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Poole RJ, Flames N, Cochella L. Neurogenesis in Caenorhabditis elegans. Genetics 2024:iyae116. [PMID: 39167071 DOI: 10.1093/genetics/iyae116] [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: 05/28/2024] [Accepted: 06/24/2024] [Indexed: 08/23/2024] Open
Abstract
Animals rely on their nervous systems to process sensory inputs, integrate these with internal signals, and produce behavioral outputs. This is enabled by the highly specialized morphologies and functions of neurons. Neuronal cells share multiple structural and physiological features, but they also come in a large diversity of types or classes that give the nervous system its broad range of functions and plasticity. This diversity, first recognized over a century ago, spurred classification efforts based on morphology, function, and molecular criteria. Caenorhabditis elegans, with its precisely mapped nervous system at the anatomical level, an extensive molecular description of most of its neurons, and its genetic amenability, has been a prime model for understanding how neurons develop and diversify at a mechanistic level. Here, we review the gene regulatory mechanisms driving neurogenesis and the diversification of neuron classes and subclasses in C. elegans. We discuss our current understanding of the specification of neuronal progenitors and their differentiation in terms of the transcription factors involved and ensuing changes in gene expression and chromatin landscape. The central theme that has emerged is that the identity of a neuron is defined by modules of gene batteries that are under control of parallel yet interconnected regulatory mechanisms. We focus on how, to achieve these terminal identities, cells integrate information along their developmental lineages. Moreover, we discuss how neurons are diversified postembryonically in a time-, genetic sex-, and activity-dependent manner. Finally, we discuss how the understanding of neuronal development can provide insights into the evolution of neuronal diversity.
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Affiliation(s)
- Richard J Poole
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia 46012, Spain
| | - Luisa Cochella
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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2
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Ghafoori SM, Sethi A, Petersen GF, Tanipour MH, Gooley PR, Forwood JK. RNA Binding Properties of SOX Family Members. Cells 2024; 13:1202. [PMID: 39056784 PMCID: PMC11274882 DOI: 10.3390/cells13141202] [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: 07/25/2023] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
SOX proteins are a family of transcription factors (TFs) that play critical functions in sex determination, neurogenesis, and chondrocyte differentiation, as well as cardiac, vascular, and lymphatic development. There are 20 SOX family members in humans, each sharing a 79-residue L-shaped high mobility group (HMG)-box domain that is responsible for DNA binding. SOX2 was recently shown to interact with long non-coding RNA and large-intergenic non-coding RNA to regulate embryonic stem cell and neuronal differentiation. The RNA binding region was shown to reside within the HMG-box domain; however, the structural details of this binding remain unclear. Here, we show that all SOX family members, except group H, interact with RNA. Our mutational experiments demonstrate that the disordered C-terminal region of the HMG-box domain plays an important role in RNA binding. Further, by determining a high-resolution structure of the HMG-box domain of the group H family member SOX30, we show that despite differences in RNA binding ability, SOX30 shares a very similar secondary structure with other SOX protein HMG-box domains. Together, our study provides insight into the interaction of SOX TFs with RNA.
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Affiliation(s)
- Seyed Mohammad Ghafoori
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Ashish Sethi
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; (A.S.); (M.H.T.); (P.R.G.)
- Australian Nuclear Science Technology Organisation, The Australian Synchrotron, 800 Blackburn Rd., Clayton, VIC 3168, Australia
| | - Gayle F. Petersen
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Mohammad Hossein Tanipour
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; (A.S.); (M.H.T.); (P.R.G.)
| | - Paul R. Gooley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; (A.S.); (M.H.T.); (P.R.G.)
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
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3
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Li M, Jin Y, Xu Y, Sun Y, Yuan R, Zhang X, Qu S, Lv M, Liao M, Liang W, Zhang L, Chen X. From degraded to deciphered: ATAC-seq's application potential in forensic diagnosis. Int J Legal Med 2024; 138:1273-1285. [PMID: 38491322 DOI: 10.1007/s00414-024-03206-2] [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: 10/25/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
In recent years, molecular biology-based diagnostic techniques have made remarkable strides and are now extensively utilized in clinical practice, providing invaluable insights for disease diagnosis and treatment. However, forensic medicine, especially forensic pathology, has witnessed relatively limited progress in the application of molecular biology technologies. A significant challenge in employing molecular techniques for forensic diagnoses lies in the quantitative and qualitative changes observed in diagnostic markers due to sample degradation-a recognized and formidable obstacle. Inspired by the success of DNA sequencing in forensic practices, which enables accurate individual identification even in cases involving degraded and deteriorated tissues and organs, we propose the application of the assay for transposase-accessible chromatin with sequencing (ATAC-seq) to identify targets at the transcriptional onset, exploring chromatin and DNA-level alterations for injury and disease inference in forensic samples. This study employs ATAC-seq to explore alterations in chromatin accessibility post-injury and their subsequent changes over a 2-h degradation period, employing traumatic brain injury (TBI) as a representative model. Our findings reveal high sensitivity of chromatin accessibility sites to injury, evidenced by shifts in thousands of peak positions post-TBI. Remarkably, these alterations remain largely unaffected by early degradation. Our results robustly endorse the notion that integrating and incorporating these specific loci for injury and disease diagnosis in forensic samples holds tremendous promise for practical application. We further validated the above results using human cortical tissue, which supported that early degradation did not significantly affect chromatin accessibility. This pioneering advancement in molecular diagnostic techniques may revolutionize the field of forensic science, especially forensic pathology.
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Affiliation(s)
- Manrui Li
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yuntian Jin
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yang Xu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yihan Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Ruixuan Yuan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Xiao Zhang
- Department of Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Xiameng Chen
- Department of Forensic Pathology and Forensic Clinical Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
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Treccarichi S, Calì F, Vinci M, Ragalmuto A, Musumeci A, Federico C, Costanza C, Bottitta M, Greco D, Saccone S, Elia M. Implications of a De Novo Variant in the SOX12 Gene in a Patient with Generalized Epilepsy, Intellectual Disability, and Childhood Emotional Behavioral Disorders. Curr Issues Mol Biol 2024; 46:6407-6422. [PMID: 39057025 PMCID: PMC11276073 DOI: 10.3390/cimb46070383] [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: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
SRY-box transcription factor (SOX) genes, a recently discovered gene family, play crucial roles in the regulation of neuronal stem cell proliferation and glial differentiation during nervous system development and neurogenesis. Whole exome sequencing (WES) in patients presenting with generalized epilepsy, intellectual disability, and childhood emotional behavioral disorder, uncovered a de novo variation within SOX12 gene. Notably, this gene has never been associated with neurodevelopmental disorders. No variants in known genes linked with the patient's symptoms have been detected by the WES Trio analysis. To date, any MIM phenotype number associated with intellectual developmental disorder has not been assigned for SOX12. In contrast, both SOX4 and SOX11 genes within the same C group (SoxC) of the Sox gene family have been associated with neurodevelopmental disorders. The variant identified in the patient here described was situated within the critical high-mobility group (HMG) functional site of the SOX12 protein. This domain, in the Sox protein family, is essential for DNA binding and bending, as well as being responsible for transcriptional activation or repression during the early stages of gene expression. Sequence alignment within SoxC (SOX12, SOX4 and SOX11) revealed a high conservation rate of the HMG region. The in silico predictive analysis described this novel variant as likely pathogenic. Furthermore, the mutated protein structure predictions unveiled notable changes with potential deleterious effects on the protein structure. The aim of this study is to establish a correlation between the SOX12 gene and the symptoms diagnosed in the patient.
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Affiliation(s)
- Simone Treccarichi
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Francesco Calì
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Mirella Vinci
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Alda Ragalmuto
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Antonino Musumeci
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Concetta Federico
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy;
| | - Carola Costanza
- Department of Sciences for Health Promotion and Mother and Child Care “G. D’Alessandro”, University of Palermo, 90128 Palermo, Italy;
| | - Maria Bottitta
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Donatella Greco
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy;
| | - Maurizio Elia
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
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Kurtova AI, Finoshin AD, Aparina MS, Gazizova GR, Kozlova OS, Voronova SN, Shagimardanova EI, Ivashkin EG, Voronezhskaya EE. Expanded expression of pro-neurogenic factor SoxB1 during larval development of gastropod Lymnaea stagnalis suggests preadaptation to prolonged neurogenesis in Mollusca. Front Neurosci 2024; 18:1346610. [PMID: 38638695 PMCID: PMC11024475 DOI: 10.3389/fnins.2024.1346610] [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: 11/29/2023] [Accepted: 03/01/2024] [Indexed: 04/20/2024] Open
Abstract
Introduction The remarkable diversity observed in the structure and development of the molluscan nervous system raises intriguing questions regarding the molecular mechanisms underlying neurogenesis in Mollusca. The expression of SoxB family transcription factors plays a pivotal role in neuronal development, thereby offering valuable insights into the strategies of neurogenesis. Methods In this study, we conducted gene expression analysis focusing on SoxB-family transcription factors during early neurogenesis in the gastropod Lymnaea stagnalis. We employed a combination of hybridization chain reaction in situ hybridization (HCR-ISH), immunocytochemistry, confocal microscopy, and cell proliferation assays to investigate the spatial and temporal expression patterns of LsSoxB1 and LsSoxB2 from the gastrula stage to hatching, with particular attention to the formation of central ring ganglia. Results Our investigation reveals that LsSoxB1 demonstrates expanded ectodermal expression from the gastrula to the hatching stage, whereas expression of LsSoxB2 in the ectoderm ceases by the veliger stage. LsSoxB1 is expressed in the ectoderm of the head, foot, and visceral complex, as well as in forming ganglia and sensory cells. Conversely, LsSoxB2 is mostly restricted to the subepithelial layer and forming ganglia cells during metamorphosis. Proliferation assays indicate a uniform distribution of dividing cells in the ectoderm across all developmental stages, suggesting the absence of distinct neurogenic zones with increased proliferation in gastropods. Discussion Our findings reveal a spatially and temporally extended pattern of SoxB1 expression in a gastropod representative compared to other lophotrochozoan species. This prolonged and widespread expression of SoxB genes may be interpreted as a form of transcriptional neoteny, representing a preadaptation to prolonged neurogenesis. Consequently, it could contribute to the diversification of nervous systems in gastropods and lead to an increase in the complexity of the central nervous system in Mollusca.
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Affiliation(s)
- Anastasia I. Kurtova
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander D. Finoshin
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Margarita S. Aparina
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Guzel R. Gazizova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Olga S. Kozlova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Svetlana N. Voronova
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Elena I. Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Life Improvement by Future Technologies Center “LIFT”, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgeny G. Ivashkin
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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Marelli E, Hughes J, Scotting PJ. SUMO-dependent transcriptional repression by Sox2 inhibits the proliferation of neural stem cells. PLoS One 2024; 19:e0298818. [PMID: 38507426 PMCID: PMC10954124 DOI: 10.1371/journal.pone.0298818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/30/2024] [Indexed: 03/22/2024] Open
Abstract
Sox2 is known for its roles in maintaining the stem cell state of embryonic stem cells and neural stem cells. In particular, it has been shown to slow the proliferation of these cell types. It is also known for its effects as an activating transcription factor. Despite this, analysis of published studies shows that it represses as many genes as it activates. Here, we identify a new set of target genes that Sox2 represses in neural stem cells. These genes are associated with centrosomes, centromeres and other aspects of cell cycle control. In addition, we show that SUMOylation of Sox2 is necessary for the repression of these genes and for its repressive effects on cell proliferation. Together, these data suggest that SUMO-dependent repression of this group of target genes is responsible for the role of Sox2 in regulating the proliferation of neural stem cells.
