Bioinformatics Analysis Of Acute Spinal Cord Injury

Background: Acute spinal cord injury(ASCI)contains primary and secondary mechanisms.In the last 10 years,numerous gene expression profiling studies investigated a large number of candidate genes related to secondary SCI.However,temporal and spatial changes of gene expression in secondary SCI are complex and still unclear.Objectives: The purpose of the work is to find out the critical genes related to ASCI,temporal and spatial changes of gene expression,and significant pathways via bioinformatics methods.Materials and Methods: The National Centre for Biotechnology Information Gene Expression Omnibus database provided microarray data GSE5296.We normalised the raw data and figured the differentially expressed genes(DEGs).Subsequently,Venny 2.1 constructed Venn diagrams by comparing the lists of DEGs.We also used the Kyoto Encyclopaedia of Genes and Genomes pathway and Gene Ontology enrichment analysis of DEGs.Finally,the PPI networks of DEGs were performed,and MCODE was used to screen the hub genes with Cytoscape software.Results: After pre-processing the data,we analysed DEGs between the post-ASCI groups and sham groups in the different regions at varying time points.As a result,there were 214,and 165 upregulated DEGs in the trauma site at 7 and 28 days,respectively,but there were not DEGs in the other different regions and varying time points.Subsequently,Venn diagram analysis of DEGs in the trauma site at 7 and28 days was conducted.There were 135 common upregulated DEGs in the trauma site at 7 and 28 days,79 uniquely upregulated DEGs in the trauma site at 7 days,and 30 uniquely upregulated DEGs in the trauma site at 28 days.Finally,after PPI network and gene module analysis,one module consisted of 28 genes was generated by 135 upregulated DEGs,and this 28 genes are associated with lysosome and innate immune cells in ASCI.one module consisted of 8 genes was generated by 79 upregulated DEGs,and this 8 genes are associated with cell cycle in ASCI.Two important modules consisted of 6 genes were generated by 79 upregulated DEGs,and this 6 genes are associated with autoimmunity in ASCI.Conclusion: This work presents the molecular mechanisms that possibly related to ASCI and figured out some critical SCI-related genes,temporal and spatial changes of gene expression,and significant pathways,building a foundation for further experiments and the advances of new targeted therapies as prospective treatments for ASCI.