1
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Emmerich K, Hageter J, Hoang T, Lyu P, Sharrock AV, Ceisel A, Thierer J, Chunawala Z, Nimmagadda S, Palazzo I, Matthews F, Zhang L, White DT, Rodriguez C, Graziano G, Marcos P, May A, Mulligan T, Reibman B, Saxena MT, Ackerley DF, Qian J, Blackshaw S, Horstick E, Mumm JS. A large-scale CRISPR screen reveals context-specific genetic regulation of retinal ganglion cell regeneration. Development 2024; 151:dev202754. [PMID: 39007397 PMCID: PMC11361637 DOI: 10.1242/dev.202754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Many genes are known to regulate retinal regeneration after widespread tissue damage. Conversely, genes controlling regeneration after limited cell loss, as per degenerative diseases, are undefined. As stem/progenitor cell responses scale to injury levels, understanding how the extent and specificity of cell loss impact regenerative processes is important. Here, transgenic zebrafish enabling selective retinal ganglion cell (RGC) ablation were used to identify genes that regulate RGC regeneration. A single cell multiomics-informed screen of 100 genes identified seven knockouts that inhibited and 11 that promoted RGC regeneration. Surprisingly, 35 out of 36 genes known and/or implicated as being required for regeneration after widespread retinal damage were not required for RGC regeneration. The loss of seven even enhanced regeneration kinetics, including the proneural factors neurog1, olig2 and ascl1a. Mechanistic analyses revealed that ascl1a disruption increased the propensity of progenitor cells to produce RGCs, i.e. increased 'fate bias'. These data demonstrate plasticity in the mechanism through which Müller glia convert to a stem-like state and context specificity in how genes function during regeneration. Increased understanding of how the regeneration of disease-relevant cell types is specifically controlled will support the development of disease-tailored regenerative therapeutics.
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Affiliation(s)
- Kevin Emmerich
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- McKusick-Nathans Institute and the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - John Hageter
- Department of Biology, West Virginia University, Morgantown, WV 26505, USA
| | - Thanh Hoang
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
| | - Pin Lyu
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Abigail V. Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Anneliese Ceisel
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - James Thierer
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Zeeshaan Chunawala
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Saumya Nimmagadda
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Isabella Palazzo
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Frazer Matthews
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Liyun Zhang
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David T. White
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Catalina Rodriguez
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Gianna Graziano
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Patrick Marcos
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Adam May
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Tim Mulligan
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Barak Reibman
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Meera T. Saxena
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jiang Qian
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Seth Blackshaw
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- McKusick-Nathans Institute and the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eric Horstick
- Department of Biology, West Virginia University, Morgantown, WV 26505, USA
- Department of Neuroscience, West Virginia University, Morgantown, WV 26506, USA
| | - Jeff S. Mumm
- Wilmer Eye Institute and the Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- McKusick-Nathans Institute and the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Center for Nanomedicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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2
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Liu Y, Chen X, Ma Y, Song C, Ma J, Chen C, Su J, Ma L, Saiyin H. Endogenous mutant Huntingtin alters the corticogenesis via lowering Golgi recruiting ARF1 in cortical organoid. Mol Psychiatry 2024:10.1038/s41380-024-02562-0. [PMID: 38654124 DOI: 10.1038/s41380-024-02562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
Pathogenic mutant huntingtin (mHTT) infiltrates the adult Huntington's disease (HD) brain and impairs fetal corticogenesis. However, most HD animal models rarely recapitulate neuroanatomical alterations in adult HD and developing brains. Thus, the human cortical organoid (hCO) is an alternative approach to decode mHTT pathogenesis precisely during human corticogenesis. Here, we replicated the altered corticogenesis in the HD fetal brain using HD patient-derived hCOs. Our HD-hCOs had pathological phenotypes, including deficient junctional complexes in the neural tubes, delayed postmitotic neuronal maturation, dysregulated fate specification of cortical neuron subtypes, and abnormalities in early HD subcortical projections during corticogenesis, revealing a causal link between impaired progenitor cells and chaotic cortical neuronal layering in the HD brain. We identified novel long, oriented, and enriched polyQ assemblies of HTTs that hold large flat Golgi stacks and scaffold clathrin+ vesicles in the neural tubes of hCOs. Flat Golgi stacks conjugated polyQ assemblies by ADP-ribosylation factor 1 (ARF1). Inhibiting ARF1 activation with Brefeldin A (BFA) disassociated polyQ assemblies from Golgi. PolyQ assembles with mHTT scaffolded fewer ARF1 and formed shorter polyQ assembles with fewer and shorter Golgi and clathrin vesicles in neural tubes of HD-hCOs compared with those in hCOs. Inhibiting the activation of ARF1 by BFA in healthy hCOs replicated impaired junctional complexes in the neural tubes. Together, endogenous polyQ assemblies with mHTT reduced the Golgi recruiting ARF1 in the neuroepithelium, impaired the Golgi structure and activities, and altered the corticogenesis in HD-hCO.
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Affiliation(s)
- Yang Liu
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinyu Chen
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yunlong Ma
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Chenyun Song
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jixin Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Cheng Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jianzhong Su
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Lixiang Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Hexige Saiyin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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3
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Engert J, Spahn B, Sommerer S, Ehret Kasemo T, Hackenberg S, Rak K, Voelker J. Adult Neurogenesis of the Medial Geniculate Body: In Vitro and Molecular Genetic Analyses Reflect the Neural Stem Cell Capacity of the Rat Auditory Thalamus over Time. Int J Mol Sci 2024; 25:2623. [PMID: 38473870 DOI: 10.3390/ijms25052623] [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: 12/23/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Neural stem cells (NSCs) have been recently identified in the neonatal rat medial geniculate body (MGB). NSCs are characterized by three cardinal features: mitotic self-renewal, formation of progenitors, and differentiation into all neuroectodermal cell lineages. NSCs and the molecular factors affecting them are particularly interesting, as they present a potential target for treating neurologically based hearing disorders. It is unclear whether an NSC niche exists in the rat MGB up to the adult stage and which neurogenic factors are essential during maturation. The rat MGB was examined on postnatal days 8, 12, and 16, and at the adult stadium. The cardinal features of NSCs were detected in MGB cells of all age groups examined by neurosphere, passage, and differentiation assays. In addition, real-time quantitative polymerase chain reaction arrays were used to compare the mRNA levels of 84 genes relevant to NSCs and neurogenesis. In summary, cells of the MGB display the cardinal features of NSCs up to the adult stage with a decreasing NSC potential over time. Neurogenic factors with high importance for MGB neurogenesis were identified on the mRNA level. These findings should contribute to a better understanding of MGB neurogenesis and its regenerative capacity.