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Affiliation(s)
- Elisa Marelli
- School of Life Sciences, University of Nottingham, Nottingham, Nottinghamshire, United Kingdom
| | - Jaime Hughes
- School of Life Sciences, University of Nottingham, Nottingham, Nottinghamshire, United Kingdom
| | - Paul J. Scotting
- School of Life Sciences, University of Nottingham, Nottingham, Nottinghamshire, United Kingdom
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Queiroz LY, Kageyama R, Cimarosti HI. SUMOylation effects on neural stem cells self-renewal, differentiation, and survival. Neurosci Res 2024; 199:1-11. [PMID: 37742800 DOI: 10.1016/j.neures.2023.09.006] [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: 06/23/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
SUMO (small ubiquitin-like modifier) conjugation or SUMOylation, a post-translational modification, is a crucial regulator of protein function and cellular processes. In the context of neural stem cells (NSCs), SUMOylation has emerged as a key player, affecting their proliferation, differentiation, and survival. By modifying transcription factors, such as SOX1, SOX2, SOX3, SOX6, Bmi1, and Nanog, SUMOylation can either enhance or impair their transcriptional activity, thus impacting on NSCs self-renewal. Moreover, SUMOylation regulates neurogenesis and neuronal differentiation by modulating key proteins, such as Foxp1, Mecp2, MEF2A, and SOX10. SUMOylation is also crucial for the survival and proliferation of NSCs in both developing and adult brains. By regulating the activity of transcription factors, coactivators, and corepressors, SUMOylation acts as a molecular switch, inducing cofactor recruitment and function during development. Importantly, dysregulation of NSCs SUMOylation has been implicated in various disorders, including embryonic defects, ischemic cerebrovascular disease, glioma, and the harmful effects of benzophenone-3 exposure. Here we review the main findings on SUMOylation-mediated regulation of NSCs self-renewal, differentiation and survival. Better understanding NSCs SUMOylation mechanisms and its functional consequences might provide new strategies to promote neuronal differentiation that could contribute for the development of novel therapies targeting neurodegenerative diseases.
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Affiliation(s)
- Letícia Yoshitome Queiroz
- Postgraduate Program in Pharmacology, Federal University of Santa Catarina (UFSC), Florianopolis, Brazil
| | - Ryoichiro Kageyama
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; RIKEN Center for Brain Science, Wako, Japan
| | - Helena I Cimarosti
- Postgraduate Program in Pharmacology, Federal University of Santa Catarina (UFSC), Florianopolis, Brazil; Postgraduate Program in Neuroscience, UFSC, Florianopolis, Brazil.
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Lim Y. Transcription factors in microcephaly. Front Neurosci 2023; 17:1302033. [PMID: 38094004 PMCID: PMC10716367 DOI: 10.3389/fnins.2023.1302033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 02/01/2024] Open
Abstract
Higher cognition in humans, compared to other primates, is often attributed to an increased brain size, especially forebrain cortical surface area. Brain size is determined through highly orchestrated developmental processes, including neural stem cell proliferation, differentiation, migration, lamination, arborization, and apoptosis. Disruption in these processes often results in either a small (microcephaly) or large (megalencephaly) brain. One of the key mechanisms controlling these developmental processes is the spatial and temporal transcriptional regulation of critical genes. In humans, microcephaly is defined as a condition with a significantly smaller head circumference compared to the average head size of a given age and sex group. A growing number of genes are identified as associated with microcephaly, and among them are those involved in transcriptional regulation. In this review, a subset of genes encoding transcription factors (e.g., homeobox-, basic helix-loop-helix-, forkhead box-, high mobility group box-, and zinc finger domain-containing transcription factors), whose functions are important for cortical development and implicated in microcephaly, are discussed.
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Affiliation(s)
- Youngshin Lim
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Biomedical Science Education, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
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Breton TS, Fike S, Francis M, Patnaude M, Murray CA, DiMaggio MA. Characterizing the SREB G protein-coupled receptor family in fish: Brain gene expression and genomic differences in upstream transcription factor binding sites. Comp Biochem Physiol A Mol Integr Physiol 2023; 285:111507. [PMID: 37611891 PMCID: PMC10529039 DOI: 10.1016/j.cbpa.2023.111507] [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: 06/07/2023] [Revised: 07/12/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
Abstract
The SREB (Super-conserved Receptors Expressed in Brain) family of orphan G protein-coupled receptors is highly conserved in vertebrates and consists of three members: SREB1 (orphan designation GPR27), SREB2 (GPR85), and SREB3 (GPR173). SREBs are associated with processes ranging from neuronal plasticity to reproductive control. Relatively little is known about similarities across the entire family, or how mammalian gene expression patterns compare to non-mammalian vertebrates. In fish, this system may be particularly complex, as some species have gained a fourth member (SREB3B) while others have lost genes. To better understand the system, the present study aimed to: 1) use qPCR to characterize sreb and related gene expression patterns in the brains of three fish species with different systems, and 2) identify possible differences in transcriptional regulation among the receptors, using upstream transcription factor binding sites across 70 ray-finned fish genomes. Overall, regional patterns of sreb expression were abundant in forebrain-related areas. However, some species-specific patterns were detected, such as abundant expression of receptors in zebrafish (Danio rerio) hypothalamic-containing sections, and divergence between sreb3a and sreb3b in pufferfish (Dichotomyctere nigroviridis). In addition, a gene possibly related to the system (dkk3a) was spatially correlated with the receptors in all three species. Genomic regions upstream of sreb2 and sreb3b, but largely not sreb1 or sreb3a, contained many highly conserved transcription factor binding sites. These results provide novel information about expression differences and transcriptional regulation across fish that may inform future research to better understand these receptors.
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Affiliation(s)
- Timothy S Breton
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA.
| | - Samantha Fike
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA
| | - Mullein Francis
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA
| | - Michael Patnaude
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA
| | - Casey A Murray
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, Ruskin, FL 33570, USA
| | - Matthew A DiMaggio
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, Ruskin, FL 33570, USA
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Gao J, Lu Y, Luo Y, Duan X, Chen P, Zhang X, Wu X, Qiu M, Shen W. β-Catenin and SOX2 Interaction Regulate Visual Experience-Dependent Cell Homeostasis in the Developing Xenopus Thalamus. Int J Mol Sci 2023; 24:13593. [PMID: 37686400 PMCID: PMC10488257 DOI: 10.3390/ijms241713593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
In the vertebrate brain, sensory experience plays a crucial role in shaping thalamocortical connections for visual processing. However, it is still not clear how visual experience influences tissue homeostasis and neurogenesis in the developing thalamus. Here, we reported that the majority of SOX2-positive cells in the thalamus are differentiated neurons that receive visual inputs as early as stage 47 Xenopus. Visual deprivation (VD) for 2 days shifts the neurogenic balance toward proliferation at the expense of differentiation, which is accompanied by a reduction in nuclear-accumulated β-catenin in SOX2-positive neurons. The knockdown of β-catenin decreases the expression of SOX2 and increases the number of progenitor cells. Coimmunoprecipitation studies reveal the evolutionary conservation of strong interactions between β-catenin and SOX2. These findings indicate that β-catenin interacts with SOX2 to maintain homeostatic neurogenesis during thalamus development.
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Affiliation(s)
- Juanmei Gao
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
- College of Life and Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yufang Lu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Yuhao Luo
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Xinyi Duan
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Peiyao Chen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Xinyu Zhang
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Xiaohua Wu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
| | - Mengsheng Qiu
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
- College of Life and Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wanhua Shen
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China (M.Q.)
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Definition and Characterization of SOX11-Derived T Cell Epitopes towards Immunotherapy of Glioma. Int J Mol Sci 2023; 24:ijms24031943. [PMID: 36768267 PMCID: PMC9916519 DOI: 10.3390/ijms24031943] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/21/2022] [Accepted: 01/12/2023] [Indexed: 01/20/2023] Open
Abstract
The transcription factor SOX11 is a tumor-associated antigen with low expression in normal cells, but overexpression in glioblastoma (GBM). So far, conventional surgery, chemotherapy, and radiotherapy have not substantially improved the dismal prognosis of relapsed/refractory GBM patients. Immunotherapy is considered a promising strategy against GBM, but there is a fervent need for better immunotargets in GBM. To this end, we performed an in silico prediction study on SOX11, which primarily yielded ten promising HLA-A*0201-restricted peptides derived from SOX11. We defined a novel peptide FMACSPVAL, which had the highest score according to in silico prediction (6.02 nM by NetMHC-4.0) and showed an exquisite binding affinity to the HLA-A*0201 molecule in the peptide-binding assays. In the IFN-γ ELISPOT assays, FMACSPVAL demonstrated a high efficiency for generating SOX11-specific CD8+ T cells. Nine out of thirty-two healthy donors showed a positive response to SOX11, as assessed by the ELISPOT assays. Therefore, this novel antigen peptide epitope seems to be promising as a target for T cell-based immunotherapy in GBM. The adoptive transfer of in vitro elicited SOX11-specific CD8+ T cells constitutes a potential approach for the treatment of GBM patients.
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12
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Stevanovic M, Lazic A, Schwirtlich M, Stanisavljevic Ninkovic D. The Role of SOX Transcription Factors in Ageing and Age-Related Diseases. Int J Mol Sci 2023; 24:851. [PMID: 36614288 PMCID: PMC9821406 DOI: 10.3390/ijms24010851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11158 Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Knez Mihailova 35, 11000 Belgrade, Serbia
| | - Andrijana Lazic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Marija Schwirtlich
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
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13
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Arnaldos-Pérez C, Vilaseca A, Naranjo L, Sabater L, Dalmau J, Ruiz-García R, Graus F. Algorithm to improve the diagnosis of paraneoplastic neurological syndromes associated with SOX1 antibodies. Front Immunol 2023; 14:1173484. [PMID: 37207233 PMCID: PMC10191251 DOI: 10.3389/fimmu.2023.1173484] [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: 02/24/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
SOX1 antibodies (SOX1-abs) are associated with paraneoplastic neurological syndromes (PNS) and small cell lung cancer (SCLC). In many clinical laboratories SOX1-abs are determined by commercial line blots without confirmation by cell-based assay (CBA) with HEK293 cells expressing SOX1. However, the diagnostic yield of commercial line blots is low and the accessibility to the CBA, that is not commercially available, limited. Here, we evaluated if the addition of the band intensity data of the line blot and the immunoreactivity in a tissue-based assay (TBA) improve the diagnostic performance of the line blot. We examined serum of 34 consecutive patients with adequate clinical information that tested positive for SOX1-abs in a commercial line blot. Samples were also assessed by TBA and CBA. SOX1-abs were confirmed by CBA in 17 (50%) patients, all (100%) had lung cancer (SCLC in 16) and 15/17 (88%) had a PNS. In the remaining 17 patients the CBA was negative and none had PNS associated with lung cancer. TBA was assessable in 30/34 patients and SOX1-abs reactivity was detected in 15/17 (88%) with positive and in 0/13 (0%) with negative CBA. Only 2 (13%) of the 15 TBA-negative patients were CBA-positive. The frequency of TBA-negative but CBA-positive increased from 10% (1/10) when the band intensity of the line blot was weak to 20% (1/5) in patients with a moderate or strong intensity band. Confirmation by CBA should be mandatory for samples (56% in this series) not assessable (4/34; 12%) or negative in the TBA (15/34; 44%).
