1
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Menz G, Engblom S. Modelling Population-Level Hes1 Dynamics: Insights from a Multi-framework Approach. Bull Math Biol 2025; 87:74. [PMID: 40379916 DOI: 10.1007/s11538-025-01447-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Accepted: 04/02/2025] [Indexed: 05/19/2025]
Abstract
Mathematical models of living cells have been successively refined with advancements in experimental techniques. A main concern is striking a balance between modelling power and the tractability of the associated mathematical analysis. In this work we model the dynamics for the transcription factor Hairy and enhancer of split-1 (Hes1), whose expression oscillates during neural development, and which critically enables stable fate decision in the embryonic brain. We design, parametrise, and analyse a detailed spatial model using ordinary differential equations (ODEs) over a grid capturing both transient oscillatory behaviour and fate decision on a population-level. We also investigate the relationship between this ODE model and a more realistic grid-based model involving intrinsic noise using mostly directly biologically motivated parameters. While we focus specifically on Hes1 in neural development, the approach of linking deterministic and stochastic grid-based models shows promise in modelling various biological processes taking place in a cell population. In this context, our work stresses the importance of the interpretability of complex computational models into a framework which is amenable to mathematical analysis.
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Affiliation(s)
- Gesina Menz
- Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05, Uppsala, Sweden
| | - Stefan Engblom
- Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05, Uppsala, Sweden.
- Science for Life Laboratory, Department of Information Technology, Uppsala University, Uppsala, Sweden.
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2
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Hsieh CW, Chang LH, Wang YH, Li WT, Chang JK, Chen CH, Ho ML. Indoxyl Sulfate Inhibits Osteogenesis in Bone Marrow Mesenchymal Stem Cells through the AhR/Hes1 Pathway. Int J Mol Sci 2024; 25:8770. [PMID: 39201457 PMCID: PMC11354967 DOI: 10.3390/ijms25168770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/05/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Uremic toxins cause bone disorders in patients with chronic kidney disease (CKD). These disorders are characterized by low turnover osteodystrophy and impaired bone formation in the early stages of CKD. Evidence indicates that the aryl hydrocarbon receptor (AhR) mediates signals that suppress early osteogenic differentiation in bone marrow mesenchymal stem cells (BMSCs). However, whether the AhR mediates the effects of indoxyl sulfate (IS), a uremic toxin, on BMSC osteogenesis remains unclear. We investigated whether IS affects osteogenesis through the AhR/Hes1 pathway. Expression levels of osteogenesis genes (Runx2, Bmp2, Alp, and Oc), AhR, and Hes1 were measured in mouse BMSCs (D1 cells). At concentrations of 2-50 μM, IS significantly reduced mineralization, particularly in the early stages of BMSC osteogenesis. Furthermore, IS significantly downregulated the expression of Runx2, Bmp2, Oc, and Alp. Notably, this downregulation could be prevented using an AhR antagonist and through Ahr knockdown. Mechanistically, IS induced the expression of Hes1 through AhR signaling, thereby suppressing the transcription of Runx2 and Bmp2. Our findings suggest that IS inhibits early osteogenesis of BMSCs through the AhR/Hes1 pathway, thus suppressing the transcription of Runx2 and Bmp2. Our findings may guide new therapeutic strategies against CKD-related bone disorders.
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Affiliation(s)
- Chin-Wen Hsieh
- Division of Nephrology, Department of Internal Medicine, Pingtung Christian Hospital, Pingtung 900, Taiwan;
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ling-Hua Chang
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yan-Hsiung Wang
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Wei-Ting Li
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
| | - Je-Ken Chang
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Orthopaedics, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Orthopedics, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung 801, Taiwan
| | - Chung-Hwan Chen
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Orthopaedics, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Orthopedics, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung 801, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Ph.D. Program in Biomedical Engineering, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Materials Engineering, College of Engineering, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Mei-Ling Ho
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Orthopaedic Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (L.-H.C.); (Y.-H.W.); (W.-T.L.); (J.-K.C.)
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Ph.D. Program in Biomedical Engineering, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Materials Engineering, College of Engineering, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- Department of Physiology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
- College of Professional Studies, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
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3
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Bilateral Feedback in Oscillator Model Is Required to Explain the Coupling Dynamics of Hes1 with the Cell Cycle. MATHEMATICS 2022. [DOI: 10.3390/math10132323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biological processes are governed by the expression of proteins, and for some proteins, their level of expression can fluctuate periodically over time (i.e., they oscillate). Many oscillatory proteins (e.g., cell cycle proteins and those from the HES family of transcription factors) are connected in complex ways, often within large networks. This complexity can be elucidated by developing intuitive mathematical models that describe the underlying critical aspects of the relationships between these processes. Here, we provide a mathematical explanation of a recently discovered biological phenomenon: the phasic position of the gene Hes1’s oscillatory expression at the beginning of the cell cycle of an individual human breast cancer stem cell can have a predictive value on how long that cell will take to complete a cell cycle. We use a two-component model of coupled oscillators to represent Hes1 and the cell cycle in the same cell with minimal assumptions. Inputting only the initial phase angles, we show that this model is capable of predicting the dynamic mitosis to mitosis behaviour of Hes1 and predicting cell cycle length patterns as found in real-world experimental data. Moreover, we discover that bidirectional coupling between Hes1 and the cell cycle is critical within the system for the data to be reproduced and that nonfixed asymmetry in the interactions between the oscillators is required. The phase dynamics we present here capture the complex interplay between Hes1 and the cell cycle, helping to explain nongenetic cell cycle variability, which has critical implications in cancer treatment contexts.