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Affiliation(s)
- Jonas Engert
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Wuerzburg, Josef-Schneider-Strasse 11, 97080 Wuerzburg, Germany
| | - Bjoern Spahn
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Wuerzburg, Josef-Schneider-Strasse 11, 97080 Wuerzburg, Germany
| | - Sabine Sommerer
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Wuerzburg, Josef-Schneider-Strasse 11, 97080 Wuerzburg, Germany
| | - Totta Ehret Kasemo
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Wuerzburg, Josef-Schneider-Strasse 11, 97080 Wuerzburg, Germany
| | - Stephan Hackenberg
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Wuerzburg, Josef-Schneider-Strasse 11, 97080 Wuerzburg, Germany
| | - Kristen Rak
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Wuerzburg, Josef-Schneider-Strasse 11, 97080 Wuerzburg, Germany
| | - Johannes Voelker
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Wuerzburg, Josef-Schneider-Strasse 11, 97080 Wuerzburg, Germany
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4
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Dorsey SG, Mocci E, Lane MV, Krueger BK. Rapid effects of valproic acid on the fetal brain transcriptome: Implications for brain development and autism. RESEARCH SQUARE 2024:rs.3.rs-3684653. [PMID: 38260618 PMCID: PMC10802704 DOI: 10.21203/rs.3.rs-3684653/v1] [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
There is an increased incidence of autism among the children of women who take the anti-epileptic, mood-stabilizing drug, valproic acid (VPA) during pregnancy; moreover, exposure to VPA in utero causes autistic-like symptoms in rodents and non-human primates. Analysis of RNA-seq data obtained from E12.5 fetal mouse brains 3 hours after VPA administration to the pregnant dam revealed that VPA rapidly and significantly increased or decreased the expression of approximately 7,300 genes. No significant sex differences in VPA-induced gene expression were observed. Expression of 399 autism risk genes was significantly altered by VPA as was expression of 255 genes that have been reported to play fundamental roles in fetal brain development but are not otherwise linked to autism. Expression of genes associated with intracellular signaling pathways, neurogenesis, and excitation-inhibition balance as well as synaptogenesis, neuronal fate determination, axon and dendritic development, neuroinflammation, circadian rhythms, and epigenetic modulation of gene expression was dysregulated by VPA. The goal of this study was to identify mouse genes that are: (a) significantly up- or down-regulated by VPA in the fetal brain and (b) known to be associated with autism and/or to play a role in embryonic neurodevelopmental processes, perturbation of which has the potential to alter brain connectivity and, consequently behavior, in the adult. The set of genes meeting these criteria provides potential targets for future hypothesis-driven studies to elucidate the proximal causes of errors in brain connectivity underlying neurodevelopmental disorders such as autism.
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Affiliation(s)
- Susan G. Dorsey
- Department of Pain and Translational Symptom Sciences, University of Maryland School of Nursing, Baltimore, MD 21201
| | - Evelina Mocci
- Department of Pain and Translational Symptom Sciences, University of Maryland School of Nursing, Baltimore, MD 21201
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Malcolm V. Lane
- Translational Toxicology/Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Bruce K. Krueger
- Departments of Physiology and Psychiatry, University of Maryland School of Medicine, Baltimore, MD 21201
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5
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Lu C, Garipler G, Dai C, Roush T, Salome-Correa J, Martin A, Liscovitch-Brauer N, Mazzoni EO, Sanjana NE. Essential transcription factors for induced neuron differentiation. Nat Commun 2023; 14:8362. [PMID: 38102126 PMCID: PMC10724217 DOI: 10.1038/s41467-023-43602-7] [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: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
Neurogenins are proneural transcription factors required to specify neuronal identity. Their overexpression in human pluripotent stem cells rapidly produces cortical-like neurons with spiking activity and, because of this, they have been widely adopted for human neuron disease models. However, we do not fully understand the key downstream regulatory effectors responsible for driving neural differentiation. Here, using inducible expression of NEUROG1 and NEUROG2, we identify transcription factors (TFs) required for directed neuronal differentiation by combining expression and chromatin accessibility analyses with a pooled in vitro CRISPR-Cas9 screen targeting all ~1900 TFs in the human genome. The loss of one of these essential TFs (ZBTB18) yields few MAP2-positive neurons. Differentiated ZBTB18-null cells have radically altered gene expression, leading to cytoskeletal defects and stunted neurites and spines. In addition to identifying key downstream TFs for neuronal differentiation, our work develops an integrative multi-omics and TFome-wide perturbation platform to rapidly characterize essential TFs for the differentiation of any human cell type.
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Affiliation(s)
- Congyi Lu
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Görkem Garipler
- Department of Biology, New York University, New York, NY, USA
| | - Chao Dai
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Timothy Roush
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Jose Salome-Correa
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Alex Martin
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Noa Liscovitch-Brauer
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY, USA.
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY, USA.
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA.
- Department of Biology, New York University, New York, NY, USA.
