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Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. SCIENCE ADVANCES 2024; 10:eadp6039. [PMID: 39028813 PMCID: PMC11259177 DOI: 10.1126/sciadv.adp6039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/13/2024] [Indexed: 07/21/2024]
Abstract
The adult hippocampus generates new granule cells (aGCs) with functional capabilities that convey unique forms of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like cells (RGLs) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to study aGC differentiation using single-nuclei RNA sequencing. Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple immature stages bearing increasing levels of effector genes supporting growth, excitability, and synaptogenesis. Analysis of differential gene expression, pseudo-time trajectory, and transcription factors (TFs) revealed critical transitions defining four cellular states: quiescent RGLs, proliferative progenitors, immature aGCs, and mature aGCs. Becoming mature aGCs involved a transcriptional switch that shuts down pathways promoting cell growth, such SoxC TFs, to activate programs that likely control neuronal homeostasis. aGCs overexpressing Sox4 or Sox11 remained immature. Our results unveil precise molecular mechanisms driving adult RGLs through the pathway of neuronal differentiation.
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Affiliation(s)
- Natalí B. Rasetto
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
| | - Damiana Giacomini
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
| | - Ariel A. Berardino
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
| | - Tomás Vega Waichman
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
| | - Maximiliano S. Beckel
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
| | - Daniela J. Di Bella
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juliana Brown
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - M. Georgina Davies-Sala
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
| | - Chiara Gerhardinger
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dieter Chichung Lie
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Paola Arlotta
- Department of Stem Cells and Regenerative Biology, Harvard University and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ariel Chernomoretz
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Integrative Systems Biology, Leloir Institute, Buenos Aires, Argentina
- University of Buenos Aires, School of Science, Phys Dept and INFINA (CONICET-UBA), Buenos Aires, Argentina
| | - Alejandro F. Schinder
- Instituto de Investigaciones Biomédicas de Buenos Aires (IIBBA) – CONICET, Buenos Aires, Argentina
- Laboratory of Neuronal Plasticity, Leloir Institute, Buenos Aires, Argentina
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2
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Huynh NPT, Osipovitch M, Foti R, Bates J, Mansky B, Cano JC, Benraiss A, Zhao C, Lu QR, Goldman SA. Shared patterns of glial transcriptional dysregulation link Huntington's disease and schizophrenia. Brain 2024:awae166. [PMID: 39028640 DOI: 10.1093/brain/awae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/22/2024] [Accepted: 05/01/2024] [Indexed: 07/21/2024] Open
Abstract
Huntington's disease and juvenile-onset schizophrenia have long been regarded as distinct disorders. However, both manifest cell-intrinsic abnormalities in glial differentiation, with resultant astrocytic dysfunction and hypomyelination. To assess whether a common mechanism might underlie the similar glial pathology of these otherwise disparate conditions, we used comparative correlation network approaches to analyse RNA-sequencing data from human glial progenitor cells (hGPCs) produced from disease-derived pluripotent stem cells. We identified gene sets preserved between Huntington's disease and schizophrenia hGPCs yet distinct from normal controls that included 174 highly connected genes in the shared disease-associated network, focusing on genes involved in synaptic signalling. These synaptic genes were largely suppressed in both schizophrenia and Huntington's disease hGPCs, and gene regulatory network analysis identified a core set of upstream regulators of this network, of which OLIG2 and TCF7L2 were prominent. Among their downstream targets, ADGRL3, a modulator of glutamatergic synapses, was notably suppressed in both schizophrenia and Huntington's disease hGPCs. Chromatin immunoprecipitation sequencing confirmed that OLIG2 and TCF7L2 each bound to the regulatory region of ADGRL3, whose expression was then rescued by lentiviral overexpression of these transcription factors. These data suggest that the disease-associated suppression of OLIG2 and TCF7L2-dependent transcription of glutamate signalling regulators may impair glial receptivity to neuronal glutamate. The consequent loss of activity-dependent mobilization of hGPCs may yield deficient oligodendrocyte production, and hence the hypomyelination noted in these disorders, as well as the disrupted astrocytic differentiation and attendant synaptic dysfunction associated with each. Together, these data highlight the importance of convergent glial molecular pathology in both the pathogenesis and phenotypic similarities of two otherwise unrelated disorders, Huntington's disease and schizophrenia.
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Affiliation(s)
- Nguyen P T Huynh
- Center for Translational Neuromedicine, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
- Center for Translational Neuromedicine and Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mikhail Osipovitch
- Center for Translational Neuromedicine, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | - Rossana Foti
- Center for Translational Neuromedicine, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | - Janna Bates
- Center for Translational Neuromedicine and Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Benjamin Mansky
- Center for Translational Neuromedicine and Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jose C Cano
- Center for Translational Neuromedicine and Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Abdellatif Benraiss
- Center for Translational Neuromedicine and Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Chuntao Zhao
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Q Richard Lu
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
- Center for Translational Neuromedicine and Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
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3
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Hulett RE, Rivera-López C, Gehrke AR, Gompers A, Srivastava M. A wound-induced differentiation trajectory for neurons. Proc Natl Acad Sci U S A 2024; 121:e2322864121. [PMID: 38976727 PMCID: PMC11260127 DOI: 10.1073/pnas.2322864121] [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: 12/28/2023] [Accepted: 05/03/2024] [Indexed: 07/10/2024] Open
Abstract
Animals capable of whole-body regeneration can replace any missing cell type and regenerate fully functional new organs, including new brains, de novo. The regeneration of a new brain requires the formation of diverse neural cell types and their assembly into an organized structure with correctly wired circuits. Recent work in various regenerative animals has revealed transcriptional programs required for the differentiation of distinct neural subpopulations, however, how these transcriptional programs are initiated in response to injury remains unknown. Here, we focused on the highly regenerative acoel worm, Hofstenia miamia, to study wound-induced transcriptional regulatory events that lead to the production of neurons and subsequently a functional brain. Footprinting analysis using chromatin accessibility data on a chromosome-scale genome assembly revealed that binding sites for the Nuclear Factor Y (NFY) transcription factor complex were significantly bound during regeneration, showing a dynamic increase in binding within one hour upon amputation specifically in tail fragments, which will regenerate a new brain. Strikingly, NFY targets were highly enriched for genes with neuronal function. Single-cell transcriptome analysis combined with functional studies identified soxC+ stem cells as a putative progenitor population for multiple neural subtypes. Further, we found that wound-induced soxC expression is likely under direct transcriptional control by NFY, uncovering a mechanism for the initiation of a neural differentiation pathway by early wound-induced binding of a transcriptional regulator.
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Affiliation(s)
- Ryan E. Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Carlos Rivera-López
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA02138
| | - Andrew R. Gehrke
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Annika Gompers
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
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Valcárcel-Hernández V, Vancamp P, Butruille L, Remaud S, Guadaño-Ferraz A. Combined deletion of Mct8 and Dio2 impairs SVZ neurogliogenesis and olfactory function in adult mice. Neurobiol Dis 2024; 199:106572. [PMID: 38901782 DOI: 10.1016/j.nbd.2024.106572] [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: 02/15/2024] [Revised: 05/30/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024] Open
Abstract
Within the adult mouse subventricular zone (SVZ), neural stem cells (NSCs) produce neuroblasts and oligodendrocyte precursor cells (OPCs). T3, the active thyroid hormone, influences renewal and commitment of SVZ progenitors. However, how regulators of T3 availability affect these processes is less understood. Using Mct8/Dio2 knockout mice, we investigated the role of MCT8, a TH transporter, and DIO2, the T3-generating enzyme, in regulating adult SVZ-neurogliogenesis. Single-cell RNA-Seq revealed Mct8 expression in various SVZ cell types in WT mice, while Dio2 was enriched in neurons, astrocytes, and quiescent NSCs. The absence of both regulators in the knockout model dysregulated gene expression, increased the neuroblast/OPC ratio and hindered OPC differentiation. Immunostainings demonstrated compromised neuroblast migration reducing their supply to the olfactory bulbs, impairing interneuron differentiation and odor discrimination. These findings underscore the pivotal roles of MCT8 and DIO2 in neuro- and oligodendrogenesis, offering targets for therapeutic avenues in neurodegenerative and demyelinating diseases.
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Affiliation(s)
- Víctor Valcárcel-Hernández
- Laboratory of Thyroid hormones and CNS, Department of Neurological Diseases and Aging, Instituto de Investigaciones Biomédicas Sols-Morreale, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Arturo Duperier 4, 28029 Madrid, Spain; Laboratory of Molecular Physiology and Adaptation, CNRS UMR 7221, Department Adaptations of Life, Muséum National d'Histoire Naturelle, F-75005 Paris, France
| | - Pieter Vancamp
- Laboratory of Molecular Physiology and Adaptation, CNRS UMR 7221, Department Adaptations of Life, Muséum National d'Histoire Naturelle, F-75005 Paris, France
| | - Lucile Butruille
- Laboratory of Molecular Physiology and Adaptation, CNRS UMR 7221, Department Adaptations of Life, Muséum National d'Histoire Naturelle, F-75005 Paris, France
| | - Sylvie Remaud
- Laboratory of Molecular Physiology and Adaptation, CNRS UMR 7221, Department Adaptations of Life, Muséum National d'Histoire Naturelle, F-75005 Paris, France.
| | - Ana Guadaño-Ferraz
- Laboratory of Thyroid hormones and CNS, Department of Neurological Diseases and Aging, Instituto de Investigaciones Biomédicas Sols-Morreale, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Arturo Duperier 4, 28029 Madrid, Spain.
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5
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Ma Y, He Z, Wang J, Zheng P, Ma Z, Liang Q, Zhang Q, Zhao X, Huang J, Weng W, Jiang J, Feng J. Mild hypothermia promotes neuronal differentiation of human neural stem cells via RBM3-SOX11 signaling pathway. iScience 2024; 27:109435. [PMID: 38523796 PMCID: PMC10960102 DOI: 10.1016/j.isci.2024.109435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/06/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Both therapeutic hypothermia and neural stem cells (NSCs) transplantation have shown promise in neuroprotection and neural repair after brain injury. However, the effects of therapeutic hypothermia on neuronal differentiation of NSCs are not elucidated. In this study, we aimed to investigate whether mild hypothermia promoted neuronal differentiation in cultured and transplanted human NSCs (hNSCs). A significant increase in neuronal differentiation rate of hNSCs was found when exposed to 35°C, from 33% to 45% in vitro and from 7% to 15% in vivo. Additionally, single-cell RNA sequencing identified upregulation of RNA-binding motif protein 3 (RBM3) in neuroblast at 35°C, which stabilized the SRY-box transcription factor 11 (SOX11) mRNA and increased its protein expression, leading to an increase in neuronal differentiation of hNSCs. In conclusion, our study highlights that mild hypothermia at 35°C enhances hNSCs-induced neurogenesis through the novel RBM3-SOX11 signaling pathway, and provides a potential treatment strategy in brain disorders.
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Affiliation(s)
- Yuxiao Ma
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Zhenghui He
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Jiangchang Wang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Ping Zheng
- Department of Neurosurgery, Shanghai Pudong New Area People’s Hospital, Shanghai 201299, China
| | - Zixuan Ma
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Qian Liang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qiao Zhang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Xiongfei Zhao
- Shanghai Angecon Biotechnology Co., Ltd., Shanghai 201318, China
| | - Jialin Huang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Weiji Weng
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Jiyao Jiang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
| | - Junfeng Feng
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Shanghai Institute of Head Trauma, Shanghai 200127, China
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6
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Morizet D, Foucher I, Alunni A, Bally-Cuif L. Reconstruction of macroglia and adult neurogenesis evolution through cross-species single-cell transcriptomic analyses. Nat Commun 2024; 15:3306. [PMID: 38632253 PMCID: PMC11024210 DOI: 10.1038/s41467-024-47484-1] [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: 04/14/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
Macroglia fulfill essential functions in the adult vertebrate brain, producing and maintaining neurons and regulating neuronal communication. However, we still know little about their emergence and diversification. We used the zebrafish D. rerio as a distant vertebrate model with moderate glial diversity as anchor to reanalyze datasets covering over 600 million years of evolution. We identify core features of adult neurogenesis and innovations in the mammalian lineage with a potential link to the rarity of radial glia-like cells in adult humans. Our results also suggest that functions associated with astrocytes originated in a multifunctional cell type fulfilling both neural stem cell and astrocytic functions before these diverged. Finally, we identify conserved elements of macroglial cell identity and function and their time of emergence during evolution.
