Gene expression signature analysis and Protein-Protein interaction network construction of Spinal Cord Injury

J. Lai, X. He, F. Wang, J.-m. Tan, J.-x. Wang, S.-m. Xing, L.-b. Shen, L.-q. Fang, P. Yang, J.-m. Tan

Department of Orthopedics, The 98th Military Hospital, Huzhou, Zhejiang Province, China. tanjunming98@gmail.com

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• Orthopedics

BACKGROUND: The aim of this study was to investigate the gene expression profile of thoracic propriospinal neurons between post-injury rat and controls.

MATERIALS AND METHODS: Microarray dataset GSE20907 was downloaded from GEO database, including 12 Spinal Cord Injury (SCI) rat and 12 controls. Student’s t test was employed to identified differentially expressed genes with a fold-change > 1.2. Then, we used DAVID to perform functional enrichment analysis to uncover dysfunctional biological processes and molecular signatures database (MsigDB) to find any potential relationship between SCI gene expression signature and other published gene expression signature. Protein-Protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape. Functional analysis of the hub protein was performed by BinGO.

RESULTS: The maximum change of gene expression profile was found at 3-days post injury and immune response was found upregulated all tested time points. Interestingly, genes upregulated 2-weeks post injury was found significantly overlapped with genes upregulated in brains from Alzheimer’s disease patients. Protein interaction network analysis found that LYN, PTPN6 and SMAD1 could be of great value for further investigation.

CONCLUSIONS: It could be inferred that understanding the underlying molecular mechanism post injury, especially at early moment, may provide novel insight for development of therapeutics strategy.

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