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6
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Dorsey SG, Mocci E, Lane MV, Krueger BK. Rapid effects of valproic acid on the fetal brain transcriptome: Implications for brain development and autism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.01.538959. [PMID: 37205520 PMCID: PMC10187231 DOI: 10.1101/2023.05.01.538959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
There is an increased incidence of autism among the children of women who take the anti-epileptic, mood stabilizing drug, valproic acid (VPA) during pregnancy; moreover, exposure to VPA in utero causes autistic-like symptoms in rodents and non-human primates. Analysis of RNAseq data obtained from fetal mouse brains 3 hr after VPA administration revealed that VPA significantly [p(FDR) ≤ 0.025] increased or decreased the expression of approximately 7,300 genes. No significant sex differences in VPA-induced gene expression were observed. Expression of genes associated with neurodevelopmental disorders such as autism as well as neurogenesis, axon growth and synaptogenesis, GABAergic, glutaminergic and dopaminergic synaptic transmission, perineuronal nets, and circadian rhythms was dysregulated by VPA. Moreover, expression of 400 autism risk genes was significantly altered by VPA as was expression of 247 genes that have been reported to play fundamental roles in the development of the nervous system, but are not linked to autism by GWAS. The goal of this study was to identify mouse genes that are: (a) significantly up- or down-regulated by VPA in the fetal brain and (b) known to be associated with autism and/or to play a role in embryonic neurodevelopmental processes, perturbation of which has the potential to alter brain connectivity in the postnatal and adult brain. The set of genes meeting these criteria provides potential targets for future hypothesis-driven approaches to elucidating the proximal underlying causes of defective brain connectivity in neurodevelopmental disorders such as autism.
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7
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Fedoseyeva VB, Novosadova EV, Nenasheva VV, Novosadova LV, Grivennikov IA, Tarantul VZ. Activation of Embryonic Gene Transcription in Neural Precursor Cells Derived from the Induced Pluripotent Stem Cells of the Patients with Parkinson's Disease. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:515-525. [PMID: 37080937 DOI: 10.1134/s0006297923040077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative diseases in the world. Despite numerous studies, the causes of this pathology remain completely unknown. This is, among other things, due to the difficulty of obtaining biological material for analysis. Neural cell cultures derived from the induced pluripotent stem cells (IPSCs) provide a great potential for studying molecular events underlying the pathogenesis of PD. This paper presents the results of bioinformatic analysis of the data obtained using RNA-seq technology in the study of neural precursors (NP) derived from IPSCs of the healthy donors and patients with PD carrying various mutations that are commonly associated with familial PD. This analysis showed that the level of transcription of multiple genes actively expressed in the nervous system at the embryonic stage of development was significantly increased in the NP cells obtained from the patients with PD, unlike in the case of healthy donors. Bioinformatic data have been, in general, confirmed using real-time PCR. The obtained data suggest that one of the causes of PD may be the shift of the gene expression pattern in neuronal cells towards embryonic gene expression pattern (termed dematuration).
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Affiliation(s)
- Viya B Fedoseyeva
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
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8
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Martins-da-Silva A, Baroni M, Salomão KB, das Chagas PF, Bonfim-Silva R, Geron L, Cruzeiro GAV, da Silva WA, Corrêa CAP, Carlotti CG, de Paula Queiroz RG, Marie SKN, Brandalise SR, Yunes JA, Scrideli CA, Valera ET, Tone LG. Clinical Prognostic Implications of Wnt Hub Genes Expression in Medulloblastoma. Cell Mol Neurobiol 2023; 43:813-826. [PMID: 35366170 DOI: 10.1007/s10571-022-01217-4] [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: 07/13/2021] [Accepted: 03/22/2022] [Indexed: 11/03/2022]
Abstract
Medulloblastoma is the most common type of pediatric malignant primary brain tumor, and about one-third of patients die due to disease recurrence and most survivors suffer from long-term side effects. MB is clinically, genetically, and epigenetically heterogeneous and subdivided into at least four molecular subgroups: WNT, SHH, Group 3, and Group 4. We evaluated common differentially expressed genes between a Brazilian RNA-seq GSE181293 dataset and microarray GSE85217 dataset cohort of pediatric MB samples using bioinformatics methodology in order to identify hub genes of the molecular subgroups based on PPI network construction, survival and functional analysis. The main finding was the identification of five hub genes from the WNT subgroup that are tumor suppressors, and whose lower expression is related to a worse prognosis for MB patients. Furthermore, the common genes correlated with the five tumor suppressors participate in important pathways and processes for tumor initiation and progression, as well as development and differentiation, and some of them control cell stemness and pluripotency. These genes have not yet been studied within the context of MB, representing new important elements for investigation in the search for therapeutic targets, prognostic markers or for understanding of MB biology.
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Affiliation(s)
- Andrea Martins-da-Silva
- Department of Pediatrics, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil.
| | - Mirella Baroni
- Department of Pediatrics, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Karina Bezerra Salomão
- Department of Pediatrics, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Pablo Ferreira das Chagas
- Department of Genetics, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Ricardo Bonfim-Silva
- Department of Surgery and Anatomy, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Lenisa Geron
- Department of Genetics, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Gustavo Alencastro Veiga Cruzeiro
- Department of Pediatrics, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil.,Department of Pediatric Oncology, Harvard Medical School - Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wilson Araújo da Silva
- Department of Genetics, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Carolina Alves Pereira Corrêa
- Department of Pediatrics, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Carlos Gilberto Carlotti
- Department of Surgery and Anatomy, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Rosane Gomes de Paula Queiroz
- Department of Pediatrics, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | | | | | | | - Carlos Alberto Scrideli
- Department of Pediatrics, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil.,Department of Genetics, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz Gonzaga Tone
- Department of Pediatrics, University Hospital - Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil.,Department of Genetics, Ribeirão Preto Medical School - University of São Paulo, Ribeirão Preto, Brazil
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9
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Schuster J, Klar J, Khalfallah A, Laan L, Hoeber J, Fatima A, Sequeira VM, Jin Z, Korol SV, Huss M, Nordgren A, Anderlid BM, Gallant C, Birnir B, Dahl N. ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function. Front Mol Neurosci 2022; 15:988993. [PMID: 36353360 PMCID: PMC9637781 DOI: 10.3389/fnmol.2022.988993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 07/30/2023] Open
Abstract
Mowat-Wilson syndrome (MWS) is a severe neurodevelopmental disorder caused by heterozygous variants in the gene encoding transcription factor ZEB2. Affected individuals present with structural brain abnormalities, speech delay and epilepsy. In mice, conditional loss of Zeb2 causes hippocampal degeneration, altered migration and differentiation of GABAergic interneurons, a heterogeneous population of mainly inhibitory neurons of importance for maintaining normal excitability. To get insights into GABAergic development and function in MWS we investigated ZEB2 haploinsufficient induced pluripotent stem cells (iPSC) of MWS subjects together with iPSC of healthy donors. Analysis of RNA-sequencing data at two time points of GABAergic development revealed an attenuated interneuronal identity in MWS subject derived iPSC with enrichment of differentially expressed genes required for transcriptional regulation, cell fate transition and forebrain patterning. The ZEB2 haploinsufficient neural stem cells (NSCs) showed downregulation of genes required for ventral telencephalon specification, such as FOXG1, accompanied by an impaired migratory capacity. Further differentiation into GABAergic interneuronal cells uncovered upregulation of transcription factors promoting pallial and excitatory neurons whereas cortical markers were downregulated. The differentially expressed genes formed a neural protein-protein network with extensive connections to well-established epilepsy genes. Analysis of electrophysiological properties in ZEB2 haploinsufficient GABAergic cells revealed overt perturbations manifested as impaired firing of repeated action potentials. Our iPSC model of ZEB2 haploinsufficient GABAergic development thus uncovers a dysregulated gene network leading to immature interneurons with mixed identity and altered electrophysiological properties, suggesting mechanisms contributing to the neuropathogenesis and seizures in MWS.
