1
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Sharma S, Majumdar A, Basu A. Regulation of Onecut2 by miR-9-5p in Japanese encephalitis virus infected neural stem/progenitor cells. Microbiol Spectr 2024; 12:e0323823. [PMID: 38319106 PMCID: PMC10913399 DOI: 10.1128/spectrum.03238-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Japanese encephalitis virus (JEV) is one of the major neurotropic viral infections that is known to dysregulate the homeostasis of neural stem/progenitor cells (NSPCs) and depletes the stem cell pool. NSPCs are multipotent stem cell population of the central nervous system (CNS) which are known to play an important role in the repair of the CNS during insults/injury caused by several factors such as ischemia, neurological disorders, CNS infections, and so on. Viruses have evolved to utilize host factors for their own benefit and during JEV infection, host factors, including the non-coding RNAs such as miRNAs, are reported to be affected, thereby cellular processes regulated by the miRNAs exhibit perturbed functionality. Previous studies from our laboratory have demonstrated the role of JEV infection in dysregulating the function of neural stem cells (NSCs) by altering the cell fate and depleting the stem cell pool leading to a decline in stem cell function in CNS repair mechanism post-infection. JEV-induced alteration in miRNA expression in the NSCs is one of the major interest to us. In prior studies, we have observed an altered expression pattern of certain miRNAs following JEV infection. In this study, we have validated the role of JEV infection in NSCs in altering the expression of miR-9-5p, which is a known regulator of neurogenesis in NSCs. Furthermore, we have validated the interaction of this miRNA with its target, Onecut2 (OC2), in primary NSCs utilizing miRNA mimic and inhibitor transfection experiments. Our findings indicate a possible role of JEV mediated dysregulated interaction between miR-9-5p and its putative target OC2 in NSPCs. IMPORTANCE MicroRNAs have emerged as key disease pathogenic markers and potential therapeutic targets. In this study, we solidify this concept by studying a key miRNA, miR-9-5p, in Japanese encephalitis virus infection of neural stem/progenitor cells. miRNA target Onecut2 has a possible role in stem cell pool biology. Here, we show a possible mechanistic axis worth investing in neurotropic viral biology.
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Affiliation(s)
| | | | - Anirban Basu
- National Brain Research Centre, Manesar, Haryana, India
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2
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Belmonte-Mateos C, Meister L, Pujades C. Hindbrain rhombomere centers harbor a heterogenous population of dividing progenitors which rely on Notch signaling. Front Cell Dev Biol 2023; 11:1268631. [PMID: 38020924 PMCID: PMC10652760 DOI: 10.3389/fcell.2023.1268631] [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: 07/28/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Tissue growth and morphogenesis are interrelated processes, whose tight coordination is essential for the production of different cell fates and the timely precise allocation of stem cell capacities. The zebrafish embryonic brainstem, the hindbrain, exemplifies such coupling between spatiotemporal cell diversity acquisition and tissue growth as the neurogenic commitment is differentially distributed over time. Here, we combined cell lineage and in vivo imaging approaches to reveal the emergence of specific cell population properties within the rhombomeres. We studied the molecular identity of hindbrain rhombomere centers and showed that they harbor different progenitor capacities that change over time. By clonal analysis, we revealed that cells within the center of rhombomeres decrease the proliferative capacity to remain mainly in the G1 phase. Proliferating progenitors give rise to neurons by asymmetric and symmetric neurogenic divisions while maintaining the pool of progenitors. The proliferative capacity of these cells differs from their neighbors, and they are delayed in the onset of Notch activity. Through functional studies, we demonstrated that they rely on Notch3 signaling to be maintained as non-committed progenitors. In this study, we show that cells in rhombomere centers, despite the neurogenic asynchrony, might share steps of a similar program with the rhombomere counterparts, to ensure proper tissue growth.
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3
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Gillis RF, Palmour RM. miRNA Expression Analysis of the Hippocampus in a Vervet Monkey Model of Fetal Alcohol Spectrum Disorder Reveals a Potential Role in Global mRNA Downregulation. Brain Sci 2023; 13:934. [PMID: 37371413 DOI: 10.3390/brainsci13060934] [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: 05/19/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
MicroRNAs (miRNAs) are short-length non-protein-coding RNA sequences that post-transcriptionally regulate gene expression in a broad range of cellular processes including neuro- development and have previously been implicated in fetal alcohol spectrum disorders (FASD). In this study, we use our vervet monkey model of FASD to follow up on a prior multivariate (developmental age × ethanol exposure) mRNA analysis (GSE173516) to explore the possibility that the global mRNA downregulation we observed in that study could be related to miRNA expression and function. We report here a predominance of upregulated and differentially expressed miRNAs. Further, the 24 most upregulated miRNAs were significantly correlated with their predicted targets (Target Scan 7.2). We then explored the relationship between these 24 miRNAs and the fold changes observed in their paired mRNA targets using two prediction platforms (Target Scan 7.2 and miRwalk 3.0). Compared to a list of non-differentially expressed miRNAs from our dataset, the 24 upregulated and differentially expressed miRNAs had a greater impact on the fold changes of their corresponding mRNA targets across both platforms. Taken together, this evidence raises the possibility that ethanol-induced upregulation of specific miRNAs might contribute functionally to the general downregulation of mRNAs observed by multiple investigators in response to prenatal alcohol exposure.
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Affiliation(s)
- Rob F Gillis
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
| | - Roberta M Palmour
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0G4, Canada
- Behavioural Science Foundation, Mansion KN 0101, Saint Kitts and Nevis
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4
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Argyris GA, Lluch Lafuente A, Tribastone M, Tschaikowski M, Vandin A. Reducing Boolean networks with backward equivalence. BMC Bioinformatics 2023; 24:212. [PMID: 37221494 DOI: 10.1186/s12859-023-05326-9] [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: 03/15/2022] [Accepted: 05/05/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Boolean Networks (BNs) are a popular dynamical model in biology where the state of each component is represented by a variable taking binary values that express, for instance, activation/deactivation or high/low concentrations. Unfortunately, these models suffer from the state space explosion, i.e., there are exponentially many states in the number of BN variables, which hampers their analysis. RESULTS We present Boolean Backward Equivalence (BBE), a novel reduction technique for BNs which collapses system variables that, if initialized with same value, maintain matching values in all states. A large-scale validation on 86 models from two online model repositories reveals that BBE is effective, since it is able to reduce more than 90% of the models. Furthermore, on such models we also show that BBE brings notable analysis speed-ups, both in terms of state space generation and steady-state analysis. In several cases, BBE allowed the analysis of models that were originally intractable due to the complexity. On two selected case studies, we show how one can tune the reduction power of BBE using model-specific information to preserve all dynamics of interest, and selectively exclude behavior that does not have biological relevance. CONCLUSIONS BBE complements existing reduction methods, preserving properties that other reduction methods fail to reproduce, and vice versa. BBE drops all and only the dynamics, including attractors, originating from states where BBE-equivalent variables have been initialized with different activation values The remaining part of the dynamics is preserved exactly, including the length of the preserved attractors, and their reachability from given initial conditions, without adding any spurious behaviours. Given that BBE is a model-to-model reduction technique, it can be combined with further reduction methods for BNs.
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Affiliation(s)
- Georgios A Argyris
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | - Alberto Lluch Lafuente
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | | | - Max Tschaikowski
- Department of Computer Science, University of Aalborg, Aalborg, Denmark
| | - Andrea Vandin
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark.
- Department of Excellence EMbeDS and Institute of Economics, Sant'Anna School for Advanced Studies, Pisa, Italy.
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5
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Kumar P. miRNA dysregulation in traumatic brain injury and epilepsy: a systematic review to identify putative biomarkers for post-traumatic epilepsy. Metab Brain Dis 2023; 38:749-765. [PMID: 36715879 DOI: 10.1007/s11011-023-01172-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
Traumatic brain injury (TBI) leads to post-traumatic epilepsy (PTE); hence, both TBI and PTE share various similar molecular mechanisms. MicroRNA (miRNA) is a small noncoding RNA that acts as a gene-silencing molecule. Notably, the dysregulation of miRNAs in various neurological diseases, including TBI and epilepsy, has been reported in several studies. However, studies on commonly dysregulated miRNAs and the regulation of shared pathways in both TBI and epilepsy that can identify potential biomarkers of PTE are still lacking. This systematic review covers the peer-review publications of TBI and database studies of epilepsy-dysregulated miRNAs of clinical studies. For TBI, 290 research articles were identified after screening, and 12 provided data for dysregulated miRNAs in humans. The compiled data suggest that 85 and 222 miRNAs are consecutively dysregulated in TBI and epilepsy. In both, 10 miRNAs were found to be commonly dysregulated, implying that they are potentially dysregulated miRNAs for PTE. Furthermore, the targets and involvement of each putative miRNA in different pathways were identified and evaluated. Additionally, clusters of predicted miRNAs were analyzed. Each miRNA's regulatory role was linked with apoptosis, inflammation, and cell cycle regulation pathways. Hence, these findings provide insight for future diagnostic biomarkers.
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Affiliation(s)
- Prince Kumar
- Department of Central Sophisticated Instrumentation Cell, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
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6
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Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development 2022; 149:276990. [PMID: 36189829 PMCID: PMC9641661 DOI: 10.1242/dev.200474] [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: 12/15/2021] [Accepted: 08/26/2022] [Indexed: 11/06/2022]
Abstract
MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.