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4
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Chen X, Chen T, Dong C, Chen H, Dong X, Yang L, Hu L, Wang H, Wu B, Yao Y, Xiong Y, Xiong M, Lin Y, Zhou W. Deletion of CHD8 in cerebellar granule neuron progenitors leads to severe cerebellar hypoplasia, ataxia and psychiatric behavior in mice. J Genet Genomics 2022; 49:859-869. [DOI: 10.1016/j.jgg.2022.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 12/22/2022]
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5
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Pfeuty B. Multistability and transitions between spatiotemporal patterns through versatile Notch-Hes signaling. J Theor Biol 2022; 539:111060. [DOI: 10.1016/j.jtbi.2022.111060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/02/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
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6
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Minguzzi M, Panichi V, D’Adamo S, Cetrullo S, Cattini L, Flamigni F, Mariani E, Borzì RM. Pleiotropic Roles of NOTCH1 Signaling in the Loss of Maturational Arrest of Human Osteoarthritic Chondrocytes. Int J Mol Sci 2021; 22:ijms222112012. [PMID: 34769441 PMCID: PMC8585104 DOI: 10.3390/ijms222112012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 02/07/2023] Open
Abstract
Notch signaling has been identified as a critical regulator of cartilage development and homeostasis. Its pivotal role was established by both several joint specific Notch signaling loss of function mouse models and transient or sustained overexpression. NOTCH1 is the most abundantly expressed NOTCH receptors in normal cartilage and its expression increases in osteoarthritis (OA), when chondrocytes exit from their healthy “maturation arrested state” and resume their natural route of proliferation, hypertrophy, and terminal differentiation. The latter are hallmarks of OA that are easily evaluated in vitro in 2-D or 3-D culture models. The aim of our study was to investigate the effect of NOTCH1 knockdown on proliferation (cell count and Picogreen mediated DNA quantification), cell cycle (flow cytometry), hypertrophy (gene and protein expression of key markers such as RUNX2 and MMP-13), and terminal differentiation (viability measured in 3-D cultures by luminescence assay) of human OA chondrocytes. NOTCH1 silencing of OA chondrocytes yielded a healthier phenotype in both 2-D (reduced proliferation) and 3-D with evidence of decreased hypertrophy (reduced expression of RUNX2 and MMP-13) and terminal differentiation (increased viability). This demonstrates that NOTCH1 is a convenient therapeutic target to attenuate OA progression.
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Affiliation(s)
- Manuela Minguzzi
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, 40138 Bologna, Italy; (M.M.); (S.D.); (E.M.)
| | - Veronica Panichi
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40138 Bologna, Italy; (V.P.); (S.C.); (F.F.)
| | - Stefania D’Adamo
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, 40138 Bologna, Italy; (M.M.); (S.D.); (E.M.)
| | - Silvia Cetrullo
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40138 Bologna, Italy; (V.P.); (S.C.); (F.F.)
| | - Luca Cattini
- Laboratorio di Immunoreumatologia e Rigenerazione Tissutale, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy;
| | - Flavio Flamigni
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, 40138 Bologna, Italy; (V.P.); (S.C.); (F.F.)
| | - Erminia Mariani
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, 40138 Bologna, Italy; (M.M.); (S.D.); (E.M.)
- Laboratorio di Immunoreumatologia e Rigenerazione Tissutale, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy;
| | - Rosa Maria Borzì
- Laboratorio di Immunoreumatologia e Rigenerazione Tissutale, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy;
- Correspondence:
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7
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Giri A, Sengupta D, Kar S. Deciphering the Role of Fluctuation Dependent Intercellular Communication in Neural Stem Cell Development. ACS Chem Neurosci 2021; 12:2360-2372. [PMID: 34170103 DOI: 10.1021/acschemneuro.1c00116] [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: 11/28/2022] Open
Abstract
Neural stem cells (NPCs) efficiently communicate in an intercellular manner to govern specific cell fate decisions during the developmental process despite withstanding the fluctuating cellular environment. How these fluctuations from diverse origins functionally affect the precise cell fate decision making remains elusive. By taking a stochastic mathematical modeling approach, we unravel that the transcriptional variability arising within an NPC population due to intermittent cell cycle events significantly influences the neuron to NPC ratio during development. Our model proficiently quantifies the impact of different sources of heterogeneities in maintaining an exact neuron to NPC ratio and predicts plausible experimental ways to fine-tune the development of NPCs. In the future, these modeling insights may lead to better therapeutic avenues to regenerate neurons from NPCs.