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Affiliation(s)
- Jens Schuster
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Ayda Khalfallah
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Loora Laan
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Jan Hoeber
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Ambrin Fatima
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Velin Marita Sequeira
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Zhe Jin
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Sergiy V. Korol
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Mikael Huss
- Wallenberg Long-Term Bioinformatics Support, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Britt Marie Anderlid
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Gallant
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Bryndis Birnir
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
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10
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Wang S, Fu Y, Miyata T, Matsumoto S, Shinoda T, Itoh K, Harada A, Hirotsune S, Jin M. Functional Cooperation of α-Synuclein and Tau Is Essential for Proper Corticogenesis. J Neurosci 2022; 42:7031-7046. [PMID: 35906071 PMCID: PMC9480882 DOI: 10.1523/jneurosci.0396-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 11/21/2022] Open
Abstract
Alpha-synuclein (αSyn) and tau are abundant multifunctional neuronal proteins, and their intracellular deposits have been linked to many neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease. Despite the disease relevance, their physiological roles remain elusive, as mice with knock-out of either of these genes do not exhibit overt phenotypes. To reveal functional cooperation, we generated αSyn-/-tau-/- double-knock-out mice and characterized the functional cross talk between these proteins during brain development. Intriguingly, deletion of αSyn and tau reduced Notch signaling and accelerated interkinetic nuclear migration of G2 phase at early embryonic stage. This significantly altered the balance between the proliferative and neurogenic divisions of progenitor cells, resulting in an overproduction of early born neurons and enhanced neurogenesis, by which the brain size was enlarged during the embryonic stage in both sexes. On the other hand, a reduction in the number of neural progenitor cells in the middle stage of corticogenesis diminished subsequent gliogenesis in the αSyn-/-tau-/- cortex. Additionally, the expansion and maturation of macroglial cells (astrocytes and oligodendrocytes) were suppressed in the αSyn-/-tau-/- postnatal brain, which in turn reduced the male αSyn-/-tau-/- brain size and cortical thickness to less than the control values. Our study identifies important functional cooperation of αSyn and tau during corticogenesis.SIGNIFICANCE STATEMENT Correct understanding of the physiological functions of αSyn and tau in CNS is critical to elucidate pathogenesis involved in the etiology of neurodegenerative diseases including Alzheimer's disease and Parkinson's disease. We show here that αSyn and tau are cooperatively involved in brain development via maintenance of progenitor cells. αSyn and tau double-knock-out mice exhibited an overproduction of early born neurons and accelerated neurogenesis at early corticogenesis. Furthermore, loss of αSyn and tau also perturbed gliogenesis at later embryonic stage, as well as the subsequent glial expansion and maturation at postnatal brain. Our findings provide new mechanistic insights and extend therapeutic opportunities for neurodegenerative diseases caused by aberrant αSyn and tau.
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Affiliation(s)
- Shengming Wang
- Department of Genetic Disease Research, Osaka Metropolitan University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Yu Fu
- Department of Genetic Disease Research, Osaka Metropolitan University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Takaki Miyata
- Department of Anatomy and Cell Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Sakiko Matsumoto
- Department of Genetic Disease Research, Osaka Metropolitan University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Tomoyasu Shinoda
- Department of Anatomy and Cell Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Akihiro Harada
- Department of Cell Biology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shinji Hirotsune
- Department of Genetic Disease Research, Osaka Metropolitan University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Mingyue Jin
- Department of Genetic Disease Research, Osaka Metropolitan University Graduate School of Medicine, Osaka 545-8585, Japan
- Guangxi Key Laboratory of Brain and Cognitive Neuroscience, Guilin Medical University, Guilin, Guangxi 541199, China
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11
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Zapata G, Yan K, Picketts DJ. Generation of a mouse model of the neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) syndrome. Hum Mol Genet 2022; 31:3405-3421. [PMID: 35604347 DOI: 10.1093/hmg/ddac119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Heterozygous variants in BPTF cause the neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL) syndrome (MIM#617755) characterized by intellectual disability (ID), speech delay, and postnatal microcephaly. BPTF functions within NURF, a complex comprising SNF2L, an ISWI chromatin remodeling protein encoded by the SMARCA1 gene. Surprisingly, ablation of Smarca1 resulted in mice with enlarged brains, a direct contrast to the phenotype of NEDDFL patients. To model the NEDDFL syndrome, we generated forebrain-specific Bptf knockout (Bptf cKO) mice. Bptf cKO mice were born in normal Mendelian ratios, survived to adulthood but were smaller in size with severe cortical hypoplasia. Prolonged progenitor cell cycle length and a high incidence of cell death reduced neuronal output. Cortical lamination was also disrupted with reduced proportions of deep layer neurons, and neuronal maturation defects that impaired the acquisition of distinct cell fates (eg. Ctip2+ neurons). RNAseq and pathway analysis identified altered expression of fate-determining transcription factors, and biological pathways involved in neural development, apoptotic signaling, and amino acid biosynthesis. Dysregulated genes were enriched for Myc binding sites, a known BPTF transcriptional co-factor. We propose Bptf cKO mice as a valuable model for further study of the NEDDFL syndrome.