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Affiliation(s)
- David Morizet
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, F-75015, Paris, France.
- Sorbonne Université, Collège doctoral, F-75005, Paris, France.
| | - Isabelle Foucher
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, F-75015, Paris, France
| | - Alessandro Alunni
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, F-75015, Paris, France
- Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, CNRS UMR9197, F-91190, Gif-sur-Yvette, France
| | - Laure Bally-Cuif
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, F-75015, Paris, France.
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Nguyen JH, Curtis MA, Imami AS, Ryan WG, Alganem K, Neifer KL, Saferin N, Nawor CN, Kistler BP, Miller GW, Shukla R, McCullumsmith RE, Burkett JP. Developmental pyrethroid exposure disrupts molecular pathways for MAP kinase and circadian rhythms in mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.28.555113. [PMID: 37745438 PMCID: PMC10515776 DOI: 10.1101/2023.08.28.555113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Neurodevelopmental disorders (NDDs) are a category of pervasive disorders of the developing nervous system with few or no recognized biomarkers. A significant portion of the risk for NDDs, including attention deficit hyperactivity disorder (ADHD), is contributed by the environment, and exposure to pyrethroid pesticides during pregnancy has been identified as a potential risk factor for NDD in the unborn child. We recently showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice causes male-biased changes to ADHD- and NDD-relevant behaviors as well as the striatal dopamine system. Here, we used an integrated multiomics approach to determine the broadest possible set of biological changes in the mouse brain caused by developmental pyrethroid exposure (DPE). Using a litter-based, split-sample design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood, euthanized them, and pulverized and divided whole brain samples for split-sample transcriptomics, kinomics and multiomics integration. Transcriptome analysis revealed alterations to multiple canonical clock genes, and kinome analysis revealed changes in the activity of multiple kinases involved in synaptic plasticity, including the mitogen-activated protein (MAP) kinase ERK. Multiomics integration revealed a dysregulated protein-protein interaction network containing primary clusters for MAP kinase cascades, regulation of apoptosis, and synaptic function. These results demonstrate that DPE causes a multi-modal biophenotype in the brain relevant to ADHD and identifies new potential mechanisms of action. NEW & NOTEWORTHY Here, we provide the first evidence that low-dose developmental exposure to the pyrethroid pesticide, deltamethrin, results in molecular disruptions in the adult mouse brain in pathways regulating circadian rhythms and neuronal growth (MAP kinase). This same exposure causes a neurodevelopmental disorder (NDD) relevant behavioral changes in adult mice, making these findings relevant to the prevention of NDDs.
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Wang G, Wang W, Zhang Y, Gou X, Zhang Q, Huang Y, Zhang K, Zhang H, Yang J, Li Y. Ethanol changes Nestin-promoter induced neural stem cells to disturb newborn dendritic spine remodeling in the hippocampus of mice. Neural Regen Res 2024; 19:416-424. [PMID: 37488906 PMCID: PMC10503613 DOI: 10.4103/1673-5374.379051] [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: 10/13/2022] [Revised: 02/14/2023] [Accepted: 05/04/2023] [Indexed: 07/26/2023] Open
Abstract
Adolescent binge drinking leads to long-lasting disorders of the adult central nervous system, particularly aberrant hippocampal neurogenesis. In this study, we applied in vivo fluorescent tracing using NestinCreERT2::Rosa26-tdTomato mice and analyzed the endogenous neurogenesis lineage progression of neural stem cells (NSCs) and dendritic spine formation of newborn neurons in the subgranular zone of the dentate gyrus. We found abnormal orientation of tamoxifen-induced tdTomato+ (tdTom+) NSCs in adult mice 2 months after treatment with EtOH (5.0 g/kg, i.p.) for 7 consecutive days. EtOH markedly inhibited tdTom+ NSCs activation and hippocampal neurogenesis in mouse dentate gyrus from adolescence to adulthood. EtOH (100 mM) also significantly inhibited the proliferation to 39.2% and differentiation of primary NSCs in vitro. Adult mice exposed to EtOH also exhibited marked inhibitions in dendritic spine growth and newborn neuron maturation in the dentate gyrus, which was partially reversed by voluntary running or inhibition of the mammalian target of rapamycin-enhancer of zeste homolog 2 pathway. In vivo tracing revealed that EtOH induced abnormal orientation of tdTom+ NSCs and spatial misposition defects of newborn neurons, thus causing the disturbance of hippocampal neurogenesis and dendritic spine remodeling in mice.
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Affiliation(s)
- Guixiang Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
| | - Wenjia Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
| | - Ye Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
| | - Xiaoying Gou
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
| | - Qingqing Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
| | - Yanmiao Huang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
| | - Kuo Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
| | - Haotian Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
| | - Jingyu Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
| | - Yuting Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, China
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9
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Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.03.565477. [PMID: 38260428 PMCID: PMC10802403 DOI: 10.1101/2023.11.03.565477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The adult hippocampus generates new granule cells (aGCs) that exhibit distinct functional capabilities along development, conveying a unique form of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like neural stem cells (RGL) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to follow newborn aGCs along differentiation using single-nuclei RNA sequencing (snRNA-seq). Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple sequential immature stages bearing increasing levels of effector genes supporting growth, excitability and synaptogenesis. Remarkably, four discrete cellular states were defined by the expression of distinct sets of transcription factors (TFs): quiescent neural stem cells, proliferative progenitors, postmitotic immature aGCs, and mature aGCs. The transition from immature to mature aCGs involved a transcriptional switch that shutdown molecular cascades promoting cell growth, such as the SoxC family of TFs, to activate programs controlling neuronal homeostasis. Indeed, aGCs overexpressing Sox4 or Sox11 remained stalled at the immature state. Our results unveil precise molecular mechanisms driving adult neural stem cells through the pathway of neuronal differentiation.
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10
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Mu C, Gao M, Xu W, Sun X, Chen T, Xu H, Qiu H. Mechanisms of microRNA-132 in central neurodegenerative diseases: A comprehensive review. Biomed Pharmacother 2024; 170:116029. [PMID: 38128185 DOI: 10.1016/j.biopha.2023.116029] [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: 09/14/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
MicroRNA-132 (miR-132) is a highly conserved molecule that plays a crucial regulatory role in central nervous system (CNS) disorders. The expression levels of miR-132 exhibit variability in various neurological disorders and have been closely linked to disease onset and progression. The expression level of miR-132 in the CNS is regulated by a diverse range of stimuli and signaling pathways, including neuronal migration and integration, dendritic outgrowth, and complexity, synaptogenesis, synaptic plasticity, as well as inflammation and apoptosis activation. The aberrant expression of miR-132 in various central neurodegenerative diseases has garnered widespread attention. Clinical studies have revealed altered miR-132 expression levels in both chronic and acute CNS diseases, positioning miR-132 as a potential biomarker or therapeutic target. An in-depth exploration of miR-132 holds the promise of enhancing our understanding of the mechanisms underlying CNS diseases, thereby offering novel insights and strategies for disease diagnosis and treatment. It is anticipated that this review will assist researchers in recognizing the potential value of miR-132 and in generating innovative ideas for clinical trials related to CNS degenerative diseases.
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Affiliation(s)
- Chenxi Mu
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Meng Gao
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Weijing Xu
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China; School of Public Health, Jiamusi University, Jiamusi 154007, Heilongjiang, China
| | - Xun Sun
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Tianhao Chen
- Basic Medical College, Jiamusi University, Jiamusi 154007, Heilongjiang, China; Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China
| | - Hui Xu
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, Jiamusi 154007, Heilongjiang, China.
| | - Hongbin Qiu
- School of Public Health, Jiamusi University, Jiamusi 154007, Heilongjiang, China.
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11
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Hussain G, Akram R, Anwar H, Sajid F, Iman T, Han HS, Raza C, De Aguilar JLG. Adult neurogenesis: a real hope or a delusion? Neural Regen Res 2024; 19:6-15. [PMID: 37488837 PMCID: PMC10479850 DOI: 10.4103/1673-5374.375317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/27/2023] [Accepted: 04/10/2023] [Indexed: 07/26/2023] Open
Abstract
Adult neurogenesis, the process of creating new neurons, involves the coordinated division, migration, and differentiation of neural stem cells. This process is restricted to neurogenic niches located in two distinct areas of the brain: the subgranular zone of the dentate gyrus of the hippocampus and the subventricular zone of the lateral ventricle, where new neurons are generated and then migrate to the olfactory bulb. Neurogenesis has been thought to occur only during the embryonic and early postnatal stages and to decline with age due to a continuous depletion of neural stem cells. Interestingly, recent years have seen tremendous progress in our understanding of adult brain neurogenesis, bridging the knowledge gap between embryonic and adult neurogenesis. Here, we discuss the current status of adult brain neurogenesis in light of what we know about neural stem cells. In this notion, we talk about the importance of intracellular signaling molecules in mobilizing endogenous neural stem cell proliferation. Based on the current understanding, we can declare that these molecules play a role in targeting neurogenesis in the mature brain. However, to achieve this goal, we need to avoid the undesired proliferation of neural stem cells by controlling the necessary checkpoints, which can lead to tumorigenesis and prove to be a curse instead of a blessing or hope.
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Affiliation(s)
- Ghulam Hussain
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Punjab, Pakistan
| | - Rabia Akram
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Punjab, Pakistan
| | - Haseeb Anwar
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Punjab, Pakistan
| | - Faiqa Sajid
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Punjab, Pakistan
| | - Tehreem Iman
- Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Punjab, Pakistan
| | - Hyung Soo Han
- Department of Physiology, School of Medicine, Clinical Omics Institute, Kyungpook National University, Daegu, Korea
| | - Chand Raza
- Department of Zoology, Faculty of Chemistry and Life Sciences, Government College University, Lahore, Pakistan
| | - Jose-Luis Gonzalez De Aguilar
- INSERM, U1118, Mécanismes Centraux et Péripheriques de la Neurodégénérescence, Strasbourg, France, Université de Strasbourg, Strasbourg, France
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12
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Ben-Tov Perry R, Tsoory M, Tolmasov M, Ulitsky I. Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation. Cell Rep 2023; 42:113168. [PMID: 37742186 PMCID: PMC10636608 DOI: 10.1016/j.celrep.2023.113168] [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: 01/10/2023] [Revised: 06/30/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are expressed in many brain circuits and types of neurons; nevertheless, their functional significance for normal brain functions remains elusive. Here, we study the functions in the central nervous system of Silc1, an lncRNA we have shown previously to be important for neuronal regeneration in the peripheral nervous system. We found that Silc1 is rapidly and strongly induced in the hippocampus upon exposure to novelty and is required for efficient spatial learning. Silc1 production is important for induction of Sox11 (its cis-regulated target gene) throughout the CA1-CA3 regions and proper expression of key Sox11 target genes. Consistent with its role in neuronal plasticity, Silc1 levels decline during aging and in models of Alzheimer's disease. Overall, we describe a plasticity pathway in which Silc1 acts as an immediate-early gene to activate Sox11 and induce a neuronal growth-associated transcriptional program important for learning.