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Affiliation(s)
- Amitava Giri
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
| | - Dola Sengupta
- Department of Chemistry, Techno India University, Salt Lake, Kolkata 700091, India
| | - Sandip Kar
- Department of Chemistry, IIT Bombay, Powai, Mumbai 400076, India
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8
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Muhr J, Hagey DW. The cell cycle and differentiation as integrated processes: Cyclins and CDKs reciprocally regulate Sox and Notch to balance stem cell maintenance. Bioessays 2021; 43:e2000285. [PMID: 34008221 DOI: 10.1002/bies.202000285] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Development and maintenance of diverse organ systems require context-specific regulation of stem cell behaviour. We hypothesize that this is achieved via reciprocal regulation between the cell cycle machinery and differentiation factors. This idea is supported by the parallel evolutionary emergence of differentiation pathways, cell cycle components and complex multicellularity. In addition, the activities of different cell cycle phases have been found to bias cells towards stem cell maintenance or differentiation. Finally, several direct mechanistic links between these two processes have been established. Here, we focus on interactions between cyclin-CDK complexes and differentiation regulators of the Notch pathway and Sox family of transcription factors within the context of pluripotent and neural stem cells. Thus, this hypothesis formalizes the links between these two processes as an integrated network. Since such factors are common to all stem cells, better understanding their interconnections will help to explain their behaviour in health and disease.
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Affiliation(s)
- Jonas Muhr
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
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9
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Theoretical study of the impact of adaptation on cell-fate heterogeneity and fractional killing. Sci Rep 2020; 10:17429. [PMID: 33060729 PMCID: PMC7562916 DOI: 10.1038/s41598-020-74238-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Fractional killing illustrates the cell propensity to display a heterogeneous fate response over a wide range of stimuli. The interplay between the nonlinear and stochastic dynamics of biochemical networks plays a fundamental role in shaping this probabilistic response and in reconciling requirements for heterogeneity and controllability of cell-fate decisions. The stress-induced fate choice between life and death depends on an early adaptation response which may contribute to fractional killing by amplifying small differences between cells. To test this hypothesis, we consider a stochastic modeling framework suited for comprehensive sensitivity analysis of dose response curve through the computation of a fractionality index. Combining bifurcation analysis and Langevin simulation, we show that adaptation dynamics enhances noise-induced cell-fate heterogeneity by shifting from a saddle-node to a saddle-collision transition scenario. The generality of this result is further assessed by a computational analysis of a detailed regulatory network model of apoptosis initiation and by a theoretical analysis of stochastic bifurcation mechanisms. Overall, the present study identifies a cooperative interplay between stochastic, adaptation and decision intracellular processes that could promote cell-fate heterogeneity in many contexts.
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10
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Urun FR, Moore AW. Visualizing Cell Cycle Phase Organization and Control During Neural Lineage Elaboration. Cells 2020; 9:E2112. [PMID: 32957483 PMCID: PMC7565168 DOI: 10.3390/cells9092112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 11/16/2022] Open
Abstract
In neural precursors, cell cycle regulators simultaneously control both progression through the cell cycle and the probability of a cell fate switch. Precursors act in lineages, where they transition through a series of cell types, each of which has a unique molecular identity and cellular behavior. Thus, investigating links between cell cycle and cell fate control requires simultaneous identification of precursor type and cell cycle phase, as well as an ability to read out additional regulatory factor expression or activity. We use a combined FUCCI-EdU labelling protocol to do this, and then applied it to the embryonic olfactory neural lineage, in which the spatial position of a cell correlates with its precursor identity. Using this integrated model, we find the CDKi p27KIP1 has different regulation relative to cell cycle phase in neural stem cells versus intermediate precursors. In addition, Hes1, which is the principle transcriptional driver of neural stem cell self-renewal, surprisingly does not regulate p27KIP1 in this cell type. Rather, Hes1 indirectly represses p27KIP1 levels in the intermediate precursor cells downstream in the lineage. Overall, the experimental model described here enables investigation of cell cycle and cell fate control linkage from a single precursor through to a lineage systems level.