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Affiliation(s)
- Gerardo Zapata
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8L6.,Departments of Biochemistry, Microbiology, & Immunology, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8L6
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada, K1H 8L6.,Departments of Biochemistry, Microbiology, & Immunology, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5.,Departments of Biochemistry, Microbiology, & Immunology, Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5.,Medicine, University of Ottawa, Ottawa, Ontario, Canada, K1H8M5
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12
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Caporale N, Leemans M, Birgersson L, Germain PL, Cheroni C, Borbély G, Engdahl E, Lindh C, Bressan RB, Cavallo F, Chorev NE, D'Agostino GA, Pollard SM, Rigoli MT, Tenderini E, Tobon AL, Trattaro S, Troglio F, Zanella M, Bergman Å, Damdimopoulou P, Jönsson M, Kiess W, Kitraki E, Kiviranta H, Nånberg E, Öberg M, Rantakokko P, Rudén C, Söder O, Bornehag CG, Demeneix B, Fini JB, Gennings C, Rüegg J, Sturve J, Testa G. From cohorts to molecules: Adverse impacts of endocrine disrupting mixtures. Science 2022; 375:eabe8244. [PMID: 35175820 DOI: 10.1126/science.abe8244] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Convergent evidence associates exposure to endocrine disrupting chemicals (EDCs) with major human diseases, even at regulation-compliant concentrations. This might be because humans are exposed to EDC mixtures, whereas chemical regulation is based on a risk assessment of individual compounds. Here, we developed a mixture-centered risk assessment strategy that integrates epidemiological and experimental evidence. We identified that exposure to an EDC mixture in early pregnancy is associated with language delay in offspring. At human-relevant concentrations, this mixture disrupted hormone-regulated and disease-relevant regulatory networks in human brain organoids and in the model organisms Xenopus leavis and Danio rerio, as well as behavioral responses. Reinterrogating epidemiological data, we found that up to 54% of the children had prenatal exposures above experimentally derived levels of concern, reaching, for the upper decile compared with the lowest decile of exposure, a 3.3 times higher risk of language delay.
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Affiliation(s)
- Nicolò Caporale
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy.,Human Technopole, V.le Rita Levi-Montalcini, 1, 20157 Milan, Italy
| | - Michelle Leemans
- UMR 7221, Phyma, CNRS-Muséum National d'Histoire Naturelle, Sorbonne Université, 75005 Paris, France
| | - Lina Birgersson
- Department of Biological and Environmental Sciences, University of Gothenburg, 41463 Gothenburg, Sweden
| | - Pierre-Luc Germain
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Cristina Cheroni
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy.,Human Technopole, V.le Rita Levi-Montalcini, 1, 20157 Milan, Italy
| | - Gábor Borbély
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden
| | - Elin Engdahl
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Department of Organismal Biology, Environmental Toxicology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Christian Lindh
- Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, SE-221 85 Lund, Sweden
| | - Raul Bardini Bressan
- Medical Research Council Centre for Regenerative Medicine and Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Francesca Cavallo
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Nadav Even Chorev
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Giuseppe Alessandro D'Agostino
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Steven M Pollard
- Medical Research Council Centre for Regenerative Medicine and Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Marco Tullio Rigoli
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Erika Tenderini
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Alejandro Lopez Tobon
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Sebastiano Trattaro
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy
| | - Flavia Troglio
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Matteo Zanella
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Åke Bergman
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Department of Environmental Science, Stockholm University, SE-10691 Stockholm, Sweden.,School of Science and Technology, Örebro University, SE-70182 Örebro, Sweden
| | - Pauliina Damdimopoulou
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Maria Jönsson
- Department of Organismal Biology, Environmental Toxicology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Wieland Kiess
- Hospital for Children and Adolescents, Department of Women and Child Health, University Hospital, University of Leipzig, 04103 Leipzig, Germany
| | - Efthymia Kitraki
- Lab of Basic Sciences, Faculty of Dentistry, National and Kapodistrian University of Athens, 152 72 Athens, Greece
| | - Hannu Kiviranta
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Kuopio 70210, Finland
| | - Eewa Nånberg
- School of Health Sciences, Örebro University, SE-70182 Örebro, Sweden
| | - Mattias Öberg
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Institute of Environmental Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Panu Rantakokko
- Department of Health Security, Finnish Institute for Health and Welfare (THL), Kuopio 70210, Finland
| | - Christina Rudén
- Department of Environmental Science, Stockholm University, SE-10691 Stockholm, Sweden
| | - Olle Söder
- Department of Women's and Children's Health, Pediatric Endocrinology Division, Karolinska Institutet and University Hospital, SE-17176 Stockholm, Sweden
| | - Carl-Gustaf Bornehag
- Faculty of Health, Science and Technology, Department of Health Sciences, Karlstad University, SE- 651 88 Karlstad, Sweden.,Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Barbara Demeneix
- UMR 7221, Phyma, CNRS-Muséum National d'Histoire Naturelle, Sorbonne Université, 75005 Paris, France
| | - Jean-Baptiste Fini
- UMR 7221, Phyma, CNRS-Muséum National d'Histoire Naturelle, Sorbonne Université, 75005 Paris, France
| | - Chris Gennings
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joëlle Rüegg
- Swedish Toxicology Sciences Research Center (SWETOX), Södertälje, Sweden.,Department of Organismal Biology, Environmental Toxicology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Joachim Sturve
- Department of Biological and Environmental Sciences, University of Gothenburg, 41463 Gothenburg, Sweden
| | - Giuseppe Testa
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141 Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy.,Human Technopole, V.le Rita Levi-Montalcini, 1, 20157 Milan, Italy
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13
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Cell-of-Origin and Genetic, Epigenetic, and Microenvironmental Factors Contribute to the Intra-Tumoral Heterogeneity of Pediatric Intracranial Ependymoma. Cancers (Basel) 2021; 13:cancers13236100. [PMID: 34885210 PMCID: PMC8657076 DOI: 10.3390/cancers13236100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Intra-tumoral heterogeneity (ITH) is a complex multifaceted phenomenon that posits major challenges for the clinical management of cancer patients. Genetic, epigenetic, and microenvironmental factors are concurrent drivers of diversity among the distinct populations of cancer cells. ITH may also be installed by cancer stem cells (CSCs), that foster unidirectional hierarchy of cellular phenotypes or, alternatively, shift dynamically between distinct cellular states. Ependymoma (EPN), a molecularly heterogeneous group of tumors, shows a specific spatiotemporal distribution that suggests a link between ependymomagenesis and alterations of the biological processes involved in embryonic brain development. In children, EPN most often arises intra-cranially and is associated with an adverse outcome. Emerging evidence shows that EPN displays large intra-patient heterogeneity. In this review, after touching on EPN inter-tumoral heterogeneity, we focus on the sources of ITH in pediatric intra-cranial EPN in the framework of the CSC paradigm. We also examine how single-cell technology has shed new light on the complexity and developmental origins of EPN and the potential impact that this understanding may have on the therapeutic strategies against this deadly pediatric malignancy.