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Affiliation(s)
- Ximena Soto
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK,Authors for correspondence (; )
| | - Joshua Burton
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Cerys S. Manning
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Thomas Minchington
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Robert Lea
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Jessica Lee
- Discovery Department, Medicines Discovery Catapult, Block 35, Mereside, Alderley Park, Alderley Edge, Cheshire, SK10 4TG, UK
| | - Jochen Kursawe
- School of Mathematics and Statistics, University of St Andrews, North Haugh, St Andrews, KY16 9SS, UK
| | - Magnus Rattray
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Nancy Papalopulu
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK,Authors for correspondence (; )
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7
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Gallicchio L, Griffiths-Jones S, Ronshaugen M. miR-9a regulates levels of both rhomboid mRNA and protein in the early Drosophila melanogaster embryo. G3 GENES|GENOMES|GENETICS 2022; 12:6526387. [PMID: 35143618 PMCID: PMC8982436 DOI: 10.1093/g3journal/jkac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 11/30/2022]
Abstract
MicroRNAs can have subtle and combinatorial effects on the levels of the targets and pathways they act on. Studying the consequences of a single microRNA knockout often proves difficult as many such knockouts exhibit phenotypes only under stress conditions. This has often led to the hypothesis that microRNAs buffer the effects of intrinsic and environmental stochasticity on gene expression. Observing and understanding this buffering effect entails quantitative analysis of microRNA and target expression in single cells. To this end, we have employed single-molecule fluorescence in situ hybridization, immunofluorescence, and high-resolution confocal microscopy to investigate the effects of miR-9a loss on the expression of the serine-protease Rhomboid in Drosophila melanogaster early embryos. Our single-cell quantitative approach shows that spatially, the rhomboid mRNA pattern is identical in WT and miR-9a knockout embryos. However, we find that the number of mRNA molecules per cell is higher when miR-9a is absent, and the level and temporal accumulation of rhomboid protein shows a more dramatic increase in the miR-9a knockout. Specifically, we see accumulation of rhomboid protein in miR-9a mutants by stage 5, much earlier than in WT. The data, therefore, show that miR-9a functions in the regulation of rhomboid mRNA and protein levels. While further work is required to establish whether rhomboid is a direct target of miR-9 in Drosophila, our results further establish the miR-9 family microRNAs as conserved regulators of timing in neurogenic processes. This study shows the power of single-cell quantification as an experimental tool to study phenotypic consequences of microRNA mis-regulation.
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Affiliation(s)
- Lorenzo Gallicchio
- School of Biological Sciences, Faculty of Medicine, Biology and Health, Michael Smith Building, The University of Manchester, Manchester M13 9GB, UK
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Medicine, Biology and Health, Michael Smith Building, The University of Manchester, Manchester M13 9GB, UK
| | - Matthew Ronshaugen
- School of Medical Sciences, Faculty of Medicine, Biology and Health, Michael Smith Building, The University of Manchester, Manchester M13 9GB, UK
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8
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Samoilova EM, Belopasov VV, Baklaushev VP. Transcription Factors of Direct Neuronal Reprogramming in Ontogenesis and Ex Vivo. Mol Biol 2021. [DOI: 10.1134/s0026893321040087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Bezerra DP, de Aguiar JP, Keasey MP, Rodrigues CG, de Oliveira JRM. MiR-9-5p Regulates Genes Linked to Cerebral Calcification in the Osteogenic Differentiation Model and Induces Generalized Alteration in the Ion Channels. J Mol Neurosci 2021; 71:1897-1905. [PMID: 34041689 DOI: 10.1007/s12031-021-01830-w] [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: 08/15/2018] [Accepted: 03/15/2021] [Indexed: 12/01/2022]
Abstract
MicroRNA-9 (miR-9) modulates gene expression and demonstrates high structural conservation and wide expression in the central nervous system. Bioinformatics analysis predicts almost 100 ion channels, membrane transporters and receptors, including genes linked to primary familial brain calcification (PFBC), as possible miR-9-5p targets. PFBC is a neurodegenerative disorder, characterized by bilateral and symmetrical calcifications in the brain, associated with motor and behavioral disturbances. In this work, we seek to study the influence of miR-9-5p in regulating genes involved in PFBC, in an osteogenic differentiation model with SaOs-2 cells. During the induced calcification process, solute carrier family 20 member 2 (SLC20A2) and platelet-derived growth factor receptor beta (PDGFRB) were downregulated, while platelet-derived growth factor beta (PDGFB) showed no significant changes. Significantly decreased levels of SLC20A2 and PDGFRB were caused by the presence of miR-9-5p, while PDGFB showed no regulation. We confirmed the findings using an miR-9-5p inhibitor and also probed the cells in electrophysiological analysis to assess whether such microRNA might affect a broader range of ion channels, membrane transporters and receptors. Our electrophysiological data show that an increase of the miR-9-5p in SaOs-2 cells decreased the density and amplitude of the output ionic currents, indicating that it may influence the activity, and perhaps the expression, of some ionic channels. Additional investigations should determine whether such an effect is specific to miR-9-5p, and whether it could be used, together with the miR-9-5p inhibitor, as a therapeutic or diagnostic tool.
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Affiliation(s)
| | | | - Matthew Philip Keasey
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | | | - João Ricardo Mendes de Oliveira
- Keizo Asami Laboratory, Federal University of Pernambuco, Recife, PE, Brazil. .,Neuropsychiatry Department, Federal University of Pernambuco, Recife, PE, Brazil.
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10
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Yuan P, Ding L, Chen H, Wang Y, Li C, Zhao S, Yang X, Ma Y, Zhu J, Qi X, Zhang Y, Xia X, Zheng JC. Neural Stem Cell-Derived Exosomes Regulate Neural Stem Cell Differentiation Through miR-9-Hes1 Axis. Front Cell Dev Biol 2021; 9:601600. [PMID: 34055767 PMCID: PMC8155619 DOI: 10.3389/fcell.2021.601600] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
Exosomes, a key element of the central nervous system microenvironment, mediate intercellular communication via horizontally transferring bioactive molecules. Emerging evidence has implicated exosomes in the regulation of neurogenesis. Recently, we compared the neurogenic potential of exosomes released from primary mouse embryonic neural stem cells (NSCs) and astrocyte-reprogrammed NSCs, and observed diverse neurogenic potential of those two exosome populations in vitro. However, the roles of NSC-derived exosomes on NSC differentiation and the underlying mechanisms remain largely unknown. In this study, we firstly demonstrated that NSC-derived exosomes facilitate the differentiation of NSCs and the maturation of both neuronal and glial cells in defined conditions. We then identified miR-9, a pro-neural miRNA, as the most abundantly expressed miRNA in NSC-derived exosomes. The silencing of miR-9 in exosomes abrogates the positive effects of NSC-derived exosomes on the differentiation of NSCs. We further identified Hes1 as miR-9 downstream target, as the transfection of Hes1 siRNA restored the differentiation promoting potential of NSC-derived exosomes after knocking down exosomal miR-9. Thus, our data indicate that NSC-derived exosomes facilitate the differentiation of NSCs via transferring miR-9, which sheds light on the development of cell-free therapeutic strategies for treating neurodegeneration.
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Affiliation(s)
- Ping Yuan
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China.,Department of Cardio-Pulmonary Circulation, School of Medicine, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Lu Ding
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Huili Chen
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Yi Wang
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Chunhong Li
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Shu Zhao
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Xiaoyu Yang
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Yizhao Ma
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Jie Zhu
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Xinrui Qi
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Yanyan Zhang
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Xiaohuan Xia
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, China
| | - Jialin C Zheng
- Center for Translational Neurodegeneration and Regenerative Therapy, Tenth People's Hospital of Tongji University, Shanghai, China.,Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, China.,Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, China
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11
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Desvignes T, Sydes J, Montfort J, Bobe J, Postlethwait JH. Evolution after Whole-Genome Duplication: Teleost MicroRNAs. Mol Biol Evol 2021; 38:3308-3331. [PMID: 33871629 PMCID: PMC8321539 DOI: 10.1093/molbev/msab105] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are important gene expression regulators implicated in many biological processes, but we lack a global understanding of how miRNA genes evolve and contribute to developmental canalization and phenotypic diversification. Whole-genome duplication events likely provide a substrate for species divergence and phenotypic change by increasing gene numbers and relaxing evolutionary pressures. To understand the consequences of genome duplication on miRNA evolution, we studied miRNA genes following the teleost genome duplication (TGD). Analysis of miRNA genes in four teleosts and in spotted gar, whose lineage diverged before the TGD, revealed that miRNA genes were retained in ohnologous pairs more frequently than protein-coding genes, and that gene losses occurred rapidly after the TGD. Genomic context influenced retention rates, with clustered miRNA genes retained more often than nonclustered miRNA genes and intergenic miRNA genes retained more frequently than intragenic miRNA genes, which often shared the evolutionary fate of their protein-coding host. Expression analyses revealed both conserved and divergent expression patterns across species in line with miRNA functions in phenotypic canalization and diversification, respectively. Finally, major strands of miRNA genes experienced stronger purifying selection, especially in their seeds and 3'-complementary regions, compared with minor strands, which nonetheless also displayed evolutionary features compatible with constrained function. This study provides the first genome-wide, multispecies analysis of the mechanisms influencing metazoan miRNA evolution after whole-genome duplication.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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12
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Moura LM, Ferreira VLDR, Loureiro RM, de Paiva JPQ, Rosa-Ribeiro R, Amaro E, Soares MBP, Machado BS. The Neurobiology of Zika Virus: New Models, New Challenges. Front Neurosci 2021; 15:654078. [PMID: 33897363 PMCID: PMC8059436 DOI: 10.3389/fnins.2021.654078] [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: 01/15/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
The Zika virus (ZIKV) attracted attention due to one striking characteristic: the ability to cross the placental barrier and infect the fetus, possibly causing severe neurodevelopmental disruptions included in the Congenital Zika Syndrome (CZS). Few years after the epidemic, the CZS incidence has begun to decline. However, how ZIKV causes a diversity of outcomes is far from being understood. This is probably driven by a chain of complex events that relies on the interaction between ZIKV and environmental and physiological variables. In this review, we address open questions that might lead to an ill-defined diagnosis of CZS. This inaccuracy underestimates a large spectrum of apparent normocephalic cases that remain underdiagnosed, comprising several subtle brain abnormalities frequently masked by a normal head circumference. Therefore, new models using neuroimaging and artificial intelligence are needed to improve our understanding of the neurobiology of ZIKV and its true impact in neurodevelopment.
