlying habenula neuron subtype-specific development and creates a framework for further interrogation of habenular development in normal and disease states.
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Affiliation(s)
- Lieke L van de Haar
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Danai Riga
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Juliska E Boer
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Oxana Garritsen
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Youri Adolfs
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Thomas E Sieburgh
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Roland E van Dijk
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, 1081 Amsterdam, the Netherlands
| | - Nicky C H van Kronenburg
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Mark H Broekhoven
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, 1081 Amsterdam, the Netherlands
| | - Frank J Meye
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - Onur Basak
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center, Utrecht University, 3584 Utrecht, the Netherlands.
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4
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Vidal B, Gulez B, Cao WX, Leyva-Diaz E, Reilly MB, Tekieli T, Hobert O. The enteric nervous system of the C. elegans pharynx is specified by the Sine oculis-like homeobox gene ceh-34. eLife 2022; 11:76003. [PMID: 35324425 PMCID: PMC8989417 DOI: 10.7554/elife.76003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/23/2022] [Indexed: 11/29/2022] Open
Abstract
Overarching themes in the terminal differentiation of the enteric nervous system, an autonomously acting unit of animal nervous systems, have so far eluded discovery. We describe here the overall regulatory logic of enteric nervous system differentiation of the nematode Caenorhabditis elegans that resides within the foregut (pharynx) of the worm. A C. elegans homolog of the Drosophila Sine oculis homeobox gene, ceh-34, is expressed in all 14 classes of interconnected pharyngeal neurons from their birth throughout their life time, but in no other neuron type of the entire animal. Constitutive and temporally controlled ceh-34 removal shows that ceh-34 is required to initiate and maintain the neuron type-specific terminal differentiation program of all pharyngeal neuron classes, including their circuit assembly. Through additional genetic loss of function analysis, we show that within each pharyngeal neuron class, ceh-34 cooperates with different homeodomain transcription factors to individuate distinct pharyngeal neuron classes. Our analysis underscores the critical role of homeobox genes in neuronal identity specification and links them to the control of neuronal circuit assembly of the enteric nervous system. Together with the pharyngeal nervous system simplicity as well as its specification by a Sine oculis homolog, our findings invite speculations about the early evolution of nervous systems.
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Affiliation(s)
- Berta Vidal
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Burcu Gulez
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Wen Xi Cao
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Eduardo Leyva-Diaz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Tessa Tekieli
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
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5
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Hobert O. Homeobox genes and the specification of neuronal identity. Nat Rev Neurosci 2021; 22:627-636. [PMID: 34446866 DOI: 10.1038/s41583-021-00497-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2021] [Indexed: 12/27/2022]
Abstract
The enormous diversity of cell types that characterizes any animal nervous system is defined by neuron-type-specific gene batteries that endow cells with distinct anatomical and functional properties. To understand how such cellular diversity is genetically specified, one needs to understand the gene regulatory programmes that control the expression of cell-type-specific gene batteries. The small nervous system of the nematode Caenorhabditis elegans has been comprehensively mapped at the cellular and molecular levels, which has enabled extensive, nervous system-wide explorations into whether there are common underlying mechanisms that specify neuronal cell-type diversity. One principle that emerged from these studies is that transcription factors termed 'terminal selectors' coordinate the expression of individual members of neuron-type-specific gene batteries, thereby assigning unique identities to individual neuron types. Systematic mutant analyses and recent nervous system-wide expression analyses have revealed that one transcription factor family, the homeobox gene family, is broadly used throughout the entire C. elegans nervous system to specify neuronal identity as terminal selectors. I propose that the preponderance of homeobox genes in neuronal identity control is a reflection of an evolutionary trajectory in which an ancestral neuron type was specified by one or more ancestral homeobox genes, and that this functional linkage then duplicated and diversified to generate distinct cell types in an evolving nervous system.
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Affiliation(s)
- Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY, USA.