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14
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Achour M, Ferdousi F, Sasaki K, Isoda H. Luteolin Modulates Neural Stem Cells Fate Determination: In vitro Study on Human Neural Stem Cells, and in vivo Study on LPS-Induced Depression Mice Model. Front Cell Dev Biol 2021; 9:753279. [PMID: 34790666 PMCID: PMC8591246 DOI: 10.3389/fcell.2021.753279] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/11/2021] [Indexed: 11/23/2022] Open
Abstract
Luteolin is a natural flavone with neurotrophic effects observed on different neuronal cell lines. In the present study, we aimed to assess the effect of luteolin on hNSCs fate determination and the LPS-induced neuroinflammation in a mouse model of depression with astrocytogenesis defect. hNSCs were cultured in basal cell culture medium (control) or medium supplemented with luteolin or AICAR, a known inducer of astrogenesis. A whole-genome transcriptomic analysis showed that luteolin upregulated the expressions of genes related to neurotrophin, dopaminergic, hippo, and Wnt signaling pathways, and downregulated the genes involved in p53, TNF, FOXO, and Notch signaling pathways. We also found that astrocyte-specific gene GFAP, as well as other genes of the key signaling pathways involved in astrogenesis such as Wnt, BMP, and JAK-STAT pathways were upregulated in luteolin-treated hNSCs. On the other hand, neurogenesis and oligodendrogenesis-related genes, TUBB3, NEUROD 1 and 6, and MBP, were downregulated in luteolin-treated hNSCs. Furthermore, immunostaining showed that percentages of GFAP+ cells were significantly higher in luteolin- and AICAR-treated hNSCs compared to control hNSCs. Additionally, RT-qPCR results showed that luteolin upregulated the expressions of GFAP, BMP2, and STAT3, whereas the expression of TUBB3 remained unchanged. Next, we evaluated the effects of luteolin in LPS-induced mice model of depression that represents defects in astrocytogenesis. We found that oral administration of luteolin (10 mg/Kg) for eight consecutive days could decrease the immobility time on tail suspension test, a mouse behavioral test measuring depression-like behavior, and attenuate LPS-induced inflammatory responses by significantly decreasing IL-6 production in mice brain-derived astrocytes and serum, and TNFα and corticosterone levels in serum. Luteolin treatment also significantly increased mature BDNF, dopamine, and noradrenaline levels in the hypothalamus of LPS-induced depression mice. Though the behavioral effects of luteolin did not reach statistical significance, global gene expression analyses of mice hippocampus and brain-derived NSCs highlighted the modulatory effects of luteolin on different signaling pathways involved in the pathophysiology of depression. Altogether, our findings suggest an astrocytogenic potential of luteolin and its possible therapeutic benefits in neuroinflammatory and neurodegenerative diseases. However, further studies are required to identify the specific mechanism of action of luteolin.
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Affiliation(s)
- Mariem Achour
- Laboratory of Metabolic Biophysics and Applied Pharmacology, Faculty of Medicine of Sousse, University of Sousse, Sousse, Tunisia.,Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan
| | - Farhana Ferdousi
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,National Institute of Advanced Industrial Science and Technology (AIST)-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba, Japan
| | - Kazunori Sasaki
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan.,National Institute of Advanced Industrial Science and Technology (AIST)-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba, Japan
| | - Hiroko Isoda
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,National Institute of Advanced Industrial Science and Technology (AIST)-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba, Japan
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15
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Girskis KM, Stergachis AB, DeGennaro EM, Doan RN, Qian X, Johnson MB, Wang PP, Sejourne GM, Nagy MA, Pollina EA, Sousa AMM, Shin T, Kenny CJ, Scotellaro JL, Debo BM, Gonzalez DM, Rento LM, Yeh RC, Song JHT, Beaudin M, Fan J, Kharchenko PV, Sestan N, Greenberg ME, Walsh CA. Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions. Neuron 2021; 109:3239-3251.e7. [PMID: 34478631 DOI: 10.1016/j.neuron.2021.08.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/02/2021] [Accepted: 08/06/2021] [Indexed: 01/21/2023]
Abstract
Human accelerated regions (HARs) are the fastest-evolving regions of the human genome, and many are hypothesized to function as regulatory elements that drive human-specific gene regulatory programs. We interrogate the in vitro enhancer activity and in vivo epigenetic landscape of more than 3,100 HARs during human neurodevelopment, demonstrating that many HARs appear to act as neurodevelopmental enhancers and that sequence divergence at HARs has largely augmented their neuronal enhancer activity. Furthermore, we demonstrate PPP1R17 to be a putative HAR-regulated gene that has undergone remarkable rewiring of its cell type and developmental expression patterns between non-primates and primates and between non-human primates and humans. Finally, we show that PPP1R17 slows neural progenitor cell cycle progression, paralleling the cell cycle length increase seen predominantly in primate and especially human neurodevelopment. Our findings establish HARs as key components in rewiring human-specific neurodevelopmental gene regulatory programs and provide an integrated resource to study enhancer activity of specific HARs.
