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Li C, Liu H, Zhang T, Zhang Y. Stability and Bifurcation Analysis of a Diffusive miR-9/Hes1 Network With Time Delay. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1870-1880. [PMID: 33417562 DOI: 10.1109/tcbb.2021.3050006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In this paper, a model of miR-9/Hes1 interaction network involving one time delay and diffusion effect under the Neumann boundary conditions is studied. First of all, the stability of the positive equilibrium and the existence of local Hopf bifurcation and Turing-Hopf bifurcation are investigated by analyzing the associated characteristic equation. Second, a algorithm for determining the direction, stability and period of the corresponding bifurcating periodic solutions is presented. The obtained results suggest that the quiescent progenitors (high steady-state Hes1) can be easily excited into oscillation by time delay whereas the differentiated state (low steady-state Hes1) is basically unaffected, and the integrated effect of delay and diffusion can induce the occurrence of spatially inhomogeneous patterns. More importantly, spatially homogeneous/inhomogeneous periodic solutions can exist simultaneously when the diffusion coefficients of Hes1 mRNA and Hes1 protein are appropriately small, conversely, there is only spatially homogeneous periodic solutions. Intriguingly, both temporal patterns and spatial-temporal patterns show that time delay can prompt Hes1 protein to shift from the high concentration state to the low concentration one ("ON" → "OFF"), where Hes1 protein shows low level whereas miR-9 shows high level. Finally, some numerical examples are presented to verify and visualize theoretical results.
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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: 3] [Impact Index Per Article: 0.5] [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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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: 0.9] [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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Ward NJ, Green D, Higgins J, Dalmay T, Münsterberg A, Moxon S, Wheeler GN. microRNAs associated with early neural crest development in Xenopus laevis. BMC Genomics 2018; 19:59. [PMID: 29347911 PMCID: PMC5774138 DOI: 10.1186/s12864-018-4436-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. NC cells arise within the dorsal neural tube where they undergo an epithelial to mesenchymal transition in order to migrate and differentiate throughout the developing embryo. The derivative cell types give rise to multiple tissues, including the craniofacial skeleton, peripheral nervous system and skin pigment cells. Several well-studied gene regulatory networks underpin NC development, which when disrupted can lead to various neurocristopathies such as craniofrontonasal dysplasia, DiGeorge syndrome and some forms of cancer. Small RNAs, such as microRNAs (miRNAs) are non-coding RNA molecules important in post-transcriptional gene silencing and critical for cellular regulation of gene expression. RESULTS To uncover novel small RNAs in NC development we used high definition adapters and next generation sequencing of libraries derived from ectodermal explants of Xenopus laevis embryos induced to form neural and NC tissue. Ectodermal and blastula animal pole (blastula) stage tissues were also sequenced. We show that miR-427 is highly abundant in all four tissue types though in an isoform specific manner and we define a set of 11 miRNAs that are enriched in the NC. In addition, we show miR-301a and miR-338 are highly expressed in both the NC and blastula suggesting a role for these miRNAs in maintaining the stem cell-like phenotype of NC cells. CONCLUSION We have characterised the miRNAs expressed in Xenopus embryonic explants treated to form ectoderm, neural or NC tissue. This has identified novel tissue specific miRNAs and highlighted differential expression of miR-427 isoforms.
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Affiliation(s)
- Nicole J. Ward
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Darrell Green
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Janet Higgins
- Regulatory Genomics, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Andrea Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Grant N. Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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Chen F, Zhang C, Wu H, Ma Y, Luo X, Gong X, Jiang F, Gui Y, Zhang H, Lu F. The E3 ubiquitin ligase SCF FBXL14 complex stimulates neuronal differentiation by targeting the Notch signaling factor HES1 for proteolysis. J Biol Chem 2017; 292:20100-20112. [PMID: 29070679 DOI: 10.1074/jbc.m117.815001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/19/2017] [Indexed: 12/30/2022] Open
Abstract
Molecular oscillators are important cellular regulators of, for example, circadian clocks, oscillations of immune regulators, and short-period (ultradian) rhythms during embryonic development. The Notch signaling factor HES1 (hairy and enhancer of split 1) is a well-known repressor of proneural genes, and HES1 ultradian oscillation is essential for keeping cells in an efficiently proliferating progenitor state. HES1 oscillation is driven by both transcriptional self-repression and ubiquitin-dependent proteolysis. However, the E3 ubiquitin ligase targeting HES1 for proteolysis remains unclear. Based on siRNA-mediated gene silencing screening, co-immunoprecipitation, and ubiquitination assays, we discovered that the E3 ubiquitin ligase SCFFBXL14 complex regulates HES1 ubiquitination and proteolysis. siRNA-mediated knockdown of the Cullin-RING E3 ubiquitin ligases RBX1 or CUL1 increased HES1 protein levels, prolonged its half-life, and dampened its oscillation. FBXL14, an F-box protein for SCF ubiquitin ligase, associates with HES1. FBXL14 silencing stabilized HES1, whereas FBXL14 overexpression decreased HES1 protein levels. Of note, the SCFFBXL14 complex promoted the ubiquitination of HES1 in vivo, and a conserved WRPW motif in HES1 was essential for HES1 binding to FBXL14 and for ubiquitin-dependent HES1 degradation. HES1 knockdown promoted neuronal differentiation, but FBXL14 silencing inhibited neuronal differentiation induced by HES1 ablation in mES and F9 cells. Our results suggest that SCFFBXL14 promotes neuronal differentiation by targeting HES1 for ubiquitin-dependent proteolysis and that the C-terminal WRPW motif in HES1 is required for this process.