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Affiliation(s)
- Fatma Rabia Urun
- Laboratory for Neurodiversity, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
- Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama 338-8570, Japan
| | - Adrian W Moore
- Laboratory for Neurodiversity, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;
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11
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Picocci S, Bizzoca A, Corsi P, Magrone T, Jirillo E, Gennarini G. Modulation of Nerve Cell Differentiation: Role of Polyphenols and of Contactin Family Components. Front Cell Dev Biol 2019; 7:119. [PMID: 31380366 PMCID: PMC6656924 DOI: 10.3389/fcell.2019.00119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/12/2019] [Indexed: 12/18/2022] Open
Abstract
In this study the mechanisms are explored, which modulate expression and function of cell surface adhesive glycoproteins of the Immunoglobulin Supergene Family (IgSF), and in particular of its Contactin subset, during neuronal precursor developmental events. In this context, a specific topic concerns the significance of the expression profile of such molecules and their ability to modulate signaling pathways activated through nutraceuticals, in particular polyphenols, administration. Both in vitro and in vivo approaches are chosen. As for the former, by using as a model the human SH-SY5Y neuroblastoma line, the effects of grape seed polyphenols are evaluated on proliferation and commitment/differentiation events along the neuronal lineage. In SH-SY5Y cell cultures, polyphenols were found to counteract precursor proliferation while promoting their differentiation, as deduced by studying their developmental parameters through the expression of cell cycle and neuronal commitment/differentiation markers as well as by measuring neurite growth. In such cultures, Cyclin E expression and BrdU incorporation were downregulated, indicating reduced precursor proliferation while increased neuronal differentiation was inferred from upregulation of cell cycle exit (p27–Kip) and neuronal commitment (NeuN) markers as well as by measuring neurite length through morphometric analysis. The polyphenol effects on developmental parameters were also explored in vivo, in cerebellar cortex, by using as a model the TAG/F3 transgenic line, which undergoes delayed neural development as a consequence of Contactin1 adhesive glycoprotein upregulation and premature expression under control of the Contactin2 gene (Cntn-2) promoter. In this transgenic line, a Notch pathway activation is known to occur and polyphenol treatment was found to counteract such an effect, demonstrated through downregulation of the Hes-1 transcription factor. Polyphenols also downregulated the expression of adhesive glycoproteins of the Contactin family themselves, demonstrated for both Contactin1 and Contactin2, indicating the involvement of changes in the expression of the underlying genes in the observed phenotype. These data support the hypothesis that the complex control exerted by polyphenols on neural development involves modulation of expression and function of the genes encoding cell adhesion molecules of the Contactin family and of the associated signaling pathways, indicating potential mechanisms whereby such compounds may control neurogenesis.
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Affiliation(s)
- Sabrina Picocci
- Laboratories of Developmental Neurobiology, Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Medical School, University of Bari Aldo Moro, Bari, Italy
| | - Antonella Bizzoca
- Laboratories of Developmental Neurobiology, Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Medical School, University of Bari Aldo Moro, Bari, Italy
| | - Patrizia Corsi
- Laboratories of Developmental Neurobiology, Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Medical School, University of Bari Aldo Moro, Bari, Italy
| | - Thea Magrone
- Laboratories of Immunology, Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Medical School, University of Bari Aldo Moro, Bari, Italy
| | - Emilio Jirillo
- Laboratories of Immunology, Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Medical School, University of Bari Aldo Moro, Bari, Italy
| | - Gianfranco Gennarini
- Laboratories of Developmental Neurobiology, Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Medical School, University of Bari Aldo Moro, Bari, Italy
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12
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Shparberg RA, Glover HJ, Morris MB. Modeling Mammalian Commitment to the Neural Lineage Using Embryos and Embryonic Stem Cells. Front Physiol 2019; 10:705. [PMID: 31354503 PMCID: PMC6637848 DOI: 10.3389/fphys.2019.00705] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/20/2019] [Indexed: 12/21/2022] Open
Abstract
Early mammalian embryogenesis relies on a large range of cellular and molecular mechanisms to guide cell fate. In this highly complex interacting system, molecular circuitry tightly controls emergent properties, including cell differentiation, proliferation, morphology, migration, and communication. These molecular circuits include those responsible for the control of gene and protein expression, as well as metabolism and epigenetics. Due to the complexity of this circuitry and the relative inaccessibility of the mammalian embryo in utero, mammalian neural commitment remains one of the most challenging and poorly understood areas of developmental biology. In order to generate the nervous system, the embryo first produces two pluripotent populations, the inner cell mass and then the primitive ectoderm. The latter is the cellular substrate for gastrulation from which the three multipotent germ layers form. The germ layer definitive ectoderm, in turn, is the substrate for multipotent neurectoderm (neural plate and neural tube) formation, representing the first morphological signs of nervous system development. Subsequent patterning of the neural tube is then responsible for the formation of most of the central and peripheral nervous systems. While a large number of studies have assessed how a competent neurectoderm produces mature neural cells, less is known about the molecular signatures of definitive ectoderm and neurectoderm and the key molecular mechanisms driving their formation. Using pluripotent stem cells as a model, we will discuss the current understanding of how the pluripotent inner cell mass transitions to pluripotent primitive ectoderm and sequentially to the multipotent definitive ectoderm and neurectoderm. We will focus on the integration of cell signaling, gene activation, and epigenetic control that govern these developmental steps, and provide insight into the novel growth factor-like role that specific amino acids, such as L-proline, play in this process.