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Affiliation(s)
| | - Andreu Vilaseca
- MS Center of Catalonia (CEMCAT), Neurooncology and Autoimmune Neurology Unit, Neurology Department, Vall d’Hebron University Hospital, Barcelona Autonoma University, Barcelona, Spain
| | - Laura Naranjo
- Immunology Department, Centre Diagnòstic Biomèdic, Hospital Clínic, Barcelona, Spain
| | - Lidia Sabater
- Neuroimmunology Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Josep Dalmau
- Neuroimmunology Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, United States
| | - Raquel Ruiz-García
- Immunology Department, Centre Diagnòstic Biomèdic, Hospital Clínic, Barcelona, Spain
- Neuroimmunology Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Francesc Graus
- Neuroimmunology Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- *Correspondence: Francesc Graus,
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14
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Single-cell transcriptomics identifies conserved regulators of neuroglandular lineages. Cell Rep 2022; 40:111370. [PMID: 36130520 DOI: 10.1016/j.celrep.2022.111370] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/01/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022] Open
Abstract
Communication in bilaterian nervous systems is mediated by electrical and secreted signals; however, the evolutionary origin and relation of neurons to other secretory cell types has not been elucidated. Here, we use developmental single-cell RNA sequencing in the cnidarian Nematostella vectensis, representing an early evolutionary lineage with a simple nervous system. Validated by transgenics, we demonstrate that neurons, stinging cells, and gland cells arise from a common multipotent progenitor population. We identify the conserved transcription factor gene SoxC as a key upstream regulator of all neuroglandular lineages and demonstrate that SoxC knockdown eliminates both neuronal and secretory cell types. While in vertebrates and many other bilaterians neurogenesis is largely restricted to early developmental stages, we show that in the sea anemone, differentiation of neuroglandular cells is maintained throughout all life stages, and follows the same molecular trajectories from embryo to adulthood, ensuring lifelong homeostasis of neuroglandular cell lineages.
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15
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Kulesh B, Reese BE, Keeley PW. Contraction of axonal and dendritic fields in Sox5-deficient cone bipolar cells is accompanied by axonal sprouting and dendritic hyper-innervation of pedicles. Front Neuroanat 2022; 16:944706. [PMID: 36093292 PMCID: PMC9459848 DOI: 10.3389/fnana.2022.944706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Multiple factors regulate the differentiation of neuronal morphology during development, including interactions with afferents, targets, and homotypic neighbors, as well as cell-intrinsic transcriptional regulation. Retinal bipolar cells provide an exemplary model system for studying the control of these processes, as there are 15 transcriptionally and morphologically distinct types, each extending their dendritic and axonal arbors in respective strata within the synaptic layers of the retina. Here we have examined the role of the transcription factor Sox5 in the control of the morphological differentiation of one type of cone bipolar cell (CBC), the Type 7 cell. We confirm selective expression of SOX5 in this single bipolar cell type, emerging at the close of the first post-natal week, prior to morphological differentiation. Conditional knockout mice were generated by crossing a bipolar cell-specific cre-expressing line with mice carrying floxed Sox5 alleles, as well as the Gustducin-gfp reporter which labels Type 7 CBCs. Loss of SOX5 was confirmed in the bipolar cell stratum, in GFP+ Type 7 cells. Such SOX5-deficient Type 7 cells differentiate axonal and dendritic arbors that are each reduced in areal extent. The axonal arbors exhibit sprouting in the inner plexiform layer (IPL), thereby extending their overall radial extent, while the dendritic arbors connect with fewer cone pedicles in the outer plexiform layer, showing an increase in the average number of dendritic contacts at each pedicle. SOX5-deficient Type 7 CBCs should therefore exhibit smaller receptive fields derived from fewer if now hyper-innervated pedicles, transmitting their signals across a broader depth through the IPL.
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Affiliation(s)
- Bridget Kulesh
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Benjamin E. Reese
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Patrick W. Keeley
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- *Correspondence: Patrick W. Keeley
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16
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The Intricate Epigenetic and Transcriptional Alterations in Pediatric High-Grade Gliomas: Targeting the Crosstalk as the Oncogenic Achilles’ Heel. Biomedicines 2022; 10:biomedicines10061311. [PMID: 35740334 PMCID: PMC9219798 DOI: 10.3390/biomedicines10061311] [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: 05/11/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/01/2023] Open
Abstract
Pediatric high-grade gliomas (pHGGs) are a deadly and heterogenous subgroup of gliomas for which the development of innovative treatments is urgent. Advances in high-throughput molecular techniques have shed light on key epigenetic components of these diseases, such as K27M and G34R/V mutations on histone 3. However, modification of DNA compaction is not sufficient by itself to drive those tumors. Here, we review molecular specificities of pHGGs subcategories in the context of epigenomic rewiring caused by H3 mutations and the subsequent oncogenic interplay with transcriptional signaling pathways co-opted from developmental programs that ultimately leads to gliomagenesis. Understanding how transcriptional and epigenetic alterations synergize in each cellular context in these tumors could allow the identification of new Achilles’ heels, thereby highlighting new levers to improve their therapeutic management.
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17
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Koch K, Bartmann K, Hartmann J, Kapr J, Klose J, Kuchovská E, Pahl M, Schlüppmann K, Zühr E, Fritsche E. Scientific Validation of Human Neurosphere Assays for Developmental Neurotoxicity Evaluation. FRONTIERS IN TOXICOLOGY 2022; 4:816370. [PMID: 35295221 PMCID: PMC8915868 DOI: 10.3389/ftox.2022.816370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/21/2022] [Indexed: 01/06/2023] Open
Abstract
There is a call for a paradigm shift in developmental neurotoxicity (DNT) evaluation, which demands the implementation of faster, more cost-efficient, and human-relevant test systems than current in vivo guideline studies. Under the umbrella of the Organisation for Economic Co-operation and Development (OECD), a guidance document is currently being prepared that instructs on the regulatory use of a DNT in vitro battery (DNT IVB) for fit-for-purpose applications. One crucial issue for OECD application of methods is validation, which for new approach methods (NAMs) requires novel approaches. Here, mechanistic information previously identified in vivo, as well as reported neurodevelopmental adversities in response to disturbances on the cellular and tissue level, are of central importance. In this study, we scientifically validate the Neurosphere Assay, which is based on human primary neural progenitor cells (hNPCs) and an integral part of the DNT IVB. It assesses neurodevelopmental key events (KEs) like NPC proliferation (NPC1ab), radial glia cell migration (NPC2a), neuronal differentiation (NPC3), neurite outgrowth (NPC4), oligodendrocyte differentiation (NPC5), and thyroid hormone-dependent oligodendrocyte maturation (NPC6). In addition, we extend our work from the hNPCs to human induced pluripotent stem cell-derived NPCs (hiNPCs) for the NPC proliferation (iNPC1ab) and radial glia assays (iNPC2a). The validation process we report for the endpoints studied with the Neurosphere Assays is based on 1) describing the relevance of the respective endpoints for brain development, 2) the confirmation of the cell type-specific morphologies observed in vitro, 3) expressions of cell type-specific markers consistent with those morphologies, 4) appropriate anticipated responses to physiological pertinent signaling stimuli and 5) alterations in specific in vitro endpoints upon challenges with confirmed DNT compounds. With these strong mechanistic underpinnings, we posit that the Neurosphere Assay as an integral part of the DNT in vitro screening battery is well poised for DNT evaluation for regulatory purposes.
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Affiliation(s)
- Katharina Koch
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Kristina Bartmann
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Julia Hartmann
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Julia Kapr
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Jördis Klose
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Eliška Kuchovská
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Melanie Pahl
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Kevin Schlüppmann
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Etta Zühr
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Ellen Fritsche
- IUF—Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
- Medical Faculty, Heinrich-Heine-University, Duesseldorf, Germany
- *Correspondence: Ellen Fritsche,
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18
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Kaewsakulthong W, Pongpaksupasin P, Nualkaew T, Hongeng S, Fucharoen S, Jearawiriyapaisarn N, Sripichai O. Lysine-specific histone demethylase 1 inhibition enhances robust fetal hemoglobin induction in human β 0-thalassemia/hemoglobin E erythroid cells. Hematol Rep 2021; 13:9215. [PMID: 35003571 PMCID: PMC8672213 DOI: 10.4081/hr.2021.9215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
Induction of fetal hemoglobin (HbF) ameliorates the clinical severity of β-thalassemias. Histone methyltransferase LSD1 enzyme removes methyl groups from the activating chromatin mark histone 3 lysine 4 at silenced genes, including the γ-globin genes. LSD1 inhibitor RN-1 induces HbF levels in cultured human erythroid cells. Here, the HbF-inducing activity of RN-1 was investigated in erythroid progenitor cells derived from β0-thalassemia/ hemoglobin E (HbE) patients. The significant and reproducible increases in γ-globin transcript and HbF expression upon RN-1 treatment were demonstrated in erythroid cells with divergent HbF baseline levels, the average of HbF induction was 17.7±0.8%. RN-1 at low concentration did not affect viability and proliferation of erythroid cells, but decreases in cell number were observed in cells treated with RN-1 at high concentration. Delayed terminal erythroid differentiation was revealed in β0-thalassemia/HbE erythroid cells treated with RN-1 as similar to other compounds that target LSD1 activity. Downregulation of repressors of γ- globin expression; NCOR1 and SOX6, was observed in RN-1 treatment. These findings provide proof of the concept that LSD1 epigenetic enzyme is a potential therapeutic target for β0-thalassemia/HbE patients.
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Affiliation(s)
- Woratree Kaewsakulthong
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok
| | - Phitchapa Pongpaksupasin
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhonpathom
| | - Tiwaporn Nualkaew
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhonpathom
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhonpathom
| | - Natee Jearawiriyapaisarn
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhonpathom
| | - Orapan Sripichai
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhonpathom.,National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
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19
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Stevanovic M, Kovacevic-Grujicic N, Mojsin M, Milivojevic M, Drakulic D. SOX transcription factors and glioma stem cells: Choosing between stemness and differentiation. World J Stem Cells 2021; 13:1417-1445. [PMID: 34786152 PMCID: PMC8567447 DOI: 10.4252/wjsc.v13.i10.1417] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/15/2021] [Accepted: 09/16/2021] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma (GBM) is the most common, most aggressive and deadliest brain tumor. Recently, remarkable progress has been made towards understanding the cellular and molecular biology of gliomas. GBM tumor initiation, progression and relapse as well as resistance to treatments are associated with glioma stem cells (GSCs). GSCs exhibit a high proliferation rate and self-renewal capacity and the ability to differentiate into diverse cell types, generating a range of distinct cell types within the tumor, leading to cellular heterogeneity. GBM tumors may contain different subsets of GSCs, and some of them may adopt a quiescent state that protects them against chemotherapy and radiotherapy. GSCs enriched in recurrent gliomas acquire more aggressive and therapy-resistant properties, making them more malignant, able to rapidly spread. The impact of SOX transcription factors (TFs) on brain tumors has been extensively studied in the last decade. Almost all SOX genes are expressed in GBM, and their expression levels are associated with patient prognosis and survival. Numerous SOX TFs are involved in the maintenance of the stemness of GSCs or play a role in the initiation of GSC differentiation. The fine-tuning of SOX gene expression levels controls the balance between cell stemness and differentiation. Therefore, innovative therapies targeting SOX TFs are emerging as promising tools for combatting GBM. Combatting GBM has been a demanding and challenging goal for decades. The current therapeutic strategies have not yet provided a cure for GBM and have only resulted in a slight improvement in patient survival. Novel approaches will require the fine adjustment of multimodal therapeutic strategies that simultaneously target numerous hallmarks of cancer cells to win the battle against GBM.