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6
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Berghoff EG, Glenwinkel L, Bhattacharya A, Sun H, Varol E, Mohammadi N, Antone A, Feng Y, Nguyen K, Cook SJ, Wood JF, Masoudi N, Cros CC, Ramadan YH, Ferkey DM, Hall DH, Hobert O. The Prop1-like homeobox gene unc-42 specifies the identity of synaptically connected neurons. eLife 2021; 10:e64903. [PMID: 34165428 PMCID: PMC8225392 DOI: 10.7554/elife.64903] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Many neuronal identity regulators are expressed in distinct populations of cells in the nervous system, but their function is often analyzed only in specific isolated cellular contexts, thereby potentially leaving overarching themes in gene function undiscovered. We show here that the Caenorhabditis elegans Prop1-like homeobox gene unc-42 is expressed in 15 distinct sensory, inter- and motor neuron classes throughout the entire C. elegans nervous system. Strikingly, all 15 neuron classes expressing unc-42 are synaptically interconnected, prompting us to investigate whether unc-42 controls the functional properties of this circuit and perhaps also the assembly of these neurons into functional circuitry. We found that unc-42 defines the routes of communication between these interconnected neurons by controlling the expression of neurotransmitter pathway genes, neurotransmitter receptors, neuropeptides, and neuropeptide receptors. Anatomical analysis of unc-42 mutant animals reveals defects in axon pathfinding and synaptic connectivity, paralleled by expression defects of molecules involved in axon pathfinding, cell-cell recognition, and synaptic connectivity. We conclude that unc-42 establishes functional circuitry by acting as a terminal selector of functionally connected neuron types. We identify a number of additional transcription factors that are also expressed in synaptically connected neurons and propose that terminal selectors may also function as 'circuit organizer transcription factors' to control the assembly of functional circuitry throughout the nervous system. We hypothesize that such organizational properties of transcription factors may be reflective of not only ontogenetic, but perhaps also phylogenetic trajectories of neuronal circuit establishment.
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Affiliation(s)
- Emily G Berghoff
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Lori Glenwinkel
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Abhishek Bhattacharya
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - HaoSheng Sun
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Erdem Varol
- Department of Statistics, Zuckerman Institute, Columbia UniversityNew YorkUnited States
| | - Nicki Mohammadi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Amelia Antone
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Yi Feng
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Ken Nguyen
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineBronxUnited States
| | - Steven J Cook
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Jordan F Wood
- Department of Biological Sciences, University at Buffalo, The State University of New YorkBuffaloUnited States
| | - Neda Masoudi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Cyril C Cros
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Yasmin H Ramadan
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Denise M Ferkey
- Department of Biological Sciences, University at Buffalo, The State University of New YorkBuffaloUnited States
| | - David H Hall
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineBronxUnited States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
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7
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Coles C, Lasek AW. Binge-Like Ethanol Drinking Increases Otx2, Wnt1, and Mdk Gene Expression in the Ventral Tegmental Area of Adult Mice. Neurosci Insights 2021; 16:26331055211009850. [PMID: 33954290 PMCID: PMC8058803 DOI: 10.1177/26331055211009850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/25/2021] [Indexed: 12/23/2022] Open
Abstract
Alcohol use disorder is associated with pathophysiological changes in the dopaminergic system. Orthodenticle homeobox 2 (OTX2) is a transcription factor important for the development of dopaminergic neurons residing in the ventral tegmental area (VTA), a critical region of the brain involved in drug reinforcement. Previous studies have demonstrated that ethanol exposure during embryonic development reduces Otx2 mRNA levels in the central nervous system. We hypothesized that levels of OTX2 would be altered by binge-like ethanol consumption in adult animals. To test this, Otx2 mRNA and protein levels in the mouse VTA were measured by quantitative real-time PCR and western blotting, respectively, after mice drank ethanol for 4 days in a procedure that elicits binge levels of ethanol consumption (drinking in the dark). Expression of known and putative OTX2 transcriptional target genes (Sema3c, Wnt1, and Mdk) were also measured in the VTA after ethanol drinking. Otx2 mRNA and protein levels were elevated in the VTA 24 hours after the fourth drinking session and there was a corresponding increase in the expression of Mdk transcript. Interestingly, Wnt1 transcript was elevated in the VTA immediately after the fourth drinking session but returned to control levels 24 hours later. We next investigated if viral-mediated reduction of Otx2 in the mouse VTA would alter ethanol or sucrose intake. Lentiviral vectors expressing a shRNA targeting Otx2 or a control shRNA were injected into the VTA and mice were tested in the drinking in the dark protocol for ethanol and sucrose drinking. Reducing levels of OTX2 in the VTA did not alter ethanol or sucrose consumption. One limitation is that the extent of OTX2 reduction may not have been sufficient. Although OTX2 in the VTA may not play a role in binge-like drinking in adult mice, OTX2 could contribute to ethanol-induced transcriptional changes in this region.
