Transcriptome-Wide Analysis to Identify the Inflammatory Role of lncRNA Neat1 in Experimental Ischemic Stroke
Fa Jin, Weiyang Ou, Boyang Wei, Haiyan Fan, Chengcong Wei, Dazhao Fang, Guangxu Li, Wenchao Liu, Jiahui Liu, Lei Jin, Xuying He, Chuanzhi Duan Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Mini...
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2021
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oai:doaj.org-article:a22fa871b57a41c385bc1a533258eebe2021-12-02T18:01:08ZTranscriptome-Wide Analysis to Identify the Inflammatory Role of lncRNA Neat1 in Experimental Ischemic Stroke1178-7031https://doaj.org/article/a22fa871b57a41c385bc1a533258eebe2021-06-01T00:00:00Zhttps://www.dovepress.com/transcriptome-wide-analysis-to-identify-the-inflammatory-role-of-lncrn-peer-reviewed-fulltext-article-JIRhttps://doaj.org/toc/1178-7031Fa Jin, Weiyang Ou, Boyang Wei, Haiyan Fan, Chengcong Wei, Dazhao Fang, Guangxu Li, Wenchao Liu, Jiahui Liu, Lei Jin, Xuying He, Chuanzhi Duan Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People’s Republic of ChinaCorrespondence: Chuanzhi Duan; Xuying He Tel +86 135 399 622 33; +86 136 888 771 33Fax +86 206 164 3010Email doctor_duanzj@163.com; 2517079319@qq.comBackground: 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.Keywords: bioinformatics, lncRNA Neat1, ischemic stroke, MCAO, microglia, neuroinflammationJin FOu WWei BFan HWei CFang DLi GLiu WLiu JJin LHe XDuan CDove Medical Pressarticlebioinformaticslncrna neat1ischemic strokemcaomicroglianeuroinflammationPathologyRB1-214Therapeutics. PharmacologyRM1-950ENJournal of Inflammation Research, Vol Volume 14, Pp 2667-2680 (2021) |
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EN |
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bioinformatics lncrna neat1 ischemic stroke mcao microglia neuroinflammation Pathology RB1-214 Therapeutics. Pharmacology RM1-950 |
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bioinformatics lncrna neat1 ischemic stroke mcao microglia neuroinflammation Pathology RB1-214 Therapeutics. Pharmacology RM1-950 Jin F Ou W Wei B Fan H Wei C Fang D Li G Liu W Liu J Jin L He X Duan C Transcriptome-Wide Analysis to Identify the Inflammatory Role of lncRNA Neat1 in Experimental Ischemic Stroke |
| description |
Fa Jin, Weiyang Ou, Boyang Wei, Haiyan Fan, Chengcong Wei, Dazhao Fang, Guangxu Li, Wenchao Liu, Jiahui Liu, Lei Jin, Xuying He, Chuanzhi Duan Neurosurgery Center, Department of Cerebrovascular Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People’s Republic of ChinaCorrespondence: Chuanzhi Duan; Xuying He Tel +86 135 399 622 33; +86 136 888 771 33Fax +86 206 164 3010Email doctor_duanzj@163.com; 2517079319@qq.comBackground: 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.Keywords: bioinformatics, lncRNA Neat1, ischemic stroke, MCAO, microglia, neuroinflammation |
| format |
article |
| author |
Jin F Ou W Wei B Fan H Wei C Fang D Li G Liu W Liu J Jin L He X Duan C |
| author_facet |
Jin F Ou W Wei B Fan H Wei C Fang D Li G Liu W Liu J Jin L He X Duan C |
| author_sort |
Jin F |
| title |
Transcriptome-Wide Analysis to Identify the Inflammatory Role of lncRNA Neat1 in Experimental Ischemic Stroke |
| title_short |
Transcriptome-Wide Analysis to Identify the Inflammatory Role of lncRNA Neat1 in Experimental Ischemic Stroke |
| title_full |
Transcriptome-Wide Analysis to Identify the Inflammatory Role of lncRNA Neat1 in Experimental Ischemic Stroke |
| title_fullStr |
Transcriptome-Wide Analysis to Identify the Inflammatory Role of lncRNA Neat1 in Experimental Ischemic Stroke |
| title_full_unstemmed |
Transcriptome-Wide Analysis to Identify the Inflammatory Role of lncRNA Neat1 in Experimental Ischemic Stroke |
| title_sort |
transcriptome-wide analysis to identify the inflammatory role of lncrna neat1 in experimental ischemic stroke |
| publisher |
Dove Medical Press |
| publishDate |
2021 |
| url |
https://doaj.org/article/a22fa871b57a41c385bc1a533258eebe |
| work_keys_str_mv |
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1718379007499567104 |