Construction of circRNA-Mediated Immune-Related ceRNA Network and Identification of Circulating circRNAs as Diagnostic Biomarkers in Acute Ischemic Stroke

References

• Wu S, Wu B, Liu M, et al. Stroke in China: advances and challenges in epidemiology, prevention, and management. Lancet Neurol. 2019;18(4):394–405. doi:10.1016/S1474-4422(18)30500-3
   PubMed Web of Science ®Google Scholar
• Zhou M, Wang H, Zeng X, et al. Mortality, morbidity, and risk factors in China and its provinces, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet. 2019;394(10204):1145–1158. doi:10.1016/S0140-6736(19)30427-1
   PubMed Web of Science ®Google Scholar
• Bonney PA, Walcott BP, Singh P, Nguyen PL, Sanossian N, Mack WJ. The continued role and value of imaging for acute ischemic stroke. Neurosurgery. 2019;85(suppl_1):S23–S30. doi:10.1093/neuros/nyz068
   PubMed Web of Science ®Google Scholar
• Easton JD, Saver JL, Albers GW, et al. Definition and evaluation of transient ischemic attack: a scientific statement for healthcare professionals from the American Heart Association/American Stroke Association Stroke Council; Council on Cardiovascular Surgery and Anesthesia; Council on Cardiovascular Radiology and Intervention; Council on Cardiovascular Nursing; and the Interdisciplinary Council on Peripheral Vascular Disease. The American Academy of Neurology affirms the value of this statement as an educational tool for neurologists. Stroke. 2009;40(6):2276–2293. doi:10.1161/STROKEAHA.108.192218
   PubMed Web of Science ®Google Scholar
• Iadecola C, Buckwalter MS, Anrather J. Immune responses to stroke: mechanisms, modulation, and therapeutic potential. J Clin Invest. 2020;130(6):2777–2788. doi:10.1172/JCI135530
   PubMed Web of Science ®Google Scholar
• Maida CD, Norrito RL, Daidone M, Tuttolomondo A, Pinto A. Neuroinflammatory mechanisms in ischemic stroke: focus on cardioembolic stroke, background, and therapeutic approaches. Int J Mol Sci. 2020;21(18):6454. doi:10.3390/ijms21186454
   PubMed Web of Science ®Google Scholar
• Mengozzi M, Kirkham FA, Girdwood EER, et al. C-reactive protein predicts further ischemic events in patients with transient ischemic attack or lacunar stroke. Front Immunol. 2020;11:1403. doi:10.3389/fimmu.2020.01403
   PubMed Web of Science ®Google Scholar
• Jenny NS, Callas PW, Judd SE, et al. Inflammatory cytokines and ischemic stroke risk: the REGARDS cohort. Neurology. 2019;92(20):e2375–e2384. doi:10.1212/WNL.0000000000007416
   PubMed Web of Science ®Google Scholar
• Katan M, Moon YP, Paik MC, et al. Procalcitonin and midregional proatrial natriuretic peptide as markers of ischemic stroke: the Northern Manhattan study. Stroke. 2016;47(7):1714–1719. doi:10.1161/STROKEAHA.115.011392
   PubMed Web of Science ®Google Scholar
• Palm F, Pussinen PJ, Safer A, et al. Serum matrix metalloproteinase-8, tissue inhibitor of metalloproteinase and myeloperoxidase in ischemic stroke. Atherosclerosis. 2018;271:9–14. doi:10.1016/j.atherosclerosis.2018.02.012
   PubMed Web of Science ®Google Scholar
• Xin R, Gao Y, Gao Y, et al. isoCirc catalogs full-length circular RNA isoforms in human transcriptomes. Nat Commun. 2021;12(1):266. doi:10.1038/s41467-020-20459-8
   PubMed Web of Science ®Google Scholar
• Mehta SL, Dempsey RJ, Vemuganti R. Role of circular RNAs in brain development and CNS diseases. Prog Neurobiol. 2020;186:101746. doi:10.1016/j.pneurobio.2020.101746
   PubMed Web of Science ®Google Scholar
• Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495(7441):384–388. doi:10.1038/nature11993
   PubMed Web of Science ®Google Scholar
• Yang J, Cheng M, Gu B, Wang J, Yan S, Xu D. CircRNA_09505 aggravates inflammation and joint damage in collagen-induced arthritis mice via miR-6089/AKT1/NF-κB axis. Cell Death Dis. 2020;11(10):833. doi:10.1038/s41419-020-03038-z
   PubMed Web of Science ®Google Scholar
• Chen J, Yang X, Liu R, et al. Circular RNA GLIS2 promotes colorectal cancer cell motility via activation of the NF-kappaB pathway. Cell Death Dis. 2020;11(9):788. doi:10.1038/s41419-020-02989-7
   PubMed Web of Science ®Google Scholar
• Zuo L, Zhang L, Zu J, et al. Circulating circular RNAs as biomarkers for the diagnosis and prediction of outcomes in acute ischemic stroke. Stroke. 2020;51(1):319–323. doi:10.1161/STROKEAHA.119.027348
   PubMed Web of Science ®Google Scholar
• Zuo L, Xie J, Liu Y, Leng S, Zhang Z, Yan F. Down-regulation of circular RNA CDC14A peripherally ameliorates brain injury in acute phase of ischemic stroke. J Neuroinflammation. 2021;18(1):283. doi:10.1186/s12974-021-02333-6