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Affiliation(s)
- Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Michael Tsoory
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael Tolmasov
- Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
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13
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Wang X, Llamas J, Trecek T, Shi T, Tao L, Makmura W, Crump JG, Segil N, Gnedeva K. SoxC transcription factors shape the epigenetic landscape to establish competence for sensory differentiation in the mammalian organ of Corti. Proc Natl Acad Sci U S A 2023; 120:e2301301120. [PMID: 37585469 PMCID: PMC10450657 DOI: 10.1073/pnas.2301301120] [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: 01/24/2023] [Accepted: 06/28/2023] [Indexed: 08/18/2023] Open
Abstract
The auditory organ of Corti is comprised of only two major cell types-the mechanosensory hair cells and their associated supporting cells-both specified from a single pool of prosensory progenitors in the cochlear duct. Here, we show that competence to respond to Atoh1, a transcriptional master regulator necessary and sufficient for induction of mechanosensory hair cells, is established in the prosensory progenitors between E12.0 and 13.5. The transition to the competent state is rapid and is associated with extensive remodeling of the epigenetic landscape controlled by the SoxC group of transcription factors. Conditional loss of Sox4 and Sox11-the two homologous family members transiently expressed in the inner ear at the time of competence establishment-blocks the ability of prosensory progenitors to differentiate as hair cells. Mechanistically, we show that Sox4 binds to and establishes accessibility of early sensory lineage-specific regulatory elements, including ones associated with Atoh1 and its direct downstream targets. Consistent with these observations, overexpression of Sox4 or Sox11 prior to developmental establishment of competence precociously induces hair cell differentiation in the cochlear progenitors. Further, reintroducing Sox4 or Sox11 expression restores the ability of postnatal supporting cells to differentiate as hair cells in vitro and in vivo. Our findings demonstrate the pivotal role of SoxC family members as agents of epigenetic and transcriptional changes necessary for establishing competence for sensory receptor differentiation in the inner ear.
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Affiliation(s)
- Xizi Wang
- Caruso Department of Otolaryngology–Head and Neck Surgery, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
| | - Juan Llamas
- Caruso Department of Otolaryngology–Head and Neck Surgery, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
| | - Talon Trecek
- Caruso Department of Otolaryngology–Head and Neck Surgery, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
| | - Tuo Shi
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
| | - Litao Tao
- Caruso Department of Otolaryngology–Head and Neck Surgery, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
| | - Welly Makmura
- Caruso Department of Otolaryngology–Head and Neck Surgery, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
| | - J. Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
| | - Neil Segil
- Caruso Department of Otolaryngology–Head and Neck Surgery, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
| | - Ksenia Gnedeva
- Caruso Department of Otolaryngology–Head and Neck Surgery, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA90033
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14
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Zeppilli S, Gurrola AO, Demetci P, Brann DH, Attey R, Zilkha N, Kimchi T, Datta SR, Singh R, Tosches MA, Crombach A, Fleischmann A. Mammalian olfactory cortex neurons retain molecular signatures of ancestral cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.13.553130. [PMID: 37645751 PMCID: PMC10461972 DOI: 10.1101/2023.08.13.553130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The cerebral cortex diversified extensively during vertebrate evolution. Intriguingly, the three-layered mammalian olfactory cortex resembles the cortical cytoarchitecture of non-mammals yet evolved alongside the six-layered neocortex, enabling unique comparisons for investigating cortical neuron diversification. We performed single-nucleus multiome sequencing across mouse three- to six-layered cortices and compared neuron types across mice, reptiles and salamander. We identified neurons that are olfactory cortex-specific or conserved across mouse cortical areas. However, transcriptomically similar neurons exhibited area-specific epigenetic states. Additionally, the olfactory cortex showed transcriptomic divergence between lab and wild-derived mice, suggesting enhanced circuit plasticity through adult immature neurons. Finally, olfactory cortex neurons displayed marked transcriptomic similarities to reptile and salamander neurons. Together, these data indicate that the mammalian olfactory cortex retains molecular signatures representative of ancestral cortical traits.
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15
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Jeyaraman M, Rajendran RL, Muthu S, Jeyaraman N, Sharma S, Jha SK, Muthukanagaraj P, Hong CM, Furtado da Fonseca L, Santos Duarte Lana JF, Ahn BC, Gangadaran P. An update on stem cell and stem cell-derived extracellular vesicle-based therapy in the management of Alzheimer's disease. Heliyon 2023; 9:e17808. [PMID: 37449130 PMCID: PMC10336689 DOI: 10.1016/j.heliyon.2023.e17808] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 05/10/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
Globally, neurological diseases pose a major burden to healthcare professionals in terms of the management and prevention of the disorder. Among neurological diseases, Alzheimer's disease (AD) accounts for 50%-70% of dementia and is the fifth leading cause of mortality worldwide. AD is a progressive, degenerative neurological disease, with the loss of neurons and synapses in the cerebral cortex and subcortical regions. The management of AD remains a debate among physicians as no standard and specific "disease-modifying" modality is available. The concept of 'Regenerative Medicine' is aimed at regenerating the degenerated neural tissues to reverse the pathology in AD. Genetically modified engineered stem cells modify the course of AD after transplantation into the brain. Extracellular vesicles (EVs) are an emerging new approach in cell communication that involves the transfer of cellular materials from parental cells to recipient cells, resulting in changes at the molecular and signaling levels in the recipient cells. EVs are a type of vesicle that can be transported between cells. Many have proposed that EVs produced from mesenchymal stem cells (MSCs) may have therapeutic promise in the treatment of AD. The biology of AD, as well as the potential applications of stem cells and their derived EVs-based therapy, were explored in this paper.
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Affiliation(s)
- Madhan Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai, Tamil Nadu, 600056, India
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
- Indian Stem Cell Study Group (ISCSG) Association, Lucknow, Uttar Pradesh, 226010, India
| | - Ramya Lakshmi Rajendran
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, 41944, Republic of Korea
| | - Sathish Muthu
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
- Indian Stem Cell Study Group (ISCSG) Association, Lucknow, Uttar Pradesh, 226010, India
- Department of Orthopedics, Government Dindigul Medical College and Hospital, Dindigul, Tamil Nadu, 624001, India
| | - Naveen Jeyaraman
- Indian Stem Cell Study Group (ISCSG) Association, Lucknow, Uttar Pradesh, 226010, India
- Department of Orthopedics, Shri Sathya Sai Medical College and Research Institute, Sri Balaji Vidyapeeth, Chengalpet, Tamil Nadu, 603108, India
| | - Shilpa Sharma
- Indian Stem Cell Study Group (ISCSG) Association, Lucknow, Uttar Pradesh, 226010, India
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - Purushothaman Muthukanagaraj
- Department of Internal Medicine & Psychiatry, SUNY-Upstate Binghamton Clinical Campus, Binghamton, NY, 13904, USA
| | - Chae Moon Hong
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, 41944, Republic of Korea
| | - Lucas Furtado da Fonseca
- Department of Orthopedics, The Federal University of São Paulo, São Paulo, 04023-062, SP, Brazil
| | | | - Byeong-Cheol Ahn
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, 41944, Republic of Korea
- BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Sciences, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea
| | - Prakash Gangadaran
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, 41944, Republic of Korea
- BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Sciences, School of Medicine, Kyungpook National University, Daegu, 41944, Republic of Korea
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16
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Hulett RE, Gehrke AR, Gompers A, Rivera-López C, Srivastava M. A wound-induced differentiation trajectory for neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540286. [PMID: 37214981 PMCID: PMC10197691 DOI: 10.1101/2023.05.10.540286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Animals capable of whole-body regeneration can replace any missing cell type and regenerate fully-functional new organs, de novo . The regeneration of a new brain requires the formation of diverse neuronal cell types and their assembly into an organized structure and correctly-wired circuits. Recent work in various regenerative animals has revealed transcriptional programs required for the differentiation of distinct neuronal subpopulations, however how these transcriptional programs are initiated upon amputation remains unknown. Here, we focused on the highly regenerative acoel worm, Hofstenia miamia , to study wound-induced transcriptional regulatory events that lead to the production of neurons. Footprinting analysis using chromatin accessibility data on an improved genome assembly revealed that binding sites for the NFY transcription factor complex were significantly bound during regeneration, showing a dynamic increase in binding within one hour upon amputation specifically in tail fragments, which will regenerate a new brain. Strikingly, NFY targets were highly enriched for genes with neuronal functional. Single-cell transcriptome analysis combined with functional studies identified sox4 + stem cells as the likely progenitor population for multiple neuronal subtypes. Further, we found that wound-induced sox4 expression is likely under direct transcriptional control by NFY, uncovering a mechanism for how early wound-induced binding of a transcriptional regulator results in the initiation of a neuronal differentiation pathway. Highlights A new chromosome-scale assembly for Hofstenia enables comprehensive analysis of transcription factor binding during regeneration NFY motifs become dynamically bound by 1hpa in regenerating tail fragments, particularly in the loci of neural genes A sox4 + neural-specialized stem cell is identified using scRNA-seq sox4 is wound-induced and required for differentiation of multiple neural cell types NFY regulates wound-induced expression of sox4 during regeneration.
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17
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Chen J, Huang L, Yang Y, Xu W, Qin Q, Qin R, Liang X, Lai X, Huang X, Xie M, Chen L. Somatic Cell Reprogramming for Nervous System Diseases: Techniques, Mechanisms, Potential Applications, and Challenges. Brain Sci 2023; 13:brainsci13030524. [PMID: 36979334 PMCID: PMC10046178 DOI: 10.3390/brainsci13030524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Nervous system diseases present significant challenges to the neuroscience community due to ethical and practical constraints that limit access to appropriate research materials. Somatic cell reprogramming has been proposed as a novel way to obtain neurons. Various emerging techniques have been used to reprogram mature and differentiated cells into neurons. This review provides an overview of somatic cell reprogramming for neurological research and therapy, focusing on neural reprogramming and generating different neural cell types. We examine the mechanisms involved in reprogramming and the challenges that arise. We herein summarize cell reprogramming strategies to generate neurons, including transcription factors, small molecules, and microRNAs, with a focus on different types of cells.. While reprogramming somatic cells into neurons holds the potential for understanding neurological diseases and developing therapeutic applications, its limitations and risks must be carefully considered. Here, we highlight the potential benefits of somatic cell reprogramming for neurological disease research and therapy. This review contributes to the field by providing a comprehensive overview of the various techniques used to generate neurons by cellular reprogramming and discussing their potential applications.
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Affiliation(s)
- Jiafeng Chen
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Lijuan Huang
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Yue Yang
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Wei Xu
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Qingchun Qin
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Rongxing Qin
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Xiaojun Liang
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Xinyu Lai
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Nanning 530021, China
| | - Xiaoying Huang
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Minshan Xie
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Li Chen
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Nanning 530021, China
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18
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The Role of SOX Transcription Factors in Ageing and Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24010851. [PMID: 36614288 PMCID: PMC9821406 DOI: 10.3390/ijms24010851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
The quest for eternal youth and immortality is as old as humankind. Ageing is an inevitable physiological process accompanied by many functional declines that are driving factors for age-related diseases. Stem cell exhaustion is one of the major hallmarks of ageing. The SOX transcription factors play well-known roles in self-renewal and differentiation of both embryonic and adult stem cells. As a consequence of ageing, the repertoire of adult stem cells present in various organs steadily declines, and their dysfunction/death could lead to reduced regenerative potential and development of age-related diseases. Thus, restoring the function of aged stem cells, inducing their regenerative potential, and slowing down the ageing process are critical for improving the health span and, consequently, the lifespan of humans. Reprograming factors, including SOX family members, emerge as crucial players in rejuvenation. This review focuses on the roles of SOX transcription factors in stem cell exhaustion and age-related diseases, including neurodegenerative diseases, visual deterioration, chronic obstructive pulmonary disease, osteoporosis, and age-related cancers. A better understanding of the molecular mechanisms of ageing and the roles of SOX transcription factors in this process could open new avenues for developing novel strategies that will delay ageing and prevent age-related diseases.