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Affiliation(s)
- Milena Stevanovic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11042, Serbia
- Chair Biochemistry and Molecular Biology, Faculty of Biology, University of Belgrade, Belgrade 11158, Serbia
- Department of Chemical and Biological Sciences, Serbian Academy of Sciences and Arts, Belgrade 11000, Serbia.
| | - Natasa Kovacevic-Grujicic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11042, Serbia
| | - Marija Mojsin
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11042, Serbia
| | - Milena Milivojevic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11042, Serbia
| | - Danijela Drakulic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade 11042, Serbia
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20
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Almasoudi SH, Schlosser G. Otic Neurogenesis in Xenopus laevis: Proliferation, Differentiation, and the Role of Eya1. Front Neuroanat 2021; 15:722374. [PMID: 34616280 PMCID: PMC8488300 DOI: 10.3389/fnana.2021.722374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/27/2021] [Indexed: 11/15/2022] Open
Abstract
Using immunostaining and confocal microscopy, we here provide the first detailed description of otic neurogenesis in Xenopus laevis. We show that the otic vesicle comprises a pseudostratified epithelium with apicobasal polarity (apical enrichment of Par3, aPKC, phosphorylated Myosin light chain, N-cadherin) and interkinetic nuclear migration (apical localization of mitotic, pH3-positive cells). A Sox3-immunopositive neurosensory area in the ventromedial otic vesicle gives rise to neuroblasts, which delaminate through breaches in the basal lamina between stages 26/27 and 39. Delaminated cells congregate to form the vestibulocochlear ganglion, whose peripheral cells continue to proliferate (as judged by EdU incorporation), while central cells differentiate into Islet1/2-immunopositive neurons from stage 29 on and send out neurites at stage 31. The central part of the neurosensory area retains Sox3 but stops proliferating from stage 33, forming the first sensory areas (utricular/saccular maculae). The phosphatase and transcriptional coactivator Eya1 has previously been shown to play a central role for otic neurogenesis but the underlying mechanism is poorly understood. Using an antibody specifically raised against Xenopus Eya1, we characterize the subcellular localization of Eya1 proteins, their levels of expression as well as their distribution in relation to progenitor and neuronal differentiation markers during otic neurogenesis. We show that Eya1 protein localizes to both nuclei and cytoplasm in the otic epithelium, with levels of nuclear Eya1 declining in differentiating (Islet1/2+) vestibulocochlear ganglion neurons and in the developing sensory areas. Morpholino-based knockdown of Eya1 leads to reduction of proliferating, Sox3- and Islet1/2-immunopositive cells, redistribution of cell polarity proteins and loss of N-cadherin suggesting that Eya1 is required for maintenance of epithelial cells with apicobasal polarity, progenitor proliferation and neuronal differentiation during otic neurogenesis.
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Affiliation(s)
| | - Gerhard Schlosser
- School of Natural Sciences, National University of Galway, Galway, Ireland
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21
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Zilova L, Weinhardt V, Tavhelidse T, Schlagheck C, Thumberger T, Wittbrodt J. Fish primary embryonic pluripotent cells assemble into retinal tissue mirroring in vivo early eye development. eLife 2021; 10:e66998. [PMID: 34252023 PMCID: PMC8275126 DOI: 10.7554/elife.66998] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Organoids derived from pluripotent stem cells promise the solution to current challenges in basic and biomedical research. Mammalian organoids are however limited by long developmental time, variable success, and lack of direct comparison to an in vivo reference. To overcome these limitations and address species-specific cellular organization, we derived organoids from rapidly developing teleosts. We demonstrate how primary embryonic pluripotent cells from medaka and zebrafish efficiently assemble into anterior neural structures, particularly retina. Within 4 days, blastula-stage cell aggregates reproducibly execute key steps of eye development: retinal specification, morphogenesis, and differentiation. The number of aggregated cells and genetic factors crucially impacted upon the concomitant morphological changes that were intriguingly reflecting the in vivo situation. High efficiency and rapid development of fish-derived organoids in combination with advanced genome editing techniques immediately allow addressing aspects of development and disease, and systematic probing of impact of the physical environment on morphogenesis and differentiation.
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Affiliation(s)
- Lucie Zilova
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Venera Weinhardt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Christina Schlagheck
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
- Heidelberg International Biosciences Graduate School HBIGS and HeiKa Graduate School on “Functional Materials”HeidelbergGermany
| | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
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22
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Bressan RB, Southgate B, Ferguson KM, Blin C, Grant V, Alfazema N, Wills JC, Marques-Torrejon MA, Morrison GM, Ashmore J, Robertson F, Williams CAC, Bradley L, von Kriegsheim A, Anderson RA, Tomlinson SR, Pollard SM. Regional identity of human neural stem cells determines oncogenic responses to histone H3.3 mutants. Cell Stem Cell 2021; 28:877-893.e9. [PMID: 33631116 PMCID: PMC8110245 DOI: 10.1016/j.stem.2021.01.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/22/2020] [Accepted: 01/20/2021] [Indexed: 01/06/2023]
Abstract
Point mutations within the histone H3.3 are frequent in aggressive childhood brain tumors known as pediatric high-grade gliomas (pHGGs). Intriguingly, distinct mutations arise in discrete anatomical regions: H3.3-G34R within the forebrain and H3.3-K27M preferentially within the hindbrain. The reasons for this contrasting etiology are unknown. By engineering human fetal neural stem cell cultures from distinct brain regions, we demonstrate here that cell-intrinsic regional identity provides differential responsiveness to each mutant that mirrors the origins of pHGGs. Focusing on H3.3-G34R, we find that the oncohistone supports proliferation of forebrain cells while inducing a cytostatic response in the hindbrain. Mechanistically, H3.3-G34R does not impose widespread transcriptional or epigenetic changes but instead impairs recruitment of ZMYND11, a transcriptional repressor of highly expressed genes. We therefore propose that H3.3-G34R promotes tumorigenesis by focally stabilizing the expression of key progenitor genes, thereby locking initiating forebrain cells into their pre-existing immature state.
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Affiliation(s)
- Raul Bardini Bressan
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
| | - Benjamin Southgate
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Kirsty M Ferguson
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Carla Blin
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Vivien Grant
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Neza Alfazema
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Jimi C Wills
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Maria Angeles Marques-Torrejon
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Gillian M Morrison
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - James Ashmore
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Faye Robertson
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Charles A C Williams
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Leanne Bradley
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Simon R Tomlinson
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK.
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23
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Yang QQ, Zhai YQ, Wang HF, Cai YC, Ma XY, Yin YQ, Li YD, Zhou GM, Zhang X, Hu G, Zhou JW. Nuclear isoform of FGF13 regulates post-natal neurogenesis in the hippocampus through an epigenomic mechanism. Cell Rep 2021; 35:109127. [PMID: 34010636 DOI: 10.1016/j.celrep.2021.109127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 02/13/2021] [Accepted: 04/22/2021] [Indexed: 10/21/2022] Open
Abstract
The hippocampus is one of two niches in the mammalian brain with persistent neurogenesis into adulthood. The neurogenic capacity of hippocampal neural stem cells (NSCs) declines with age, but the molecular mechanisms of this process remain unknown. In this study, we find that fibroblast growth factor 13 (FGF13) is essential for the post-natal neurogenesis in mouse hippocampus, and FGF13 deficiency impairs learning and memory. In particular, we find that FGF13A, the nuclear isoform of FGF13, is involved in the maintenance of NSCs and the suppression of neuronal differentiation during post-natal hippocampal development. Furthermore, we find that FGF13A interacts with ARID1B, a unit of Brahma-associated factor chromatin remodeling complex, and suppresses the expression of neuron differentiation-associated genes through chromatin modification. Our results suggest that FGF13A is an important regulator for maintaining the self-renewal and neurogenic capacity of NSCs in post-natal hippocampus, revealing an epigenomic regulatory function of FGFs in neurogenesis.
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Affiliation(s)
- Qiao-Qiao Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Ying-Qi Zhai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Hai-Fang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Chen Cai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin-Yue Ma
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Yan-Qing Yin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan-Dong Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Min Zhou
- Department of Anatomy, Histology and Embryology, Shanghai Medical School of Fudan University, Shanghai 200032, China
| | - Xu Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Gang Hu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu 210029, China; Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Jia-Wei Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China; Co-innovation Center of Neuroregeneration, School of Medicine, Nantong University, Nantong, Jiangsu 226001, China.
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24
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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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25
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Li J, Sun L, Peng XL, Yu XM, Qi SJ, Lu ZJ, Han JDJ, Shen Q. Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons. PLoS Genet 2021; 17:e1009355. [PMID: 33760820 PMCID: PMC7990179 DOI: 10.1371/journal.pgen.1009355] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 01/12/2021] [Indexed: 01/02/2023] Open
Abstract
Neurogenesis in the developing neocortex begins with the generation of the preplate, which consists of early-born neurons including Cajal-Retzius (CR) cells and subplate neurons. Here, utilizing the Ebf2-EGFP transgenic mouse in which EGFP initially labels the preplate neurons then persists in CR cells, we reveal the dynamic transcriptome profiles of early neurogenesis and CR cell differentiation. Genome-wide RNA-seq and ChIP-seq analyses at multiple early neurogenic stages have revealed the temporal gene expression dynamics of early neurogenesis and distinct histone modification patterns in early differentiating neurons. We have identified a new set of coding genes and lncRNAs involved in early neuronal differentiation and validated with functional assays in vitro and in vivo. In addition, at E15.5 when Ebf2-EGFP+ cells are mostly CR neurons, single-cell sequencing analysis of purified Ebf2-EGFP+ cells uncovers molecular heterogeneities in CR neurons, but without apparent clustering of cells with distinct regional origins. Along a pseudotemporal trajectory these cells are classified into three different developing states, revealing genetic cascades from early generic neuronal differentiation to late fate specification during the establishment of CR neuron identity and function. Our findings shed light on the molecular mechanisms governing the early differentiation steps during cortical development, especially CR neuron differentiation. Neural stem cells and progenitor cells in the embryonic brain give rise to neurons following a precise temporal order after initial expansion. Early-born neurons including Cajal-Retzius (CR) cells and subplate neurons form the preplate in the developing cerebral cortex, then CR neurons occupy the layer 1, playing an important role in cortical histogenesis. The molecular mechanisms governing the early neuronal differentiation processes remain to be explored. Here, by genome-wide approaches including bulk RNA-seq, single-cell RNA-seq and ChIP-seq, we comprehensively characterized the temporal dynamic gene expression profile and epigenetic status at different stages during early cortical development and uncovered molecularly heterogeneous subpopulations within the CR cells. We revealed CR neuron signatures and cell type-specific histone modification patterns along early neuron specification. Using in vitro and in vivo assays, we identified novel lncRNAs as potential functional regulators in preplate differentiation and CR neuron identity establishment. Our study provides a comprehensive analysis of the genetic and epigenetic programs during neuronal differentiation and would help bring new insights into the early cortical neurogenesis process, particularly the differentiation of CR neurons.