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Affiliation(s)
| | | | | | | | | | - Edson Amaro
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Milena Botelho Pereira Soares
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ), Bahia, Brazil.,University Center SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Advanced Health Systems (CIMATEC ISI SAS), National Service of Industrial Learning - SENAI, Bahia, Brazil
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13
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Alwin Prem Anand A, Alvarez-Bolado G, Wizenmann A. MiR-9 and the Midbrain-Hindbrain Boundary: A Showcase for the Limited Functional Conservation and Regulatory Complexity of MicroRNAs. Front Cell Dev Biol 2020; 8:586158. [PMID: 33330463 PMCID: PMC7719755 DOI: 10.3389/fcell.2020.586158] [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: 07/22/2020] [Accepted: 10/23/2020] [Indexed: 11/15/2022] Open
Abstract
MicroRNAs regulate gene expression at post-transcriptional levels. Some of them appear to regulate brain development and are involved in neurodevelopmental disorders. This has led to the suggestion that the role of microRNAs in neuronal development and function may be more central than previously appreciated. Here, we review the data about miR-9 function to depict the subtlety, complexity, flexibility and limited functional conservation of this essential developmental regulatory system. On this basis we propose that species-specific actions of miR-9 could underlie to a large degree species differences in brain size, shape and function.
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Affiliation(s)
- A Alwin Prem Anand
- Institute of Clinical Anatomy and Cell Analysis, University of Tuebingen, Tuebingen, Germany
| | | | - Andrea Wizenmann
- Institute of Clinical Anatomy and Cell Analysis, University of Tuebingen, Tuebingen, Germany
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14
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Galagali H, Kim JK. The multifaceted roles of microRNAs in differentiation. Curr Opin Cell Biol 2020; 67:118-140. [PMID: 33152557 DOI: 10.1016/j.ceb.2020.08.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are major drivers of cell fate specification and differentiation. The post-transcriptional regulation of key molecular factors by microRNAs contributes to the progression of embryonic and postembryonic development in several organisms. Following the discovery of lin-4 and let-7 in Caenorhabditis elegans and bantam microRNAs in Drosophila melanogaster, microRNAs have emerged as orchestrators of cellular differentiation and developmental timing. Spatiotemporal control of microRNAs and associated protein machinery can modulate microRNA activity. Additionally, adaptive modulation of microRNA expression and function in response to changing environmental conditions ensures that robust cell fate specification during development is maintained. Herein, we review the role of microRNAs in the regulation of differentiation during development.
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Affiliation(s)
- Himani Galagali
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.
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15
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Haghani A, Johnson RG, Woodward NC, Feinberg JI, Lewis K, Ladd-Acosta C, Safi N, Jaffe AE, Sioutas C, Allayee H, Campbell DB, Volk HE, Finch CE, Morgan TE. Adult mouse hippocampal transcriptome changes associated with long-term behavioral and metabolic effects of gestational air pollution toxicity. Transl Psychiatry 2020; 10:218. [PMID: 32636363 PMCID: PMC7341755 DOI: 10.1038/s41398-020-00907-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 12/30/2022] Open
Abstract
Gestational exposure to air pollution increases the risk of autism spectrum disorder and cognitive impairments with unresolved molecular mechanisms. This study exposed C57BL/6J mice throughout gestation to urban-derived nanosized particulate matter (nPM). Young adult male and female offspring were studied for behavioral and metabolic changes using forced swim test, fat gain, glucose tolerance, and hippocampal transcriptome. Gestational nPM exposure caused increased depressive behaviors, decreased neurogenesis in the dentate gyrus, and increased glucose tolerance in adult male offspring. Both sexes gained fat and body weight. Gestational nPM exposure induced 29 differentially expressed genes (DEGs) in adult hippocampus related to cytokine production, IL17a signaling, and dopamine degradation in both sexes. Stratification by sex showed twofold more DEGs in males than females (69 vs 37), as well as male-specific enrichment of DEGs mediating serotonin signaling, endocytosis, Gαi, and cAMP signaling. Gene co-expression analysis (WCGNA) identified a module of 43 genes with divergent responses to nPM between the sexes. Chronic changes in 14 DEGs (e.g., microRNA9-1) were associated with depressive behaviors, adiposity and glucose intolerance. These genes enriched neuroimmune pathways such as HMGB1 and TLR4. Based on cerebral cortex transcriptome data of neonates, we traced the initial nPM responses of HMGB1 pathway. In vitro, mixed glia responded to 24 h nPM with lower HMGB1 protein and increased proinflammatory cytokines. This response was ameliorated by TLR4 knockdown. In sum, we identified transcriptional changes that could be associated with air pollution-mediated behavioral and phenotypic changes. These identified genes merit further mechanistic studies for therapeutic intervention development.
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Affiliation(s)
- Amin Haghani
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Richard G Johnson
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Nicholas C Woodward
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Jason I Feinberg
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kristy Lewis
- Department of Pediatrics and Human Development, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Nikoo Safi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Andrew E Jaffe
- Lieber Institute of Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Constantinos Sioutas
- Department of Civil and Environmental Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Hooman Allayee
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daniel B Campbell
- Department of Pediatrics and Human Development, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Heather E Volk
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Caleb E Finch
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Todd E Morgan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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16
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Ala U. Competing Endogenous RNAs, Non-Coding RNAs and Diseases: An Intertwined Story. Cells 2020; 9:E1574. [PMID: 32605220 PMCID: PMC7407898 DOI: 10.3390/cells9071574] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 01/17/2023] Open
Abstract
MicroRNAs (miRNAs), a class of small non-coding RNA molecules, are responsible for RNA silencing and post-transcriptional regulation of gene expression. They can mediate a fine-tuned crosstalk among coding and non-coding RNA molecules sharing miRNA response elements (MREs). In a suitable environment, both coding and non-coding RNA molecules can be targeted by the same miRNAs and can indirectly regulate each other by competing for them. These RNAs, otherwise known as competing endogenous RNAs (ceRNAs), lead to an additional post-transcriptional regulatory layer, where non-coding RNAs can find new significance. The miRNA-mediated interplay among different types of RNA molecules has been observed in many different contexts. The analyses of ceRNA networks in cancer and other pathologies, as well as in other physiological conditions, provide new opportunities for interpreting omics data for the field of personalized medicine. The development of novel computational tools, providing putative predictions of ceRNA interactions, is a rapidly growing field of interest. In this review, I discuss and present the current knowledge of the ceRNA mechanism and its implications in a broad spectrum of different pathologies, such as cardiovascular or autoimmune diseases, cancers and neurodegenerative disorders.
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Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Turin, 10124 Turin, Italy
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17
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Soto X, Biga V, Kursawe J, Lea R, Doostdar P, Thomas R, Papalopulu N. Dynamic properties of noise and Her6 levels are optimized by miR-9, allowing the decoding of the Her6 oscillator. EMBO J 2020; 39:e103558. [PMID: 32395844 PMCID: PMC7298297 DOI: 10.15252/embj.2019103558] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 03/25/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023] Open
Abstract
Noise is prevalent in biology and has been widely quantified using snapshot measurements. This static view obscures our understanding of dynamic noise properties and how these affect gene expression and cell state transitions. Using a CRISPR/Cas9 Zebrafish her6::Venus reporter combined with mathematical and in vivo experimentation, we explore how noise affects the protein dynamics of Her6, a basic helix-loop-helix transcriptional repressor. During neurogenesis, Her6 expression transitions from fluctuating to oscillatory at single-cell level. We identify that absence of miR-9 input generates high-frequency noise in Her6 traces, inhibits the transition to oscillatory protein expression and prevents the downregulation of Her6. Together, these impair the upregulation of downstream targets and cells accumulate in a normally transitory state where progenitor and early differentiation markers are co-expressed. Computational modelling and double smFISH of her6 and the early neurogenesis marker, elavl3, suggest that the change in Her6 dynamics precedes the downregulation in Her6 levels. This sheds light onto the order of events at the moment of cell state transition and how this is influenced by the dynamic properties of noise. Our results suggest that Her/Hes oscillations, facilitated by dynamic noise optimization by miR-9, endow progenitor cells with the ability to make a cell state transition.
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Affiliation(s)
- Ximena Soto
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Veronica Biga
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Jochen Kursawe
- School of Mathematics and StatisticsUniversity of St AndrewsSt AndrewsUK
| | - Robert Lea
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Parnian Doostdar
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Riba Thomas
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
| | - Nancy Papalopulu
- Faculty of Biology Medicine and HealthSchool of Medical SciencesThe University of ManchesterManchesterUK
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18
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MicroRNAs as regulators of brain function and targets for treatment of epilepsy. Nat Rev Neurol 2020; 16:506-519. [DOI: 10.1038/s41582-020-0369-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
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19
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Jurisch-Yaksi N, Yaksi E, Kizil C. Radial glia in the zebrafish brain: Functional, structural, and physiological comparison with the mammalian glia. Glia 2020; 68:2451-2470. [PMID: 32476207 DOI: 10.1002/glia.23849] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 02/01/2023]
Abstract
The neuroscience community has witnessed a tremendous expansion of glia research. Glial cells are now on center stage with leading roles in the development, maturation, and physiology of brain circuits. Over the course of evolution, glia have highly diversified and include the radial glia, astroglia or astrocytes, microglia, oligodendrocytes, and ependymal cells, each having dedicated functions in the brain. The zebrafish, a small teleost fish, is no exception to this and recent evidences point to evolutionarily conserved roles for glia in the development and physiology of its nervous system. Due to its small size, transparency, and genetic amenability, the zebrafish has become an increasingly prominent animal model for brain research. It has enabled the study of neural circuits from individual cells to entire brains, with a precision unmatched in other vertebrate models. Moreover, its high neurogenic and regenerative potential has attracted a lot of attention from the research community focusing on neural stem cells and neurodegenerative diseases. Hence, studies using zebrafish have the potential to provide fundamental insights about brain development and function, and also elucidate neural and molecular mechanisms of neurological diseases. We will discuss here recent discoveries on the diverse roles of radial glia and astroglia in neurogenesis, in modulating neuronal activity and in regulating brain homeostasis at the brain barriers. By comparing insights made in various animal models, particularly mammals and zebrafish, our goal is to highlight the similarities and differences in glia biology among species, which could set new paradigms relevant to humans.
