Transcriptome-Wide Analysis to Identify the Inflammatory Role of lncRNA Neat1 in Experimental Ischemic Stroke

BACKGROUND: Ischemic stroke is one of the leading causes of mortality and disability worldwide. Following stroke, there is secondary neuroinflammation that promotes further injury. Identifying the long non-coding RNA (lncRNA) involved in neuroinflammation after cerebral ischemic stroke will promote the discovery of potential therapeutic targets. METHODS: We identified differentially expressed genes from genome-wide RNA-seq profiles of mice with focal ischemia using Gene Ontology Term Enrichment, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment analyses. Immune cell infiltration deconvolution, protein-protein interaction network construction, and co-expression network analyses were also used to screen lncRNAs. In further experiments, lncRNA Neat1 knockdown animal models were developed by intraventricular injection of the antisense oligonucleotide before performing middle cerebral artery occlusion (MCAO). An enzyme-linked immunosorbent assay was performed to measure the level of cytokines. Hematoxylin-eosin staining and immunohistochemical staining were used to observe the changes in morphology. RESULTS: Enrichment analysis revealed that differential mRNAs induced neuroinflammation after MCAO. Immune deconvolution showed that the proportion of microglia gradually increased while monocytes decreased within 24 h. We identified six hub lncRNAs (Neat1, Gm10827, Trp53cor1, Mir670hg, C730002L08Rik, and Mir181a-hg) that were highly correlated with activated-microglia mRNAs (cor > 0.8). We found that Neat1 had the highest correlation coefficient with pro-inflammatory factor mRNA levels. In vivo experiments demonstrated that Neat1 had abnormally high expression after MCAO. Knockdown of Neat1 could significantly alleviate brain damage by reducing the number of activated microglia and reducing their release of proinflammatory cytokines. CONCLUSION: We identified inflammation-associated lncRNA Neat1 as crucial, which means it is a potential target for ischemic stroke treatment.