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Affiliation(s)
- Jia Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- PTN graduate program, School of Life Sciences, Peking University, Beijing, China
- School of Medicine, Tsinghua University, Beijing, China
| | - Lei Sun
- PTN graduate program, School of Life Sciences, Tsinghua University, Beijing, China
| | | | - Xiao-Ming Yu
- School of Medicine, Tsinghua University, Beijing, China
| | - Shao-Jun Qi
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- School of Medicine, Tsinghua University, Beijing, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing-Dong J. Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qin Shen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Frontier Science Center for Stem Cell Research, Ministry of Education, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Brain and Spinal Cord Clinical Research Center, Tongji University, Shanghai, China
- * E-mail:
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26
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Batool S, Kayani MA, Valis M, Kuca K. Neural Differentiation of Mouse Embryonic Stem Cells-An in vitro Approach to Profile DNA Methylation of Reprogramming Factor Sox2-SRR2. Front Genet 2021; 12:641095. [PMID: 33828585 PMCID: PMC8019947 DOI: 10.3389/fgene.2021.641095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/02/2021] [Indexed: 12/30/2022] Open
Abstract
Sox2 is one of the core transcription factors maintaining the embryonic stem cells (ES) pluripotency and, also indispensable for cellular reprogramming. However, limited data is available about the DNA methylation of pluripotency genes during lineage-specific differentiations. This study investigated the DNA methylation of Sox2 regulatory region 2 (SRR2) during directed differentiation of mouse ES into neural lineage. ES cells were first grown to form embryoid bodies in suspension which were then dissociated, and cultured in defined medium to promote neural differentiation. Typical neuronal morphology together with the up-regulation of Pax6, neuroepithelial stem cell intermediate filament and β-tubulin III and, down-regulation of pluripotency genes Oct4, Nanog and Sox2 showed the existence of neural phenotype in cells undergoing differentiation. Three CpGs in the core enhancer region of neural-specific SRR2 were individually investigated by direct DNA sequencing post-bisulfite treatment and, found to be unmethylated in differentiated cells at time-points chosen for analysis. This analysis does not limit the possibility of methylation at other CpG sites than those profiled here and/or transient methylation. Hence, similar analyses exploring the DNA methylation at other regions of the Sox2 gene could unravel the onset and transitions of epigenetic signatures influencing the outcome of differentiation pathways and neural development. The data presented here shows that in vitro neural differentiation of embryonic stem cells can be employed to study and characterize molecular regulatory mechanisms governing neurogenesis by applying diverse pharmacological and toxicological agents.
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Affiliation(s)
- Sajida Batool
- Cancer Genetics and Epigenetics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Martin Valis
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Hradec Kralove, Czechia
| | - Kamil Kuca
- Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czechia
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27
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Ataei A, Poorebrahim M, Rajabpour A, Rizvanov A, Shahriar Arab S. Topological Analysis of Regulatory Networks Reveals Functionally Key Genes and miRNAs Involved in the Differentiation of Mesenchymal Stem Cells. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2565. [PMID: 34179189 PMCID: PMC8217530 DOI: 10.30498/ijb.2021.2565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background The details of molecular mechanisms underlying the differentiation of Mesenchymal Stem Cells (MSCs) into specific lineages are not well understood. Objectives We aimed to construct the interactome network and topology analysis of bone marrow mesenchymal stem cell of CAGE data. Applying the enrichment results, we wanted to introduce the common genes and hub-microRNA and hub-genes of these giant network. Materials and Methods In this study, we constructed gene regulatory networks for each non-mesenchymal cell lineage according to their gene expression profiles obtained from FANTOM5 database. The putative interactions of TF-gene and protein-protein were determined using TRED, STRING, HPRD and GeneMANIA servers. In parallel, a regulatory network including corresponding miRNAs and total differentially expressed genes (DEGs) was constructed for each cell lineage. Results The results indicated that analysis of networks' topology can significantly distinguish the hub regulatory genes and miRNAs involved in the differentiation of MSCs. The functional annotation of identified hub genes and miRNAs revealed that several signal transduction pathways i.e. AKT, WNT and TGFβ and cell proliferation related pathways play a pivotal role in the regulation of MSCs differentiation. We also classified cell lineages into two groups based on their predicted miRNA profiles. Conclusions In conclusion, we found a number of hub genes and miRNAs which seem to have key regulatory functions during differentiation of MSCs. Our results also introduce a number of new regulatory genes and miRNAs which can be considered as the new candidates for genetic manipulation of MSCs in vitro.
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Affiliation(s)
- Atousa Ataei
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.,Equal contribution
| | - Mansour Poorebrahim
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, University of Medical Sciences, Tehran, Iran.,Equal contribution
| | - Azam Rajabpour
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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28
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Zhao X, Chen J, Xiao P, Feng J, Nie Q, Zhao XM. Identifying age-specific gene signatures of the human cerebral cortex with joint analysis of transcriptomes and functional connectomes. Brief Bioinform 2020; 22:6048938. [PMID: 33367491 DOI: 10.1093/bib/bbaa388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/10/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
The human cerebral cortex undergoes profound structural and functional dynamic variations across the lifespan, whereas the underlying molecular mechanisms remain unclear. Here, with a novel method transcriptome-connectome correlation analysis (TCA), which integrates the brain functional magnetic resonance images and region-specific transcriptomes, we identify age-specific cortex (ASC) gene signatures for adolescence, early adulthood and late adulthood. The ASC gene signatures are significantly correlated with the cortical thickness (P-value <2.00e-3) and myelination (P-value <1.00e-3), two key brain structural features that vary in accordance with brain development. In addition to the molecular underpinning of age-related brain functions, the ASC gene signatures allow delineation of the molecular mechanisms of neuropsychiatric disorders, such as the regulation between ARNT2 and its target gene ETF1 involved in Schizophrenia. We further validate the ASC gene signatures with published gene sets associated with the adult cortex, and confirm the robustness of TCA on other brain image datasets. Availability: All scripts are written in R. Scripts for the TCA method and related statistics result can be freely accessed at https://github.com/Soulnature/TCA. Additional data related to this paper may be requested from the authors.
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Affiliation(s)
- Xingzhong Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, China
| | - Peipei Xiao
- Department of Electronic and Information Engineering, Tongji University, China
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, China
| | - Qing Nie
- Department of Biomedical Engineering, University of California, Irvine, USA
| | - Xing-Ming Zhao
- ISTBI, RIICS, Fudan University, and MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and Frontiers Center for Brain Science, China
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29
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Schock EN, LaBonne C. Sorting Sox: Diverse Roles for Sox Transcription Factors During Neural Crest and Craniofacial Development. Front Physiol 2020; 11:606889. [PMID: 33424631 PMCID: PMC7793875 DOI: 10.3389/fphys.2020.606889] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022] Open
Abstract
Sox transcription factors play many diverse roles during development, including regulating stem cell states, directing differentiation, and influencing the local chromatin landscape. Of the twenty vertebrate Sox factors, several play critical roles in the development the neural crest, a key vertebrate innovation, and the subsequent formation of neural crest-derived structures, including the craniofacial complex. Herein, we review the specific roles for individual Sox factors during neural crest cell formation and discuss how some factors may have been essential for the evolution of the neural crest. Additionally, we describe how Sox factors direct neural crest cell differentiation into diverse lineages such as melanocytes, glia, and cartilage and detail their involvement in the development of specific craniofacial structures. Finally, we highlight several SOXopathies associated with craniofacial phenotypes.
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Affiliation(s)
- Elizabeth N. Schock
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, United States
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30
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Ectopic activation of GABA B receptors inhibits neurogenesis and metamorphosis in the cnidarian Nematostella vectensis. Nat Ecol Evol 2020; 5:111-121. [PMID: 33168995 DOI: 10.1038/s41559-020-01338-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 09/29/2020] [Indexed: 01/22/2023]
Abstract
The metabotropic gamma-aminobutyric acid B receptor (GABABR) is a G protein-coupled receptor that mediates neuronal inhibition by the neurotransmitter GABA. While GABABR-mediated signalling has been suggested to play central roles in neuronal differentiation and proliferation across evolution, it has mostly been studied in the mammalian brain. Here, we demonstrate that ectopic activation of GABABR signalling affects neurogenic functions in the sea anemone Nematostella vectensis. We identified four putative Nematostella GABABR homologues presenting conserved three-dimensional extracellular domains and residues needed for binding GABA and the GABABR agonist baclofen. Moreover, sustained activation of GABABR signalling reversibly arrests the critical metamorphosis transition from planktonic larva to sessile polyp life stage. To understand the processes that underlie the developmental arrest, we combined transcriptomic and spatial analyses of control and baclofen-treated larvae. Our findings reveal that the cnidarian neurogenic programme is arrested following the addition of baclofen to developing larvae. Specifically, neuron development and neurite extension were inhibited, resulting in an underdeveloped and less organized nervous system and downregulation of proneural factors including NvSoxB(2), NvNeuroD1 and NvElav1. Our results thus point to an evolutionarily conserved function of GABABR in neurogenesis regulation and shed light on early cnidarian development.
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31
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Mahmoodazdeh A, Shafiee SM, Sisakht M, Khoshdel Z, Takhshid MA. Adrenomedullin protects rat dorsal root ganglion neurons against doxorubicin-induced toxicity by ameliorating oxidative stress. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2020; 23:1197-1206. [PMID: 32963742 PMCID: PMC7491506 DOI: 10.22038/ijbms.2020.45134.10514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/13/2020] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Despite effective anticancer effects, the use of doxorubicin (DOX) is hindered due to its cardio and neurotoxicity. The neuroprotective effect of adrenomedullin (AM) was shown in several studies. The present study aimed to evaluate the possible protective effects of AM against DOX-induced toxicity in dorsal root ganglia (DRGs) neurons. MATERIALS AND METHODS Rat embryonic DRG neurons were isolated and cultured. The effect of various concentrations of DOX (0.0 to 100 µM) in the absence or presence of AM (3.125 -100 nM) on cell death, apoptosis, oxidative stress, expression of tumor necrosis-α (TNF-α), interleukin1- β (IL-1β), inducible nitric oxide synthase (iNOS), matrix metalloproteinase (MMP) 3 and 13, and SRY-related protein 9 (SOX9) were examined. RESULTS Based on MTT assay data, DOX decreased the viability of DRG neurons in a dose and time-dependent manner (IC50=6.88 µm) while dose-dependently, AM protected DRG neurons against DOX-induced cell death. Furthermore, results of annexin V apoptosis assay revealed the protective effects of AM (25 nm) against DOX (6.88 µM)-induced apoptosis and necrosis of DRG neurons. Also, AM significantly ameliorated DOX-induced oxidative stress in DRG neurons. Real-time PCR results showed a significant increase in the expression of TNF-α, IL-1β, iNOS, MMP 3, and MMP 13, and a decrease in the expression of SOX9 following treatment with DOX. Treatment with AM (25 nM) significantly reversed the effects of DOX on the above-mentioned genes expression. CONCLUSION Our findings suggest that AM can be considered a novel ameliorating drug against DOX-induced neurotoxicity.
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Affiliation(s)
- Amir Mahmoodazdeh
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sayed Mohammad Shafiee
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Sisakht
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Khoshdel
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Ali Takhshid
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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32
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Nejad SM, Hodjat M, Mousavi SA, Baeeri M, Rezvanfar MA, Rahimifard M, Sabuncuoglu S, Abdollahi M. Alteration of gene expression profile in mouse embryonic stem cells and neural differentiation deficits by ethephon. Hum Exp Toxicol 2020; 39:1518-1527. [PMID: 32519556 DOI: 10.1177/0960327120930255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ethephon, a member of the organophosphorus compounds, is one of the most widely used plant growth regulators for artificial ripening. Although million pounds of this chemical is being used annually, the knowledge regarding its molecular toxicity is yet not sufficient. The purpose of this study was to evaluate the potential developmental toxicity of ethephon using embryonic stem cell model. The mouse embryonic stem cells (mESCs) were exposed to various concentrations of ethephon and the viability, cell cycle alteration and changes in the gene expression profile were evaluated using high-throughput RNA sequencing. Further, the effect of ethephon on neural differentiation potential was examined. The results showed that ethephon at noncytotoxic doses induced cell cycle arrest in mESCs. Gene ontology enrichment analysis showed that terms related to cell fate and organismal development, including neuron fate commitment, embryo development and cardiac cell differentiation, were markedly enriched in ethephon-treated cells. Neural induction of mESCs in the presence of ethephon was inhibited and the expression of neural genes was decreased in differentiated cells. Results obtained from this work clearly demonstrate that ethephon affects the gene expression profile of undifferentiated mESCs and prevents neural differentiation. Therefore, more caution against the frequent application of ethephon is advised.