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Affiliation(s)
| | | | - Michael B. Morris
- Embryonic Stem Cell Laboratory, Discipline of Physiology, School of Medical Sciences, Bosch Institute, University of Sydney, Sydney, NSW, Australia
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13
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Polioudakis D, de la Torre-Ubieta L, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, Hinz FI, Sabri S, Lowry WE, Gerstein MB, Plath K, Geschwind DH. A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation. Neuron 2019; 103:785-801.e8. [PMID: 31303374 DOI: 10.1016/j.neuron.2019.06.011] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/20/2019] [Accepted: 06/12/2019] [Indexed: 01/05/2023]
Abstract
We performed RNA sequencing on 40,000 cells to create a high-resolution single-cell gene expression atlas of developing human cortex, providing the first single-cell characterization of previously uncharacterized cell types, including human subplate neurons, comparisons with bulk tissue, and systematic analyses of technical factors. These data permit deconvolution of regulatory networks connecting regulatory elements and transcriptional drivers to single-cell gene expression programs, significantly extending our understanding of human neurogenesis, cortical evolution, and the cellular basis of neuropsychiatric disease. We tie cell-cycle progression with early cell fate decisions during neurogenesis, demonstrating that differentiation occurs on a transcriptomic continuum; rather than only expressing a few transcription factors that drive cell fates, differentiating cells express broad, mixed cell-type transcriptomes before telophase. By mapping neuropsychiatric disease genes to cell types, we implicate dysregulation of specific cell types in ASD, ID, and epilepsy. We developed CoDEx, an online portal to facilitate data access and browsing.
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Affiliation(s)
- Damon Polioudakis
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Luis de la Torre-Ubieta
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Andrew G Elkins
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Xu Shi
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jason L Stein
- Department of Genetics & UNC Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Celine K Vuong
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Susanne Nichterwitz
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Melinda Gevorgian
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Biology, CSUN, Northridge, CA, USA
| | - Carli K Opland
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daning Lu
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - William Connell
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Elizabeth K Ruzzo
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jennifer K Lowe
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Tarik Hadzic
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Flora I Hinz
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Shan Sabri
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - William E Lowry
- Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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14
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Tyrovola JB. The "mechanostat" principle in cell differentiation. The osteochondroprogenitor paradigm. J Cell Biochem 2018; 120:37-44. [PMID: 30144147 DOI: 10.1002/jcb.27509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/25/2018] [Indexed: 12/13/2022]
Abstract
The "mechanostat" principle may be depicted as an oscillating signal of a signaling molecule, in which the amplitude, frequency, cumulative level, delay, and duration of the curve encode the information for concrete cellular responses and biological activities. When the oscillating signal is kept sustained (present delay), cell exit may be performed, whereas when the oscillating signal remains robust, cell proliferation may take place. B-catenin-Wnt signaling pathway has a key role in the differentiation of osteochondroprogenitor cells. Sustained downregulation of the β-catenin-Wnt pathway forces osteochondroprogenitors to a chondrogenic fate instead of an osteoblastic one. Other signaling, for example, bone morphogenetic protein and Notch signaling pathways interact with the Wnt pathway. The crosstalk between biochemical and mechanical stimuli produces the final information that leads to the final cell fate decisions, through the "mechanostat" principle.
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15
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Zammit V, Baron B, Ayers D. MiRNA Influences in Neuroblast Modulation: An Introspective Analysis. Genes (Basel) 2018; 9:genes9010026. [PMID: 29315268 PMCID: PMC5793179 DOI: 10.3390/genes9010026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/22/2017] [Accepted: 12/29/2017] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma (NB) is the most common occurring solid paediatric cancer in children under the age of five years. Whether of familial or sporadic origin, chromosome abnormalities contribute to the development of NB and cause dysregulation of microRNAs (miRNAs). MiRNAs are small non-coding, single stranded RNAs that target messenger RNAs at the post-transcriptional levels by repressing translation within all facets of human physiology. Such gene 'silencing' activities by miRNAs allows the development of regulatory feedback loops affecting multiple functions within the cell, including the possible differentiation of neural stem cell (NSC) lineage selection. Neurogenesis includes stages of self-renewal and fate specification of NSCs, migration and maturation of young neurones, and functional integration of new neurones into the neural circuitry, all of which are regulated by miRNAs. The role of miRNAs and their interaction in cellular processes are recognised aspects of cancer genetics, and miRNAs are currently employed as biomarkers for prognosis and tumour characterisation in multiple cancer models. Consequently, thorough understanding of the mechanisms of how these miRNAs interplay at the transcriptomic level will definitely lead to the development of novel, bespoke and efficient therapeutic measures, with this review focusing on the influences of miRNAs on neuroblast modulations leading to neuroblastoma.