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Affiliation(s)
- Cassandre Coles
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA.,Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, USA
| | - Amy W Lasek
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
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8
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Wang GT, Pan HY, Lang WH, Yu YD, Hsieh CH, Kuan YS. Three-dimensional multi-gene expression maps reveal cell fate changes associated with laterality reversal of zebrafish habenula. J Neurosci Res 2021; 99:1632-1645. [PMID: 33638209 DOI: 10.1002/jnr.24806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 11/09/2022]
Abstract
The conserved bilateral habenular nuclei (HA) in vertebrate diencephalon develop into compartmentalized structures containing neurons derived from different cell lineages. Despite extensive studies demonstrated that zebrafish larval HA display distinct left-right (L-R) asymmetry in gene expression and connectivity, the spatial gene expression domains were mainly obtained from two-dimensional (2D) snapshots of colorimetric RNA in situ hybridization staining which could not properly reflect different HA neuronal lineages constructed in three-dimension (3D). Combing the tyramide-based fluorescent mRNA in situ hybridization, confocal microscopy and customized imaging processing procedures, we have created spatial distribution maps of four genes for 4-day-old zebrafish and in sibling fish whose L-R asymmetry was spontaneously reversed. 3D volumetric analyses showed that ratios of cpd2, lov, ron, and nrp1a expression in L-R reversed HA were reversed according to the parapineal positions. However, the quantitative changes of gene expression in reversed larval brains do not mirror the gene expression level in the obverse larval brains. There were a total 87.78% increase in lov+ nrp1a+ and a total 12.45% decrease in lov+ ron+ double-positive neurons when the L-R asymmetry of HA was reversed. Thus, our volumetric analyses of the 3D maps indicate that changes of HA neuronal cell fates are associated with the reversal of HA laterality. These changes likely account for the behavior changes associated with HA laterality alterations.
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Affiliation(s)
- Guo-Tzau Wang
- National Center for High-Performance Computing, Hsinchu, Taiwan R.O.C
| | - He-Yen Pan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan R.O.C
| | - Wei-Han Lang
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan R.O.C
| | - Yuan-Ding Yu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan R.O.C
| | - Chang-Huain Hsieh
- National Center for High-Performance Computing, Hsinchu, Taiwan R.O.C
| | - Yung-Shu Kuan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan R.O.C.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan R.O.C.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan R.O.C.,Neuroscience Program, Academia Sinica, Taipei, Taiwan R.O.C
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9
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García-Guillén IM, Alonso A, Puelles L, Marín F, Aroca P. Multiple Regionalized Genes and Their Putative Networks in the Interpeduncular Nucleus Suggest Complex Mechanisms of Neuron Development and Axon Guidance. Front Neuroanat 2021; 15:643320. [PMID: 33664652 PMCID: PMC7921722 DOI: 10.3389/fnana.2021.643320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/26/2021] [Indexed: 12/27/2022] Open
Abstract
The interpeduncular nucleus (IPN) is a highly conserved limbic structure in the vertebrate brain, located in the isthmus and rhombomere 1. It is formed by various populations that migrate from different sites to the distinct domains within the IPN: the prodromal, rostral interpeduncular, and caudal interpeduncular nuclei. The aim here was to identify genes that are differentially expressed across these domains, characterizing their putative functional roles and interactions. To this end, we screened the 2,038 genes in the Allen Developing Mouse Brain Atlas database expressed at E18.5 and we identified 135 genes expressed within the IPN. The functional analysis of these genes highlighted an overrepresentation of gene families related to neuron development, cell morphogenesis and axon guidance. The interactome analysis within each IPN domain yielded specific networks that mainly involve members of the ephrin/Eph and Cadherin families, transcription factors and molecules related to synaptic neurotransmission. These results bring to light specific mechanisms that might participate in the formation, molecular regionalization, axon guidance and connectivity of the different IPN domains. This genoarchitectonic model of the IPN enables data on gene expression and interactions to be integrated and interpreted, providing a basis for the further study of the connectivity and function of this poorly understood nuclear complex under both normal and pathological conditions.