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Affiliation(s)
- S Mohammadi Nejad
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - M Hodjat
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - S A Mousavi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - M Baeeri
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - M A Rezvanfar
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - M Rahimifard
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - S Sabuncuoglu
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - M Abdollahi
- Toxicology and Diseases Group, Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.,Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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Li B, Chen J, Du Q, Wang B, Qu Y, Chang Z. Toxic effects of dechlorane plus on the common carp (Cyprinus carpio) embryonic development. CHEMOSPHERE 2020; 249:126481. [PMID: 32209501 DOI: 10.1016/j.chemosphere.2020.126481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
Dechlorane Plus (DP) is a widely used chlorinated flame retardant, which has been extensively detected in the environment. Although DP content in the surface water is low, it can pose a continuous exposure risk to aquatic organisms due to its strong bioaccumulation. Considering that the related studies on the toxicity mechanism of DP exposure are limited, the effect of DP on carp embryo development was evaluated. In the present work, carp embryos were exposed to different concentrations (0, 30, 60, and 120 μg/L) of DP at 3 h post-fertilization (hpf). The expression levels of neural and skeletal development-associated genes, such as sox2, sox19a, Mef2c and BMP4, were detected with quantitative PCR, and the changes in different developmental toxicity endpoints were observed. Our results demonstrated that the expression levels of sox2, sox19a, Mef2c and BMP4 were significantly altered and several developmental abnormalities were found in DP-exposed carp embryos, such as DNA damage, increased mortality rate, delayed hatching time, reduced hatching rate, decreased body length, and increased morphological deformities. In addition, the activities of reactive oxygen species and malondialdehyde were remarkably higher in 60 and 120 μg/L DP exposure groups than in control group. These results suggest that DP can exhibit a unique modes of action, which lead to aberration occurrence in the early development stage of common carps, which may be related to some gene damage and oxidative stress. Besides, the parameters evaluated here can be used as tools to access the environmental risk for biota and humans exposed to DP.
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Affiliation(s)
- Baohua Li
- College of Life Science, Henan Normal University, Xinxiang, 453007, PR China; College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China
| | - Jianjun Chen
- College of Life Science, Henan Normal University, Xinxiang, 453007, PR China
| | - Qiyan Du
- College of Life Science, Henan Normal University, Xinxiang, 453007, PR China
| | - Beibei Wang
- College of Life Science, Henan Normal University, Xinxiang, 453007, PR China
| | - Ying Qu
- College of Life Science, Henan Normal University, Xinxiang, 453007, PR China
| | - Zhongjie Chang
- College of Life Science, Henan Normal University, Xinxiang, 453007, PR China.
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34
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Sun CP, Sun D, Luan ZL, Dai X, Bie X, Ming WH, Sun XW, Huo XX, Lu TL, Zhang D. Association of SOX11 Polymorphisms in distal 3'UTR with Susceptibility for Schizophrenia. J Clin Lab Anal 2020; 34:e23306. [PMID: 32207210 PMCID: PMC7439430 DOI: 10.1002/jcla.23306] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 12/25/2022] Open
Abstract
Background Diverse and circumstantial evidence suggests that schizophrenia is a neurodevelopmental disorder. Genes contributing to neurodevelopment may be potential candidates for schizophrenia. The human SOX11 gene is a member of the developmentally essential SOX (Sry‐related HMG box) transcription factor gene family and mapped to chromosome 2p, a potential candidate region for schizophrenia. Methods Our previous genome‐wide association study (GWAS) implicated an involvement of SOX11 with schizophrenia in a Chinese Han population. To further investigate the association between SOX11 polymorphisms and schizophrenia, we performed an independent replication case‐control association study in a sample including 768 cases and 1348 controls. Results After Bonferroni correction, four SNPs in SOX11 distal 3′UTR significantly associated with schizophrenia in the allele frequencies: rs16864067 (allelic P = .0022), rs12478711 (allelic P = .0009), rs2564045 (allelic P = .0027), and rs2252087 (allelic P = .0025). The haplotype analysis of the selected SNPs showed different haplotype frequencies for two blocks (rs4371338‐rs7596062‐rs16864067‐rs12478711 and rs2564045‐rs2252087‐rs2564055‐rs1366733) between cases and controls. Further luciferase assay and electrophoretic mobility shift assay (EMSA) revealed the schizophrenia‐associated SOX11 SNPs may influence SOX11 gene expression, and the risk and non‐risk alleles may have different affinity to certain transcription factors and can recruit divergent factors. Conclusions Our results suggest SOX11 as a susceptibility gene for schizophrenia, and SOX11 polymorphisms and haplotypes in the distal 3′UTR of the gene might modulate transcriptional activity by serving as cis‐regulatory elements and recruiting transcriptional activators or repressors. Also, these SNPs may potentiate as diagnostic markers for the disease.
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Affiliation(s)
- Cheng-Peng Sun
- Advanced Institute for Medical Sciences, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Dong Sun
- Department of Otolaryngology-Head and Neck Surgery, The 2nd Affiliated Hospital to Dalian Medical University, Dalian, China
| | - Zhi-Lin Luan
- Advanced Institute for Medical Sciences, College of Pharmacy, Dalian Medical University, Dalian, China.,Peking University Sixth Hospital (Institute of Mental Health), Beijing, China.,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health (Peking University), Ministry of Health, Beijing, China
| | - Xin Dai
- Department of Neuroscience, Medical Physiology, University Medical Center Groningen, Groningen, the Netherlands
| | - Xu Bie
- Department of Otolaryngology-Head and Neck Surgery, The 2nd Affiliated Hospital to Dalian Medical University, Dalian, China
| | - Wen-Hua Ming
- Advanced Institute for Medical Sciences, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Xiao-Wan Sun
- Advanced Institute for Medical Sciences, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Xiao-Xiao Huo
- Advanced Institute for Medical Sciences, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Tian-Lan Lu
- Peking University Sixth Hospital (Institute of Mental Health), Beijing, China.,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health (Peking University), Ministry of Health, Beijing, China
| | - Dai Zhang
- Peking University Sixth Hospital (Institute of Mental Health), Beijing, China.,National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health (Peking University), Ministry of Health, Beijing, China
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35
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Tait CM, Chinnaiya K, Manning E, Murtaza M, Ashton JP, Furley N, Hill CJ, Alves CH, Wijnholds J, Erdmann KS, Furley A, Rashbass P, Das RM, Storey KG, Placzek M. Crumbs2 mediates ventricular layer remodelling to form the spinal cord central canal. PLoS Biol 2020; 18:e3000470. [PMID: 32150534 PMCID: PMC7108746 DOI: 10.1371/journal.pbio.3000470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/31/2020] [Accepted: 02/18/2020] [Indexed: 11/27/2022] Open
Abstract
In the spinal cord, the central canal forms through a poorly understood process termed dorsal collapse that involves attrition and remodelling of pseudostratified ventricular layer (VL) cells. Here, we use mouse and chick models to show that dorsal ventricular layer (dVL) cells adjacent to dorsal midline Nestin(+) radial glia (dmNes+RG) down-regulate apical polarity proteins, including Crumbs2 (CRB2) and delaminate in a stepwise manner; live imaging shows that as one cell delaminates, the next cell ratchets up, the dmNes+RG endfoot ratchets down, and the process repeats. We show that dmNes+RG secrete a factor that promotes loss of cell polarity and delamination. This activity is mimicked by a secreted variant of Crumbs2 (CRB2S) which is specifically expressed by dmNes+RG. In cultured MDCK cells, CRB2S associates with apical membranes and decreases cell cohesion. Analysis of Crb2F/F/Nestin-Cre+/- mice, and targeted reduction of Crb2/CRB2S in slice cultures reveal essential roles for transmembrane CRB2 (CRB2TM) and CRB2S on VL cells and dmNes+RG, respectively. We propose a model in which a CRB2S-CRB2TM interaction promotes the progressive attrition of the dVL without loss of overall VL integrity. This novel mechanism may operate more widely to promote orderly progenitor delamination.
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Affiliation(s)
- Christine M Tait
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Kavitha Chinnaiya
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Elizabeth Manning
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Mariyam Murtaza
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - John-Paul Ashton
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Nicholas Furley
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Chris J Hill
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - C Henrique Alves
- Department of Ophthalmology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Kai S Erdmann
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Andrew Furley
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Penny Rashbass
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Raman M Das
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kate G Storey
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Marysia Placzek
- Department of Biomedical Science and Bateson Centre, University of Sheffield, Sheffield, United Kingdom
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36
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Yu Y, Andreu-Agullo C, Liu BF, Barboza L, Toth M, Lai EC. Regulation of embryonic and adult neurogenesis by Ars2. Development 2020; 147:147/2/dev180018. [PMID: 31969356 DOI: 10.1242/dev.180018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/20/2019] [Indexed: 11/20/2022]
Abstract
Neural development is controlled at multiple levels to orchestrate appropriate choices of cell fate and differentiation. Although more attention has been paid to the roles of neural-restricted factors, broadly expressed factors can have compelling impacts on tissue-specific development. Here, we describe in vivo conditional knockout analyses of murine Ars2, which has mostly been studied as a general RNA-processing factor in yeast and cultured cells. Ars2 protein expression is regulated during neural lineage progression, and is required for embryonic neural stem cell (NSC) proliferation. In addition, Ars2 null NSCs can still transition into post-mitotic neurons, but fail to undergo terminal differentiation. Similarly, adult-specific deletion of Ars2 compromises hippocampal neurogenesis and results in specific behavioral defects. To broaden evidence for Ars2 as a chromatin regulator in neural development, we generated Ars2 ChIP-seq data. Notably, Ars2 preferentially occupies DNA enhancers in NSCs, where it colocalizes broadly with NSC regulator SOX2. Ars2 association with chromatin is markedly reduced following NSC differentiation. Altogether, Ars2 is an essential neural regulator that interacts dynamically with DNA and controls neural lineage development.
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Affiliation(s)
- Yang Yu
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Celia Andreu-Agullo
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Bing Fang Liu
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Luendreo Barboza
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Miklos Toth
- Department of Pharmacology, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Eric C Lai
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, Box 252, New York, NY 10065, USA
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37
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Yang J, Hu Y, Han J, Xiao K, Liu X, Tan C, Zeng Q, Du H. Genome-wide analysis of the Chinese sturgeon sox gene family: identification, characterisation and expression profiles of different tissues. JOURNAL OF FISH BIOLOGY 2020; 96:175-184. [PMID: 31713865 DOI: 10.1111/jfb.14199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
The sox family is assumed to be responsible for a number of developmental systems. Genome sequencing technology makes it possible to scan sox genes and conduct characteristic analyses of different species. In fish, full characterisation of sox genes at the genome-wide level has been reported for pufferfish Takifugu rubripes, medaka Oryzias latipes, tilapia Oreochromis niloticus and channel catfish Ictalurus punctatus. However, no systematic investigation of the sox family in sturgeons (Acipenseridae) has been reported to date. This study conducted genome-wide identification of the sox genes in the Chinese sturgeon Acipenser sinensis and profiled their tissue distribution between male and female individuals. In total, 19 sox genes were identified, including soxb1, b2, c, d, e, f and h, in the Chinese sturgeon. Genomic structure analysis indicated relatively conserved exon-intron structures in each sox group and phylogenetic analysis supported the previous classification of the sox family. Most of the sox genes showed a tissue-specific expression pattern, indicating the possible involvement of Chinese sturgeon sox genes at different developmental processes such as cardiac and gonadal development. This study provides a comprehensive resource of Chinese sturgeon sox genes and enables a better understanding of the evolution and function of the sox family.