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Affiliation(s)
- Nathalie Jurisch-Yaksi
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Neurology and Clinical Neurophysiology, St Olav University Hospital, Trondheim, Norway
| | - Emre Yaksi
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway
| | - Caghan Kizil
- German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Dresden, Germany.,Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden, Dresden, Germany
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20
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Tambalo M, Mitter R, Wilkinson DG. A single cell transcriptome atlas of the developing zebrafish hindbrain. Development 2020; 147:dev184143. [PMID: 32094115 PMCID: PMC7097387 DOI: 10.1242/dev.184143] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/11/2020] [Indexed: 12/31/2022]
Abstract
Segmentation of the vertebrate hindbrain leads to the formation of rhombomeres, each with a distinct anteroposterior identity. Specialised boundary cells form at segment borders that act as a source or regulator of neuronal differentiation. In zebrafish, there is spatial patterning of neurogenesis in which non-neurogenic zones form at boundaries and segment centres, in part mediated by Fgf20 signalling. To further understand the control of neurogenesis, we have carried out single cell RNA sequencing of the zebrafish hindbrain at three different stages of patterning. Analyses of the data reveal known and novel markers of distinct hindbrain segments, of cell types along the dorsoventral axis, and of the transition of progenitors to neuronal differentiation. We find major shifts in the transcriptome of progenitors and of differentiating cells between the different stages analysed. Supervised clustering with markers of boundary cells and segment centres, together with RNA-seq analysis of Fgf-regulated genes, has revealed new candidate regulators of cell differentiation in the hindbrain. These data provide a valuable resource for functional investigations of the patterning of neurogenesis and the transition of progenitors to neuronal differentiation.
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Affiliation(s)
- Monica Tambalo
- Neural Development Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David G Wilkinson
- Neural Development Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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21
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Balasubramanian S, Raghunath A, Perumal E. Role of epigenetics in zebrafish development. Gene 2019; 718:144049. [DOI: 10.1016/j.gene.2019.144049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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22
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Chi L, Jiao D, Nan G, Yuan H, Shen J, Gao Y. miR-9-5p attenuates ischemic stroke through targeting ERMP1-mediated endoplasmic reticulum stress. Acta Histochem 2019; 121:151438. [PMID: 31500865 DOI: 10.1016/j.acthis.2019.08.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/07/2019] [Accepted: 08/30/2019] [Indexed: 12/20/2022]
Abstract
Ischemic stroke (IS) is a cerebrovascular disease with serious neurological function impairment, which may activate endoplasmic reticulum (ER) stress. However, the underlying regulatory mechanism of ER stress under IS remains unclear. miR-9-5p is enriched in the brain tissues and plays a role in the pathological process of IS. Therefore, the purpose of this study is to explore the effect of miR-9 on ER stress and underlying mechanism in IS. Here, a middle cerebral artery occlusion (MCAO) rat model was utilized to examine the alteration of brain pathology, and the expressions of miR-9 and ER stress-related proteins. Then SH-SY5Y cells with oxygen-glucose deprivation (OGD) were performed to further evaluate the functional role of miR-9 and preliminary mechanism. The results showed that miR-9 levels were decreased in the ischemic region of rats after MCAO. MCAO significantly increased the brain infract volume, reduced Nissl bodies and cell apoptosis, and increased ER stress-related proteins (ERMP1, GRP78, p-PERK, p-eIF2α and CHOP). Furthermore, overexpression of miR-9 by miR-9 mimics increased cell viability, inhibited LDH activity and cell apoptosis, and inactivated ER stress in OGD-neurons. Luciferase activity results showed that miR-9 negatively regulated ERMP1 expression by directly targeting ERMP1 3' UTR. Subsequently, we found that ERMP1 overexpression reversed the inhibition of miR-9 on GRP78-PERK-CHOP pathway in OGD neurons. In summary, our results suggest that the attenuation of miR-9 on ischemic injury may be involved in targeting ERMP1-mediated ER stress, which provides an available target for IS treatment.
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23
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Sunohara T, Morizane A, Matsuura S, Miyamoto S, Saito H, Takahashi J. MicroRNA-Based Separation of Cortico-Fugal Projection Neuron-Like Cells Derived From Embryonic Stem Cells. Front Neurosci 2019; 13:1141. [PMID: 31708734 PMCID: PMC6819314 DOI: 10.3389/fnins.2019.01141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022] Open
Abstract
The purification of pluripotent stem cell-derived cortico-fugal projection neurons (PSC-CFuPNs) is useful for disease modeling and cell therapies related to the dysfunction of cortical motor neurons, such as amyotrophic lateral sclerosis (ALS) or stroke. However, no CFuPN-specific surface markers for the purification are known. Recently, microRNAs (miRNAs) have been reported as alternatives to surface markers. Here, we investigated this possibility by applying the miRNA switch, an mRNA technology, to enrich PSC-CFuPNs. An array study of miRNAs in mouse fetal brain tissue revealed that CFuPNs highly express miRNA-124-3p at E14.5 and E16.5. In response, we designed a miRNA switched that responds to miRNA-124-3p and applied it to mouse embryonic stem cell (ESC)-derived cortical neurons. Flow cytometry and quantitative polymerase chain reaction (qPCR) analyses showed the miRNA-124-3p switch enriched CFuPN-like cells from this population. Immunocytechemical analysis confirmed vGlut1/Emx1/Bcl11b triple positive CFuPN-like cells were increased from 6.5 to 42%. Thus, our miRNA-124-3p switch can uniquely enrich live CFuPN-like cells from mouse ESC-derived cortical neurons.
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Affiliation(s)
- Tadashi Sunohara
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.,Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Asuka Morizane
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Satoshi Matsuura
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Susumu Miyamoto
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Jun Takahashi
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.,Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
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24
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MicroRNA Profiling During Neural Differentiation of Induced Pluripotent Stem Cells. Int J Mol Sci 2019; 20:ijms20153651. [PMID: 31357387 PMCID: PMC6696086 DOI: 10.3390/ijms20153651] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNA) play an essential role in the regulation of gene expression and influence signaling networks responsible for several cellular processes like differentiation of pluripotent stem cells. Despite several studies on the neurogenesis process, no global analysis of microRNA expression during differentiation of induced pluripotent stem cells (iPSC) to neuronal stem cells (NSC) has been done. Therefore, we compared the profile of microRNA expression in iPSC lines and in NSC lines derived from them, using microarray-based analysis. Two different protocols for NSC formation were used: Direct and two-step via neural rosette formation. We confirmed the new associations of previously described miRNAs in regulation of NSC differentiation from iPSC. We discovered upregulation of miR-10 family, miR-30 family and miR-9 family and downregulation of miR-302 and miR-515 family expression. Moreover, we showed that miR-10 family play a crucial role in the negative regulation of genes expression belonging to signaling pathways involved in neural differentiation: WNT signaling pathway, focal adhesion, and signaling pathways regulating pluripotency of stem cells.
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25
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Madelaine R, Notwell JH, Skariah G, Halluin C, Chen CC, Bejerano G, Mourrain P. A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human. Nucleic Acids Res 2019. [PMID: 29518216 PMCID: PMC5909433 DOI: 10.1093/nar/gky166] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Thousands of human disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding genome, but only a handful have been demonstrated to affect gene expression and human biology. We computationally identified risk-associated SNPs in deeply conserved non-exonic elements (CNEs) potentially contributing to 45 human diseases. We further demonstrated that human CNE1/rs17421627 associated with retinal vasculature defects showed transcriptional activity in the zebrafish retina, while introducing the risk-associated allele completely abolished CNE1 enhancer activity. Furthermore, deletion of CNE1 led to retinal vasculature defects and to a specific downregulation of microRNA-9, rather than MEF2C as predicted by the original genome-wide association studies. Consistent with these results, miR-9 depletion affects retinal vasculature formation, demonstrating MIR-9-2 as a critical gene underpinning the associated trait. Importantly, we validated that other CNEs act as transcriptional enhancers that can be disrupted by conserved non-coding SNPs. This study uncovers disease-associated non-coding mutations that are deeply conserved, providing a path for in vivo testing to reveal their cis-regulated genes and biological roles.
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Affiliation(s)
- Romain Madelaine
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Sleep Sciences and Medicine, Stanford, CA 94305, USA
| | | | - Gemini Skariah
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Sleep Sciences and Medicine, Stanford, CA 94305, USA
| | - Caroline Halluin
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Sleep Sciences and Medicine, Stanford, CA 94305, USA
| | | | - Gill Bejerano
- Department of Computer Science, Stanford, CA 94305, USA.,Department of Developmental Biology, Stanford, CA 94305, USA.,Division of Medical Genetics, Department of Pediatrics, Stanford, CA 94305, USA
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford Center for Sleep Sciences and Medicine, Stanford, CA 94305, USA.,INSERM 1024, Ecole Normale Supérieure Paris, 75005, France
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26
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Shu P, Wu C, Ruan X, Liu W, Hou L, Fu H, Wang M, Liu C, Zeng Y, Chen P, Yin B, Yuan J, Qiang B, Peng X, Zhong W. Opposing Gradients of MicroRNA Expression Temporally Pattern Layer Formation in the Developing Neocortex. Dev Cell 2019; 49:764-785.e4. [PMID: 31080058 DOI: 10.1016/j.devcel.2019.04.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 11/08/2018] [Accepted: 04/07/2019] [Indexed: 12/24/2022]
Abstract
The precisely timed generation of different neuronal types is a hallmark of development from invertebrates to vertebrates. In the developing mammalian neocortex, neural stem cells change competence over time to sequentially produce six layers of functionally distinct neurons. Here, we report that microRNAs (miRNAs) are dispensable for stem-cell self-renewal and neuron production but essential for timing neocortical layer formation and specifying laminar fates. Specifically, as neurogenesis progresses, stem cells reduce miR-128 expression and miR-9 activity but steadily increase let-7 expression, whereas neurons initially maintain the differences in miRNA expression present at birth. Moreover, miR-128, miR-9, and let-7 are functionally distinct; capable of specifying neurons for layer VI and layer V and layers IV, III, and II, respectively; and transiently altering their relative levels of expression can modulate stem-cell competence in a neurogenic-stage-specific manner to shift neuron production between earlier-born and later-born fates, partly by temporally regulating a neurogenesis program involving Hmga2.