   PubMed Web of Science ®Google Scholar
• Barr TL, Conley Y, Ding J, et al. Genomic biomarkers and cellular pathways of ischemic stroke by RNA gene expression profiling. Neurology. 2010;75(11):1009–1014. doi:10.1212/WNL.0b013e3181f2b37f
   PubMed Web of Science ®Google Scholar
• Tiedt S, Prestel M, Malik R, et al. RNA-Seq identifies circulating miR-125a-5p, miR-125b-5p, and miR-143-3p as potential biomarkers for acute ischemic stroke. Circ Res. 2017;121(8):970–980. doi:10.1161/CIRCRESAHA.117.311572
   PubMed Web of Science ®Google Scholar
• Bhattacharya S, Dunn P, Thomas CG, et al. ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. Sci Data. 2018;5:180015. doi:10.1038/sdata.2018.15
   PubMed Web of Science ®Google Scholar
• Breuer K, Foroushani AK, Laird MR, et al. InnateDB: systems biology of innate immunity and beyond–recent updates and continuing curation. Nucleic Acids Res. 2013;41(Databaseissue):D1228–1233. doi:10.1093/nar/gks1147
   PubMed Web of Science ®Google Scholar
• Glažar P, Papavasileiou P, Rajewsky N. circBase: a database for circular RNAs. RNA. 2014;20(11):1666–1670. doi:10.1261/rna.043687.113
   PubMed Web of Science ®Google Scholar
• Kozomara A, Birgaoanu M, Griffiths-Jones S. miRBase: from microRNA sequences to function. Nucleic Acids Res. 2019;47(D1):D155–D162. doi:10.1093/nar/gky1141
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
   PubMed Web of Science ®Google Scholar
• Wu T, Hu E, Xu S, et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation. 2021;2(3):100141. doi:10.1016/j.xinn.2021.100141
   Web of Science ®Google Scholar
• Sticht C, De La Torre C, Parveen A, Gretz N. miRWalk: an online resource for prediction of microRNA binding sites. PLoS One. 2018;13(10):e0206239. doi:10.1371/journal.pone.0206239
   PubMed Web of Science ®Google Scholar
• Liu M, Wang Q, Shen J, Yang BB, Ding X. Circbank: a comprehensive database for circRNA with standard nomenclature. RNA Biol. 2019;16(7):899–905. doi:10.1080/15476286.2019.1600395
   PubMed Web of Science ®Google Scholar
• Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014;505(7483):344–352. doi:10.1038/nature12986
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi:10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Gable AL, Nastou KC, et al. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 2021;49(D1):D605–D612. doi:10.1093/nar/gkaa1074
   PubMed Web of Science ®Google Scholar
• Scardoni G, Petterlini M, Laudanna C. Analyzing biological network parameters with CentiScaPe. Bioinformatics. 2009;25(21):2857–2859. doi:10.1093/bioinformatics/btp517
   PubMed Web of Science ®Google Scholar
• Dong Z, Deng L, Peng Q, Pan J, Wang Y. CircRNA expression profiles and function prediction in peripheral blood mononuclear cells of patients with acute ischemic stroke. J Cell Physiol. 2020;235(3):2609–2618. doi:10.1002/jcp.29165
   PubMed Web of Science ®Google Scholar
• Zhang SR, Phan TG, Sobey CG. Targeting the immune system for ischemic stroke. Trends Pharmacol Sci. 2021;42(2):96–105. doi:10.1016/j.tips.2020.11.010
   PubMed Web of Science ®Google Scholar
• Han B, Zhang Y, Zhang Y, et al. Novel insight into circular RNA HECTD1 in astrocyte activation via autophagy by targeting MIR142-TIPARP: implications for cerebral ischemic stroke. Autophagy. 2018;14(7):1164–1184. doi:10.1080/15548627.2018.1458173
   PubMed Web of Science ®Google Scholar
• Yang L, Han B, Zhang Z, et al. Extracellular vesicle-mediated delivery of circular RNA SCMH1 promotes functional recovery in rodent and nonhuman primate ischemic stroke models. Circulation. 2020;142(6):556–574. doi:10.1161/CIRCULATIONAHA.120.045765
   PubMed Web of Science ®Google Scholar
• Johnston SC, Gress DR, Browner WS, Sidney S. Short-term prognosis after emergency department diagnosis of TIA. JAMA. 2000;284(22):2901–2906. doi:10.1001/jama.284.22.2901
   PubMed Web of Science ®Google Scholar
• Ali-Ahmed F, Federspiel JJ, Liang L, et al. Intravenous tissue plasminogen activator in stroke mimics. Circ Cardiovasc Qual Outcomes. 2019;12(8):e005609. doi:10.1161/CIRCOUTCOMES.119.005609
   PubMed Web of Science ®Google Scholar
• Wan H, You T, Luo W. circ_0003204 regulates cell growth, oxidative stress, and inflammation in ox-LDL-induced vascular endothelial cells via regulating miR-942-5p/HDAC9 axis. Front Cardiovasc Med. 2021;8:646832. doi:10.3389/fcvm.2021.646832
   PubMed Web of Science ®Google Scholar
• Ravetch JV, Bolland S. IgG Fc receptors. Annu Rev Immunol. 2001;19:275–290. doi:10.1146/annurev.immunol.19.1.275
   PubMed Web of Science ®Google Scholar