Expression Profiles of Long Non-Coding RNAs and Messenger RNAs in a Rat Model of Spinal Cord Injury

Spinal cord injury (SCI) is a serious disorder of the central nervous system with a high disability rate. Long non-coding RNAs (lncRNAs) are reported to mediate many biological processes. The aim of this study was to explore lncRNA and mRNA expression profiles and functional networks after SCI.We identified 5465 differentially expressed lncRNAs (DE lncRNAs) and 8366 differentially expressed mRNAs (DE mRNAs) in the SCI group compared with the sham group (fold change >2.0, P<0.05). Four genes were confirmed by real-time PCR which were consistent with the microarray data. GSEA analysis showed that most marked changes occurred in pathways related to immune inflammation and nerve cell function, including cytokine-cytokine receptor interaction (rno04060), TNF signaling pathway (rno04668), neuroactive ligand-receptor interaction (rno04080)，and GABAergic synapse (rno04727). Enrichment analysis identified 30 signaling pathways, including those associated with inflammation and the immune response. A total of 40 key lncRNAs were identified using the SVM-RFE algorithm. A key lncRNA-mRNAs co-expression network was generated for 230 951 lncRNA-mRNA pairs with half showing positive correlations. Several key DE lncRNAs were predicted to have “cis” or “trans”-regulated target genes. The transcription factors, Sp1, JUN, and SOX10, may regulate the interaction between XR_001837123.1 and ETS 1. In addition, five pairs of ceRNA regulatory sequences were identified. 6 male SD rats were randomly divided into two groups, including 3 in spinal cord injury group and 3 underwent the same laminectomy procedure without subsequent damage to the spinal cord. Rats were anesthetized at 3 days post-SCI, and the T10 spinal cord segments centered on and enclosing the injured site were collected. Microarray analysis was performed to investigate the lncRNA and mRNAs expression patterns in rat spinal cord three days after SCI.