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19
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Cao M, Deng Y, Deng Y, Wu J, Yang C, Wang Z, Hou Q, Fu H, Ren Z, Xia X, Li Y, Wang W, Xu H, Liao X, Shu Y. Characterization of immature ovarian teratomas through single-cell transcriptome. Front Immunol 2023; 14:1131814. [PMID: 36936909 PMCID: PMC10020330 DOI: 10.3389/fimmu.2023.1131814] [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: 12/26/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Immature ovarian teratomas are a type of malignant germ cell tumor composed of complicated cell types and are characterized by pathological features of immature neuroectodermal tubules/rosettes. However, there is a lack of understanding of patient-derived immature ovarian teratomas (PDT) at the single cell level. Moreover, whether stem cell lines derived from immature teratomas (CDT) can be used as models for research on PDT remains to be elucidated. Methods Single-cell RNA sequencing (scRNA-seq) and subsequent bioinformatic analysis was performed on three patient-derived immature ovarian teratomas (PDT) samples to reveal the heterogeneity, evolution trajectory, and cell communication within the tumor microenvironment of PDT. Validations were conducted in additional seven samples through multiplex immunofluorescence. Result A total of qualified 22,153 cells were obtained and divided into 28 clusters, which can match to the scRNA-seq annotation of CDT as well as human fetal Cell Atlas, but with higher heterogeneity and more prolific cell-cell crosstalk. Radial glia cells (tagged by SOX2) and immature neuron (tagged by DCX) exhibited mutually exclusive expression and differentiated along distinct evolutionary trajectory from cycling neural progenitors. Proportions of these neuroectodermal cell subtypes may play important roles in PDT through contributing to the internal heterogeneity of PDTs. Moreover, the immune cells in PDTs were infiltrated rather than teratoma-derived, with more abundant macrophage in immature neuron than those in radial glia cells, and the infiltrated macrophage subtypes (i.e., M1 and M2) were significantly correlated to clinical grade. Overall, suppressed evolution process and transcriptome regulation in neuroectodermal cells, reduced cell-cell crosstalk, higher M1/M2 proportion ratio, and enhanced T cell effects in tumor microenvironment are enriched in patients with favorable prognosis. Discussion This study provides a comprehensive profile of PDT at the single cell level, shedding light on the heterogeneity and evolution of neuroectodermal cells within PDTs and the role of immune cells within the tumor microenvironment. Also, our findings highlight the potential usage of CDTs as a model for research on PDT.
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Affiliation(s)
- Minyuan Cao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yun Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yiqi Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chongyi Yang
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zijun Wang
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Qianqian Hou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huancheng Fu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhixiang Ren
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xuyang Xia
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yue Li
- Research Core Facility of West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wei Wang
- Department of Pathology, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Division of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Yang Shu, ; Xin Liao, ; Heng Xu,
| | - Xin Liao
- Department of Pathology, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Yang Shu, ; Xin Liao, ; Heng Xu,
| | - Yang Shu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Yang Shu, ; Xin Liao, ; Heng Xu,
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20
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Alatawneh R, Salomon Y, Eshel R, Orenstein Y, Birnbaum RY. Deciphering transcription factors and their corresponding regulatory elements during inhibitory interneuron differentiation using deep neural networks. Front Cell Dev Biol 2023; 11:1034604. [PMID: 36891511 PMCID: PMC9986276 DOI: 10.3389/fcell.2023.1034604] [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: 09/01/2022] [Accepted: 01/23/2023] [Indexed: 02/22/2023] Open
Abstract
During neurogenesis, the generation and differentiation of neuronal progenitors into inhibitory gamma-aminobutyric acid-containing interneurons is dependent on the combinatorial activity of transcription factors (TFs) and their corresponding regulatory elements (REs). However, the roles of neuronal TFs and their target REs in inhibitory interneuron progenitors are not fully elucidated. Here, we developed a deep-learning-based framework to identify enriched TF motifs in gene REs (eMotif-RE), such as poised/repressed enhancers and putative silencers. Using epigenetic datasets (e.g., ATAC-seq and H3K27ac/me3 ChIP-seq) from cultured interneuron-like progenitors, we distinguished between active enhancer sequences (open chromatin with H3K27ac) and non-active enhancer sequences (open chromatin without H3K27ac). Using our eMotif-RE framework, we discovered enriched motifs of TFs such as ASCL1, SOX4, and SOX11 in the active enhancer set suggesting a cooperativity function for ASCL1 and SOX4/11 in active enhancers of neuronal progenitors. In addition, we found enriched ZEB1 and CTCF motifs in the non-active set. Using an in vivo enhancer assay, we showed that most of the tested putative REs from the non-active enhancer set have no enhancer activity. Two of the eight REs (25%) showed function as poised enhancers in the neuronal system. Moreover, mutated REs for ZEB1 and CTCF motifs increased their in vivo activity as enhancers indicating a repressive effect of ZEB1 and CTCF on these REs that likely function as repressed enhancers or silencers. Overall, our work integrates a novel framework based on deep learning together with a functional assay that elucidated novel functions of TFs and their corresponding REs. Our approach can be applied to better understand gene regulation not only in inhibitory interneuron differentiation but in other tissue and cell types.
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Affiliation(s)
- Rawan Alatawneh
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yahel Salomon
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Reut Eshel
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yaron Orenstein
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Department of Computer Science, Bar-Ilan University, Ramat Gan, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Ramon Y Birnbaum
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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21
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Fong BC, Chakroun I, Iqbal MA, Paul S, Bastasic J, O’Neil D, Yakubovich E, Bejjani AT, Ahmadi N, Carter A, Clark A, Leone G, Park DS, Ghanem N, Vandenbosch R, Slack RS. The Rb/E2F axis is a key regulator of the molecular signatures instructing the quiescent and activated adult neural stem cell state. Cell Rep 2022; 41:111578. [DOI: 10.1016/j.celrep.2022.111578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 08/11/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
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22
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The Genomic Architecture of Pregnancy-Associated Plasticity in the Maternal Mouse Hippocampus. eNeuro 2022; 9:ENEURO.0117-22.2022. [PMID: 36239981 PMCID: PMC9522463 DOI: 10.1523/eneuro.0117-22.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/10/2022] [Accepted: 08/25/2022] [Indexed: 12/15/2022] Open
Abstract
Pregnancy is associated with extraordinary plasticity in the maternal brain. Studies in humans and other mammals suggest extensive structural and functional remodeling of the female brain during and after pregnancy. However, we understand remarkably little about the molecular underpinnings of this natural phenomenon. To gain insight into pregnancy-associated hippocampal plasticity, we performed single nucleus RNA sequencing (snRNA-seq) and snATAC-seq from the mouse hippocampus before, during, and after pregnancy. We identified cell type-specific transcriptional and epigenetic signatures associated with pregnancy and postpartum adaptation. In addition, we analyzed receptor-ligand interactions and transcription factor (TF) motifs that inform hippocampal cell type identity and provide evidence of pregnancy-associated adaption. In total, these data provide a unique resource of coupled transcriptional and epigenetic data across a dynamic time period in the mouse hippocampus and suggest opportunities for functional interrogation of hormone-mediated plasticity.
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23
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Shafik AM, Allen EG, Jin P. Epitranscriptomic dynamics in brain development and disease. Mol Psychiatry 2022; 27:3633-3646. [PMID: 35474104 PMCID: PMC9596619 DOI: 10.1038/s41380-022-01570-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/08/2023]
Abstract
Distinct cell types are generated at specific times during brain development and are regulated by epigenetic, transcriptional, and newly emerging epitranscriptomic mechanisms. RNA modifications are known to affect many aspects of RNA metabolism and have been implicated in the regulation of various biological processes and in disease. Recent studies imply that dysregulation of the epitranscriptome may be significantly associated with neuropsychiatric, neurodevelopmental, and neurodegenerative disorders. Here we review the current knowledge surrounding the role of the RNA modifications N6-methyladenosine, 5-methylcytidine, pseudouridine, A-to-I RNA editing, 2'O-methylation, and their associated machinery, in brain development and human diseases. We also highlight the need for the development of new technologies in the pursuit of directly mapping RNA modifications in both genome- and single-molecule-level approach.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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24
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García-Corzo L, Calatayud-Baselga I, Casares-Crespo L, Mora-Martínez C, Julián Escribano-Saiz J, Hortigüela R, Asenjo-Martínez A, Jordán-Pla A, Ercoli S, Flames N, López-Alonso V, Vilar M, Mira H. The transcription factor LEF1 interacts with NFIX and switches isoforms during adult hippocampal neural stem cell quiescence. Front Cell Dev Biol 2022; 10:912319. [PMID: 35938168 PMCID: PMC9355129 DOI: 10.3389/fcell.2022.912319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022] Open
Abstract
Stem cells in adult mammalian tissues are held in a reversible resting state, known as quiescence, for prolonged periods of time. Recent studies have greatly increased our understanding of the epigenetic and transcriptional landscapes that underlie stem cell quiescence. However, the transcription factor code that actively maintains the quiescence program remains poorly defined. Similarly, alternative splicing events affecting transcription factors in stem cell quiescence have been overlooked. Here we show that the transcription factor T-cell factor/lymphoid enhancer factor LEF1, a central player in canonical β-catenin-dependent Wnt signalling, undergoes alternative splicing and switches isoforms in quiescent neural stem cells. We found that active β-catenin and its partner LEF1 accumulated in quiescent hippocampal neural stem and progenitor cell (Q-NSPC) cultures. Accordingly, Q-NSPCs showed enhanced TCF/LEF1-driven transcription and a basal Wnt activity that conferred a functional advantage to the cultured cells in a Wnt-dependent assay. At a mechanistic level, we found a fine regulation of Lef1 gene expression. The coordinate upregulation of Lef1 transcription and retention of alternative spliced exon 6 (E6) led to the accumulation of a full-length protein isoform (LEF1-FL) that displayed increased stability in the quiescent state. Prospectively isolated GLAST + cells from the postnatal hippocampus also underwent E6 retention at the time quiescence is established in vivo. Interestingly, LEF1 motif was enriched in quiescence-associated enhancers of genes upregulated in Q-NSPCs and quiescence-related NFIX transcription factor motifs flanked the LEF1 binding sites. We further show that LEF1 interacts with NFIX and identify putative LEF1/NFIX targets. Together, our results uncover an unexpected role for LEF1 in gene regulation in quiescent NSPCs, and highlight alternative splicing as a post-transcriptional regulatory mechanism in the transition from stem cell activation to quiescence.
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Affiliation(s)
- Laura García-Corzo
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Isabel Calatayud-Baselga
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Lucía Casares-Crespo
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Carlos Mora-Martínez
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
- Evo-devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juan Julián Escribano-Saiz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | | | | | - Antonio Jordán-Pla
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Stefano Ercoli
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Nuria Flames
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | | | - Marçal Vilar
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
| | - Helena Mira
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), València, Spain
- *Correspondence: Helena Mira,
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25
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Reprogramming neurons for regeneration: The fountain of youth. Prog Neurobiol 2022; 214:102284. [PMID: 35533809 DOI: 10.1016/j.pneurobio.2022.102284] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/03/2022] [Accepted: 05/02/2022] [Indexed: 01/22/2023]
Abstract
Neurons in the central nervous system (CNS) are terminally differentiated cells that gradually lose their ability to support regeneration during maturation due to changes in transcriptomic and chromatin landscape. Similar transcriptomic changes also occur during development when stem cells differentiate into different types of somatic cells. Importantly, differentiated cells can be reprogrammed back to induced pluripotent stems cells (iPSCs) via global epigenetic remodeling by combined overexpression of pluripotent reprogramming factors, including Oct4, Sox2, Klf4, c-Myc, Nanog, and/or Lin28. Moreover, recent findings showed that many proneural transcription factors were able to convert non-neural somatic cells into neurons bypassing the pluripotent stage via direct reprogramming. Interestingly, many of these factors have recently been identified as key regulators of CNS neural regeneration. Recent studies indicated that these factors could rejuvenate mature CNS neurons back to a younger state through cellular state reprogramming, thus favoring regeneration. Here we will review some recent findings regarding the roles of genetic cellular state reprogramming in regulation of neural regeneration and explore the potential underlying molecular mechanisms. Moreover, by using newly emerging techniques, such as multiomics sequencing with big data analysis and Crispr-based gene editing, we will discuss future research directions focusing on better revealing cellular state reprogramming-induced remodeling of chromatin landscape and potential translational application.
