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Shefa U, Jung J. Comparative study of microarray and experimental data on Schwann cells in peripheral nerve degeneration and regeneration: big data analysis. Neural Regen Res 2019; 14:1099-1104. [PMID: 30762025 PMCID: PMC6404495 DOI: 10.4103/1673-5374.250632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A Schwann cell has regenerative capabilities and is an important cell in the peripheral nervous system. This microarray study is part of a bioinformatics study that focuses mainly on Schwann cells. Microarray data provide information on differences between microarray-based and experiment-based gene expression analyses. According to microarray data, several genes exhibit increased expression (fold change) but they are weakly expressed in experimental studies (based on morphology, protein and mRNA levels). In contrast, some genes are weakly expressed in microarray data and highly expressed in experimental studies; such genes may represent future target genes in Schwann cell studies. These studies allow us to learn about additional genes that could be used to achieve targeted results from experimental studies. In the current big data study by retrieving more than 5000 scientific articles from PubMed or NCBI, Google Scholar, and Google, 1016 (up- and downregulated) genes were determined to be related to Schwann cells. However, no experiment was performed in the laboratory; rather, the present study is part of a big data analysis. Our study will contribute to our understanding of Schwann cell biology by aiding in the identification of genes. Based on a comparative analysis of all microarray data, we conclude that the microarray could be a good tool for predicting the expression and intensity of different genes of interest in actual experiments.
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Affiliation(s)
- Ulfuara Shefa
- Department of Biomedical Science, Graduate School, Kyung Hee University, Dongdaemun-gu, Seoul, Republic of Korea
| | - Junyang Jung
- Department of Biomedical Science, Graduate School; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, Dongdaemun-gu, Seoul, Republic of Korea
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2
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Shi Y, Guo S, Wang Y, Liu X, Li Q, Li T. Lamprey Prohibitin2 Arrest G2/M Phase Transition of HeLa Cells through Down-regulating Expression and Phosphorylation Level of Cell Cycle Proteins. Sci Rep 2018; 8:3932. [PMID: 29500418 PMCID: PMC5834496 DOI: 10.1038/s41598-018-22212-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 02/20/2018] [Indexed: 01/13/2023] Open
Abstract
Prohibitin 2(PHB2) is a member of the SFPH trans-membrane family proteins. It is a highly conserved and functionally diverse protein that plays an important role in preserving the structure and function of the mitochondria. In this study, the lamprey PHB2 gene was expressed in HeLa cells to investigate its effect on cell proliferation. The effect of Lm-PHB2 on the proliferation of HeLa cells was determined by treating the cells with pure Lm-PHB2 protein followed by MTT assay. Using the synchronization method with APC-BrdU and PI double staining revealed rLm-PHB2 treatment induced the decrease of both S phase and G0/G1 phase and then increase of G2/M phase. Similarly, cells transfected with pEGFP-N1-Lm-PHB2 also exhibited remarkable reduction in proliferation. Western blot and quantitative real-time PCR(qRT-PCR) assays suggested that Lm-PHB2 caused cell cycle arrest in HeLa cells through inhibition of CDC25C and CCNB1 expression. According to our western blot analysis, Lm-PHB2 was also found to reduce the expression level of Wee1 and PLK1 and the phosphorylation level of CCNB1, CDC25C and CDK1 in HeLa cells. Lamprey prohibitin 2 could arrest G2/M phase transition of HeLa cells through down-regulating expression and phosphorylation level of cell cycle proteins.
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Affiliation(s)
- Ying Shi
- College of Life Sciences, Lamprey Research Center, Liaoning Provincial Key Laboratory of Biotechnology and Drug discovery, Liaoning Normal University, Dalian, 116081, China
| | - Sicheng Guo
- College of Life Sciences, Lamprey Research Center, Liaoning Provincial Key Laboratory of Biotechnology and Drug discovery, Liaoning Normal University, Dalian, 116081, China
| | - Ying Wang
- 210th Hospital of PLA, Dalian, 116011, China
| | - Xin Liu
- College of Life Sciences, Lamprey Research Center, Liaoning Provincial Key Laboratory of Biotechnology and Drug discovery, Liaoning Normal University, Dalian, 116081, China
| | - Qingwei Li
- College of Life Sciences, Lamprey Research Center, Liaoning Provincial Key Laboratory of Biotechnology and Drug discovery, Liaoning Normal University, Dalian, 116081, China.
| | - Tiesong Li
- College of Life Sciences, Lamprey Research Center, Liaoning Provincial Key Laboratory of Biotechnology and Drug discovery, Liaoning Normal University, Dalian, 116081, China.
