Identification of hub genes in the subacute spinal cord injury in rats
Abstract Background Spinal cord injury (SCI) is a common trauma in clinical practices. Subacute SCI is mainly characterized by neuronal apoptosis, axonal demyelination, Wallerian degeneration, axonal remodeling, and glial scar formation. It has been discovered in recent years that inflammatory respo...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-08-01
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| Series: | BMC Neuroscience |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12868-022-00737-5 |
| _version_ | 1817998774789734400 |
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| author | Lei Yan Jiawei Fu Xiong Dong Baishen Chen Hongxiang Hong Zhiming Cui |
| author_facet | Lei Yan Jiawei Fu Xiong Dong Baishen Chen Hongxiang Hong Zhiming Cui |
| author_sort | Lei Yan |
| collection | DOAJ |
| description | Abstract Background Spinal cord injury (SCI) is a common trauma in clinical practices. Subacute SCI is mainly characterized by neuronal apoptosis, axonal demyelination, Wallerian degeneration, axonal remodeling, and glial scar formation. It has been discovered in recent years that inflammatory responses are particularly important in subacute SCI. However, the mechanisms mediating inflammation are not completely clear. Methods The gene expression profiles of GSE20907, GSE45006, and GSE45550 were downloaded from the GEO database. The models of the three gene expression profiles were all for SCI to the thoracic segment of the rat. The differentially expressed genes (DEGs) and weighted correlation network analysis (WGCNA) were performed using R software, and functional enrichment analysis and protein–protein interaction (PPI) network were performed using Metascape. Module analysis was performed using Cytoscape. Finally, the relative mRNA expression level of central genes was verified by RT-PCR. Results A total of 206 candidate genes were identified, including 164 up-regulated genes and 42 down-regulated genes. The PPI network was evaluated, and the candidate genes enrichment results were mainly related to the production of tumor necrosis factors and innate immune regulatory response. Twelve core genes were identified, including 10 up-regulated genes and 2 down-regulated genes. Finally, seven hub genes with statistical significance in both the RT-PCR results and expression matrix were identified, namely Itgb1, Ptprc, Cd63, Lgals3, Vav1, Shc1, and Casp4. They are all related to the activation process of microglia. Conclusion In this study, we identified the hub genes and signaling pathways involved in subacute SCI using bioinformatics methods, which may provide a molecular basis for the future treatment of SCI. |
| first_indexed | 2024-04-14T02:57:48Z |
| format | Article |
| id | doaj.art-4101ca09ee74402892064966d1c72093 |
| institution | Directory Open Access Journal |
| issn | 1471-2202 |
| language | English |
| last_indexed | 2024-04-14T02:57:48Z |
| publishDate | 2022-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Neuroscience |
| spelling | doaj.art-4101ca09ee74402892064966d1c720932022-12-22T02:16:00ZengBMCBMC Neuroscience1471-22022022-08-0123111410.1186/s12868-022-00737-5Identification of hub genes in the subacute spinal cord injury in ratsLei Yan0Jiawei Fu1Xiong Dong2Baishen Chen3Hongxiang Hong4Zhiming Cui5The Second Affiliated Hospital of Nantong UniversityThe Second Affiliated Hospital of Nantong UniversityThe Second Affiliated Hospital of Nantong UniversityThe Second Affiliated Hospital of Nantong UniversityThe Second Affiliated Hospital of Nantong UniversityThe Second Affiliated Hospital of Nantong UniversityAbstract Background Spinal cord injury (SCI) is a common trauma in clinical practices. Subacute SCI is mainly characterized by neuronal apoptosis, axonal demyelination, Wallerian degeneration, axonal remodeling, and glial scar formation. It has been discovered in recent years that inflammatory responses are particularly important in subacute SCI. However, the mechanisms mediating inflammation are not completely clear. Methods The gene expression profiles of GSE20907, GSE45006, and GSE45550 were downloaded from the GEO database. The models of the three gene expression profiles were all for SCI to the thoracic segment of the rat. The differentially expressed genes (DEGs) and weighted correlation network analysis (WGCNA) were performed using R software, and functional enrichment analysis and protein–protein interaction (PPI) network were performed using Metascape. Module analysis was performed using Cytoscape. Finally, the relative mRNA expression level of central genes was verified by RT-PCR. Results A total of 206 candidate genes were identified, including 164 up-regulated genes and 42 down-regulated genes. The PPI network was evaluated, and the candidate genes enrichment results were mainly related to the production of tumor necrosis factors and innate immune regulatory response. Twelve core genes were identified, including 10 up-regulated genes and 2 down-regulated genes. Finally, seven hub genes with statistical significance in both the RT-PCR results and expression matrix were identified, namely Itgb1, Ptprc, Cd63, Lgals3, Vav1, Shc1, and Casp4. They are all related to the activation process of microglia. Conclusion In this study, we identified the hub genes and signaling pathways involved in subacute SCI using bioinformatics methods, which may provide a molecular basis for the future treatment of SCI.https://doi.org/10.1186/s12868-022-00737-5Spinal cord injuryWGCNAPPIBioinformatics analysis |
| spellingShingle | Lei Yan Jiawei Fu Xiong Dong Baishen Chen Hongxiang Hong Zhiming Cui Identification of hub genes in the subacute spinal cord injury in rats BMC Neuroscience Spinal cord injury WGCNA PPI Bioinformatics analysis |
| title | Identification of hub genes in the subacute spinal cord injury in rats |
| title_full | Identification of hub genes in the subacute spinal cord injury in rats |
| title_fullStr | Identification of hub genes in the subacute spinal cord injury in rats |
| title_full_unstemmed | Identification of hub genes in the subacute spinal cord injury in rats |
| title_short | Identification of hub genes in the subacute spinal cord injury in rats |
| title_sort | identification of hub genes in the subacute spinal cord injury in rats |
| topic | Spinal cord injury WGCNA PPI Bioinformatics analysis |
| url | https://doi.org/10.1186/s12868-022-00737-5 |
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