Identification and coregulation pattern analysis of long noncoding RNAs following subacute spinal cord injury

Abstract

Long noncoding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in posttranscriptional and transcriptional regulation in eukaryotic cells.However, the characteristics of many lncRNAs, particularly their expression patterns in the lesion epicenter of spinal tissues following subacute spinal cord injury (SCI), remain unclear. In this study, we determined the expression profiles of lncRNAs in the lesion epicenter of spinal tissues after traumatic SCI and predicted latent regulatory networks. Standard Allen's drop surgery was conducted on mice, and hematoxylin and eosin staining was used to observe the damaged area. Highthroughput sequencing was performed to identify the differential expression profiles of lncRNAs. Quantitative real-time polymerase chain reaction was conducted to evaluate the quality of the sequencing results. Bioinformatics analyses, including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, coexpression analysis, and protein-protein interaction analysis, were performed.Targeted binding of lncRNA-miRNA-mRNA was predicted by TargetScan and miRanda. A total of 230 differentially expressed lncRNAs were identified and preliminarily verified, and some potential regulatory networks were constructed. These findings improve our understanding of the mechanisms underlying subacute SCI; differentially expressed lncRNAs are closely involved in pathophysiological processes by regulating multiple pathways. Further studies are essential for revealingThis is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Identification and coregulation pattern analysis of long noncoding RNAs in the mouse brain after Angiostrongylus cantonensis infection

“…After larval infection, brain tissues were collected at 1, 7, 14, and 21 days, fixed in 4% paraformaldehyde, embedded in paraffin, dewaxed in xylene, immersed in different concentrations of ethanol and stained with H&E. Pathological changes in the brains of infected mice at different infection times were observed through H&E staining. After H&E staining, the nuclei were stained blue, and the cytoplasm was stained pink [ 29 ].…”

Research Progress of Long Non-coding RNAs in Spinal Cord Injury

“…A total of 230 DE LncRNAs were identified, of which 172 were up-regulated and 58 were down-regulated [21]. The authors also constructed a ceRNA network to predict the targeting relationship between LncRNAs and miRNAs, which facilitates the screening of novel biomarkers that is critical in the molecular mechanism of SCI [21]. Duran RNA sequencing in the subacute and chronic stages of SCI [22].…”

“…Similarly, the authors reported a ceRNA network of LncRNAs-miRNAs-mRNAs interactions, including 655 nodes and 10,564 edges, in which LncRNA 1700020I14Rik, LncRNA Neat1, Lnc RNAXist and LncRNA Malat1 were identified to play a crucial part in regulating biological signaling pathways in SCI by interacting with other types of RNAs [ 20 ]. In another study, Wenzhao et al identified the expression profiles of LncRNAs after the subacute stage of SCI [ 21 ]. High-throughput sequencing were performed to identify DE LncRNAs, miRNAs and mRNAs in SCI at the transcriptome level, and the results were validated by qRT-PCR [ 21 ].…”

“…In another study, Wenzhao et al identified the expression profiles of LncRNAs after the subacute stage of SCI [ 21 ]. High-throughput sequencing were performed to identify DE LncRNAs, miRNAs and mRNAs in SCI at the transcriptome level, and the results were validated by qRT-PCR [ 21 ]. A total of 230 DE LncRNAs were identified, of which 172 were up-regulated and 58 were down-regulated [ 21 ].…”

“…High-throughput sequencing were performed to identify DE LncRNAs, miRNAs and mRNAs in SCI at the transcriptome level, and the results were validated by qRT-PCR [ 21 ]. A total of 230 DE LncRNAs were identified, of which 172 were up-regulated and 58 were down-regulated [ 21 ]. The authors also constructed a ceRNA network to predict the targeting relationship between LncRNAs and miRNAs, which facilitates the screening of novel biomarkers that is critical in the molecular mechanism of SCI [ 21 ].…”