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Affiliation(s)
- Kelly M Girskis
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ellen M DeGennaro
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan N Doan
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xuyu Qian
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew B Johnson
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Peter P Wang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gabrielle M Sejourne
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Aurel Nagy
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Pollina
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Taehwan Shin
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston MA, USA
| | - Connor J Kenny
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julia L Scotellaro
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian M Debo
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dilenny M Gonzalez
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lariza M Rento
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebecca C Yeh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Janet H T Song
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc Beaudin
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jean Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Nenad Sestan
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Michael E Greenberg
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Program in Neuroscience, Harvard Medical School, Boston, MA, USA.
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16
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Larrigan S, Shah S, Fernandes A, Mattar P. Chromatin Remodeling in the Brain-a NuRDevelopmental Odyssey. Int J Mol Sci 2021; 22:ijms22094768. [PMID: 33946340 PMCID: PMC8125410 DOI: 10.3390/ijms22094768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 01/07/2023] Open
Abstract
During brain development, the genome must be repeatedly reconfigured in order to facilitate neuronal and glial differentiation. A host of chromatin remodeling complexes facilitates this process. At the genetic level, the non-redundancy of these complexes suggests that neurodevelopment may require a lexicon of remodelers with different specificities and activities. Here, we focus on the nucleosome remodeling and deacetylase (NuRD) complex. We review NuRD biochemistry, genetics, and functions in neural progenitors and neurons.
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Affiliation(s)
- Sarah Larrigan
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Alex Fernandes
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Pierre Mattar
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Correspondence:
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17
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Oproescu AM, Han S, Schuurmans C. New Insights Into the Intricacies of Proneural Gene Regulation in the Embryonic and Adult Cerebral Cortex. Front Mol Neurosci 2021; 14:642016. [PMID: 33658912 PMCID: PMC7917194 DOI: 10.3389/fnmol.2021.642016] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/26/2021] [Indexed: 12/21/2022] Open
Abstract
Historically, the mammalian brain was thought to lack stem cells as no new neurons were found to be made in adulthood. That dogma changed ∼25 years ago with the identification of neural stem cells (NSCs) in the adult rodent forebrain. However, unlike rapidly self-renewing mature tissues (e.g., blood, intestinal crypts, skin), the majority of adult NSCs are quiescent, and those that become 'activated' are restricted to a few neurogenic zones that repopulate specific brain regions. Conversely, embryonic NSCs are actively proliferating and neurogenic. Investigations into the molecular control of the quiescence-to-proliferation-to-differentiation continuum in the embryonic and adult brain have identified proneural genes encoding basic-helix-loop-helix (bHLH) transcription factors (TFs) as critical regulators. These bHLH TFs initiate genetic programs that remove NSCs from quiescence and drive daughter neural progenitor cells (NPCs) to differentiate into specific neural cell subtypes, thereby contributing to the enormous cellular diversity of the adult brain. However, new insights have revealed that proneural gene activities are context-dependent and tightly regulated. Here we review how proneural bHLH TFs are regulated, with a focus on the murine cerebral cortex, drawing parallels where appropriate to other organisms and neural tissues. We discuss upstream regulatory events, post-translational modifications (phosphorylation, ubiquitinylation), protein-protein interactions, epigenetic and metabolic mechanisms that govern bHLH TF expression, stability, localization, and consequent transactivation of downstream target genes. These tight regulatory controls help to explain paradoxical findings of changes to bHLH activity in different cellular contexts.
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Affiliation(s)
- Ana-Maria Oproescu
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Sisu Han
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Carol Schuurmans
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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18
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Dupont J, Vieira JP, Tavares ALT, Conceição CR, Khan S, Bertoli-Avella AM, Sousa AB. Adding evidence to the role of NEUROG1 in congenital cranial dysinnervation disorders. Clin Genet 2021; 99:588-593. [PMID: 33439489 DOI: 10.1111/cge.13922] [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: 11/11/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 11/28/2022]
Abstract
Congenital cranial dysinnervation disorders (CCDDs) are a heterogeneous group of neurodevelopmental phenotypes caused by a primary disturbance of innervation due to deficient, absent, or misguided cranial nerves. Although some CCDDs genes are known, several clinical phenotypes and their aetiologies remain to be elucidated. We describe a 12-year-old boy with hypotonia, developmental delay, sensorineural hearing loss, and keratoconjunctivitis due to lack of corneal reflex. He had a long expressionless face, severe oromotor dysfunction, bilateral agenesis/severe hypoplasia of the VIII nerve with marked atresia of the internal auditory canals and cochlear labyrinth malformation. Trio-exome sequencing identified a homozygous loss of function variant in the NEUROG1 gene (NM_006161.2: c.202G > T, p.Glu68*). NEUROG1 is considered a causal candidate for CCDDs based on (i) the previous report of a patient with a homozygous gene deletion and developmental delay, deafness due to absent bilateral VIII nerves, and severe oromotor dysfunction; (ii) a second patient with a homozygous NEUROG1 missense variant and corneal opacity, absent corneal reflex and intellectual disability; and (iii) the knockout mouse model phenotype which highly resembles the disorder observed in humans. Our findings support the growing compelling evidence that loss of NEUROG1 leads to a very distinctive disorder of cranial nerves development.
