Identification of Aberrantly Expressed Genes during Aging in Rat Nucleus Pulposus Cells
Nucleus pulposus cells (NPCs) play a vital role in maintaining the homeostasis of the intervertebral disc (IVD). Previous studies have discovered that NPCs exhibited malfunction due to cellular senescence during disc aging and degeneration; this might be one of the key factors of IVD degeneration. T...
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| Format: | Article |
| Language: | English |
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Wiley
2019-01-01
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| Series: | Stem Cells International |
| Online Access: | http://dx.doi.org/10.1155/2019/2785207 |
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| author | Shi Cheng Xiaochuan Li Linghan Lin Zhiwei Jia Yachao Zhao Deli Wang Dike Ruan Yu Zhang |
| author_facet | Shi Cheng Xiaochuan Li Linghan Lin Zhiwei Jia Yachao Zhao Deli Wang Dike Ruan Yu Zhang |
| author_sort | Shi Cheng |
| collection | DOAJ |
| description | Nucleus pulposus cells (NPCs) play a vital role in maintaining the homeostasis of the intervertebral disc (IVD). Previous studies have discovered that NPCs exhibited malfunction due to cellular senescence during disc aging and degeneration; this might be one of the key factors of IVD degeneration. Thus, we conducted this study in order to investigate the altered biofunction and the underlying genes and pathways of senescent NPCs. We isolated and identified NPCs from the tail discs of young (2 months) and old (24 months) SD rats and confirmed the senescent phenotype through SA-β-gal staining. CCK-8 assay, transwell assay, and cell scratch assay were adopted to detect the proliferous and migratory ability of two groups. Then, a rat Gene Chip Clariom™ S array was used to detect differentially expressed genes (DEGs). After rigorous bioinformatics analysis of the raw data, totally, 1038 differentially expressed genes with a fold change>1.5 were identified out of 23189 probes. Among them, 617 were upregulated and 421 were downregulated. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted and revealed numerous number of enriched GO terms and signaling pathways associated with senescence of NPCs. A protein-protein interaction (PPI) network of the DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape software. Module analysis was conducted for the PPI network using the MCODE plugin in Cytoscape. Hub genes were identified by the CytoHubba plugin in Cytoscape. Derived 5 hub genes and most significantly up- or downregulated genes were further verified by real-time PCR. The present study investigated underlying mechanisms in the senescence of NPCs on a genome-wide scale. The illumination of molecular mechanisms of NPCs senescence may assist the development of novel biological methods to treat degenerative disc diseases. |
| format | Article |
| id | doaj-art-da72d9eb831f461e8653a670ca826574 |
| institution | OA Journals |
| issn | 1687-966X 1687-9678 |
| language | English |
| publishDate | 2019-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Stem Cells International |
| spelling | doaj-art-da72d9eb831f461e8653a670ca8265742025-08-20T02:21:25ZengWileyStem Cells International1687-966X1687-96782019-01-01201910.1155/2019/27852072785207Identification of Aberrantly Expressed Genes during Aging in Rat Nucleus Pulposus CellsShi Cheng0Xiaochuan Li1Linghan Lin2Zhiwei Jia3Yachao Zhao4Deli Wang5Dike Ruan6Yu Zhang7Department of Orthopedics, Guangdong General Hospital, Guangdong Academy of Medical Science, South China University of Technology, Guangzhou 510080, ChinaDepartment of Orthopedic Surgery, Gaozhou People’s Hospital, Guangdong 525200, ChinaDepartment of Orthopaedics, The Sixth Medical Centre of PLA General Hospital, 100048 Beijing, ChinaDepartment of Orthopaedics, The 306th Hospital of People’s Liberation Army, Beijing, ChinaDepartment of Orthopaedics, The Sixth Medical Centre of PLA General Hospital, 100048 Beijing, ChinaDepartment of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036 Guangdong, ChinaDepartment of Orthopaedics, The Sixth Medical Centre of PLA General Hospital, 100048 Beijing, ChinaDepartment of Orthopedics, Guangdong General Hospital, Guangdong Academy of Medical Science, South China University of Technology, Guangzhou 510080, ChinaNucleus pulposus cells (NPCs) play a vital role in maintaining the homeostasis of the intervertebral disc (IVD). Previous studies have discovered that NPCs exhibited malfunction due to cellular senescence during disc aging and degeneration; this might be one of the key factors of IVD degeneration. Thus, we conducted this study in order to investigate the altered biofunction and the underlying genes and pathways of senescent NPCs. We isolated and identified NPCs from the tail discs of young (2 months) and old (24 months) SD rats and confirmed the senescent phenotype through SA-β-gal staining. CCK-8 assay, transwell assay, and cell scratch assay were adopted to detect the proliferous and migratory ability of two groups. Then, a rat Gene Chip Clariom™ S array was used to detect differentially expressed genes (DEGs). After rigorous bioinformatics analysis of the raw data, totally, 1038 differentially expressed genes with a fold change>1.5 were identified out of 23189 probes. Among them, 617 were upregulated and 421 were downregulated. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted and revealed numerous number of enriched GO terms and signaling pathways associated with senescence of NPCs. A protein-protein interaction (PPI) network of the DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape software. Module analysis was conducted for the PPI network using the MCODE plugin in Cytoscape. Hub genes were identified by the CytoHubba plugin in Cytoscape. Derived 5 hub genes and most significantly up- or downregulated genes were further verified by real-time PCR. The present study investigated underlying mechanisms in the senescence of NPCs on a genome-wide scale. The illumination of molecular mechanisms of NPCs senescence may assist the development of novel biological methods to treat degenerative disc diseases.http://dx.doi.org/10.1155/2019/2785207 |
| spellingShingle | Shi Cheng Xiaochuan Li Linghan Lin Zhiwei Jia Yachao Zhao Deli Wang Dike Ruan Yu Zhang Identification of Aberrantly Expressed Genes during Aging in Rat Nucleus Pulposus Cells Stem Cells International |
| title | Identification of Aberrantly Expressed Genes during Aging in Rat Nucleus Pulposus Cells |
| title_full | Identification of Aberrantly Expressed Genes during Aging in Rat Nucleus Pulposus Cells |
| title_fullStr | Identification of Aberrantly Expressed Genes during Aging in Rat Nucleus Pulposus Cells |
| title_full_unstemmed | Identification of Aberrantly Expressed Genes during Aging in Rat Nucleus Pulposus Cells |
| title_short | Identification of Aberrantly Expressed Genes during Aging in Rat Nucleus Pulposus Cells |
| title_sort | identification of aberrantly expressed genes during aging in rat nucleus pulposus cells |
| url | http://dx.doi.org/10.1155/2019/2785207 |
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