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Original Research

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

ORCID Icon, , , , , , , , , , & ORCID Icon show all
Pages 2667-2680 | Published online: 22 Jun 2021

References

  • Moskowitz MA, Lo EH, Iadecola C. The science of stroke: mechanisms in search of treatments. Neuron. 2010;67(2):181–198. doi:10.1016/j.neuron.2010.07.002
  • Kang R, Gamdzyk M, Lenahan C, Tang J, Tan S, Zhang JH. The dual role of microglia in blood-brain barrier dysfunction after stroke. Curr Neuropharmacol. 2020;18(12):1237–1249. doi:10.2174/1570159X18666200529150907
  • Zhang L, Wang H. Long non-coding RNA in CNS injuries: a new target for therapeutic intervention. Mol Ther Nucleic Acids. 2019;17:754–766. doi:10.1016/j.omtn.2019.07.013
  • Jin R, Yang G, Li G. Inflammatory mechanisms in ischemic stroke: role of inflammatory cells. J Leukoc Biol. 2010;87(5):779–789. doi:10.1189/jlb.1109766
  • Gülke E, Gelderblom M, Magnus T. Danger signals in stroke and their role on microglia activation after ischemia. Ther Adv Neurol Disord. 2018;11:1756286418774254. doi:10.1177/1756286418774254
  • Perego C, Fumagalli S, De Simoni M-G. Temporal pattern of expression and colocalization of microglia/macrophage phenotype markers following brain ischemic injury in mice. J Neuroinflammation. 2011;8(1):174. doi:10.1186/1742-2094-8-174
  • Roberts TC, Morris KV, Weinberg MS. Perspectives on the mechanism of transcriptional regulation by long non-coding RNAs. Epigenetics. 2014;9(1):13–20. doi:10.4161/epi.26700
  • Bai Y, Nie S, Jiang G, et al. Regulation of CARD8 expression by ANRIL and association of CARD8 single nucleotide polymorphism rs2043211 (p.C10X) with ischemic stroke. Stroke. 2014;45(2):383–388. doi:10.1161/STROKEAHA.113.003393
  • Zhang X, Tang X, Liu K, Hamblin MH, Yin K-J. Long noncoding RNA malat1 regulates cerebrovascular pathologies in ischemic stroke. J Neurosci. 2017;37(7):1797–1806. doi:10.1523/JNEUROSCI.3389-16.2017
  • Liu J, Li Q, Zhang K, et al. Downregulation of the long non-coding RNA Meg3 promotes angiogenesis after ischemic brain injury by activating notch signaling. Mol Neurobiol. 2017;54(10):8179–8190. doi:10.1007/s12035-016-0270-z
  • Zhang X, Zhu X-L, Ji B-Y, et al. LncRNA-1810034E14Rik reduces microglia activation in experimental ischemic stroke. J Neuroinflammation. 2019;16(1):75. doi:10.1186/s12974-019-1464-x
  • Sasaki YTF, Ideue T, Sano M, Mituyama T, Hirose T. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci U S A. 2009;106(8):2525–2530. doi:10.1073/pnas.0807899106
  • Yamazaki T, Souquere S, Chujo T, et al. Functional domains of NEAT1 architectural lncRNA induce paraspeckle assembly through phase separation. Mol Cell. 2018;70(6):1038–1053.e7. doi:10.1016/j.molcel.2018.05.019
  • Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 2009;19(3):347–359. doi:10.1101/gr.087775.108
  • Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i890. doi:10.1093/bioinformatics/bty560
  • Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907–915. doi:10.1038/s41587-019-0201-4
  • Liao Y, Smyth GK, Shi W. Featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–930. doi:10.1093/bioinformatics/btt656
  • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi:10.1186/s13059-014-0550-8
  • Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
  • Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431–432. doi:10.1093/bioinformatics/btq675
  • Bindea G, Mlecnik B, Hackl H, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091–1093. doi:10.1093/bioinformatics/btp101
  • Chen Z, Quan L, Huang A, et al. seq-ImmuCC: cell-centric view of tissue transcriptome measuring cellular compositions of immune microenvironment from mouse RNA-seq data. Front Immunol. 2018;9:1286. doi:10.3389/fimmu.2018.01286