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Affiliation(s)
- Pengcheng Shu
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Chao Wu
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Xiangbin Ruan
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Wei Liu
- Department of Anatomy and Histology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Lin Hou
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Hongye Fu
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Ming Wang
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Chang Liu
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yi Zeng
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Pan Chen
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Bin Yin
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Jiangang Yuan
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Boqin Qiang
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Xiaozhong Peng
- The State Key Laboratory of Medical Molecular Biology, Neuroscience Center, Medical Primates Research Center and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China; Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China.
| | - Weimin Zhong
- Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520, USA.
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27
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Kittelmann S, McGregor AP. Modulation and Evolution of Animal Development through microRNA Regulation of Gene Expression. Genes (Basel) 2019; 10:genes10040321. [PMID: 31027314 PMCID: PMC6523689 DOI: 10.3390/genes10040321] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/20/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022] Open
Abstract
microRNAs regulate gene expression by blocking the translation of mRNAs and/or promoting their degradation. They, therefore, play important roles in gene regulatory networks (GRNs) by modulating the expression levels of specific genes and can tune GRN outputs more broadly as part of feedback loops. These roles for microRNAs provide developmental buffering on one hand but can facilitate evolution of development on the other. Here we review how microRNAs can modulate GRNs during animal development as part of feedback loops and through their individual or combinatorial targeting of multiple different genes in the same network. We then explore how changes in the expression of microRNAs and consequently targets can facilitate changes in GRNs that alter development and lead to phenotypic evolution. The reviewed studies exemplify the key roles played by microRNAs in the regulation and evolution of gene expression during developmental processes in animals.
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Affiliation(s)
- Sebastian Kittelmann
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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28
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Bloch S, Thomas M, Colin I, Galant S, Machado E, Affaticati P, Jenett A, Yamamoto K. Mesencephalic origin of the inferior lobe in zebrafish. BMC Biol 2019; 17:22. [PMID: 30849972 PMCID: PMC6407210 DOI: 10.1186/s12915-019-0631-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/22/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Although the overall brain organization is shared in vertebrates, there are significant differences within subregions among different groups, notably between Sarcopterygii (lobe-finned fish) and Actinopterygii (ray-finned fish). Recent comparative studies focusing on the ventricular morphology have revealed a large diversity of the hypothalamus. Here, we study the development of the inferior lobe (IL), a prominent structure forming a bump on the ventral surface of the teleost brain. Based on its position, IL has been thought to be part of the hypothalamus (therefore forebrain). RESULTS Taking advantage of genetic lineage-tracing techniques in zebrafish, we reveal that cells originating from her5-expressing progenitors in the midbrain-hindbrain boundary (MHB) participate in the formation of a large part of the IL. 3D visualization demonstrated how IL develops in relation to the ventricular system. We found that IL is constituted by two developmental components: the periventricular zone of hypothalamic origin and the external zone of mesencephalic origin. The mesencephalic external zone grows progressively until adulthood by adding new cells throughout development. CONCLUSION Our results disprove a homology between the IL and the mammalian lateral hypothalamus. We suggest that the IL is likely to be involved in multimodal sensory integration rather than feeding motivation. The teleost brain is not a simpler version of the mammalian brain, and our study highlights the evolutionary plasticity of the brain which gives rise to novel structures.
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Affiliation(s)
- Solal Bloch
- Paris-Saclay Institute of Neuroscience (Neuro-PSI), CNRS UMR9197, Univ Paris Sud, Université Paris-Saclay, CNRS Bâtiment 5, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Manon Thomas
- Paris-Saclay Institute of Neuroscience (Neuro-PSI), CNRS UMR9197, Univ Paris Sud, Université Paris-Saclay, CNRS Bâtiment 5, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
- Present address: Plateau de phénotypage TEFOR, LPGP-INRA UR1037, 35042, Rennes, France
| | - Ingrid Colin
- Paris-Saclay Institute of Neuroscience (Neuro-PSI), CNRS UMR9197, Univ Paris Sud, Université Paris-Saclay, CNRS Bâtiment 5, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Sonya Galant
- Paris-Saclay Institute of Neuroscience (Neuro-PSI), CNRS UMR9197, Univ Paris Sud, Université Paris-Saclay, CNRS Bâtiment 5, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Elodie Machado
- TEFOR Paris-Saclay, CNRS UMS2010, INRA UMS1451, Univ Paris Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Pierre Affaticati
- TEFOR Paris-Saclay, CNRS UMS2010, INRA UMS1451, Univ Paris Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Arnim Jenett
- TEFOR Paris-Saclay, CNRS UMS2010, INRA UMS1451, Univ Paris Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Kei Yamamoto
- Paris-Saclay Institute of Neuroscience (Neuro-PSI), CNRS UMR9197, Univ Paris Sud, Université Paris-Saclay, CNRS Bâtiment 5, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France.
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29
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Ma Q, Zhang L, Pearce WJ. MicroRNAs in brain development and cerebrovascular pathophysiology. Am J Physiol Cell Physiol 2019; 317:C3-C19. [PMID: 30840494 DOI: 10.1152/ajpcell.00022.2019] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
MicroRNAs (miRNAs) are a class of highly conserved non-coding RNAs with 21-25 nucleotides in length and play an important role in regulating gene expression at the posttranscriptional level via base-paring with complementary sequences of the 3'-untranslated region of the target gene mRNA, leading to either transcript degradation or translation inhibition. Brain-enriched miRNAs act as versatile regulators of brain development and function, including neural lineage and subtype determination, neurogenesis, synapse formation and plasticity, neural stem cell proliferation and differentiation, and responses to insults. Herein, we summarize the current knowledge regarding the role of miRNAs in brain development and cerebrovascular pathophysiology. We review recent progress of the miRNA-based mechanisms in neuronal and cerebrovascular development as well as their role in hypoxic-ischemic brain injury. These findings hold great promise, not just for deeper understanding of basic brain biology but also for building new therapeutic strategies for prevention and treatment of pathologies such as cerebral ischemia.
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Affiliation(s)
- Qingyi Ma
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine , Loma Linda, California
| | - Lubo Zhang
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine , Loma Linda, California
| | - William J Pearce
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine , Loma Linda, California
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30
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Kizil C, Bhattarai P. Is Alzheimer's Also a Stem Cell Disease? - The Zebrafish Perspective. Front Cell Dev Biol 2018; 6:159. [PMID: 30533414 PMCID: PMC6265475 DOI: 10.3389/fcell.2018.00159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/06/2018] [Indexed: 12/22/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease and is the leading form of dementia. AD entails chronic inflammation, impaired synaptic integrity and reduced neurogenesis. The clinical and molecular onsets of the disease do not temporally overlap and the initiation phase of the cellular changes might start with a complex causativeness between chronic inflammation, reduced neural stem cell plasticity and neurogenesis. Although the immune and neuronal aspects in AD are well studied, the neural stem cell-related features are far less investigated. An intriguing question is, therefore, whether a stem cell can ever be made proliferative and neurogenic during the prevalent AD in the brain. Recent findings affirm this hypothesis and thus a plausible way to circumvent the AD phenotypes could be to mobilize the endogenous stem cells by enhancing their proliferative and neurogenic capacity as well as to provide the newborn neurons the potential to survive and integrate into the existing circuitry. To address these questions, zebrafish offers unprecedented information and tools, which can be effectively translated into mammalian experimental systems.
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Affiliation(s)
- Caghan Kizil
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence, Technische Universität Dresden, Dresden, Germany
| | - Prabesh Bhattarai
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence, Technische Universität Dresden, Dresden, Germany
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31
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Upregulation of MicroRNA miR-9 Is Associated with Microcephaly and Zika Virus Infection in Mice. Mol Neurobiol 2018; 56:4072-4085. [DOI: 10.1007/s12035-018-1358-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/19/2018] [Indexed: 12/31/2022]
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32
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Vieira MS, Santos AK, Vasconcellos R, Goulart VAM, Parreira RC, Kihara AH, Ulrich H, Resende RR. Neural stem cell differentiation into mature neurons: Mechanisms of regulation and biotechnological applications. Biotechnol Adv 2018; 36:1946-1970. [PMID: 30077716 DOI: 10.1016/j.biotechadv.2018.08.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023]
Abstract
The abilities of stem cells to self-renew and form different mature cells expand the possibilities of applications in cell-based therapies such as tissue recomposition in regenerative medicine, drug screening, and treatment of neurodegenerative diseases. In addition to stem cells found in the embryo, various adult organs and tissues have niches of stem cells in an undifferentiated state. In the central nervous system of adult mammals, neurogenesis occurs in two regions: the subventricular zone and the dentate gyrus in the hippocampus. The generation of the different neural lines originates in adult neural stem cells that can self-renew or differentiate into astrocytes, oligodendrocytes, or neurons in response to specific stimuli. The regulation of the fate of neural stem cells is a finely controlled process relying on a complex regulatory network that extends from the epigenetic to the translational level and involves extracellular matrix components. Thus, a better understanding of the mechanisms underlying how the process of neurogenesis is induced, regulated, and maintained will provide elues for development of novel for strategies for neurodegenerative therapies. In this review, we focus on describing the mechanisms underlying the regulation of the neuronal differentiation process by transcription factors, microRNAs, and extracellular matrix components.