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26
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Bhawe K, Das JK, Yoo C, Felty Q, Gong Z, Deoraj A, Liuzzi JP, Ehtesham NZ, Hasnain SE, Singh VP, Mohapatra I, Komotar RJ, Roy D. Nuclear respiratory factor 1 transcriptomic signatures as prognostic indicators of recurring aggressive mesenchymal glioblastoma and resistance to therapy in White American females. J Cancer Res Clin Oncol 2022; 148:1641-1682. [PMID: 35441887 DOI: 10.1007/s00432-022-03987-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/17/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE The mechanisms contributing to recurrence of glioblastoma (GBM), an aggressive neuroepithelial brain tumor, remain unknown. We have recently shown that nuclear respiratory factor 1 (NRF1) is an oncogenic transcription factor and its transcriptional activity is associated with the progression and prognosis of GBM. Herein, we extend our efforts to (1) identify influential NRF1-driven gene and microRNA (miRNA) expression for the aggressiveness of mesenchymal GBM; and (2) understand the molecular basis for its poor response to therapy. METHODS Clinical data and RNA-Seq from four independent GBM cohorts were analyzed by Bayesian Network Inference with Java Objects (BANJO) and Markov chain Monte Carlo (MCMC)-based gene order to identify molecular drivers of mesenchymal GBM as well as prognostic indicators of poor response to radiation and chemotherapy. RESULTS We are the first to report sex-specific NRF1 motif enriched gene signatures showing increased susceptibility to GBM. Risk estimates for GBM were increased by greater than 100-fold with the joint effect of NRF1-driven gene signatures-CDK4, DUSP6, MSH2, NRF1, and PARK7 in female GBM patients and CDK4, CASP2, H6PD, and NRF1 in male GBM patients. NRF1-driven causal Bayesian network genes were predictive of poor survival and resistance to chemoradiation in IDH1 wild-type mesenchymal GBM patients. NRF1-regulatable miRNAs were also associated with poor response to chemoradiation therapy in female IDH1 wild-type mesenchymal GBM. Stable overexpression of NRF1 reprogramed human astrocytes into neural stem cell-like cells expressing SOX2 and nestin. These cells differentiated into neurons and form tumorospheroids. CONCLUSIONS In summary, our novel discovery shows that NRF1-driven causal genes and miRNAs involved in cancer cell stemness and mesenchymal features contribute to cancer aggressiveness and recurrence of aggressive therapy-resistant glioblastoma.
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Affiliation(s)
- Kaumudi Bhawe
- Department of Environmental Health Sciences, Florida International University, Miami, FL, 33199, USA
| | - Jayanta K Das
- Department of Environmental Health Sciences, Florida International University, Miami, FL, 33199, USA
| | - Changwon Yoo
- Department of Biostatistics, Florida International University, Miami, FL, 33199, USA
| | - Quentin Felty
- Department of Environmental Health Sciences, Florida International University, Miami, FL, 33199, USA
| | - Zhenghua Gong
- Department of Biostatistics, Florida International University, Miami, FL, 33199, USA
| | - Alok Deoraj
- Department of Environmental Health Sciences, Florida International University, Miami, FL, 33199, USA
| | - Juan P Liuzzi
- Department of Dietetics and Nutrition, Florida International University, Miami, FL, 33199, USA
| | - Nasreen Z Ehtesham
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Delhi (IIT-D), Indian Institute of Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - Varindera Paul Singh
- Institute of Neuroscience, Medanta-The Medicity, Gurugram, Haryana, 12200, India
| | - Ishani Mohapatra
- Institute of Neuroscience, Medanta-The Medicity, Gurugram, Haryana, 12200, India
| | - Ricardo Jorge Komotar
- Department of Neurological Surgery, University of Miami School of Medicine, Miami, FL, USA
| | - Deodutta Roy
- Department of Environmental Health Sciences, Florida International University, Miami, FL, 33199, USA.
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27
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Abulaiti X, Wang A, Zhang H, Su H, Gao R, Chen J, Gao S, Li L. Disrupted mossy fiber connections from defective embryonic neurogenesis contribute to SOX11-associated schizophrenia. Cell Mol Life Sci 2022; 79:180. [PMID: 35254515 PMCID: PMC11072709 DOI: 10.1007/s00018-022-04206-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/29/2022] [Accepted: 02/09/2022] [Indexed: 11/26/2022]
Abstract
Abnormal mossy fiber connections in the hippocampus have been implicated in schizophrenia. However, it remains unclear whether this abnormality in the patients is genetically determined and whether it contributes to the onset of schizophrenia. Here, we showed that iPSC-derived hippocampal NPCs from schizophrenia patients with the A/A allele at SNP rs16864067 exhibited abnormal NPC polarity, resulting from the downregulation of SOX11 by this high-risk allele. In the SOX11-deficient mouse brain, abnormal NPC polarity was also observed in the hippocampal dentate gyrus, and this abnormal NPC polarity led to defective hippocampal neurogenesis-specifically, irregular neuroblast distribution and disrupted granule cell morphology. As granule cell synapses, the mossy fiber pathway was disrupted, and this disruption was resistant to activity-induced mossy fiber remodeling in SOX11 mutant mice. Moreover, these mutant mice exhibited diminished PPI and schizophrenia-like behaviors. Activation of hippocampal neurogenesis in the embryonic brain, but not in the adult brain, partially alleviated disrupted mossy fiber connections and improved schizophrenia-related behaviors in mutant mice. We conclude that disrupted mossy fiber connections are genetically determined and strongly correlated with schizophrenia-like behaviors in SOX11-deficient mice. This disruption may reflect the pathological substrate of SOX11-associated schizophrenia.
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Affiliation(s)
- Xianmixinuer Abulaiti
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Shanghai Advanced Research Institute Chinese Academy of Sciences, Shanghai, 201210, China
| | - Aifang Wang
- Shanghai Advanced Research Institute Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Han Zhang
- Shanghai Advanced Research Institute Chinese Academy of Sciences, Shanghai, 201210, China
| | - Hang Su
- Shanghai Advanced Research Institute Chinese Academy of Sciences, Shanghai, 201210, China
- Henan Provincial People's Hospital of Zhengzhou University, Zhengzhou, 450003, Henan, China
| | - Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Lingsong Li
- Shanghai Advanced Research Institute Chinese Academy of Sciences, Shanghai, 201210, China.
- Henan Provincial People's Hospital of Zhengzhou University, Zhengzhou, 450003, Henan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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Stenudd M, Sabelström H, Llorens-Bobadilla E, Zamboni M, Blom H, Brismar H, Zhang S, Basak O, Clevers H, Göritz C, Barnabé-Heider F, Frisén J. Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties. Cell Rep 2022; 38:110440. [PMID: 35235796 DOI: 10.1016/j.celrep.2022.110440] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 11/30/2021] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
Spinal cord ependymal cells display neural stem cell properties in vitro and generate scar-forming astrocytes and remyelinating oligodendrocytes after injury. We report that ependymal cells are functionally heterogeneous and identify a small subpopulation (8% of ependymal cells and 0.1% of all cells in a spinal cord segment), which we denote ependymal A (EpA) cells, that accounts for the in vitro stem cell potential in the adult spinal cord. After spinal cord injury, EpA cells undergo self-renewing cell division as they give rise to differentiated progeny. Single-cell transcriptome analysis revealed a loss of ependymal cell gene expression programs as EpA cells gained signaling entropy and dedifferentiated to a stem-cell-like transcriptional state after an injury. We conclude that EpA cells are highly differentiated cells that can revert to a stem cell state and constitute a therapeutic target for spinal cord repair.
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Affiliation(s)
- Moa Stenudd
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Hanna Sabelström
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | | | - Margherita Zamboni
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Hans Blom
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, 171 21 Solna, Sweden
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, 171 21 Solna, Sweden
| | - Shupei Zhang
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Onur Basak
- Hubrecht Institute for Developmental Biology and Stem Cell Research, 3584 CT Utrecht, the Netherlands; University Medical Centre Utrecht, 3584 GC, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research, 3584 CT Utrecht, the Netherlands; University Medical Centre Utrecht, 3584 GC, Utrecht, the Netherlands
| | - Christian Göritz
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Fanie Barnabé-Heider
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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29
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Li L, Medina-Menéndez C, García-Corzo L, Córdoba-Beldad CM, Quiroga AC, Calleja Barca E, Zinchuk V, Muñoz-López S, Rodríguez-Martín P, Ciorraga M, Colmena I, Fernández S, Vicario C, Nicolis SK, Lefebvre V, Mira H, Morales AV. SoxD genes are required for adult neural stem cell activation. Cell Rep 2022; 38:110313. [PMID: 35108528 DOI: 10.1016/j.celrep.2022.110313] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/20/2021] [Accepted: 01/07/2022] [Indexed: 01/17/2023] Open
Abstract
The adult neurogenic niche in the hippocampus is maintained through activation of reversibly quiescent neural stem cells (NSCs) with radial glia-like morphology (RGLs). Here, we show that the expression of SoxD transcription factors Sox5 and Sox6 is enriched in activated RGLs. Using inducible deletion of Sox5 or Sox6 in the adult mouse brain, we show that both genes are required for RGL activation and the generation of new neurons. Conversely, Sox5 overexpression in cultured NSCs interferes with entry in quiescence. Mechanistically, expression of the proneural protein Ascl1 (a key RGL regulator) is severely downregulated in SoxD-deficient RGLs, and Ascl1 transcription relies on conserved Sox motifs. Additionally, loss of Sox5 hinders the RGL activation driven by neurogenic stimuli such as environmental enrichment. Altogether, our data suggest that SoxD genes are key mediators in the transition of adult RGLs from quiescence to an activated mitotic state under physiological situations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Carlos Vicario
- Instituto Cajal, CSIC, 28002 Madrid, Spain; CIBERNED-Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | | | - Helena Mira
- Instituto de Biomedicina de Valencia, CSIC, 46010 Valencia, Spain
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30
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Sharma S, Jeyaraman M, Muthu S. Role of stem cell therapy in neurosciences. ESSENTIALS OF EVIDENCE-BASED PRACTICE OF NEUROANESTHESIA AND NEUROCRITICAL CARE 2022:163-179. [DOI: 10.1016/b978-0-12-821776-4.00012-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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31
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Direct neuronal reprogramming: Fast forward from new concepts toward therapeutic approaches. Neuron 2021; 110:366-393. [PMID: 34921778 DOI: 10.1016/j.neuron.2021.11.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/25/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022]
Abstract
Differentiated cells have long been considered fixed in their identity. However, about 20 years ago, the first direct conversion of glial cells into neurons in vitro opened the field of "direct neuronal reprogramming." Since then, neuronal reprogramming has achieved the generation of fully functional, mature neurons with remarkable efficiency, even in diseased brain environments. Beyond their clinical implications, these discoveries provided basic insights into crucial mechanisms underlying conversion of specific cell types into neurons and maintenance of neuronal identity. Here we discuss such principles, including the importance of the starter cell for shaping the outcome of neuronal reprogramming. We further highlight technical concerns for in vivo reprogramming and propose a code of conduct to avoid artifacts and pitfalls. We end by pointing out next challenges for development of less invasive cell replacement therapies for humans.
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32
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Gillotin S, Sahni V, Lepko T, Hanspal MA, Swartz JE, Alexopoulou Z, Marshall FH. Targeting impaired adult hippocampal neurogenesis in ageing by leveraging intrinsic mechanisms regulating Neural Stem Cell activity. Ageing Res Rev 2021; 71:101447. [PMID: 34403830 DOI: 10.1016/j.arr.2021.101447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/14/2021] [Accepted: 08/10/2021] [Indexed: 02/06/2023]
Abstract
Deficits in adult neurogenesis may contribute to the aetiology of many neurodevelopmental, psychiatric and neurodegenerative diseases. Genetic ablation of neurogenesis provides proof of concept that adult neurogenesis is required to sustain complex and dynamic cognitive functions, such as learning and memory, mostly by providing a high degree of plasticity to neuronal circuits. In addition, adult neurogenesis is reactive to external stimuli and the environment making it particularly susceptible to impairment and consequently contributing to comorbidity. In the human brain, the dentate gyrus of the hippocampus is the main active source of neural stem cells that generate granule neurons throughout life. The regulation and preservation of the pool of neural stem cells is central to ensure continuous and healthy adult hippocampal neurogenesis (AHN). Recent advances in genetic and metabolic profiling alongside development of more predictive animal models have contributed to the development of new concepts and the emergence of molecular mechanisms that could pave the way to the implementation of new therapeutic strategies to treat neurological diseases. In this review, we discuss emerging molecular mechanisms underlying AHN that could be embraced in drug discovery to generate novel concepts and targets to treat diseases of ageing including neurodegeneration. To support this, we review cellular and molecular mechanisms that have recently been identified to assess how AHN is sustained throughout life and how AHN is associated with diseases. We also provide an outlook on strategies for developing correlated biomarkers that may accelerate the translation of pre-clinical and clinical data and review clinical trials for which modulation of AHN is part of the therapeutic strategy.