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Affiliation(s)
- Jing Yang
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Yacheng Hu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Jilu Han
- China Three Gorges Corporation, Yichang, China
| | - Kan Xiao
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Xueqing Liu
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Chun Tan
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Qingkai Zeng
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Hejun Du
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
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38
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Li X, Zhou W, Li X, Gao M, Ji S, Tian W, Ji G, Du J, Hao A. SOX19b regulates the premature neuronal differentiation of neural stem cells through EZH2-mediated histone methylation in neural tube development of zebrafish. Stem Cell Res Ther 2019; 10:389. [PMID: 31842983 PMCID: PMC6915949 DOI: 10.1186/s13287-019-1495-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/29/2019] [Accepted: 11/14/2019] [Indexed: 12/15/2022] Open
Abstract
Objective Neural tube defects (NTDs) are the most serious and common birth defects in the clinic. The SRY-related HMG box B1 (SoxB1) gene family has been implicated in different processes of early embryogenesis. Sox19b is a maternally expressed gene in the SoxB1 family that is found in the region of the presumptive central nervous system (CNS), but its role and mechanism in embryonic neural stem cells (NSCs) during neural tube development have not yet been explored. Considering that Sox19b is specific to bony fish, we intended to investigate the role and mechanism of Sox19b in neural tube development in zebrafish embryos. Material and methods Morpholino (MO) antisense oligonucleotides were used to construct a Sox19b loss-of-function zebrafish model. The phenotype and the expression of related genes were analysed by in situ hybridization and immunolabelling. Epigenetic modifications were detected by western blot and chromatin immunoprecipitation. Results In this study, we found that zebrafish embryos exhibited a reduced or even deleted forebrain phenotype after the expression of the Sox19b gene was inhibited. Moreover, we found for the first time that knockdown of Sox19b reduced the proliferation of NSCs; increased the transcription levels of Ngn1, Ascl1, HuC, Islet1, and cyclin-dependent kinase (CDK) inhibitors; and led to premature differentiation of NSCs. Finally, we found that knockdown of Sox19b decreased the levels of EZH2/H3K27me3 and decreased the level of H3K27me3 at the promoters of Ngn1 and ascl1a. Conclusion Together, our data demonstrate that Sox19b plays an essential role in early NSC proliferation and differentiation through EZH2-mediated histone methylation in neural tube development. This study established the role of transcription factor Sox19b and epigenetic factor EZH2 regulatory network on NSC development, which provides new clues and theoretical guidance for the clinical treatment of neural tube defects.
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Affiliation(s)
- Xian Li
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shandong University, 44#, Wenhua Xi Road, Jinan, 250012, Shandong, China.,Foot and Ankle Surgery Center of Shandong University and Department of Hand and Foot Surgery, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Wenjuan Zhou
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shandong University, 44#, Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Xinyue Li
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shandong University, 44#, Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Ming Gao
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shandong University, 44#, Wenhua Xi Road, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Center for Reproductive Medicine, Shandong University, Jinan, China
| | - Shufang Ji
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shandong University, 44#, Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Wenyu Tian
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shandong University, 44#, Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Guangyu Ji
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shandong University, 44#, Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Jingyi Du
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shandong University, 44#, Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Aijun Hao
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shandong University, 44#, Wenhua Xi Road, Jinan, 250012, Shandong, China.
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DeOliveira-Mello L, Lara JM, Arevalo R, Velasco A, Mack AF. Sox2 expression in the visual system of two teleost species. Brain Res 2019; 1722:146350. [DOI: 10.1016/j.brainres.2019.146350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/20/2019] [Accepted: 07/23/2019] [Indexed: 12/13/2022]
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40
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Shparberg RA, Glover HJ, Morris MB. Modeling Mammalian Commitment to the Neural Lineage Using Embryos and Embryonic Stem Cells. Front Physiol 2019; 10:705. [PMID: 31354503 PMCID: PMC6637848 DOI: 10.3389/fphys.2019.00705] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/20/2019] [Indexed: 12/21/2022] Open
Abstract
Early mammalian embryogenesis relies on a large range of cellular and molecular mechanisms to guide cell fate. In this highly complex interacting system, molecular circuitry tightly controls emergent properties, including cell differentiation, proliferation, morphology, migration, and communication. These molecular circuits include those responsible for the control of gene and protein expression, as well as metabolism and epigenetics. Due to the complexity of this circuitry and the relative inaccessibility of the mammalian embryo in utero, mammalian neural commitment remains one of the most challenging and poorly understood areas of developmental biology. In order to generate the nervous system, the embryo first produces two pluripotent populations, the inner cell mass and then the primitive ectoderm. The latter is the cellular substrate for gastrulation from which the three multipotent germ layers form. The germ layer definitive ectoderm, in turn, is the substrate for multipotent neurectoderm (neural plate and neural tube) formation, representing the first morphological signs of nervous system development. Subsequent patterning of the neural tube is then responsible for the formation of most of the central and peripheral nervous systems. While a large number of studies have assessed how a competent neurectoderm produces mature neural cells, less is known about the molecular signatures of definitive ectoderm and neurectoderm and the key molecular mechanisms driving their formation. Using pluripotent stem cells as a model, we will discuss the current understanding of how the pluripotent inner cell mass transitions to pluripotent primitive ectoderm and sequentially to the multipotent definitive ectoderm and neurectoderm. We will focus on the integration of cell signaling, gene activation, and epigenetic control that govern these developmental steps, and provide insight into the novel growth factor-like role that specific amino acids, such as L-proline, play in this process.
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Affiliation(s)
| | | | - Michael B. Morris
- Embryonic Stem Cell Laboratory, Discipline of Physiology, School of Medical Sciences, Bosch Institute, University of Sydney, Sydney, NSW, Australia
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41
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Evolution of Snail-mediated regulation of neural crest and placodes from an ancient role in bilaterian neurogenesis. Dev Biol 2019; 453:180-190. [PMID: 31211947 DOI: 10.1016/j.ydbio.2019.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022]
Abstract
A major challenge in vertebrate evolution is to identify the gene regulatory mechanisms that facilitated the origin of neural crest cells and placodes from ancestral precursors in invertebrates. Here, we show in lamprey, a primitively jawless vertebrate, that the transcription factor Snail is expressed simultaneously throughout the neural plate, neural plate border, and pre-placodal ectoderm in the early embryo and is then upregulated in the CNS throughout neurogenesis. Using CRISPR/Cas9-mediated genome editing, we demonstrate that Snail plays functional roles in all of these embryonic domains or their derivatives. We first show that Snail patterns the neural plate border by repressing lateral expansion of Pax3/7 and activating nMyc and ZicA. We also present evidence that Snail is essential for DlxB-mediated establishment of the pre-placodal ectoderm but is not required for SoxB1a expression during formation of the neural plate proper. At later stages, Snail regulates formation of neural crest-derived and placode-derived PNS neurons and controls CNS neural differentiation in part by promoting cell survival. Taken together with established functions of invertebrate Snail genes, we identify a pan-bilaterian mechanism that extends to jawless vertebrates for regulating neurogenesis that is dependent on Snail transcription factors. We propose that ancestral vertebrates deployed an evolutionarily conserved Snail expression domain in the CNS and PNS for neurogenesis and then acquired derived functions in neural crest and placode development by recruitment of regulatory genes downstream of neuroectodermal Snail activity. Our results suggest that Snail regulatory mechanisms in vertebrate novelties such as the neural crest and placodes may have emerged from neurogenic roles that originated early in bilaterian evolution.
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Ruiz-García R, Martínez-Hernández E, García-Ormaechea M, Español-Rego M, Sabater L, Querol L, Illa I, Dalmau J, Graus F. Caveats and Pitfalls of SOX1 Autoantibody Testing With a Commercial Line Blot Assay in Paraneoplastic Neurological Investigations. Front Immunol 2019; 10:769. [PMID: 31031763 PMCID: PMC6473043 DOI: 10.3389/fimmu.2019.00769] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 03/25/2019] [Indexed: 01/15/2023] Open
Abstract
SOX1 autoantibodies are considered markers of small cell lung cancer (SCLC) and paraneoplastic neurological syndromes (PNS) and are usually determined by commercial line blot in many clinical services. Recent studies suggested that SOX1 autoantibodies also occur in patients with neuropathies unrelated to SCLC, questioning the value of SOX1 autoantibodies as paraneoplastic biomarkers. Here, we compared the specificity and sensitivity of a commercial line blot (Euroimmun, Lübeck, Germany) with those of an in house cell-based assay (CBA) with HEK293 cells transfected with SOX1. Overall, 210 patients were included in the study, 139 patients with polyneuropathies without SCLC, and 71 with disorders associated with SOX1 autoantibodies detected with the in-house CBA. Forty one of these 71 cases had been referred to our laboratory for onconeuronal antibody assessment and 30/71 were patients with known PNS and SCLC. None of the patients with polyneuropathies had SOX1 autoantibodies by either line blot or CBA (specificity of the immunoblot: 100%; 95%C.I.: 97.8-100). Among the 71 patients with CBA SOX1 autoantibodies, only 53 were positive by line blot (sensitivity: 74.6%; 95%C.I.: 62.9-84.2). Lung cancer was detected in 37/41 (90%; 34 with SCLC) patients referred for onconeuronal antibody assessment and 34 of them also had a PNS. Our study confirms the association of SOX1 autoantibodies with SCLC and PNS. The line blot test misses 25% of the cases; therefore, to minimize the frequency of false negative results we recommend the use of a confirmatory test, such as CBA, in patients suspected to have a SCLC-related PNS.
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Affiliation(s)
- Raquel Ruiz-García
- Immunology Department, Centre Diagnóstic Biomédic, Hospital Clínic, Barcelona, Spain
| | - Eugenia Martínez-Hernández
- Neuroimmunology Program, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Service of Neurology, Hospital Clinic, Barcelona, Spain
| | | | - Marta Español-Rego
- Immunology Department, Centre Diagnóstic Biomédic, Hospital Clínic, Barcelona, Spain
| | - Lidia Sabater
- Neuroimmunology Program, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Luis Querol
- Neuromuscular Disorders Unit, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Centro de Investigaciones Biomédicas en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Isabel Illa
- Neuromuscular Disorders Unit, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Centro de Investigaciones Biomédicas en Red en Enfermedades Raras (CIBERER), Valencia, Spain.,Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Josep Dalmau
- Neuroimmunology Program, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Neurology, University of Pennsylvania, Philadelphia, PA, United States
| | - Francesc Graus
- Neuroimmunology Program, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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Ando H, Sato T, Ito T, Yamamoto J, Sakamoto S, Nitta N, Asatsuma-Okumura T, Shimizu N, Mizushima R, Aoki I, Imai T, Yamaguchi Y, Berk AJ, Handa H. Cereblon Control of Zebrafish Brain Size by Regulation of Neural Stem Cell Proliferation. iScience 2019; 15:95-108. [PMID: 31055217 PMCID: PMC6501120 DOI: 10.1016/j.isci.2019.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 01/03/2019] [Accepted: 04/04/2019] [Indexed: 01/13/2023] Open
Abstract
Thalidomide is a teratogen that causes multiple malformations in the developing baby through its interaction with cereblon (CRBN), a substrate receptor subunit of the CRL4 E3 ubiquitin ligase complex. CRBN was originally reported as a gene associated with autosomal recessive non-syndromic mild mental retardation. However, the function of CRBN during brain development remains largely unknown. Here we demonstrate that CRBN promotes brain development by facilitating the proliferation of neural stem cells (NSCs). Knockdown of CRBN in zebrafish embryos impaired brain development and led to small brains, as did treatment with thalidomide. By contrast, overexpression of CRBN resulted in enlarged brains, leading to the expansion of NSC regions and increased cell proliferation in the early brain field and an expanded expression of brain region-specific genes and neural and glial marker genes. These results demonstrate that CRBN functions in the determination of brain size by regulating the proliferation of NSCs during development. CRBN is a determinant of head and brain size during zebrafish development Thalidomide causes a reduction in head and brain size by binding to CRBN CRBN prevents apoptosis and promotes NSC proliferation during brain development crbn overexpression results in a concomitant increase in neurons and glial cells
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Affiliation(s)
- Hideki Ando
- Department of Nanoparticle Translational Research, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Tomomi Sato
- Department of Nanoparticle Translational Research, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Takumi Ito
- Department of Nanoparticle Translational Research, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan; PRESTO, JST, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012 Japan
| | - Junichi Yamamoto
- Department of Nanoparticle Translational Research, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Satoshi Sakamoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Nobuhiro Nitta
- National Institute of Radiological Sciences (NIRS), Chiba 263-8555, Japan
| | - Tomoko Asatsuma-Okumura
- Department of Nanoparticle Translational Research, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Nobuyuki Shimizu
- Department of Nanoparticle Translational Research, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Ryota Mizushima
- Department of Nanoparticle Translational Research, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Ichio Aoki
- National Institute of Radiological Sciences (NIRS), Chiba 263-8555, Japan
| | - Takeshi Imai
- National Center for Geriatrics and Gerontology (NCGG), Aichi 474-8511, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Arnold J Berk
- Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California, Los Angeles 90095, USA
| | - Hiroshi Handa
- Department of Nanoparticle Translational Research, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan.