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Xu HH, Liu SJ, Song SH, Wang RX, Wang WQ, Song SQ. Proteomics analysis reveals distinct involvement of embryo and endosperm proteins during seed germination in dormant and non-dormant rice seeds. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 103:219-42. [PMID: 27035683 DOI: 10.1016/j.plaphy.2016.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 03/01/2016] [Accepted: 03/04/2016] [Indexed: 05/09/2023]
Abstract
Seed germination is a complex trait which is influenced by many genetic, endogenous and environmental factors, but the key event(s) associated with seed germination are still poorly understood. In present study, the non-dormant cultivated rice Yannong S and the dormant Dongxiang wild rice seeds were used as experimental materials, we comparatively investigated the water uptake, germination time course, and the differential proteome of the effect of embryo and endosperm on germination of these two types of seeds. A total of 231 and 180 protein spots in embryo and endosperm, respectively, showed a significant change in abundance during germination. We observed that the important proteins associated with seed germination included those involved in metabolism, energy production, protein synthesis and destination, storage protein, cell growth and division, signal transduction, cell defense and rescue. The contribution of embryo and endosperm to seed germination is different. In embryo, the proteins involved in amino acid activation, sucrose cleavage, glycolysis, fermentation and protein synthesis increased; in endosperm, the proteins involved in sucrose cleavage and glycolysis decreased, and those with ATP and CoQ synthesis and proteolysis increased. Our results provide some new knowledge to understand further the mechanism of seed germination.
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Affiliation(s)
- Heng-Heng Xu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shu-Jun Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shun-Hua Song
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Rui-Xia Wang
- College of Life Science, Linyi University, Linyi 276005, China
| | - Wei-Qing Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Song-Quan Song
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Poitelon Y, Bogni S, Matafora V, Della-Flora Nunes G, Hurley E, Ghidinelli M, Katzenellenbogen BS, Taveggia C, Silvestri N, Bachi A, Sannino A, Wrabetz L, Feltri ML. Spatial mapping of juxtacrine axo-glial interactions identifies novel molecules in peripheral myelination. Nat Commun 2015; 6:8303. [PMID: 26383514 PMCID: PMC4576721 DOI: 10.1038/ncomms9303] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 08/07/2015] [Indexed: 12/13/2022] Open
Abstract
Cell–cell interactions promote juxtacrine signals in specific subcellular domains, which are difficult to capture in the complexity of the nervous system. For example, contact between axons and Schwann cells triggers signals required for radial sorting and myelination. Failure in this interaction causes dysmyelination and axonal degeneration. Despite its importance, few molecules at the axo-glial surface are known. To identify novel molecules in axo-glial interactions, we modified the ‘pseudopodia' sub-fractionation system and isolated the projections that glia extend when they receive juxtacrine signals from axons. By proteomics we identified the signalling networks present at the glial-leading edge, and novel proteins, including members of the Prohibitin family. Glial-specific deletion of Prohibitin-2 in mice impairs axo-glial interactions and myelination. We thus validate a novel method to model morphogenesis and juxtacrine signalling, provide insights into the molecular organization of the axo-glial contact, and identify a novel class of molecules in myelination. Neuron–glia interactions are critical in the nervous system, where they result in the extension of glial pseudopodia. Poitelon et al. isolate these protrusions using an in vitro assay, and, by characterising their proteomes, identify Prohibitin-2 as a regulator of myelination.