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33
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Hau AC, Mommaerts E, Laub V, Müller T, Dittmar G, Schulte D. Transcriptional cooperation of PBX1 and PAX6 in adult neural progenitor cells. Sci Rep 2021; 11:21013. [PMID: 34697387 PMCID: PMC8545929 DOI: 10.1038/s41598-021-99968-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
PAX6 is a highly conserved transcription factor and key regulator of several neurogenic processes, including the continuous generation of dopaminergic/GABAergic interneurons in the adult ventricular-subventricular (V-SVZ) neurogenic system in mice. Here we report that PAX6 cooperates with the TALE-homeodomain transcription factor PBX1 in this context. Chromatin-immunoprecipitation showed that PBX1 and PAX6 co-occupy shared genomic binding sites in adult V-SVZ stem- and progenitor cell cultures and mouse embryonic stem cells, while depletion of Pbx1 revealed that association of PAX6 with these sites requires the presence of PBX1. Expression profiling together with viral overexpression or knockdown of Pax6 or Pbx1 identified novel PBX1-PAX6 co-regulated genes, including several transcription factors. Computational modeling of genome wide expression identified novel cross-regulatory networks among these very transcription factors. Taken together, the results presented here highlight the intimate link that exists between PAX6 and TALE-HD family proteins and contribute novel insights into how the orchestrated activity of transcription factors shapes adult V-SVZ neurogenesis.
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Affiliation(s)
- Ann-Christin Hau
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany. .,NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Strassen, Luxembourg. .,National Center of Pathology, Laboratoire National de Santé, 1 rue Louis Rech, 3555, Dudelange, Luxembourg.
| | - Elise Mommaerts
- Quantitative Biology Unit, LUXGEN, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Vera Laub
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany
| | - Tamara Müller
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany
| | - Gunnar Dittmar
- Quantitative Biology Unit, LUXGEN, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Dorothea Schulte
- Neurological Institute, Edinger Institute, University Hospital, Goethe University, Heinrich-Hoffmann-Str. 7, 60528, Frankfurt, Germany.
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Turan S, Boerstler T, Kavyanifar A, Loskarn S, Reis A, Winner B, Lie DC. A novel human stem cell model for Coffin-Siris syndrome-like syndrome reveals the importance of SOX11 dosage for neuronal differentiation and survival. Hum Mol Genet 2021; 28:2589-2599. [PMID: 31035284 DOI: 10.1093/hmg/ddz089] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/03/2019] [Accepted: 04/17/2019] [Indexed: 11/14/2022] Open
Abstract
The SOXC transcription factors Sox4, Sox11 and Sox12, are critical neurodevelopmental regulators that are thought to function in a highly redundant fashion. Surprisingly, heterozygous missense mutations or deletions of SOX11 were recently detected in patients with Coffin-Siris syndrome-like syndrome (CSSLS), a neurodevelopmental disorder associated with intellectual disability, demonstrating that in humans SOX11 haploinsufficiency cannot be compensated and raising the question of the function of SOX11 in human neurodevelopment. Here, we describe the generation of SOX11+/- heterozygous human embryonic stem cell (hESC) lines by CRISPR/Cas9 genome engineering. SOX11 haploinsufficiency impaired the generation of neurons and resulted in a proliferation/differentiation imbalance of neural precursor cells and enhanced neuronal cell death. Using the SOX11+/- hESC model we provide for the first time experimental evidence that SOX11 haploinsufficiency is sufficient to impair key processes of human neurodevelopment, giving a first insight into the pathophysiology of CSSLS and SOX11 function in human neurodevelopment.
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Affiliation(s)
- Soeren Turan
- Institute of Biochemistry.,Department of Stem Cell Biology
| | | | | | | | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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36
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Afanasyeva EA, Gartlgruber M, Ryl T, Decaesteker B, Denecker G, Mönke G, Toprak UH, Florez A, Torkov A, Dreidax D, Herrmann C, Okonechnikov K, Ek S, Sharma AK, Sagulenko V, Speleman F, Henrich KO, Westermann F. Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma. Life Sci Alliance 2021; 4:e201900332. [PMID: 33658318 PMCID: PMC8017594 DOI: 10.26508/lsa.201900332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The migrational propensity of neuroblastoma is affected by cell identity, but the mechanisms behind the divergence remain unknown. Using RNAi and time-lapse imaging, we show that ADRN-type NB cells exhibit RAC1- and kalirin-dependent nucleokinetic (NUC) migration that relies on several integral components of neuronal migration. Inhibition of NUC migration by RAC1 and kalirin-GEF1 inhibitors occurs without hampering cell proliferation and ADRN identity. Using three clinically relevant expression dichotomies, we reveal that most of up-regulated mRNAs in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells are associated with low-risk characteristics. The computational analysis shows that, in a context of overall gene set poverty, the upregulomes in RAC1- and kalirin-GEF1-suppressed ADRN-type cells are a batch of AU-rich element-containing mRNAs, which suggests a link between NUC migration and mRNA stability. Gene set enrichment analysis-based search for vulnerabilities reveals prospective weak points in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells, including activities of H3K27- and DNA methyltransferases. Altogether, these data support the introduction of NUC inhibitors into cancer treatment research.
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Affiliation(s)
- Elena A Afanasyeva
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Moritz Gartlgruber
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Tatsiana Ryl
- Department of Neurosurgery, University of Duisburg Essen, Essen, Germany
| | - Bieke Decaesteker
- Center for Medical Genetics, Ghent University, and Cancer Research Institute Ghent, Ghent, Belgium
| | - Geertrui Denecker
- Center for Medical Genetics, Ghent University, and Cancer Research Institute Ghent, Ghent, Belgium
| | - Gregor Mönke
- European Molecular Biology Laboratories, Heidelberg, Germany
| | - Umut H Toprak
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Andres Florez
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
- Center for Systems Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Alica Torkov
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Daniel Dreidax
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Carl Herrmann
- Group of Cancer Regulatory Genomics B086, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Department of Pediatric Neurooncology, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Sara Ek
- Department of Immunotechnology, CREATE Health, Faculty of Engineering, Lund University, Lund, Sweden
| | - Ashwini Kumar Sharma
- Institute for Pharmacy and Molecular Biotechnology and BioQuant, Heidelberg University, Heidelberg, Germany
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vitaliya Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, and Cancer Research Institute Ghent, Ghent, Belgium
| | - Kai-Oliver Henrich
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
| | - Frank Westermann
- Department of Neuroblastoma Genomics, Hopp-Children's Cancer Center at the (NCT) Nationales Centrum für Tumorerkrankungen Heidelberg (KiTZ), Heidelberg, Germany
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37
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Stevanovic M, Drakulic D, Lazic A, Ninkovic DS, Schwirtlich M, Mojsin M. SOX Transcription Factors as Important Regulators of Neuronal and Glial Differentiation During Nervous System Development and Adult Neurogenesis. Front Mol Neurosci 2021; 14:654031. [PMID: 33867936 PMCID: PMC8044450 DOI: 10.3389/fnmol.2021.654031] [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: 01/15/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
The SOX proteins belong to the superfamily of transcription factors (TFs) that display properties of both classical TFs and architectural components of chromatin. Since the cloning of the Sox/SOX genes, remarkable progress has been made in illuminating their roles as key players in the regulation of multiple developmental and physiological processes. SOX TFs govern diverse cellular processes during development, such as maintaining the pluripotency of stem cells, cell proliferation, cell fate decisions/germ layer formation as well as terminal cell differentiation into tissues and organs. However, their roles are not limited to development since SOX proteins influence survival, regeneration, cell death and control homeostasis in adult tissues. This review summarized current knowledge of the roles of SOX proteins in control of central nervous system development. Some SOX TFs suspend neural progenitors in proliferative, stem-like state and prevent their differentiation. SOX proteins function as pioneer factors that occupy silenced target genes and keep them in a poised state for activation at subsequent stages of differentiation. At appropriate stage of development, SOX members that maintain stemness are down-regulated in cells that are competent to differentiate, while other SOX members take over their functions and govern the process of differentiation. Distinct SOX members determine down-stream processes of neuronal and glial differentiation. Thus, sequentially acting SOX TFs orchestrate neural lineage development defining neuronal and glial phenotypes. In line with their crucial roles in the nervous system development, deregulation of specific SOX proteins activities is associated with neurodevelopmental disorders (NDDs). The overview of the current knowledge about the link between SOX gene variants and NDDs is presented. We outline the roles of SOX TFs in adult neurogenesis and brain homeostasis and discuss whether impaired adult neurogenesis, detected in neurodegenerative diseases, could be associated with deregulation of SOX proteins activities. We present the current data regarding the interaction between SOX proteins and signaling pathways and microRNAs that play roles in nervous system development. Finally, future research directions that will improve the knowledge about distinct and various roles of SOX TFs in health and diseases are presented and discussed.
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Affiliation(s)
- Milena Stevanovic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.,Faculty of Biology, University of Belgrade, Belgrade, Serbia.,Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Danijela Drakulic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Andrijana Lazic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Danijela Stanisavljevic Ninkovic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marija Schwirtlich
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marija Mojsin
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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38
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Colquitt BM, Merullo DP, Konopka G, Roberts TF, Brainard MS. Cellular transcriptomics reveals evolutionary identities of songbird vocal circuits. Science 2021; 371:371/6530/eabd9704. [PMID: 33574185 DOI: 10.1126/science.abd9704] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
Birds display advanced behaviors, including vocal learning and problem-solving, yet lack a layered neocortex, a structure associated with complex behavior in mammals. To determine whether these behavioral similarities result from shared or distinct neural circuits, we used single-cell RNA sequencing to characterize the neuronal repertoire of the songbird song motor pathway. Glutamatergic vocal neurons had considerable transcriptional similarity to neocortical projection neurons; however, they displayed regulatory gene expression patterns more closely related to neurons in the ventral pallium. Moreover, while γ-aminobutyric acid-releasing neurons in this pathway appeared homologous to those in mammals and other amniotes, the most abundant avian class is largely absent in the neocortex. These data suggest that songbird vocal circuits and the mammalian neocortex have distinct developmental origins yet contain transcriptionally similar neurons.
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Affiliation(s)
- Bradley M Colquitt
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Departments of Physiology and Psychiatry, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Devin P Merullo
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Todd F Roberts
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Michael S Brainard
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. .,Departments of Physiology and Psychiatry, University of California-San Francisco, San Francisco, CA 94158, USA
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39
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Castellan M, Guarnieri A, Fujimura A, Zanconato F, Battilana G, Panciera T, Sladitschek HL, Contessotto P, Citron A, Grilli A, Romano O, Bicciato S, Fassan M, Porcù E, Rosato A, Cordenonsi M, Piccolo S. Single-cell analyses reveal YAP/TAZ as regulators of stemness and cell plasticity in Glioblastoma. NATURE CANCER 2021; 2:174-188. [PMID: 33644767 PMCID: PMC7116831 DOI: 10.1038/s43018-020-00150-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/28/2020] [Indexed: 02/07/2023]
Abstract
Glioblastoma (GBM) is a devastating human malignancy. GBM stem-like cells (GSCs) drive tumor initiation and progression. Yet, the molecular determinants defining GSCs in their native state in patients remain poorly understood. Here we used single cell datasets and identified GSCs at the apex of the differentiation hierarchy of GBM. By reconstructing the GSCs' regulatory network, we identified the YAP/TAZ coactivators as master regulators of this cell state, irrespectively of GBM subtypes. YAP/TAZ are required to install GSC properties in primary cells downstream of multiple oncogenic lesions, and required for tumor initiation and maintenance in vivo in different mouse and human GBM models. YAP/TAZ act as main roadblock of GSC differentiation and their inhibition irreversibly lock differentiated GBM cells into a non-tumorigenic state, preventing plasticity and regeneration of GSC-like cells. Thus, GSC identity is linked to a key molecular hub integrating genetics and microenvironmental inputs within the multifaceted biology of GBM.