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Affiliation(s)
- Vanessa Zammit
- National Blood Transfusion Service, St. Luke's Hospital, PTA1010 G'Mangia, Malta.
- School of Biomedical Science and Physiology, University of Wolverhampton, Wolverhampton WV1 1LY, UK.
| | - Byron Baron
- Centre for Molecular Medicine and Biobanking, Faculty of Medicine and Surgery, University of Malta, MSD2080 Msida, Malta.
| | - Duncan Ayers
- Centre for Molecular Medicine and Biobanking, Faculty of Medicine and Surgery, University of Malta, MSD2080 Msida, Malta.
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK.
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16
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Boareto M, Iber D, Taylor V. Differential interactions between Notch and ID factors control neurogenesis by modulating Hes factor autoregulation. Development 2017; 144:3465-3474. [PMID: 28974640 PMCID: PMC5665482 DOI: 10.1242/dev.152520] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/14/2017] [Indexed: 12/25/2022]
Abstract
During embryonic and adult neurogenesis, neural stem cells (NSCs) generate the correct number and types of neurons in a temporospatial fashion. Control of NSC activity and fate is crucial for brain formation and homeostasis. Neurogenesis in the embryonic and adult brain differ considerably, but Notch signaling and inhibitor of DNA-binding (ID) factors are pivotal in both. Notch and ID factors regulate NSC maintenance; however, it has been difficult to evaluate how these pathways potentially interact. Here, we combined mathematical modeling with analysis of single-cell transcriptomic data to elucidate unforeseen interactions between the Notch and ID factor pathways. During brain development, Notch signaling dominates and directly regulates Id4 expression, preventing other ID factors from inducing NSC quiescence. Conversely, during adult neurogenesis, Notch signaling and Id2/3 regulate neurogenesis in a complementary manner and ID factors can induce NSC maintenance and quiescence in the absence of Notch. Our analyses unveil key molecular interactions underlying NSC maintenance and mechanistic differences between embryonic and adult neurogenesis. Similar Notch and ID factor interactions may be crucial in other stem cell systems. Summary: Computational analysis of transcriptome data from neural stem cells reveals key differences in the synergistic interactions between Notch and inhibitor of DNA-binding factors during embryonic and adult neurogenesis.
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Affiliation(s)
- Marcelo Boareto
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland .,Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland .,Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Verdon Taylor
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
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17
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Bielefeld P, Schouten M, Lucassen PJ, Fitzsimons CP. Transcription factor oscillations in neural stem cells: Implications for accurate control of gene expression. NEUROGENESIS 2017; 4:e1262934. [PMID: 28321433 PMCID: PMC5345753 DOI: 10.1080/23262133.2016.1262934] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 01/14/2023]
Abstract
Naturally occurring oscillations in glucocorticoids induce a cyclic activation of the glucocorticoid receptor (GR), a well-characterized ligand-activated transcription factor. These cycles of GR activation/deactivation result in rapid GR exchange at genomic response elements and GR recycling through the chaperone machinery, ultimately generating pulses of GR-mediated transcriptional activity of target genes. In a recent article we have discussed the implications of circadian and high-frequency (ultradian) glucocorticoid oscillations for the dynamic control of gene expression in hippocampal neural stem/progenitor cells (NSPCs) (Fitzsimons et al., Front. Neuroendocrinol., 2016). Interestingly, this oscillatory transcriptional activity is common to other transcription factors, many of which regulate key biological functions in NSPCs, such as NF-kB, p53, Wnt and Notch. Here, we discuss the oscillatory behavior of these transcription factors, their role in a biologically accurate target regulation and the potential importance for a dynamic control of transcription activity and gene expression in NSPCs.