  • National Research Council (US) Committee for the Update of the Guide for the Care and Use of Laboratory Animals. Guide for the Care and Use of Laboratory Animals. 8th ed. National Academies Press (US); 2011. Available from: http://www.ncbi.nlm.nih.gov/books/NBK54050/. Accessed May 16, 2021.
  • Engel O, Kolodziej S, Dirnagl U, Prinz V. Modeling stroke in mice - middle cerebral artery occlusion with the filament model. J Vis Exp. 2011;(47). doi:10.3791/2423
  • Johnson PD, Besselsen DG. Practical aspects of experimental design in animal research. ILAR J. 2002;43(4):202–206. doi:10.1093/ilar.43.4.202
  • Schaar KL, Brenneman MM, Savitz SI. Functional assessments in the rodent stroke model. Exp Transl Stroke Med. 2010;2(1):13. doi:10.1186/2040-7378-2-13
  • Michael B, Janine G, Anne-Carina S, et al. Validity and reliability of neurological scores in mice exposed to middle cerebral artery occlusion. Stroke. 2019;50(10):2875–2882. doi:10.1161/STROKEAHA.119.026652
  • Jayaraj RL, Azimullah S, Beiram R, Jalal FY, Rosenberg GA. Neuroinflammation: friend and foe for ischemic stroke. J Neuroinflammation. 2019;16(1):142. doi:10.1186/s12974-019-1516-2
  • Lennox KA, Behlke MA. Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Res. 2016;44(2):863–877. doi:10.1093/nar/gkv1206
  • Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10(3):155–159. doi:10.1038/nrg2521
  • Bao M-H, Szeto V, Yang BB, Zhu S, Sun H-S, Feng Z-P. Long non-coding RNAs in ischemic stroke. Cell Death Dis. 2018;9(3). doi:10.1038/s41419-018-0282-x
  • Ni X, Su Q, Xia W, et al. Knockdown lncRNA NEAT1 regulates the activation of microglia and reduces AKT signaling and neuronal apoptosis after cerebral ischemic reperfusion. Sci Rep. 2020;10(1):19658. doi:10.1038/s41598-020-71411-1
  • Li P, Duan S, Fu A. Long noncoding RNA NEAT1 correlates with higher disease risk, worse disease condition, decreased miR-124 and miR-125a and predicts poor recurrence-free survival of acute ischemic stroke. J Clin Lab Anal. 2020;34(2):e23056. doi:10.1002/jcla.23056
  • Akira S, Uematsu S, Takeuchi O. Pathogen recognition and innate immunity. Cell. 2006;124(4):783–801. doi:10.1016/j.cell.2006.02.015
  • Iadecola C, Anrather J. The immunology of stroke: from mechanisms to translation. Nat Med. 2011;17(7):796–808. doi:10.1038/nm.2399
  • Taylor RA, Sansing LH. Microglial responses after ischemic stroke and intracerebral hemorrhage. Clin Dev Immunol. 2013;2013:1–10. doi:10.1155/2013/746068
  • Mosser DM, Edwards JP. Exploring the full spectrum of macrophage activation. Nat Rev Immunol. 2008;8(12):958–969. doi:10.1038/nri2448
  • Hu X, Li P, Guo Y, et al. Microglia/macrophage polarization dynamics reveal novel mechanism of injury expansion after focal cerebral ischemia. Stroke. 2012;43(11):3063–3070. doi:10.1161/STROKEAHA.112.659656
  • Wang W, Guo Z-H. Downregulation of lncRNA NEAT1 ameliorates LPS-induced inflammatory responses by promoting macrophage M2 polarization via miR-125a-5p/TRAF6/TAK1 axis. Inflammation. 2020;43(4):1548–1560. doi:10.1007/s10753-020-01231-y
  • Zhang P, Cao L, Zhou R, Yang X, Wu M. The lncRNA Neat1 promotes activation of inflammasomes in macrophages. Nat Commun. 2019;10. doi:10.1038/s41467-019-09482-6
  • Zhao S, Ma L, Chu Z, Xu H, Wu W, Liu F. Regulation of microglial activation in stroke. Acta Pharmacol Sin. 2017;38(4):445–458. doi:10.1038/aps.2016.162
  • Gordon S, Taylor PR. Monocyte and macrophage heterogeneity. Nat Rev Immunol. 2005;5(12):953–964. doi:10.1038/nri1733
  • Giladi A, Amit I. Single-cell genomics: a stepping stone for future immunology discoveries. Cell. 2018;172(1–2):14–21. doi:10.1016/j.cell.2017.11.011
  • Papalexi E, Satija R. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat Rev Immunol. 2018;18(1):35–45. doi:10.1038/nri.2017.76
  • Doetschman T, Georgieva T. Gene editing with CRISPR/Cas9 RNA-directed nuclease. Circ Res. 2017;120(5):876–894. doi:10.1161/CIRCRESAHA.116.309727