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Bonatto Paese CL, Leite DJ, Schönauer A, McGregor AP, Russell S. Duplication and expression of Sox genes in spiders. BMC Evol Biol 2018; 18:205. [PMID: 30587109 PMCID: PMC6307133 DOI: 10.1186/s12862-018-1337-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/17/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The Sox family of transcription factors is an important part of the genetic 'toolbox' of all metazoans examined to date and is known to play important developmental roles in vertebrates and insects. However, outside the commonly studied Drosophila model little is known about the repertoire of Sox family transcription factors in other arthropod species. Here we characterise the Sox family in two chelicerate species, the spiders Parasteatoda tepidariorum and Stegodyphus mimosarum, which have experienced a whole genome duplication (WGD) in their evolutionary history. RESULTS We find that virtually all of the duplicate Sox genes have been retained in these spiders after the WGD. Analysis of the expression of Sox genes in P. tepidariorum embryos suggests that it is likely that some of these genes have neofunctionalised after duplication. Our expression analysis also strengthens the view that an orthologue of vertebrate Group B1 genes, SoxNeuro, is implicated in the earliest events of CNS specification in both vertebrates and invertebrates. In addition, a gene in the Dichaete/Sox21b class is dynamically expressed in the spider segment addition zone, suggestive of an ancient regulatory mechanism controlling arthropod segmentation as recently suggested for flies and beetles. Together with the recent analysis of Sox gene expression in the embryos of other arthropods, our findings support the idea of conserved functions for some of these genes, including a potential role for SoxC and SoxD genes in CNS development and SoxF in limb development. CONCLUSIONS Our study provides a new chelicerate perspective to understanding the evolution and function of Sox genes and how the retention of duplicates of such important tool-box genes after WGD has contributed to different aspects of spider embryogenesis. Future characterisation of the function of these genes in spiders will help us to better understand the evolution of the regulation of important developmental processes in arthropods and other metazoans including neurogenesis and segmentation.
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Affiliation(s)
- Christian L Bonatto Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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Zhang S, Chen X, Wang M, Zhang W, Pan J, Qin Q, Zhong L, Shao J, Sun M, Jiang H, Bian W. Genome-wide identification, phylogeny and expressional profile of the Sox gene family in channel catfish (Ictalurus punctatus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:17-26. [DOI: 10.1016/j.cbd.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 12/11/2017] [Accepted: 03/05/2018] [Indexed: 01/10/2023]
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King AJ, Higgs DR. Potential new approaches to the management of the Hb Bart's hydrops fetalis syndrome: the most severe form of α-thalassemia. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2018; 2018:353-360. [PMID: 30504332 PMCID: PMC6246003 DOI: 10.1182/asheducation-2018.1.353] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The α-thalassemia trait, associated with deletions removing both α-globin genes from 1 chromosome (genotype ζ αα/ζ--), is common throughout Southeast Asia. Consequently, many pregnancies in couples of Southeast Asian origin carry a 1 in 4 risk of producing a fetus inheriting no functional α-globin genes (ζ--/ζ--), leading to hemoglobin (Hb) Bart's hydrops fetalis syndrome (BHFS). Expression of the embryonic α-globin genes (ζ-globin) is normally limited to the early stages of primitive erythropoiesis, and so when the ζ-globin genes are silenced, at ∼6 weeks of gestation, there should be no α-like globin chains to pair with the fetal γ-globin chains of Hb, which consequently form nonfunctional tetramers (γ4) known as Hb Bart's. When deletions leave the ζ-globin gene intact, a low level of ζ-globin gene expression continues in definitive erythroid cells, producing small amounts of Hb Portland (ζ2γ2), a functional form of Hb that allows the fetus to survive up to the second or third trimester. Untreated, all affected individuals die at these stages of development. Prevention is therefore of paramount importance. With improvements in early diagnosis, intrauterine transfusion, and advanced perinatal care, there are now a small number of individuals with BHFS who have survived, with variable outcomes. A deeper understanding of the mechanism underlying the switch from ζ- to α-globin expression could enable persistence or reactivation of embryonic globin synthesis in definitive cells, thereby providing new therapeutic options for such patients.
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Affiliation(s)
- Andrew J King
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Douglas R Higgs
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
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Connor B, Firmin E, McCaughey-Chapman A, Monk R, Lee K, Liot S, Geiger J, Rudolph C, Jones K. Conversion of adult human fibroblasts into neural precursor cells using chemically modified mRNA. Heliyon 2018; 4:e00918. [PMID: 30450440 PMCID: PMC6226601 DOI: 10.1016/j.heliyon.2018.e00918] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/11/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
Direct reprogramming offers a unique approach by which to generate neural lineages for the study and treatment of neurological disorders. Our objective is to develop a clinically viable reprogramming strategy to generate neural precursor cells for the treatment of neurological disorders through cell replacement therapy. We initially developed a method for directly generating neural precursor cells (iNPs) from adult human fibroblasts by transient expression of the neural transcription factors, SOX2 and PAX6 using plasmid DNA. This study advances these findings by examining the use of chemically modified mRNA (cmRNA) for direct-to-iNP reprogramming. Chemically modified mRNA has the benefit of being extremely stable and non-immunogenic, offering a clinically suitable gene delivery system. The use of SOX2 and PAX6 cmRNA resulted in high co-transfection efficiency and cell viability compared with plasmid transfection. Neural positioning and fate determinant genes were observed throughout reprogramming with ion channel and synaptic marker genes detected during differentiation. Differentiation of cmRNA-derived iNPs generated immature GABAergic or glutamatergic neuronal phenotypes in conjunction with astrocytes. This represents the first time a cmRNA approach has been used to directly reprogram adult human fibroblasts to iNPs, potentially providing an efficient system by which to generate human neurons for both research and clinical application.
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Affiliation(s)
- Bronwen Connor
- Department of Pharmacology & Clinical Pharmacology, Centre for Brain Research, School of Medical Science, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Erin Firmin
- Department of Pharmacology & Clinical Pharmacology, Centre for Brain Research, School of Medical Science, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Amy McCaughey-Chapman
- Department of Pharmacology & Clinical Pharmacology, Centre for Brain Research, School of Medical Science, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Ruth Monk
- Department of Pharmacology & Clinical Pharmacology, Centre for Brain Research, School of Medical Science, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Kevin Lee
- Department of Physiology, Centre for Brain Research, School of Medical Science, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Sophie Liot
- Department of Pharmacology & Clinical Pharmacology, Centre for Brain Research, School of Medical Science, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | | | | | - Kathryn Jones
- Department of Pharmacology & Clinical Pharmacology, Centre for Brain Research, School of Medical Science, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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48
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Zaletel I, Schwirtlich M, Perović M, Jovanović M, Stevanović M, Kanazir S, Puškaš N. Early Impairments of Hippocampal Neurogenesis in 5xFAD Mouse Model of Alzheimer’s Disease Are Associated with Altered Expression of SOXB Transcription Factors. J Alzheimers Dis 2018; 65:963-976. [DOI: 10.3233/jad-180277] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ivan Zaletel
- Institute of Histology and Embryology “Aleksandar Đ Kostić”, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marija Schwirtlich
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Milka Perović
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Mirna Jovanović
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Milena Stevanović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Selma Kanazir
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Nela Puškaš
- Institute of Histology and Embryology “Aleksandar Đ Kostić”, School of Medicine, University of Belgrade, Belgrade, Serbia
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Direct Conversion of Mouse Fibroblasts into Neural Stem Cells by Chemical Cocktail Requires Stepwise Activation of Growth Factors and Nup210. Cell Rep 2018; 24:1355-1362.e3. [DOI: 10.1016/j.celrep.2018.06.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 05/14/2018] [Accepted: 06/27/2018] [Indexed: 11/18/2022] Open
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50
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Ueha R, Ueha S, Kondo K, Kikuta S, Yamasoba T. Cigarette Smoke-Induced Cell Death Causes Persistent Olfactory Dysfunction in Aged Mice. Front Aging Neurosci 2018; 10:183. [PMID: 29950987 PMCID: PMC6008309 DOI: 10.3389/fnagi.2018.00183] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 05/30/2018] [Indexed: 11/21/2022] Open
Abstract
Introduction: Exposure to cigarette smoke is a cause of olfactory dysfunction. We previously reported that in young mice, cigarette smoke damaged olfactory progenitors and decreased mature olfactory receptor neurons (ORNs), then, mature ORNs gradually recovered after smoking cessation. However, in aged populations, the target cells in ORNs by cigarette smoke, the underlying molecular mechanisms by which cigarette smoke impairs the regenerative ORNs, and the degree of ORN regeneration after smoking cessation remain unclear. Objectives: To explore the effects of cigarette smoke on the ORN cell system using an aged mouse model of smoking, and to investigate the extent to which smoke-induced damage to ORNs recovers following cessation of exposure to cigarette smoke in aged mice. Methods: We intranasally administered a cigarette smoke solution (CSS) to 16-month-old male mice over 24 days, then examined ORN existence, cell survival, changes of inflammatory cytokines in the olfactory epithelium (OE), and olfaction using histological analyses, gene analyses and olfactory habituation/dishabituation tests. Results: CSS administration reduced the number of mature ORNs in the OE and induced olfactory dysfunction. These changes coincided with an increase in the number of apoptotic cells and Tumor necrosis factor (TNF) expression and a decrease in Il6 expression. Notably, the reduction in mature ORNs did not recover even on day 28 after cessation of treatment with CSS, resulting in persistent olfactory dysfunction. Conclusion: In aged mice, by increasing ORN death, CSS exposure could eventually overwhelm the regenerative capacity of the OE, resulting in continued reduction in the number of mature ORNs and olfactory dysfunction.
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Affiliation(s)
- Rumi Ueha
- Department of Otolaryngology and Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Ueha
- Division of Molecular Regulation of Inflammatory and Immune Diseases Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Kenji Kondo
- Department of Otolaryngology and Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shu Kikuta
- Department of Otolaryngology and Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Yamasoba
- Department of Otolaryngology and Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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