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Affiliation(s)
- Pascal Bielefeld
- Neuroscience Program, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam
| | - Marijn Schouten
- Neuroscience Program, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam
| | - Paul J Lucassen
- Neuroscience Program, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam
| | - Carlos P Fitzsimons
- Neuroscience Program, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam
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18
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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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19
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Liu L, Zhang Q, Cai Y, Sun D, He X, Wang L, Yu D, Li X, Xiong X, Xu H, Yang Q, Fan X. Resveratrol counteracts lipopolysaccharide-induced depressive-like behaviors via enhanced hippocampal neurogenesis. Oncotarget 2016; 7:56045-56059. [PMID: 27517628 PMCID: PMC5302895 DOI: 10.18632/oncotarget.11178] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/20/2016] [Indexed: 11/25/2022] Open
Abstract
Radial glial-like cells (RGLs) in the adult dentate gyrus (DG) function as progenitor cells for adult hippocampal neurogenesis, a process involved in the stress-related pathophysiology and treatment efficiency of depression. Resveratrol (RSV) has been demonstrated to be a potent activator of neurogenesis. The present study investigated whether chronic RSV treatment has antidepressant potential in relation to hippocampal neurogenesis. Mice received two weeks of RSV (20 mg/kg) or dimethylsulfoxide (DMSO) treatment, followed by lipopolysaccharide (LPS; 1 mg/kg) or saline injections for 5 days. We found that RSV treatment abrogated the increased immobility in the forced swimming test and tail suspension test induced by LPS. Immunohistochemical staining revealed that RSV treatment reversed the increase in microglial activation and the inhibition in DG neurogenesis. RSV treatment also attenuated LPS-induced defects in the expanding of RGLs through promoting symmetric division. In addition, RSV ameliorated LPS-induced NF-κB activation in the hippocampus coincides with the up-regulation levels of Sirt1 and Hes1. Taken together, these data indicated that RSV-induced Sirt1 activation counteracts LPS-induced depression-like behaviors via a neurogenic mechanism. A new model to understand the role of RSV in treating depression may result from these findings.
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Affiliation(s)
- Liang Liu
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
- Department of Neurology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Qin Zhang
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Yulong Cai
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Dayu Sun
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
- Department of Neurology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Xie He
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Lian Wang
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Dan Yu
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Xin Li
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Xiaoyi Xiong
- Department of Neurology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Haiwei Xu
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Qingwu Yang
- Department of Neurology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Xiaotang Fan
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
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20
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Pfeuty B, Kaneko K. Requirements for efficient cell-type proportioning: regulatory timescales, stochasticity and lateral inhibition. Phys Biol 2016; 13:026007. [PMID: 27172110 DOI: 10.1088/1478-3975/13/2/026007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell types. This developmental differentiation process typically involves intracellular regulatory and stochastic mechanisms to generate cell-fate diversity as well as intercellular signaling mechanisms to coordinate cell-fate decisions at tissue level. We thus surmise that key insights about the developmental regulation of cell-type proportion can be captured by the modeling study of clustering dynamics in population of inhibitory-coupled noisy bistable systems. This general class of dynamical system is shown to exhibit a very stable two-cluster state, but also metastability, collective oscillations or noise-induced state hopping, which can prevent from timely and reliably reaching a robust and well-proportioned clustered state. To circumvent these obstacles or to avoid fine-tuning, we highlight a general strategy based on dual-time positive feedback loops, such as mediated through transcriptional versus epigenetic mechanisms, which improves proportion regulation by coordinating early and flexible lineage priming with late and firm commitment. This result sheds new light on the respective and cooperative roles of multiple regulatory feedback, stochasticity and lateral inhibition in developmental dynamics.
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Affiliation(s)
- B Pfeuty
- Université de Lille, CNRS, Laboratoire de Physique des Lasers, Atomes, et Molécules, F-59000, Lille, France
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21
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Bivik C, MacDonald RB, Gunnar E, Mazouni K, Schweisguth F, Thor S. Control of Neural Daughter Cell Proliferation by Multi-level Notch/Su(H)/E(spl)-HLH Signaling. PLoS Genet 2016; 12:e1005984. [PMID: 27070787 PMCID: PMC4829154 DOI: 10.1371/journal.pgen.1005984] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 03/17/2016] [Indexed: 11/18/2022] Open
Abstract
The Notch pathway controls proliferation during development and in adulthood, and is frequently affected in many disorders. However, the genetic sensitivity and multi-layered transcriptional properties of the Notch pathway has made its molecular decoding challenging. Here, we address the complexity of Notch signaling with respect to proliferation, using the developing Drosophila CNS as model. We find that a Notch/Su(H)/E(spl)-HLH cascade specifically controls daughter, but not progenitor proliferation. Additionally, we find that different E(spl)-HLH genes are required in different neuroblast lineages. The Notch/Su(H)/E(spl)-HLH cascade alters daughter proliferation by regulating four key cell cycle factors: Cyclin E, String/Cdc25, E2f and Dacapo (mammalian p21CIP1/p27KIP1/p57Kip2). ChIP and DamID analysis of Su(H) and E(spl)-HLH indicates direct transcriptional regulation of the cell cycle genes, and of the Notch pathway itself. These results point to a multi-level signaling model and may help shed light on the dichotomous proliferative role of Notch signaling in many other systems.