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Affiliation(s)
- Fangfang Chen
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China; Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China
| | - Chunxiao Zhang
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China; Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154
| | - Haonan Wu
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Yue Ma
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Xiaomin Luo
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China
| | - Xinqi Gong
- Institute for Mathematical Sciences, Renmin University of China, Beijing 100872, China
| | - Fan Jiang
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Yaoting Gui
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
| | - Hui Zhang
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154.
| | - Fei Lu
- Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.
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Affiliation(s)
- Alexander A. Spector
- Department
of Biomedical Engineering and ‡Translational Tissue Engineering
Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Institute for Nanobiotechnology (INBT) and ∥Department of Material Sciences & Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore 21218, Maryland, United States
| | - Warren L. Grayson
- Department
of Biomedical Engineering and ‡Translational Tissue Engineering
Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Institute for Nanobiotechnology (INBT) and ∥Department of Material Sciences & Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore 21218, Maryland, United States
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Dhanesh SB, Subashini C, James J. Hes1: the maestro in neurogenesis. Cell Mol Life Sci 2016; 73:4019-42. [PMID: 27233500 PMCID: PMC11108451 DOI: 10.1007/s00018-016-2277-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 10/21/2022]
Abstract
The process of neurogenesis is well orchestrated by the harmony of multiple cues in a spatiotemporal manner. In this review, we focus on how a dynamic gene, Hes1, is involved in neurogenesis with the view of its regulation and functional implications. Initially, we have reviewed the immense functional significance drawn by this maestro during neural development in a context-dependent manner. How this indispensable role of Hes1 in conferring the competency for neural differentiation partly relies on the direct/indirect mode of repression mediated by very specific structural and functional arms of this protein has also been outlined here. We also review the detailed molecular mechanisms behind the well-tuned oscillatory versus sustained expression of this antineurogenic bHLH repressor, which indeed makes it a master gene to implement the elusive task of neural progenitor propensity. Apart from the functional aspects of Hes1, we also discuss the molecular insights into the endogenous regulatory machinery that regulates its expression. Though Hes1 is a classical target of the Notch signaling pathway, we discuss here its differential expression at the molecular, cellular, and/or regional level. Moreover, we describe how its expression is fine-tuned by all possible ways of gene regulation such as epigenetic, transcriptional, post-transcriptional, post-translational, and environmental factors during vertebrate neurogenesis.
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Affiliation(s)
- Sivadasan Bindu Dhanesh
- Neuro Stem Cell Biology Laboratory, Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, 695 014, Kerala, India
| | - Chandramohan Subashini
- Neuro Stem Cell Biology Laboratory, Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, 695 014, Kerala, India
| | - Jackson James
- Neuro Stem Cell Biology Laboratory, Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Thiruvananthapuram, 695 014, Kerala, India.
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Shi X, Yan C, Liu B, Yang C, Nie X, Wang X, Zheng J, Wang Y, Zhu Y. miR-381 Regulates Neural Stem Cell Proliferation and Differentiation via Regulating Hes1 Expression. PLoS One 2015; 10:e0138973. [PMID: 26431046 PMCID: PMC4591969 DOI: 10.1371/journal.pone.0138973] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/08/2015] [Indexed: 11/18/2022] Open
Abstract
Neural stem cells are self-renewing, multipotent and undifferentiated precursors that retain the capacity for differentiation into both glial (astrocytes and oligodendrocytes) and neuronal lineages. Neural stem cells offer cell-based therapies for neurological disorders such as Alzheimer's disease, Parkinson's disease, Huntington's disease and spinal cord injuries. However, their cellular behavior is poorly understood. MicroRNAs (miRNAs) are a class of small noncoding RNAs involved in cell development, proliferation and differentiation through regulating gene expression at post-transcriptional level. The role of miR-381 in the development of neural stem cells remains unknown. In this study, we showed that overexpression of miR-381 promoted neural stem cells proliferation. It induced the neural stem cells differentiation to neurons and inhibited their differentiation to astrocytes. Furthermore, we identified HES1 as a direct target of miR-381 in neural stem cells. Moreover, re-expression of HES1 impaired miR-381-induced promotion of neural stem cells proliferation and induce neural stem cells differentiation to neurons. In conclusion, miR-381 played important role in neural stem cells proliferation and differentiation.
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Affiliation(s)
- Xiaodong Shi
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, PR China
| | - Chunhua Yan
- Department of Respiratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, PR China
| | - Baoquan Liu
- Department of anatomy, Harbin Medical University, Harbin, 150081, PR China
| | - Chunxiao Yang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, PR China
| | - Xuedan Nie
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, PR China
| | - Xiaokun Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, PR China
| | - Jiaolin Zheng
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, PR China
| | - Yue Wang
- Department of Occupational Health, College of Public Health, Harbin Medical University, Harbin, 150081, PR China
| | - Yulan Zhu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, PR China
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