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Affiliation(s)
- Mariana S Vieira
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Instituto Nanocell, Divinopólis, MG, Brazil
| | - Anderson K Santos
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rebecca Vasconcellos
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Instituto Nanocell, Divinopólis, MG, Brazil
| | - Vânia A M Goulart
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ricardo C Parreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Instituto Nanocell, Divinopólis, MG, Brazil
| | - Alexandre H Kihara
- Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Henning Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil.
| | - Rodrigo R Resende
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Instituto Nanocell, Divinopólis, MG, Brazil.
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33
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Chen W, Zhang L, Shi C, Ren G, Kong Q, Qin C. Comprehensive analysis of hippocampal miRNAomes in humans and mice. Epigenomics 2018; 10:813-828. [PMID: 29979109 DOI: 10.2217/epi-2017-0161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM This study aims to explore the similarity and difference of hippocampal miRNAomes between humans and mice. MATERIALS & METHODS A systematic comparison of the miRNAomes between healthy human and mouse hippocampi was performed using high-throughput sequencing followed by bioinformatic analyses. RESULTS A novel miRNA termed novel-21-5p and a human-specific miR-656-3p were identified in human hippocampi, which were expressed ubiquitously and predicted to be associated with neural activities. Compared with mouse, abundantly expressed miRNAs in human hippocampus were notably enriched in pathways pertaining to neural activities, such as neurotrophin TRK receptor signaling pathway, axon guidance and synaptic transmission. Expression pattern of orthologous miRNAs between human and mouse hippocampi was conserved. Meanwhile, the expression conservation was positively correlated with the sequence conservation. CONCLUSION Hippocampal miRNAomes between humans and mice were overall comparable; the differences in expression or function across species should be considered when constructing mouse models.
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Affiliation(s)
- Wei Chen
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China.,Experimental & Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China
| | - Ling Zhang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China
| | - Changhua Shi
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China
| | - Guanhua Ren
- Library of Peking University First Hospital, Beijing, PR China
| | - Qi Kong
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China
| | - Chuan Qin
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Centre, Peking Union Medical Collage (PUMC), Beijing, PR China
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34
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Naldi A, Hernandez C, Abou-Jaoudé W, Monteiro PT, Chaouiya C, Thieffry D. Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0. Front Physiol 2018; 9:646. [PMID: 29971008 PMCID: PMC6018412 DOI: 10.3389/fphys.2018.00646] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/11/2018] [Indexed: 11/13/2022] Open
Abstract
The logical formalism is well adapted to model large cellular networks, in particular when detailed kinetic data are scarce. This tutorial focuses on this well-established qualitative framework. Relying on GINsim (release 3.0), a software implementing this formalism, we guide the reader step by step toward the definition, the analysis and the simulation of a four-node model of the mammalian p53-Mdm2 network.
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Affiliation(s)
- Aurélien Naldi
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Sante et de la Recherche Médicale, PSL Université, Paris, France
| | - Céline Hernandez
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Sante et de la Recherche Médicale, PSL Université, Paris, France
| | - Wassim Abou-Jaoudé
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Sante et de la Recherche Médicale, PSL Université, Paris, France
| | - Pedro T. Monteiro
- INESC-ID, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | | | - Denis Thieffry
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Sante et de la Recherche Médicale, PSL Université, Paris, France
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35
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Zhang Y, Li L, Yu C, Senyuk V, Li F, Quigley JG, Zhu T, Qian Z. miR-9 upregulation leads to inhibition of erythropoiesis by repressing FoxO3. Sci Rep 2018; 8:6519. [PMID: 29695725 PMCID: PMC5916915 DOI: 10.1038/s41598-018-24628-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/04/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are emerging as critical regulators of normal and malignant hematopoiesis. In previous studies of acute myeloid leukemia miR-9 overexpression was commonly observed. Here, we show that ectopic expression of miR-9 in vitro and in vivo significantly blocks differentiation of erythroid progenitor cells with an increase in reactive oxygen species (ROS) production. Consistent with this observation, ROS scavenging enzymes, including superoxide dismutase (Sod2), Catalase (Cat), and glutathine peroxidase (Gpx1), are down-regulated by miR-9. In addition, miR-9 suppresses expression of the erythroid transcriptional regulator FoxO3, and its down-stream targets Btg1 and Cited 2 in erythroid progenitor cells, while expression of a constitutively active form of FoxO3 (FoxO3-3A) reverses miR-9-induced suppression of erythroid differentiation, and inhibits miR-9-induced ROS production. Thus, our findings indicate that aberrant expression of miR-9 blocks erythropoiesis by deregulating FoxO3-mediated pathways, which may contribute to the ineffective erythropoiesis observed in patients with hematological malignancies.
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Affiliation(s)
- Yunyuan Zhang
- Department of Clinical laboratory, The Affiliated Hospital of Qingdao University Medical College, Qingdao, 266003, China
- Department of Medicine and Cancer Research Center, University of Illinois Hospital and Health Sciences System, Chicago, IL, USA
| | - Liping Li
- Department of Medicine and Cancer Research Center, University of Illinois Hospital and Health Sciences System, Chicago, IL, USA
- Fudan University ZhongShan Hospital, Shanghai, China
| | - Chunjie Yu
- Department of Medicine and Cancer Research Center, University of Illinois Hospital and Health Sciences System, Chicago, IL, USA
| | - Vitalyi Senyuk
- Department of Medicine and Cancer Research Center, University of Illinois Hospital and Health Sciences System, Chicago, IL, USA
| | - Fuxing Li
- Department of Medicine and Cancer Research Center, University of Illinois Hospital and Health Sciences System, Chicago, IL, USA
- Department of Pediatrics, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - John G Quigley
- Department of Medicine and Cancer Research Center, University of Illinois Hospital and Health Sciences System, Chicago, IL, USA
| | - Tongyu Zhu
- Fudan University ZhongShan Hospital, Shanghai, China
| | - Zhijian Qian
- Department of Medicine and Cancer Research Center, University of Illinois Hospital and Health Sciences System, Chicago, IL, USA.
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36
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Madelaine R, Sloan SA, Huber N, Notwell JH, Leung LC, Skariah G, Halluin C, Paşca SP, Bejerano G, Krasnow MA, Barres BA, Mourrain P. MicroRNA-9 Couples Brain Neurogenesis and Angiogenesis. Cell Rep 2018; 20:1533-1542. [PMID: 28813666 DOI: 10.1016/j.celrep.2017.07.051] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/30/2017] [Accepted: 07/19/2017] [Indexed: 12/22/2022] Open
Abstract
In the developing brain, neurons expressing VEGF-A and blood vessels grow in close apposition, but many of the molecular pathways regulating neuronal VEGF-A and neurovascular system development remain to be deciphered. Here, we show that miR-9 links neurogenesis and angiogenesis through the formation of neurons expressing VEGF-A. We found that miR-9 directly targets the transcription factors TLX and ONECUTs to regulate VEGF-A expression. miR-9 inhibition leads to increased TLX and ONECUT expression, resulting in VEGF-A overexpression. This untimely increase of neuronal VEGF-A signal leads to the thickening of blood vessels at the expense of the normal formation of the neurovascular network in the brain and retina. Thus, this conserved transcriptional cascade is critical for proper brain development in vertebrates. Because of this dual role on neural stem cell proliferation and angiogenesis, miR-9 and its downstream targets are promising factors for cellular regenerative therapy following stroke and for brain tumor treatment.
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Affiliation(s)
- Romain Madelaine
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Steven A Sloan
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Nina Huber
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - James H Notwell
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Louis C Leung
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Gemini Skariah
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Caroline Halluin
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Sergiu P Paşca
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Mark A Krasnow
- HHMI and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Ben A Barres
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Philippe Mourrain
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; INSERM 1024, École Normale Supérieure, Paris 75005, France.
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37
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Sengupta D, Kar S. Alteration in MicroRNA Expression Governs the Nature and Timing of Cellular Fate Commitment. ACS Chem Neurosci 2018; 9:725-737. [PMID: 29181975 DOI: 10.1021/acschemneuro.7b00423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the central nervous system, the expression level of transcriptional repressor Hes1 (hairy and enhancer of split-1) tightly controls the alternative cell fate commitment during differentiation as well as the time required for such cellular transitions. A microRNA, miR-9, that interacts with Hes1 in a mutually antagonistic manner, influences both the process of lineage specification and timing of differentiation significantly, but the impact of the miR-9 in guiding these events still remains poorly understood. Here, we proposed a stochastic mathematical model of the miR-9/Hes1 double-negative feedback interaction network that at the outset shows how alternative cell fate such as quiescence, progenitor, and neuronal states can be accomplished through fine-tuning the Hes1 dynamics by altering the expression level of miR-9. The model simulations further foretell a correlated variation of the period of oscillation of Hes1, and the time delay observed between Hes1 mRNA and protein as the transcription rate of miR-9 increases during the neural progenitor state attainment. Importantly, the model simulations aided by the systematic sensitivity analysis predict that the timing of differentiation to the neuronal state crucially depends on the negative regulators (miR-9 and Hes6) of the Hes1. Our results indicate that miR-9/Hes1 interaction network can be effectively exploited for an efficient and well-timed neuronal transformation.