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Affiliation(s)
- Caroline Bivik
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - Ryan B. MacDonald
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - Erika Gunnar
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - Khalil Mazouni
- Institut Pasteur, Paris, France
- CNRS, URA2578, Paris, France
| | | | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
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22
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Uriu K. Genetic oscillators in development. Dev Growth Differ 2016; 58:16-30. [PMID: 26753997 DOI: 10.1111/dgd.12262] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/19/2015] [Accepted: 11/19/2015] [Indexed: 02/03/2023]
Abstract
In development, morphogenetic processes are strictly coordinated in time. Cells in a developing tissue would need mechanisms for time-keeping. One such time-keeping mechanism is to use oscillations of gene expression. Oscillatory gene expression can be generated by transcriptional/translational feedback loops, usually referred to as a genetic oscillator. In this review article, we discuss genetic oscillators in the presence of developmental processes such as cell division, cell movement and cell differentiation. We first introduce the gene regulatory network for generating a rhythm of gene expression. We then discuss how developmental processes influence genetic oscillators. Examples include vertebrate somitogenesis and neural progenitor cell differentiation, as well as the circadian clock for comparison. To understand the behaviors of genetic oscillators in development, it is necessary to consider both gene expression dynamics and cellular behaviors simultaneously. Theoretical modeling combined with live imaging at single-cell resolution will be a powerful tool to analyze genetic oscillators in development.
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Affiliation(s)
- Koichiro Uriu
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
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23
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Phillips NE, Manning CS, Pettini T, Biga V, Marinopoulou E, Stanley P, Boyd J, Bagnall J, Paszek P, Spiller DG, White MRH, Goodfellow M, Galla T, Rattray M, Papalopulu N. Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation. eLife 2016; 5:e16118. [PMID: 27700985 PMCID: PMC5050025 DOI: 10.7554/elife.16118] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/24/2016] [Indexed: 01/27/2023] Open
Abstract
Recent studies suggest that cells make stochastic choices with respect to differentiation or division. However, the molecular mechanism underlying such stochasticity is unknown. We previously proposed that the timing of vertebrate neuronal differentiation is regulated by molecular oscillations of a transcriptional repressor, HES1, tuned by a post-transcriptional repressor, miR-9. Here, we computationally model the effects of intrinsic noise on the Hes1/miR-9 oscillator as a consequence of low molecular numbers of interacting species, determined experimentally. We report that increased stochasticity spreads the timing of differentiation in a population, such that initially equivalent cells differentiate over a period of time. Surprisingly, inherent stochasticity also increases the robustness of the progenitor state and lessens the impact of unequal, random distribution of molecules at cell division on the temporal spread of differentiation at the population level. This advantageous use of biological noise contrasts with the view that noise needs to be counteracted.
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Affiliation(s)
- Nick E Phillips
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Cerys S Manning
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Tom Pettini
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Veronica Biga
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Elli Marinopoulou
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Peter Stanley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James Boyd
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Pawel Paszek
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David G Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michael RH White
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Marc Goodfellow
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom,Centre for Biomedical Modelling and Analysis, University of Exeter, Exeter, United Kingdom,EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter, United Kingdom
| | - Tobias Galla
- Theoretical Physics, School of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Nancy Papalopulu
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom,
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24
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Pfeuty B. Neuronal specification exploits the inherent flexibility of cell-cycle gap phases. NEUROGENESIS 2015; 2:e1095694. [PMID: 27606329 PMCID: PMC4973608 DOI: 10.1080/23262133.2015.1095694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/30/2015] [Accepted: 09/14/2015] [Indexed: 12/26/2022]
Abstract
Starting from pluripotent stem cells that virtually proliferate indefinitely, the orderly emergence during organogenesis of lineage-restricted cell types exhibiting a decreased proliferative capacity concurrently with an increasing range of differentiation traits implies the occurrence of a stringent spatiotemporal coupling between cell-cycle progression and cell differentiation. A recent computational modeling study has explored in the context of neurogenesis whether and how the peculiar pattern of connections among the proneural Neurog2 factor, the Hes1 Notch effector and antagonistically-acting G1-phase regulators would be instrumental in this event. This study highlighted that the strong opposition to G1/S transit imposed by accumulating Neurog2 and CKI enables a sensitive control of G1-phase lengthening and terminal differentiation to occur concomitantly with late-G1 exit. Contrastingly, Hes1 promotes early-G1 cell-cycle arrest and its cell-autonomous oscillations combined with a lateral inhibition mechanism help maintain a labile proliferation state in dynamic balance with diverse cell-fate outputs, thereby, offering cells the choice to either keep self-renewing or differentiate into distinct cell types. These results, discussed in connection with Ascl1-dependent neural differentiation, suggest that developmental fate decisions exploit the inherent flexibility of cell-cycle gap phases to generate diversity by selecting subtly-differing patterns of connections among components of the cell-cycle machinery and differentiation pathways.
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Affiliation(s)
- Benjamin Pfeuty
- Laboratoire de Physique des Lasers Atomes et Molécules; CNRS; Université de Lille ; Villeneuve d'Ascq, France
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25
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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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