Identification of key microRNAs and the underlying molecular mechanism in spinal cord ischemia-reperfusion injury in rats

Abstract

Spinal cord ischemia-reperfusion injury (SCII) is a pathological process with severe complications such as paraplegia and paralysis. Aberrant miRNA expression is involved in the development of SCII. Differences in the experimenters, filtering conditions, control selection, and sequencing platform may lead to different miRNA expression results. This study systematically analyzes the available SCII miRNA expression data to explore the key differently expressed miRNAs (DEmiRNAs) and the underlying molecular mechanism in SCII. A systematic bioinformatics analysis was performed on 23 representative rat SCII miRNA datasets from PubMed. The target genes of key DEmiRNAs were predicted on miRDB. The DAVID and TFactS databases were utilized for functional enrichment and transcription factor binding analyses. In this study, 19 key DEmiRNAs involved in SCII were identified, 9 of which were upregulated (miR-144-3p, miR-3568, miR-204, miR-30c, miR-34c-3p, miR-155-3p, miR-200b, miR-463, and miR-760-5p) and 10 downregulated (miR-28-5p, miR-21-5p, miR-702-3p, miR-291a-3p, miR-199a-3p, miR-352, miR-743b-3p, miR-125b-2-3p, miR-129-1-3p, and miR-136). KEGG enrichment analysis on the target genes of the upregulated DEmiRNAs revealed that the involved pathways were mainly the cGMP-PKG and cAMP signaling pathways. KEGG enrichment analysis on the target genes of the downregulated DEmiRNAs revealed that the involved pathways were mainly the Chemokine and MAPK signaling pathways. GO enrichment analysis indicated that the target genes of the upregulated DEmiRNAs were markedly enriched in biological processes such as brain development and the positive regulation of transcription from RNA polymerase II promoter. Target genes of the downregulated DEmiRNAs were mainly enriched in biological processes such as intracellular signal transduction and negative regulation of cell proliferation. According to the transcription factor analysis, the four transcription factors, including SP1, GLI1, GLI2, and FOXO3, had important regulatory effects on the target genes of the key DEmiRNAs. Among the upregulated DEmiRNAs, miR-3568 was especially interesting. While SCII causes severe neurological deficits of lower extremities, the anti-miRNA oligonucleotides (AMOs) of miR-3568 improve neurological function. Cleaved caspase-3 and Bax was markedly upregulated in SCII comparing to the sham group, and miR-3568 AMO reduced the upregulation. Bcl-2 expression levels showed a opposite trend as cleaved caspase-3. The expression of GATA6, GATA4, and RBPJ decreased after SCII and miR-3568 AMO attenuated this upregulation. In conclusion, 19 significant DEmiRNAs in the pathogenesis of SCII were identified, and the underlying molecular mechanisms were validated. The DEmiRNAs could serve as potential intervention targets for SCII. Moreover, inhibition of miR-3568 preserved hind limb function after SCII by reducing apoptosis, possibly through regulating GATA6, GATA4, and RBPJ in SCII.

Effects of Extracorporeal Shockwave Therapy on Functional Recovery and Circulating miR-375 and miR-382-5p after Subacute and Chronic Spinal Cord Contusion Injury in Rats

“…Significant downregulation of miR-199a-3p after SCI constitutes this miRNA as a potential marker for SCI, as also observed by other authors [ 58 , 59 , 60 ]. Furthermore, miR-199a-3p was upregulated at week 14, which indicates the beneficial effects of ESWT.…”

Transcription Profiling of a Revealed the Potential Molecular Mechanism of Governor Vessel Electroacupuncture for Spinal Cord Injury in Rats

“…After spinal cord ischemia-reperfusion injury, mir-144-3p is upregulated, with the main target gene involved in GMP-PKG and cAMP signaling pathways. 42 Our ceRNA regulatory network results indicate that TCONS_ 00125346-miR-125a-3p-SCARB1, TCONS_00128041-miR-338-3p-TPM1, and 1:163182618|163216364-miR-134-5p-LIMK1 are markedly altered in the post-SCI pathophysiological process, providing comprehensive insight toward identifying potential GV-EA therapeutic targets. In this case, additional, specific pathways and molecular mechanisms need to be further studied.…”

“…Therefore, GV-EA may effectively regulate the interaction between TLR2 and miR-144-3p, further reducing the inflammatory response. After spinal cord ischemia-reperfusion injury, mir-144-3p is upregulated, with the main target gene involved in GMP-PKG and cAMP signaling pathways [ 42 ]. Our ceRNA regulatory network results indicate that TCONS_00125346-miR-125a-3p-SCARB1, TCONS_00128041-miR-338-3p-TPM1, and 1:163182618|163216364-miR-134-5p-LIMK1 are markedly altered in the post-SCI pathophysiological process, providing comprehensive insight toward identifying potential GV-EA therapeutic targets.…”

Tanshinone IIA improves Alzheimer’s disease via RNA nuclear-enriched abundant transcript 1/microRNA-291a-3p/member RAS oncogene family Rab22a axis

“…For example, a study by Zhao et al [ 16 ] showed that the lncRNA nuclear-enriched abundant transcript 1 (NEAT1) promotes the development of AD through the miR-124/beta-site amyloid precursor protein-cleaving enzyme axis. In addition, miR-291a-3p, which is associated with inflammation, oxidative stress, and apoptosis, may be downregulated in neural injury[ 17 , 18 ]; however, its role and mechanism of function in AD remain unclear.…”