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Affiliation(s)
- Dola Sengupta
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
| | - Sandip Kar
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
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38
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Nonprotein-coding RNAs in Fetal Alcohol Spectrum Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:299-342. [PMID: 29933954 DOI: 10.1016/bs.pmbts.2017.11.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Early developmental exposure to ethanol, a known teratogen, can result in a range of neurodevelopmental disorders, collectively referred to as Fetal Alcohol Spectrum Disorders (FASDs). Changes in the environment, including exposure to teratogens, can result in long term alterations to the epigenetic landscape of a cell, thereby altering gene expression. Noncoding RNAs (ncRNAs) can affect transcription and translation of networks of genes. ncRNAs are dynamically expressed during development and have been identified as a target of alcohol. ncRNAs therefore make for attractive targets for novel therapeutics to address the developmental deficits associated with FASDs.
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39
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Alwin Prem Anand A, Huber C, Asnet Mary J, Gallus N, Leucht C, Klafke R, Hirt B, Wizenmann A. Expression and function of microRNA-9 in the mid-hindbrain area of embryonic chick. BMC DEVELOPMENTAL BIOLOGY 2018; 18:3. [PMID: 29471810 PMCID: PMC5824543 DOI: 10.1186/s12861-017-0159-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 11/27/2017] [Indexed: 12/21/2022]
Abstract
Background MiR-9 is a small non-coding RNA that is highly conserved between species and primarily expressed in the central nervous system (CNS). It is known to influence proliferation and neuronal differentiation in the brain and spinal cord of different vertebrates. Different studies have pointed to regional and species-specific differences in the response of neural progenitors to miR-9. Methods In ovo and ex ovo electroporation was used to overexpress or reduce miR-9 followed by mRNA in situ hybridisation and immunofluorescent stainings to evaluate miR- expression and the effect of changed miR-9 expression. Results We have investigated the expression and function of miR-9 during early development of the mid-hindbrain region (MH) in chick. Our analysis reveals a closer relationship of chick miR-9 to mammalian miR-9 than to fish and a dynamic expression pattern in the chick neural tube. Early in development, miR-9 is diffusely expressed in the entire brain, bar the forebrain, and it becomes more restricted to specific areas of the CNS at later stages. MiR-9 overexpression at HH9–10 results in a reduction of FGF8 expression and premature neuronal differentiation in the mid-hindbrain boundary (MHB). Within the midbrain miR-9 does not cause premature neuronal differentiation it rather reduces proliferation in the midbrain. Conclusion Our findings indicate that miR-9 has regional specific effects in the developing mid-hindbrain region with a divergence of response of regional progenitors. Electronic supplementary material The online version of this article (10.1186/s12861-017-0159-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A Alwin Prem Anand
- Institute of Clinical Anatomy and Cell Analysis, University of Tuebingen, Oesterbergstrasse 3, D-72074, Tuebingen, Germany
| | - Carola Huber
- Institute of Clinical Anatomy and Cell Analysis, University of Tuebingen, Oesterbergstrasse 3, D-72074, Tuebingen, Germany.,Robert-Bosch-Krankenhaus, Auerbachstraße 110, 70376, Stuttgart, Germany
| | - John Asnet Mary
- Department of Zoology, Fatima College, Madurai, Tamilnadu, 625018, India
| | - Nancy Gallus
- Institute of Clinical Anatomy and Cell Analysis, University of Tuebingen, Oesterbergstrasse 3, D-72074, Tuebingen, Germany.,Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Christoph Leucht
- Institute of Developmental Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Ruth Klafke
- Institute of Developmental Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Bernhard Hirt
- Institute of Clinical Anatomy and Cell Analysis, University of Tuebingen, Oesterbergstrasse 3, D-72074, Tuebingen, Germany
| | - Andrea Wizenmann
- Institute of Clinical Anatomy and Cell Analysis, University of Tuebingen, Oesterbergstrasse 3, D-72074, Tuebingen, Germany.
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40
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Identification of microRNAs differentially expressed in glioblastoma stem-like cells and their association with patient survival. Sci Rep 2018; 8:2836. [PMID: 29434344 PMCID: PMC5809429 DOI: 10.1038/s41598-018-20929-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 01/25/2018] [Indexed: 01/29/2023] Open
Abstract
Glioblastoma stem-like cells (GSCs) are critical for the aggressiveness and progression of glioblastoma (GBM) and contribute to its resistance to adjuvant treatment. MicroRNAs (miRNAs) are small, non-coding RNAs controlling gene expression at the post-transcriptional level, which are known to be important regulators of the stem-like features. Moreover, miRNAs have been previously proved to be promising diagnostic biomarkers in several cancers including GBM. Using global expression analysis of miRNAs in 10 paired in-vitro as well as in-vivo characterized primary GSC and non-stem glioblastoma cultures, we identified a miRNA signature associated with the stem-like phenotype in GBM. 51 most deregulated miRNAs classified the cell cultures into GSC and non-stem cell clusters and identified a subgroup of GSC cultures with more pronounced stem-cell characteristics. The importance of the identified miRNA signature was further supported by demonstrating that a Risk Score based on the expression of seven miRNAs overexpressed in GSC predicted overall survival in GBM patients in the TCGA dataset independently of the IDH1 status. In summary, we identified miRNAs differentially expressed in GSCs and described their association with GBM patient survival. We propose that these miRNAs participate on GSC features and could represent helpful prognostic markers and potential therapeutic targets in GBM.
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Abstract
The mouse embryo forebrain is the most commonly employed system for studying mammalian neurogenesis during development. However, the highly folded forebrain neuroepithelium is not amenable to wholemount analysis to examine organ-wide neurogenesis patterns. Moreover, defining the mechanisms of forebrain neurogenesis is not necessarily predictive of neurogenesis in other parts of the brain; for example, due to the presence of forebrain-specific progenitor subtypes. The mouse hindbrain provides an alternative model for studying embryonic neurogenesis that is amenable to wholemount analysis, as well as tissue sections to observe the spatiotemporal distribution and behavior of neural progenitors. Moreover, it is easily dissected for other downstream applications, such as cell isolation or molecular biology analysis. As the mouse hindbrain can be readily analyzed in the vast number of cell lineage reporter and mutant mouse strains that have become available, it offers a powerful model for studying the cellular and molecular mechanisms of developmental neurogenesis in a mammalian organism. Here, we present a simple and quick method to use the mouse embryo hindbrain for analyzing mammalian neural progenitor cell (NPC) behavior in wholemount preparations and tissue sections.
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Kizil C. Mechanisms of Pathology-Induced Neural Stem Cell Plasticity and Neural Regeneration in Adult Zebrafish Brain. CURRENT PATHOBIOLOGY REPORTS 2018; 6:71-77. [PMID: 29938129 PMCID: PMC5978899 DOI: 10.1007/s40139-018-0158-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Purpose of the Review The purpose of this study is to review the current knowledge on the damage-induced molecular programs that underlie the regenerative ability in zebrafish brain. Recent Findings Neural stem cells are the reservoir for new neurons during development and regeneration of the vertebrate brains. Pathological conditions such as neurodegenerative diseases hamper neural stem cell plasticity and neurogenic outcome in humans, whereas adult zebrafish brain can enhance proliferation and neurogenic capacity of its neural stem cells despite the incipient pathology. Evidence suggests that zebrafish uses damage-induced molecular programs to enable neural stem cells to efficiently initiate regeneration. Since this aptitude may be harnessed for regenerative therapies in human brain, understanding the molecular programs regulating neural stem cell proliferation and quiescence in zebrafish is of utmost importance for clinical efforts. Summary Specific molecular programs that are different than those in the homeostatic conditions regulate adult zebrafish neural stem cell plasticity and the regenerative capacity after injury and neurodegeneration. These programs can serve as candidates for stem cell-based regenerative therapies in humans.
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Affiliation(s)
- Caghan Kizil
- 1German Centre for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Arnoldstrasse 18, 01307 Dresden, Germany.,2Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Fetscherstrasse 105, 01307 Dresden, Germany
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Zebrafish Zic Genes Mediate Developmental Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1046:157-177. [PMID: 29442322 DOI: 10.1007/978-981-10-7311-3_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The introduction of genomics into the field of developmental biology led to a vast expansion of knowledge about developmental genes and signaling mechanisms they are involved in. Unlike mammals, the zebrafish features seven Zic genes. This provides an interesting insight into Zic gene evolution. In addition, an unprecedented bioimaging capability of semitransparent zebrafish embryos turns to be a crucial factor in medium- to large-scale analysis of the activity of potential regulatory elements. The Zic family of zinc finger proteins plays an important, relatively well-established, role in the regulation of stem cells and neural development and, in particular, during neural fate commitment and determination. At the same time, some Zic genes are expressed in mesodermal lineages, and their deficiency causes a number of developmental defects in axis formation, establishing body symmetry and cardiac morphogenesis. In stem cells, Zic genes are required to maintain pluripotency by binding to the proximal promoters of pluripotency genes (Oct4, Nanog, Sox2, etc.). During embryogenesis, the dynamic nature of Zic transcriptional regulation is manifested by the interaction of these factors with distal enhancers and other regulatory elements associated with the control of gene transcription and, in particular, with the Nodal and Wnt signaling pathways that play a role in establishing basic organization of the vertebrate body. Zic transcription factors may regulate development through acting alone as well as in combination with other transcription factors. This is achieved due to Zic binding to sites adjacent to the binding sites of other transcription factors, including Gli. This probably leads to the formation of multi-transcription factor complexes associated with enhancers.
