Bioinformatics analyses of differentially expressed genes associated with spinal cord injury: A microarray-based analysis in a mouse model

Abstract Background: Sarcopenia caused by spinal cord injury seriously affects the muscle function, which impairs the locomotion function of patients. As an effective physiotherapeutic, functional electrical stimulation is benefit to the recovery of muscle function without exact mechanisms. So the objection of the study is to explore the biological regulatory factors related to functional electrical stimulation for muscle function recovery of patients with sarcopenia after spinal cord injury using bioinformatics methods.Methods: The related microarray datasets GSE142426 and GSE33886 were downloaded from the Gene Expression Omnibus database. We used the R software to merge the two datasets, correct the inter-batch differences and screen the differentially expressed genes. Gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway were analyzed by using the DAVID online tool. The STRING database was used to analyze the interaction of differentially encoded proteins. The key genes were selected to draw the ROC curves, and CYCS was used to perform gene set enrichment analysis.Results: A total of 114 differentially expressed genes were selected, including 44 up-regulated genes and 70 down-regulated genes, and four hub genes were identified including CYCS, SUCLG1, ATP5B and ATP5C1. ROC curve showed that CYCS was considered as the best indicator and GSEA analysis showed that up-regulation of CYCS was related to mitochondria and energy metabolism.Conclusion: The mechanism of function electrical stimulation on muscle function recovery of spinal cord injury patients with sarcopenia is mainly related to regulate mitochondrial energy metabolism and scavenge reactive oxygen species to mitigate the oxidative damage.

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Aberrant LncRNA Expression Profile in a Contusion Spinal Cord Injury Mouse Model

BioMed Research International ◽

10.1155/2016/9249401 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 16

Author(s):

Ya Ding ◽

Zhiwen Song ◽

Jinbo Liu

Keyword(s):

Spinal Cord ◽

Spinal Cord Injury ◽

Mouse Model ◽

Expression Profiles ◽

Focal Adhesions ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Receptor Interaction ◽

Lncrna Expression ◽

Cord Injury

Long noncoding RNAs (LncRNAs) play a crucial role in cell growth, development, and various diseases related to the central nervous system. However, LncRNA differential expression profiles in spinal cord injury are yet to be reported. In this study, we profiled the expression pattern of LncRNAs using a microarray method in a contusion spinal cord injury (SCI) mouse model. Compared with a spinal cord without injury, few changes in LncRNA expression levels were noted 1 day after injury. The differential changes in LncRNA expression peaked 1 week after SCI and subsequently declined until 3 weeks after injury. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the reliability of the microarray, demonstrating that the results were reliable. Gene ontology (GO) analysis indicated that differentially expressed mRNAs were involved in transport, cell adhesion, ion transport, and metabolic processes, among others. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the neuroactive ligand-receptor interaction, the PI3K-Akt signaling pathway, and focal adhesions were potentially implicated in SCI pathology. We constructed a dynamic LncRNA-mRNA network containing 264 LncRNAs and 949 mRNAs to elucidate the interactions between the LncRNAs and mRNAs. Overall, the results from this study indicate for the first time that LncRNAs are differentially expressed in a contusion SCI mouse model.

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