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Affiliation(s)
| | | | - Atsushi Fujimura
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Giusy Battilana
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Tito Panciera
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | | | - Anna Citron
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Andrea Grilli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Matteo Fassan
- Department of Medicine - Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
| | - Elena Porcù
- Department of Woman and Children Health, University of Padua, Padua, Italy
| | - Antonio Rosato
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua, Padua, Italy.
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.
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40
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Chiang SY, Wu HC, Lin SY, Chen HY, Wang CF, Yeh NH, Shih JH, Huang YS, Kuo HC, Chou SJ, Chen RH. Usp11 controls cortical neurogenesis and neuronal migration through Sox11 stabilization. SCIENCE ADVANCES 2021; 7:7/7/eabc6093. [PMID: 33579706 PMCID: PMC7880594 DOI: 10.1126/sciadv.abc6093] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/23/2020] [Indexed: 06/01/2023]
Abstract
The role of protein stabilization in cortical development remains poorly understood. A recessive mutation in the USP11 gene is found in a rare neurodevelopmental disorder with intellectual disability, but its pathogenicity and molecular mechanism are unknown. Here, we show that mouse Usp11 is expressed highly in embryonic cerebral cortex, and Usp11 deficiency impairs layer 6 neuron production, delays late-born neuronal migration, and disturbs cognition and anxiety behaviors. Mechanistically, these functions are mediated by a previously unidentified Usp11 substrate, Sox11. Usp11 ablation compromises Sox11 protein accumulation in the developing cortex, despite the induction of Sox11 mRNA. The disease-associated Usp11 mutant fails to stabilize Sox11 and is unable to support cortical neurogenesis and neuronal migration. Our findings define a critical function of Usp11 in cortical development and highlight the importance of orchestrating protein stabilization mechanisms into transcription regulatory programs for a robust induction of cell fate determinants during early brain development.
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Affiliation(s)
- Shang-Yin Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 100, Taiwan
| | - Hsin-Chieh Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Shu-Yu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Hsin-Yi Chen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Chia-Fang Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | - Nai-Hsing Yeh
- Insititute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Jou-Ho Shih
- Insititute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Shuian Huang
- Insititute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | - Shen-Ju Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan.
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 100, Taiwan
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41
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Sharif N, Calzolari F, Berninger B. Direct In Vitro Reprogramming of Astrocytes into Induced Neurons. Methods Mol Biol 2021; 2352:13-29. [PMID: 34324177 DOI: 10.1007/978-1-0716-1601-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Spontaneous neuronal replacement is almost absent in the postnatal mammalian nervous system. However, several studies have shown that both early postnatal and adult astroglia can be reprogrammed in vitro or in vivo by forced expression of proneural transcription factors, such as Neurogenin-2 or Achaete-scute homolog 1 (Ascl1), to acquire a neuronal fate. The reprogramming process stably induces properties such as distinctly neuronal morphology, expression of neuron-specific proteins, and the gain of mature neuronal functional features. Direct conversion of astroglia into neurons thus possesses potential as a basis for cell-based strategies against neurological diseases. In this chapter, we describe a well-established protocol used for direct reprogramming of postnatal cortical astrocytes into functional neurons in vitro and discuss available tools and approaches to dissect molecular and cell biological mechanisms underlying the reprogramming process.
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Affiliation(s)
- Nesrin Sharif
- Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University Mainz, Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics and Genome Stability, Mainz, Germany
| | - Filippo Calzolari
- Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University Mainz, Mainz, Germany
| | - Benedikt Berninger
- Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University Mainz, Mainz, Germany.
- Institute of Psychiatry, Psychology, and Neuroscience, Centre for Developmental Neurobiology, King's College London, London, UK.
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.
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42
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Niklison-Chirou MV, Agostini M, Amelio I, Melino G. Regulation of Adult Neurogenesis in Mammalian Brain. Int J Mol Sci 2020; 21:ijms21144869. [PMID: 32660154 PMCID: PMC7402357 DOI: 10.3390/ijms21144869] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
Adult neurogenesis is a multistage process by which neurons are generated and integrated into existing neuronal circuits. In the adult brain, neurogenesis is mainly localized in two specialized niches, the subgranular zone (SGZ) of the dentate gyrus and the subventricular zone (SVZ) adjacent to the lateral ventricles. Neurogenesis plays a fundamental role in postnatal brain, where it is required for neuronal plasticity. Moreover, perturbation of adult neurogenesis contributes to several human diseases, including cognitive impairment and neurodegenerative diseases. The interplay between extrinsic and intrinsic factors is fundamental in regulating neurogenesis. Over the past decades, several studies on intrinsic pathways, including transcription factors, have highlighted their fundamental role in regulating every stage of neurogenesis. However, it is likely that transcriptional regulation is part of a more sophisticated regulatory network, which includes epigenetic modifications, non-coding RNAs and metabolic pathways. Here, we review recent findings that advance our knowledge in epigenetic, transcriptional and metabolic regulation of adult neurogenesis in the SGZ of the hippocampus, with a special attention to the p53-family of transcription factors.
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Affiliation(s)
- Maria Victoria Niklison-Chirou
- Centre for Therapeutic Innovation (CTI-Bath), Department of Pharmacy & Pharmacology, University of Bath, Bath BA2 7AY, UK;
- Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Massimiliano Agostini
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy; (M.A.); (I.A.)
| | - Ivano Amelio
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy; (M.A.); (I.A.)
- School of Life Sciences, University of Nottingham, Nottingham NG7 2HU, UK
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy; (M.A.); (I.A.)
- Correspondence:
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43
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von Wittgenstein J, Zheng F, Wittmann MT, Balta EA, Ferrazzi F, Schäffner I, Häberle BM, Valero-Aracama MJ, Koehl M, Miranda CJ, Kaspar BK, Ekici AB, Reis A, Abrous DN, Alzheimer C, Lie DC. Sox11 is an Activity-Regulated Gene with Dentate-Gyrus-Specific Expression Upon General Neural Activation. Cereb Cortex 2020; 30:3731-3743. [PMID: 32080705 DOI: 10.1093/cercor/bhz338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 01/21/2023] Open
Abstract
Neuronal activity initiates transcriptional programs that shape long-term changes in plasticity. Although neuron subtypes differ in their plasticity response, most activity-dependent transcription factors (TFs) are broadly expressed across neuron subtypes and brain regions. Thus, how region- and neuronal subtype-specific plasticity are established on the transcriptional level remains poorly understood. We report that in young adult (i.e., 6-8 weeks old) mice, the developmental TF SOX11 is induced in neurons within 6 h either by electroconvulsive stimulation or by exploration of a novel environment. Strikingly, SOX11 induction was restricted to the dentate gyrus (DG) of the hippocampus. In the novel environment paradigm, SOX11 was observed in a subset of c-FOS expressing neurons (ca. 15%); whereas around 75% of SOX11+ DG granule neurons were c-FOS+, indicating that SOX11 was induced in an activity-dependent fashion in a subset of neurons. Environmental enrichment or virus-mediated overexpression of SOX11 enhanced the excitability of DG granule cells and downregulated the expression of different potassium channel subunits, whereas conditional Sox11/4 knock-out mice presented the opposite phenotype. We propose that Sox11 is regulated in an activity-dependent fashion, which is specific to the DG, and speculate that activity-dependent Sox11 expression may participate in the modulation of DG neuron plasticity.
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Affiliation(s)
- Julia von Wittgenstein
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.,Department of Biology, Animal Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Fang Zheng
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Marie-Theres Wittmann
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.,Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Elli-Anna Balta
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Fulvia Ferrazzi
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Iris Schäffner
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Benjamin M Häberle
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Maria J Valero-Aracama
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Muriel Koehl
- Neurocentre Magendie U1215, INSERM and Université de Bordeaux, Bordeaux 33000, France
| | - Carlos J Miranda
- The Research Institute, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Brian K Kaspar
- The Research Institute, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Djoher Nora Abrous
- Neurocentre Magendie U1215, INSERM and Université de Bordeaux, Bordeaux 33000, France
| | - Christian Alzheimer
- Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - D Chichung Lie
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
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44
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Shafik AM, Allen EG, Jin P. Dynamic N6-methyladenosine RNA methylation in brain and diseases. Epigenomics 2020; 12:371-380. [PMID: 32081027 DOI: 10.2217/epi-2019-0260] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) is a dynamic RNA modification that regulates various aspects of RNA metabolism and has been implicated in many biological processes and transitions. m6A is highly abundant in the brain; however, only recently has the role of m6A in brain development been a focus. The machinery that controls m6A is critically important for proper neurodevelopment, and the precise mechanisms by which m6A regulates these processes are starting to emerge. However, the role of m6A in neurodegenerative and neuropsychiatric diseases still requires much elucidation. This review discusses and summarizes the current body of knowledge surrounding the function of the m6A modification in regulating normal brain development, neurodegenerative diseases and outlines possible future directions.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
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45
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Decoding the development of the human hippocampus. Nature 2020; 577:531-536. [PMID: 31942070 DOI: 10.1038/s41586-019-1917-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 11/12/2019] [Indexed: 01/08/2023]
Abstract
The hippocampus is an important part of the limbic system in the human brain that has essential roles in spatial navigation and the consolidation of information from short-term memory to long-term memory1,2. Here we use single-cell RNA sequencing and assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis to illustrate the cell types, cell linage, molecular features and transcriptional regulation of the developing human hippocampus. Using the transcriptomes of 30,416 cells from the human hippocampus at gestational weeks 16-27, we identify 47 cell subtypes and their developmental trajectories. We also identify the migrating paths and cell lineages of PAX6+ and HOPX+ hippocampal progenitors, and regional markers of CA1, CA3 and dentate gyrus neurons. Multiomic data have uncovered transcriptional regulatory networks of the dentate gyrus marker PROX1. We also illustrate spatially specific gene expression in the developing human prefrontal cortex and hippocampus. The molecular features of the human hippocampus at gestational weeks 16-20 are similar to those of the mouse at postnatal days 0-5 and reveal gene expression differences between the two species. Transient expression of the primate-specific gene NBPF1 leads to a marked increase in PROX1+ cells in the mouse hippocampus. These data provides a blueprint for understanding human hippocampal development and a tool for investigating related diseases.
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Zakopoulou V, Vlaikou AM, Darsinou M, Papadopoulou Z, Theodoridou D, Papageorgiou K, Alexiou GA, Bougias H, Siafaka V, Zoccolotti P, Chroussos GP, Syrrou M, Michaelidis TM. Linking Early Life Hypothalamic-Pituitary-Adrenal Axis Functioning, Brain Asymmetries, and Personality Traits in Dyslexia: An Informative Case Study. Front Hum Neurosci 2019; 13:327. [PMID: 31632253 PMCID: PMC6779713 DOI: 10.3389/fnhum.2019.00327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022] Open
Abstract
Developmental dyslexia (DD) is a multi-system disorder, combining influences of susceptibility genes and environmental factors. The causative interaction between specific genetic factors, brain regions, and personality/mental disorders, as well as specific learning disabilities, has been thoroughly investigated with regard to the approach of developing a multifaceted diagnostic procedure with an intervention strategy potential. In an attempt to add new translational evidence to the interconnection of the above factors in the occurrence of DD, we performed a combinatorial analysis of brain asymmetries, personality traits, cognitive and learning skills, and expression profiles of selected genes in an adult, early diagnosed with DD, and in his son of typical development. We focused on the expression of genes, based on the assumption that the regulation of transcription may be affected by genetic and epigenetic factors. The results highlighted a potential chain link between neuroplasticity-related as well as stress-related genes, such as BDNF, Sox4, mineralocorticoid receptor (MR), and GILZ, leftward asymmetries in the amygdala and selective cerebellum lobules, and tendencies for personality disorders and dyslexia. This correlation may reflect the presence of a specific neuro-epigenetic component of DD, ensuing from the continuous, multifaceted difficulties in the acquisition of cognitive and learning skills, which in turn may act as a fostering mechanism for the onset of long-term disorders. This is in line with recent findings demonstrating a dysfunction in processes supported by rapid neural adaptation in children and adults with dyslexia. Accordingly, the co-evaluation of all the above parameters may indicate a stress-related dyslexia endophenotype that should be carefully considered for a more integrated diagnosis and effective intervention.