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Katz S, Cussigh D, Urbán N, Blomfield I, Guillemot F, Bally-Cuif L, Coolen M. A Nuclear Role for miR-9 and Argonaute Proteins in Balancing Quiescent and Activated Neural Stem Cell States. Cell Rep 2017; 17:1383-1398. [PMID: 27783951 PMCID: PMC5098119 DOI: 10.1016/j.celrep.2016.09.088] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/07/2016] [Accepted: 09/26/2016] [Indexed: 01/08/2023] Open
Abstract
Throughout life, adult neural stem cells (NSCs) produce new neurons and glia that contribute to crucial brain functions. Quiescence is an essential protective feature of adult NSCs; however, the establishment and maintenance of this state remain poorly understood. We demonstrate that in the adult zebrafish pallium, the brain-enriched miR-9 is expressed exclusively in a subset of quiescent NSCs, highlighting a heterogeneity within these cells, and is necessary to maintain NSC quiescence. Strikingly, miR-9, along with Argonaute proteins (Agos), is localized to the nucleus of quiescent NSCs, and manipulating their nuclear/cytoplasmic ratio impacts quiescence. Mechanistically, miR-9 permits efficient Notch signaling to promote quiescence, and we identify the RISC protein TNRC6 as a mediator of miR-9/Agos nuclear localization in vivo. We propose a conserved non-canonical role for nuclear miR-9/Agos in controlling the balance between NSC quiescence and activation, a key step in maintaining adult germinal pools.
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Affiliation(s)
- Shauna Katz
- Zebrafish Neurogenetics Group, Paris-Saclay Institute of Neuroscience (Neuro-PSI), UMR 9197, CNRS-University Paris-Sud, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Delphine Cussigh
- Zebrafish Neurogenetics Group, Paris-Saclay Institute of Neuroscience (Neuro-PSI), UMR 9197, CNRS-University Paris-Sud, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France; Department of Developmental and Stem Cell Biology, Institut Pasteur and CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Noelia Urbán
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Isabelle Blomfield
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - François Guillemot
- Mill Hill Laboratory, The Francis Crick Institute, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Laure Bally-Cuif
- Zebrafish Neurogenetics Group, Paris-Saclay Institute of Neuroscience (Neuro-PSI), UMR 9197, CNRS-University Paris-Sud, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France; Department of Developmental and Stem Cell Biology, Institut Pasteur and CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France.
| | - Marion Coolen
- Zebrafish Neurogenetics Group, Paris-Saclay Institute of Neuroscience (Neuro-PSI), UMR 9197, CNRS-University Paris-Sud, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France; Department of Developmental and Stem Cell Biology, Institut Pasteur and CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France.
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Saraiva C, Esteves M, Bernardino L. MicroRNA: Basic concepts and implications for regeneration and repair of neurodegenerative diseases. Biochem Pharmacol 2017; 141:118-131. [DOI: 10.1016/j.bcp.2017.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/07/2017] [Indexed: 12/25/2022]
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Rajman M, Schratt G. MicroRNAs in neural development: from master regulators to fine-tuners. Development 2017; 144:2310-2322. [DOI: 10.1242/dev.144337] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The proper formation and function of neuronal networks is required for cognition and behavior. Indeed, pathophysiological states that disrupt neuronal networks can lead to neurodevelopmental disorders such as autism, schizophrenia or intellectual disability. It is well-established that transcriptional programs play major roles in neural circuit development. However, in recent years, post-transcriptional control of gene expression has emerged as an additional, and probably equally important, regulatory layer. In particular, it has been shown that microRNAs (miRNAs), an abundant class of small regulatory RNAs, can regulate neuronal circuit development, maturation and function by controlling, for example, local mRNA translation. It is also becoming clear that miRNAs are frequently dysregulated in neurodevelopmental disorders, suggesting a role for miRNAs in the etiology and/or maintenance of neurological disease states. Here, we provide an overview of the most prominent regulatory miRNAs that control neural development, highlighting how they act as ‘master regulators’ or ‘fine-tuners’ of gene expression, depending on context, to influence processes such as cell fate determination, cell migration, neuronal polarization and synapse formation.
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Affiliation(s)
- Marek Rajman
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Gerhard Schratt
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg 35043, Germany
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Abstract
Notch signaling is evolutionarily conserved from Drosophila to human. It plays critical roles in neural stem cell maintenance and neurogenesis in the embryonic brain as well as in the adult brain. Notch functions greatly depend on careful regulation and cross-talk with other regulatory mechanisms. Deregulation of Notch signaling is involved in many neurodegenerative diseases and brain disorders. Here, we summarize the fundamental role of Notch in neuronal development and specification and discuss how epigenetic regulation and pathway cross-talk contribute to Notch function. In addition, we cover aberrant alterations of Notch signaling in the diseased brain. The aim of this review is to provide an insight into how Notch signaling works in different contexts to control neurogenesis and its potential effects in diagnoses and therapies of neurodegeneration, brain tumors and disorders.
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Affiliation(s)
- Runrui Zhang
- Embryology and Stem Cell Biology, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Anna Engler
- Embryology and Stem Cell Biology, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Verdon Taylor
- Embryology and Stem Cell Biology, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland.
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Li YW, Chiang KY, Li YH, Wu SY, Liu W, Lin CR, Wu JL. MiR-145 mediates zebrafish hepatic outgrowth through progranulin A signaling. PLoS One 2017; 12:e0177887. [PMID: 28531199 PMCID: PMC5439702 DOI: 10.1371/journal.pone.0177887] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/04/2017] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRs) are mRNA-regulatory molecules that fine-tune gene expression and modulate both processes of development and tumorigenesis. Our previous studies identified progranulin A (GrnA) as a growth factor which induces zebrafish hepatic outgrowth through MET signaling. We also found that miR-145 is one of potential fine-tuning regulators of GrnA involved in embryonic hepatic outgrowth. The low level of miR-145 seen in hepatocarinogenesis has been shown to promote pathological liver growth. However, little is known about the regulatory mechanism of miR-145 in embryonic liver development. In this study, we demonstrate a significant decrease in miR-145 expression during hepatogenesis. We modulate miR-145 expression in zebrafish embryos by injection with a miR-145 mimic or a miR-145 hairpin inhibitor. Altered embryonic liver outgrowth is observed in response to miR-145 expression modulation. We also confirm a critical role of miR-145 in hepatic outgrowth by using whole-mount in situ hybridization. Loss of miR-145 expression in embryos results in hepatic cell proliferation, and vice versa. Furthermore, we demonstrate that GrnA is a target of miR-145 and GrnA-induced MET signaling is also regulated by miR-145 as determined by luciferase reporter assay and gene expression analysis, respectively. In addition, co-injection of GrnA mRNA with miR-145 mimic or MO-GrnA with miR-145 inhibitor restores the liver defects caused by dysregulation of miR-145 expression. In conclusion, our findings suggest an important role of miR-145 in regulating GrnA-dependent hepatic outgrowth in zebrafish embryonic development.
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Affiliation(s)
- Ya-Wen Li
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Keng-Yu Chiang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Department of Life science, National Taiwan University, Taipei, Taiwan
| | - Yen-Hsing Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Sung-Yu Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Wangta Liu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Lipid Science and Aging Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Ray Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jen-Leih Wu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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Roese-Koerner B, Stappert L, Brüstle O. Notch/Hes signaling and miR-9 engage in complex feedback interactions controlling neural progenitor cell proliferation and differentiation. NEUROGENESIS 2017; 4:e1313647. [PMID: 28573150 PMCID: PMC5443189 DOI: 10.1080/23262133.2017.1313647] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/27/2016] [Accepted: 01/18/2017] [Indexed: 02/04/2023]
Abstract
Canonical Notch signaling has diverse functions during nervous system development and is critical for neural progenitor self-renewal, timing of differentiation and specification of various cell fates. A key feature of Notch-mediated self-renewal is its fluctuating activity within the neural progenitor cell population and the oscillatory expression pattern of the Notch effector Hes1 and its target genes. A negative feedback loop between Hes1 and neurogenic microRNA miR-9 was found to be part of this oscillatory clock. In a recent study we discovered that miR-9 expression is further modulated by direct binding of the Notch intracellular domain/RBPj transcriptional complex to the miR-9_2 promoter. In turn, miR-9 not only targets Hes1 but also Notch2 to attenuate Notch signaling and promote neuronal differentiation. Here, we discuss how the two interwoven feedback loops may provide an additional fail-save mechanism to control proliferation and differentiation within the neural progenitor cell population. Furthermore, we explore potential implications of miR-9-mediated regulation of Notch/Hes1 signaling with regard to neural progenitor homeostasis, patterning, timing of differentiation and tumor formation.
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Affiliation(s)
- Beate Roese-Koerner
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn Medical Faculty, Bonn, Germany
| | - Laura Stappert
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn Medical Faculty, Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, LIFE & BRAIN Center, University of Bonn Medical Faculty, Bonn, Germany
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50
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Nowak JS, Hobor F, Downie Ruiz Velasco A, Choudhury NR, Heikel G, Kerr A, Ramos A, Michlewski G. Lin28a uses distinct mechanisms of binding to RNA and affects miRNA levels positively and negatively. RNA (NEW YORK, N.Y.) 2017; 23:317-332. [PMID: 27881476 PMCID: PMC5311490 DOI: 10.1261/rna.059196.116] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/22/2016] [Indexed: 05/29/2023]
Abstract
Lin28a inhibits the biogenesis of let-7 miRNAs by triggering the polyuridylation and degradation of their precursors by terminal uridylyltransferases TUT4/7 and 3'-5' exoribonuclease Dis3l2, respectively. Previously, we showed that Lin28a also controls the production of neuro-specific miRNA-9 via a polyuridylation-independent mechanism. Here we reveal that the sequences and structural characteristics of pre-let-7 and pre-miRNA-9 are eliciting two distinct modes of binding to Lin28a. We present evidence that Dis3l2 controls miRNA-9 production. Finally, we show that the constitutive expression of untagged Lin28a during neuronal differentiation in vitro positively and negatively affects numerous other miRNAs. Our findings shed light on the role of Lin28a in differentiating cells and on the ways in which one RNA-binding protein can perform multiple roles in the regulation of RNA processing.
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Affiliation(s)
- Jakub Stanislaw Nowak
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Fruzsina Hobor
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6XA, United Kingdom
| | | | - Nila Roy Choudhury
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Gregory Heikel
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Alastair Kerr
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Andres Ramos
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6XA, United Kingdom
| | - Gracjan Michlewski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
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