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Affiliation(s)
- Juliette Dupont
- Genetics Department, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, Lisbon, Portugal
| | - José Pedro Vieira
- Neurology Department, Hospital de Dona Estefânia, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Ana Lisa Taylor Tavares
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Health, Genomics England, Queen Mary University of London, Charterhouse Square, London, UK
| | - Carla Ribeiro Conceição
- Neuroradiology Department, Hospital de Dona Estefânia, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Suliman Khan
- Research Data Analysis, CENTOGENE AG, Rostock, Germany
| | | | - Ana Berta Sousa
- Genetics Department, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, Lisbon, Portugal.,Laboratório de Imunologia Básica, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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19
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Gojo J, Englinger B, Jiang L, Hübner JM, Shaw ML, Hack OA, Madlener S, Kirchhofer D, Liu I, Pyrdol J, Hovestadt V, Mazzola E, Mathewson ND, Trissal M, Lötsch D, Dorfer C, Haberler C, Halfmann A, Mayr L, Peyrl A, Geyeregger R, Schwalm B, Mauermann M, Pajtler KW, Milde T, Shore ME, Geduldig JE, Pelton K, Czech T, Ashenberg O, Wucherpfennig KW, Rozenblatt-Rosen O, Alexandrescu S, Ligon KL, Pfister SM, Regev A, Slavc I, Berger W, Suvà ML, Kool M, Filbin MG. Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma. Cancer Cell 2020; 38:44-59.e9. [PMID: 32663469 PMCID: PMC7479515 DOI: 10.1016/j.ccell.2020.06.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/26/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023]
Abstract
Ependymoma is a heterogeneous entity of central nervous system tumors with well-established molecular groups. Here, we apply single-cell RNA sequencing to analyze ependymomas across molecular groups and anatomic locations to investigate their intratumoral heterogeneity and developmental origins. Ependymomas are composed of a cellular hierarchy initiating from undifferentiated populations, which undergo impaired differentiation toward three lineages of neuronal-glial fate specification. While prognostically favorable groups of ependymoma predominantly harbor differentiated cells, aggressive groups are enriched for undifferentiated cell populations. The delineated transcriptomic signatures correlate with patient survival and define molecular dependencies for targeted treatment approaches. Taken together, our analyses reveal a developmental hierarchy underlying ependymomas relevant to biological and clinical behavior.
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Affiliation(s)
- Johannes Gojo
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jens M Hübner
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - McKenzie L Shaw
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Olivia A Hack
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Dominik Kirchhofer
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Ilon Liu
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jason Pyrdol
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emanuele Mazzola
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan D Mathewson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Maria Trissal
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daniela Lötsch
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Angela Halfmann
- Clinical Cell Biology, Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Rene Geyeregger
- Clinical Cell Biology, Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - Benjamin Schwalm
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Monica Mauermann
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Marni E Shore
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jack E Geduldig
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Orr Ashenberg
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Keith L Ligon
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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20
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Vaid S, Huttner WB. Transcriptional Regulators and Human-Specific/Primate-Specific Genes in Neocortical Neurogenesis. Int J Mol Sci 2020; 21:ijms21134614. [PMID: 32610533 PMCID: PMC7369782 DOI: 10.3390/ijms21134614] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022] Open
Abstract
During development, starting from a pool of pluripotent stem cells, tissue-specific genetic programs help to shape and develop functional organs. To understand the development of an organ and its disorders, it is important to understand the spatio-temporal dynamics of the gene expression profiles that occur during its development. Modifications in existing genes, the de-novo appearance of new genes, or, occasionally, even the loss of genes, can greatly affect the gene expression profile of any given tissue and contribute to the evolution of organs or of parts of organs. The neocortex is evolutionarily the most recent part of the brain, it is unique to mammals, and is the seat of our higher cognitive abilities. Progenitors that give rise to this tissue undergo sequential waves of differentiation to produce the complete sets of neurons and glial cells that make up a functional neocortex. We will review herein our understanding of the transcriptional regulators that control the neural precursor cells (NPCs) during the generation of the most abundant class of neocortical neurons, the glutametergic neurons. In addition, we will discuss the roles of recently-identified human- and primate-specific genes in promoting neurogenesis, leading to neocortical expansion.
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21
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Adnani L, Dixit R, Chen X, Balakrishnan A, Modi H, Touahri Y, Logan C, Schuurmans C. Plag1 and Plagl2 have overlapping and distinct functions in telencephalic development. Biol Open 2018; 7:bio.038661. [PMID: 30361413 PMCID: PMC6262857 DOI: 10.1242/bio.038661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Plag gene family has three members; Plagl1/Zac1, which is a tumor suppressor gene, and Plag1 and Plagl2, which are proto-oncogenes. All three genes are known to be expressed in embryonic neural progenitors, and Zac1 regulates proliferation, neuronal differentiation and migration in the developing neocortex. Here we examined the functions of Plag1 and Plagl2 in neocortical development. We first attempted, and were unable to generate, E12.5 Plag1;Plagl2 double mutants, indicating that at least one Plag1 or Plagl2 gene copy is required for embryonic survival. We therefore focused on single mutants, revealing a telencephalic patterning defect in E12.5 Plagl2 mutants and a proliferation/differentiation defect in Plag1 mutant neocortices. Specifically, the ventral pallium, a dorsal telencephalic territory, expands into the ventral telencephalon in Plagl2 mutants. In contrast, Plag1 mutants develop normal regional territories, but neocortical progenitors proliferate less and instead produce more neurons. Finally, in gain-of-function studies, both Plag1 and Plagl2 reduce neurogenesis and increase BrdU-uptake, indicative of enhanced proliferation, but while Plagl2 effects on proliferation are more immediate, Plag1 effects are delayed. Taken together, we found that the Plag proto-oncogenes genes are essential regulators of neocortical development and although Plag1 and Plagl2 functions are similar, they do not entirely overlap. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Lata Adnani
- Sunnybrook Research Institute, Biological Sciences, Room S1-16A, 2075 Bayview Ave, Toronto, ON, Canada M4N 3M5.,Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute and Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Rajiv Dixit
- Sunnybrook Research Institute, Biological Sciences, Room S1-16A, 2075 Bayview Ave, Toronto, ON, Canada M4N 3M5.,Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute and Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Xingyu Chen
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute and Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Anjali Balakrishnan
- Sunnybrook Research Institute, Biological Sciences, Room S1-16A, 2075 Bayview Ave, Toronto, ON, Canada M4N 3M5.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Harshil Modi
- Sunnybrook Research Institute, Biological Sciences, Room S1-16A, 2075 Bayview Ave, Toronto, ON, Canada M4N 3M5
| | - Yacine Touahri
- Sunnybrook Research Institute, Biological Sciences, Room S1-16A, 2075 Bayview Ave, Toronto, ON, Canada M4N 3M5
| | - Cairine Logan
- Department of Cell Biology and Anatomy, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 4N1
| | - Carol Schuurmans
- Sunnybrook Research Institute, Biological Sciences, Room S1-16A, 2075 Bayview Ave, Toronto, ON, Canada M4N 3M5 .,Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute and Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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