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Affiliation(s)
- Isabel M García-Guillén
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia and IMIB-Arrixaca, Murcia, Spain
| | - Antonia Alonso
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia and IMIB-Arrixaca, Murcia, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia and IMIB-Arrixaca, Murcia, Spain
| | - Faustino Marín
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia and IMIB-Arrixaca, Murcia, Spain
| | - Pilar Aroca
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia and IMIB-Arrixaca, Murcia, Spain
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10
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García-Guillén IM, Alonso A, Morales-Delgado N, Andrés B, Puelles L, López-Bendito G, Marín F, Aroca P. Netrin-1/DCC Signaling Differentially Regulates the Migration of Pax7, Nkx6.1, Irx2, Otp, and Otx2 Cell Populations in the Developing Interpeduncular Nucleus. Front Cell Dev Biol 2020; 8:588851. [PMID: 33195252 PMCID: PMC7606981 DOI: 10.3389/fcell.2020.588851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/30/2020] [Indexed: 12/27/2022] Open
Abstract
The interpeduncular nucleus (IPN) is a hindbrain structure formed by three main subdivisions, the prodromal (Pro) domain located at the isthmus (Ist), and the rostral and caudal interpeduncular domains (IPR, IPC) within rhombomere 1 (r1). Various cell populations can be detected in the IPN through the expression of the Nkx6.1, Otp, Otx2, Pax7, and/or Irx2 transcription factors. These cell populations follow independent dorsoventral tangential and radial migratory routes targeting the ventral paramedian region of Ist and r1. Here we set out to examine the influence of the Netrin-1/DCC pathway on these migrations, since it is known to regulate other processes of neuronal migration in the brain. To this end, we analyzed IPN development in late gestational wild-type and DCC-/- mice, using mainly in situ hybridization (ISH) to identify the cells expressing each of the aforementioned genes. We found that the migration of Nkx6.1 + and Irx2 + cells into the Pro domain was strongly disrupted by the loss of DCC, as occurred with the migration of Pax7 +, Irx2 +, and Otp + cells that would normally form the IPR. In addition, there was mild impairment of the migration of the Pax7 + and Otx2 + cells that form the IPC. These results demonstrate that the Netrin-1/DCC signaling pathway is involved in the migration of most of the IPN populations, mainly affecting those of the Pro and IPR domains of this nucleus. There are psychiatric disorders that involve the medial habenula (mHb)-IPN system, so that this experimental model could provide a basis to study their neurodevelopmental etiology.
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Affiliation(s)
- Isabel M García-Guillén
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain.,Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | - Antonia Alonso
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain.,Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | - Nicanor Morales-Delgado
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain.,Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain.,Department of Histology and Anatomy, School of Medicine, Miguel Hernández University, Alicante, Spain
| | - Belén Andrés
- Instituto de Neurociencias de Alicante, CSIC, Universidad Miguel Hernández, Alicante, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain.,Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | | | - Faustino Marín
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain.,Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
| | - Pilar Aroca
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain.,Biomedical Research Institute of Murcia (IMIB-Arrixaca), Murcia, Spain
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Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain. Cell Rep 2020; 33:108268. [PMID: 33053343 DOI: 10.1016/j.celrep.2020.108268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/09/2020] [Accepted: 09/22/2020] [Indexed: 12/18/2022] Open
Abstract
Tegmental nuclei in the ventral midbrain and anterior hindbrain control motivated behavior, mood, memory, and movement. These nuclei contain inhibitory GABAergic and excitatory glutamatergic neurons, whose molecular diversity and development remain largely unraveled. Many tegmental neurons originate in the embryonic ventral rhombomere 1 (r1), where GABAergic fate is regulated by the transcription factor (TF) Tal1. We used single-cell mRNA sequencing of the mouse ventral r1 to characterize the Tal1-dependent and independent neuronal precursors. We describe gene expression dynamics during bifurcation of the GABAergic and glutamatergic lineages and show how active Notch signaling promotes GABAergic fate selection in post-mitotic precursors. We identify GABAergic precursor subtypes that give rise to distinct tegmental nuclei and demonstrate that Sox14 and Zfpm2, two TFs downstream of Tal1, are necessary for the differentiation of specific tegmental GABAergic neurons. Our results provide a framework for understanding the development of cellular diversity in the tegmental nuclei.
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