Bioinformatics Analysis On Key Pathways In Axon Regeneration After Spinal Cord Injury In Zebrafish

【Objective】Spinal cord injury(SCI)is a common injury of the central nervous system,which can lead to loss of sensory and motor functions in severe cases.The main reason is that the axons can not regenerate after SCI in mammals.Unlike mammals,zebrafish can regenerate axons after SCI and regain sensory and motor functions within 6-8 weeks after injury.In the present study,bioinformatics method was applied to analyze the differential genes between the regenerated axons and non-regenerated axons in zebrafish after spinal cord injury,so as to explore the key genes and pathways of axon regeneration in zebrafish after SCI,and provide new research targets for the treatment of mammalian spinal cord injury.【Methods】Microarray GSE56842 contains the expression of each gene in the neuron samples of axonal regeneration after spinal cord injury in zebrafish and those without axonal regeneration.In the Gene Expression Omnibus(GEO)database,the differentially expressed genes of microarray GSE56842 were analyzed by online tool GEO2 R,and then the differentially expressed genes with statistical significance were obtained under the selection conditions of P < 0.05 and [logFC] > 1.The original series and platform data of GSE56842 were downloaded,and the heat map of the top 50 upregulated and downregulated DEGs of the gene expression profiles were obtained by an online tool Morpheus.Gene ontology(GO)enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)signal pathway enrichment analysis of differentially expressed genes were performed by online tool DAVID.Cytoscape was used to analyze the protein interaction of differentially expressed genes,and the genes and modules with the highest correlation were screened out.And then,the genes in the interaction module were analyzed for functional enrichment.Finally,the differentially expressed genes and all bioinformatics results were retrieved and analyzed in the database,and the genes and pathways that might play a role in the repair of spinal cord injury in zebrafish and mammals were screened.【Results】1.The present study identified 636 differentially expressed genes(DEGs),including 255 upregulated genes and 381 downregulated genes in the regenerated neuron samples,compared to non-regenerated neuron samples.2.The GO enrichment analysis of the differentially expressed genes showed that the differentially expressed genes were mainly enriched in the Neuron differentiation,cytoskeleton,mitochondrial electron transfer,etc.The up-regulated differentially expressed genes were mainly concentrated in cytochrome oxidase activity,cytoskeleton,mitochondrial electron transport,ion transport,nervous system development and other related items.Down-regulated differentially expressed genes are mainly concentrated in the development of multicellular organisms,the negative regulation of neurogenesis,cell differentiation,Notch signaling pathway,myelin formation and other related items.3.Enrichment results of KEGG signaling pathway of differentially expressed genes showed that up-regulated differentially expressed genes were mainly enriched in oxidative phosphorylation,Wnt signaling pathway,meiosis,fatty acid degradation in neurons with axonal regeneration after spinal cord injury.Downregulated genes are mainly concentrated in amino acid metabolism,amino acid synthesis,TGF-beta signaling pathway,and Notch signaling pathway.4.The results of Protein–Protein Interaction(PPI)network analysis showed that the interaction network contained 480 node genes and 1976 edges.The top 10 genes with the highest correlation and top 2 modules with the highest score were obtained.In the first module,genes were mainly enriched in focal adhesion,tight junction,and regulation of actin cytoskeleton.In the second module,genes were mainly enriched in cardiac muscle contraction,cytokine-cytokine receptor interaction,and TGF-β signaling pathway.【Conclusions】Spectrin may promote axonal regeneration after SCI in zebrafish,and repair effect of spectrin on mammals after SCI is also worthy of further study,while TGF-signal may inhibit repair after SCI in zebrafish.In addition,focal adhesion and tight junction may play an important role in the migration and proliferation of some cells such as schwann cells or neural progenitor cells after SCI in zebrafish.