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Affiliation(s)
- Y Poitelon
- Hunter James Kelly Research Institute, Department Biochemistry, University at Buffalo, Buffalo, New York 14203, USA.,Division of Genetics and Cell Biology, San Raffaele Hospital, Milano 20132, Italy
| | - S Bogni
- Division of Genetics and Cell Biology, San Raffaele Hospital, Milano 20132, Italy
| | - V Matafora
- Division of Genetics and Cell Biology, San Raffaele Hospital, Milano 20132, Italy
| | - G Della-Flora Nunes
- Hunter James Kelly Research Institute, Department Biochemistry, University at Buffalo, Buffalo, New York 14203, USA
| | - E Hurley
- Hunter James Kelly Research Institute, Department Biochemistry, University at Buffalo, Buffalo, New York 14203, USA
| | - M Ghidinelli
- Hunter James Kelly Research Institute, Department Biochemistry, University at Buffalo, Buffalo, New York 14203, USA.,Division of Genetics and Cell Biology, San Raffaele Hospital, Milano 20132, Italy
| | - B S Katzenellenbogen
- Department of Molecular and Integrative Physiology, University of Illinois and College of Medicine, Urbana Illinois 61801, USA
| | - C Taveggia
- Division of Neuroscience, San Raffaele Hospital, Milano 20132, Italy
| | - N Silvestri
- Department of Neurology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - A Bachi
- Division of Genetics and Cell Biology, San Raffaele Hospital, Milano 20132, Italy
| | - A Sannino
- Department of Engineering for Innovation, University of Salento, Lecce 73100, Italy
| | - L Wrabetz
- Hunter James Kelly Research Institute, Department Biochemistry, University at Buffalo, Buffalo, New York 14203, USA.,Division of Genetics and Cell Biology, San Raffaele Hospital, Milano 20132, Italy.,Department of Neurology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - M L Feltri
- Hunter James Kelly Research Institute, Department Biochemistry, University at Buffalo, Buffalo, New York 14203, USA.,Division of Genetics and Cell Biology, San Raffaele Hospital, Milano 20132, Italy.,Department of Neurology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
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Geuna S. The sciatic nerve injury model in pre-clinical research. J Neurosci Methods 2015; 243:39-46. [PMID: 25629799 DOI: 10.1016/j.jneumeth.2015.01.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 12/15/2022]
Abstract
In the pre-clinical view, the study of peripheral nerve repair and regeneration still needs to be carried out in animal models due to the structural complexity of this organ which can be only partly simulated in vitro. The far most used experimental model is based on the injury of the sciatic nerve, the largest nerve trunk in mammals. In this paper, the potential application of the sciatic nerve injury model in pre-clinical research is critically reviewed. This paper is aimed at helping researchers in properly employing this in vivo model for the study of nerve repair and regeneration as well as interpreting the results in a clinical translation perspective.
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Affiliation(s)
- Stefano Geuna
- Neuroscience Institute of the Cavalieri Ottolenghi Foundation & Department of Clinical and Biological Sciences, University of Turin, Italy.
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Involvement of upregulated SYF2 in Schwann cell differentiation and migration after sciatic nerve crush. Cell Mol Neurobiol 2014; 34:1023-36. [PMID: 24962097 DOI: 10.1007/s10571-014-0078-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 06/02/2014] [Indexed: 01/22/2023]
Abstract
SYF2 is a putative homolog of human p29 in Saccharomyces cerevisiae. It seems to be involved in pre-mRNA splicing and cell cycle progression. Disruption of SYF2 leads to reduced α-tubulin expression and delayed nerve system development in zebrafish. Due to the potential of SYF2 in modulating microtubule dynamics in nervous system, we investigated the spatiotemporal expression of SYF2 in a rat sciatic nerve crush (SNC) model. We found that SNC resulted in a significant upregulation of SYF2 from 3 days to 1 week and subsequently returned to the normal level at 4 weeks. At its peak expression, SYF2 distributed predominantly in Schwann cells. In addition, upregulation of SYF2 was approximately in parallel with Oct-6, and numerous Schwann cells expressing SYF2 were Oct-6 positive. In vitro, we observed enhanced expression of SYF2 during the process of cyclic adenosine monophosphate (cAMP)-induced Schwann cell differentiation. SYF2-specific siRNA-transfected Schwann cells did not show significant morphological change in the process of Schwann cell differentiation. Also, we found shorter and disorganized microtubule structure and a decreased migration in SYF2-specific siRNA-transfected Schwann cells. Together, these findings indicated that the upregulation of SYF2 was associated with Schwann cell differentiation and migration following sciatic nerve crush.
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