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Affiliation(s)
- Victoria Zakopoulou
- Department of Speech and Language Therapy, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Angeliki-Maria Vlaikou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Marousa Darsinou
- Department of Biomedical Research, Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology, Ioannina, Greece.,Department of Biological Applications and Technologies, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Zoe Papadopoulou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Daniela Theodoridou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Kyriaki Papageorgiou
- Department of Biomedical Research, Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology, Ioannina, Greece.,Department of Biological Applications and Technologies, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - George A Alexiou
- Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Haralambos Bougias
- Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Vassiliki Siafaka
- Department of Speech and Language Therapy, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Pierluigi Zoccolotti
- Neuropsychology Unit, Department of Psychology, IRCCS (National Institute for Research and Treatment) Fondazione Santa Lucia, Sapienza University of Rome, Rome, Italy
| | - George P Chroussos
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Maria Syrrou
- Laboratory of Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Theologos M Michaelidis
- Department of Biomedical Research, Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology, Ioannina, Greece.,Department of Biological Applications and Technologies, School of Health Sciences, University of Ioannina, Ioannina, Greece
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47
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Lepko T, Pusch M, Müller T, Schulte D, Ehses J, Kiebler M, Hasler J, Huttner HB, Vandenbroucke RE, Vandendriessche C, Modic M, Martin‐Villalba A, Zhao S, LLorens‐Bobadilla E, Schneider A, Fischer A, Breunig CT, Stricker SH, Götz M, Ninkovic J. Choroid plexus-derived miR-204 regulates the number of quiescent neural stem cells in the adult brain. EMBO J 2019; 38:e100481. [PMID: 31304985 PMCID: PMC6717894 DOI: 10.15252/embj.2018100481] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022] Open
Abstract
Regulation of adult neural stem cell (NSC) number is critical for lifelong neurogenesis. Here, we identified a post-transcriptional control mechanism, centered around the microRNA 204 (miR-204), to control the maintenance of quiescent (q)NSCs. miR-204 regulates a spectrum of transcripts involved in cell cycle regulation, neuronal migration, and differentiation in qNSCs. Importantly, inhibition of miR-204 function reduced the number of qNSCs in the subependymal zone (SEZ) by inducing pre-mature activation and differentiation of NSCs without changing their neurogenic potential. Strikingly, we identified the choroid plexus of the mouse lateral ventricle as the major source of miR-204 that is released into the cerebrospinal fluid to control number of NSCs within the SEZ. Taken together, our results describe a novel mechanism to maintain adult somatic stem cells by a niche-specific miRNA repressing activation and differentiation of stem cells.
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Affiliation(s)
- Tjasa Lepko
- Institute of Stem Cell ResearchHelmholtz Center MunichNeuherbergGermany
- Graduate School of Systemic NeurosciencesLudwig‐Maximilians UniversitaetPlanegg‐MartinsriedGermany
- Physiological GenomicsBiomedical CenterMedical FacultyLudwig‐Maximilians UniversitaetPlanegg‐MartinsriedGermany
| | - Melanie Pusch
- Institute of Stem Cell ResearchHelmholtz Center MunichNeuherbergGermany
| | - Tamara Müller
- Institute of Neurology (Edinger Institute)University HospitalGoethe University FrankfurtFrankfurtGermany
| | - Dorothea Schulte
- Institute of Neurology (Edinger Institute)University HospitalGoethe University FrankfurtFrankfurtGermany
| | - Janina Ehses
- Department for Cell Biology and AnatomyBiomedical CenterLudwig‐Maximilians UniversitaetPlanegg‐MartinsriedGermany
| | - Michael Kiebler
- Department for Cell Biology and AnatomyBiomedical CenterLudwig‐Maximilians UniversitaetPlanegg‐MartinsriedGermany
| | - Julia Hasler
- Institute of Stem Cell ResearchHelmholtz Center MunichNeuherbergGermany
| | - Hagen B Huttner
- Department of NeurologyUniversity Hospital ErlangenFriedrich‐Alexander‐University Erlangen‐NürnbergErlangenGermany
| | - Roosmarijn E Vandenbroucke
- VIB Center for Inflammation Research, VIBGhentBelgium
- Department of Biomedical Molecular BiologyGhent UniversityGhentBelgium
- Ghent Gut Inflammation Group (GGIG)Ghent UniversityGhentBelgium
| | - Charysse Vandendriessche
- VIB Center for Inflammation Research, VIBGhentBelgium
- Department of Biomedical Molecular BiologyGhent UniversityGhentBelgium
- Ghent Gut Inflammation Group (GGIG)Ghent UniversityGhentBelgium
| | - Miha Modic
- The Francis Crick InstituteLondonUK
- Department for Neuromuscular DiseasesUCL Queen Square Institute of NeurologyLondonUK
| | | | - Sheng Zhao
- Molecular NeurobiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | | | - Anja Schneider
- Translational Dementia Research GroupGerman Center for Neurodegenerative Diseases (DZNE) BonnBonnGermany
- Department of Neurodegenerative Diseases and Geriatric PsychiatryUniversity Clinic BonnBonnGermany
| | - Andre Fischer
- Department for Epigenetics and Systems MedicineGerman Center for Neurodegenerative Diseases (DZNE) GöttingenGöttingenGermany
| | - Christopher T Breunig
- MCN Junior Research GroupMunich Center for NeurosciencesBioMedical CenterLudwig‐Maximilians UniversitaetPlanegg‐MartinsriedGermany
- Epigenetic EngineeringHelmholtz Zentrum MünchenNeuherbergGermany
| | - Stefan H Stricker
- MCN Junior Research GroupMunich Center for NeurosciencesBioMedical CenterLudwig‐Maximilians UniversitaetPlanegg‐MartinsriedGermany
- Epigenetic EngineeringHelmholtz Zentrum MünchenNeuherbergGermany
| | - Magdalena Götz
- Institute of Stem Cell ResearchHelmholtz Center MunichNeuherbergGermany
- Physiological GenomicsBiomedical CenterMedical FacultyLudwig‐Maximilians UniversitaetPlanegg‐MartinsriedGermany
- Munich Cluster for Systems Neurology (SyNergy)MunichGermany
| | - Jovica Ninkovic
- Institute of Stem Cell ResearchHelmholtz Center MunichNeuherbergGermany
- Physiological GenomicsBiomedical CenterMedical FacultyLudwig‐Maximilians UniversitaetPlanegg‐MartinsriedGermany
- Department for Cell Biology and AnatomyBiomedical CenterLudwig‐Maximilians UniversitaetPlanegg‐MartinsriedGermany
- Munich Cluster for Systems Neurology (SyNergy)MunichGermany
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48
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Moreno CS. SOX4: The unappreciated oncogene. Semin Cancer Biol 2019; 67:57-64. [PMID: 31445218 DOI: 10.1016/j.semcancer.2019.08.027] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 01/10/2023]
Abstract
SOX4 is an essential developmental transcription factor that regulates stemness, differentiation, progenitor development, and multiple developmental pathways including PI3K, Wnt, and TGFβ signaling. The SOX4 gene is frequently amplified and overexpressed in over 20 types of malignancies, and multiple lines of evidence support that notion that SOX4 is an oncogene. Its overexpression is due to both gene amplification and to activation of PI3K, Wnt, and TGFβ pathways that SOX4 regulates. SOX4 interacts with multiple other transcription factors, rendering many of its impacts on gene expression context and tissue-specific. Nevertheless, there are common themes that run through many of the effects of SOX4 hyperactivity, such as the promotion of cell survival, stemness, the epithelial to mesenchymal transition, migration, and metastasis. Specific targeting of SOX4 remains a challenge for future cancer research and drug development.
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Affiliation(s)
- Carlos S Moreno
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Whitehead Bldg, Rm 105J, 615 Michael St. Atlanta, GA, USA.
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49
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Jacob A, Wüst HM, Thalhammer JM, Fröb F, Küspert M, Reiprich S, Balta EA, Lie DC, Wegner M, Sock E. The transcription factor prospero homeobox protein 1 is a direct target of SoxC proteins during developmental vertebrate neurogenesis. J Neurochem 2019; 146:251-268. [PMID: 29749639 DOI: 10.1111/jnc.14456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/20/2018] [Accepted: 04/16/2018] [Indexed: 11/29/2022]
Abstract
The high-mobility-group domain containing SoxC transcription factors Sox4 and Sox11 are expressed and required in the vertebrate central nervous system in neuronal precursors and neuroblasts. To identify genes that are widely regulated by SoxC proteins during vertebrate neurogenesis we generated expression profiles from developing mouse brain and chicken neural tube with reduced SoxC expression and found the transcription factor prospero homeobox protein 1 (Prox1) strongly down-regulated under both conditions. This led us to hypothesize that Prox1 expression depends on SoxC proteins in the developing central nervous system of mouse and chicken. By combining luciferase reporter assays and over-expression in the chicken neural tube with in vivo and in vitro binding studies, we identify the Prox1 gene promoter and two upstream enhancers at -44 kb and -40 kb relative to the transcription start as regulatory regions that are bound and activated by SoxC proteins. This argues that Prox1 is a direct target gene of SoxC proteins during neurogenesis. Electroporations in the chicken neural tube furthermore show that Prox1 activates a subset of SoxC target genes, whereas it has no effects on others. We propose that the transcriptional control of Prox1 by SoxC proteins may ensure coupling of two types of transcription factors that are both required during early neurogenesis, but have at least in part distinct functions. Open Data: Materials are available on https://cos.io/our-services/open-science-badges/ https://osf.io/93n6m/.
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Affiliation(s)
- Anne Jacob
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hannah M Wüst
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes M Thalhammer
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Franziska Fröb
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Melanie Küspert
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Simone Reiprich
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Elli-Anna Balta
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - D Chichung Lie
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Elisabeth Sock
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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50
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Genome-Wide Mapping of Bivalent Histone Modifications in Hepatic Stem/Progenitor Cells. Stem Cells Int 2019; 2019:9789240. [PMID: 31065285 PMCID: PMC6466853 DOI: 10.1155/2019/9789240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/22/2018] [Accepted: 01/06/2019] [Indexed: 01/20/2023] Open
Abstract
The "bivalent domain," a distinctive histone modification signature, is characterized by repressive trimethylation of histone H3 at lysine 27 (H3K27me3) and active trimethylation of histone H3 at lysine 4 (H3K4me3) marks. Maintenance and dynamic resolution of these histone marks play important roles in regulating differentiation processes in various stem cell systems. However, little is known regarding their roles in hepatic stem/progenitor cells. In the present study, we conducted the chromatin immunoprecipitation (ChIP) assay followed by high-throughput DNA sequencing (ChIP-seq) analyses in purified delta-like 1 protein (Dlk+) hepatic stem/progenitor cells and successfully identified 562 genes exhibiting bivalent domains within 2 kb of the transcription start site. Gene ontology analysis revealed that these genes were enriched in developmental functions and differentiation processes. Microarray analyses indicated that many of these genes exhibited derepression after differentiation toward hepatocyte and cholangiocyte lineages. Among these, 72 genes, including Cdkn2a and Sox4, were significantly upregulated after differentiation toward hepatocyte or cholangiocyte lineages. Knockdown of Sox4 in Dlk+ cells suppressed colony propagation and resulted in increased numbers of albumin+/cytokeratin 7+ progenitor cells in colonies. These findings implicate that derepression of Sox4 expression is required to induce normal differentiation processes. In conclusion, combined ChIP-seq and microarray analyses successfully identified bivalent genes. Functional analyses of these genes will help elucidate the epigenetic machinery underlying the terminal differentiation of hepatic stem/progenitor cells.
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