Integrative Analysis of the Roles of lncRNAs and mRNAs in Itaconate-Mediated Protection Against Liver Ischemia-Reperfusion Injury in Mice

References

• Zhai Y, Petrowsky H, Hong JC, Busuttil RW, Kupiec-Weglinski JW. Ischaemia-reperfusion injury in liver transplantation–from bench to bedside. Nat Rev Gastroenterol Hepatol. 2013;10(2):79–89.
   PubMed Web of Science ®Google Scholar
• Lu TF, Yang TH, Zhong CP, et al. Dual effect of hepatic macrophages on liver ischemia and reperfusion injury during liver transplantation. Immune Netw. 2018;18(3):e24.
   PubMed Web of Science ®Google Scholar
• Sun YY, Li XF, Meng XM, Huang C, Zhang L, Li J. Macrophage phenotype in liver injury and repair. Scand J Immunol. 2017;85(3):166–174.
   PubMed Web of Science ®Google Scholar
• Konishi T, Lentsch AB. Hepatic ischemia/reperfusion: mechanisms of tissue injury, repair, and regeneration. Gene Expr. 2017;17(4):277–287.
   PubMedGoogle Scholar
• Hooftman A, O’Neill LAJ. The immunomodulatory potential of the metabolite itaconate. Trends Immunol. 2019;40(8):687–698.
   PubMed Web of Science ®Google Scholar
• Lampropoulou V, Sergushichev A, Bambouskova M, et al. Itaconate links inhibition of succinate dehydrogenase with macrophage metabolic remodeling and regulation of inflammation. Cell Metab. 2016;24(1):158–166.
   PubMed Web of Science ®Google Scholar
• Mills EL, Ryan DG, Prag HA, et al. Itaconate is an anti-inflammatory metabolite that activates Nrf2 via alkylation of KEAP1. Nature. 2018;556(7699):113–117.
   PubMed Web of Science ®Google Scholar
• Zheng Y, Chen Z, She C, et al. Four-octyl itaconate activates Nrf2 cascade to protect osteoblasts from hydrogen peroxide-induced oxidative injury. Cell Death Dis. 2020;11(9):772.
   PubMed Web of Science ®Google Scholar
• Yi Z, Deng M, Scott MJ, et al. Immune-responsive gene 1/itaconate activates nuclear factor erythroid 2-related factor 2 in hepatocytes to protect against liver ischemia-reperfusion injury. Hepatology. 2020;72(4):1394–1411.
   PubMed Web of Science ®Google Scholar
• Tang B, Bao N, He G, Wang J. Long noncoding RNA HOTAIR regulates autophagy via the miR-20b-5p/ATG7 axis in hepatic ischemia/reperfusion injury. Gene. 2019;686:56–62.
   PubMed Web of Science ®Google Scholar
• Huang X, Gao Y, Qin J, Lu S. The mechanism of long non-coding RNA MEG3 for hepatic ischemia-reperfusion: mediated by miR-34a/Nrf2 signaling pathway. J Cell Biochem. 2018;119(1):1163–1172.
   PubMed Web of Science ®Google Scholar
• Chen Z, Jia S, Li D, et al. Silencing of long noncoding RNA AK139328 attenuates ischemia/reperfusion injury in mouse livers. PLoS One. 2013;8(11):e80817.
   PubMed Web of Science ®Google Scholar
• Dai B, Qiao L, Zhang M, et al. lncRNA AK054386 functions as a ceRNA to sequester miR-199 and induce sustained endoplasmic reticulum stress in hepatic reperfusion injury. Oxid Med Cell Longev. 2019;2019:8189079.
   PubMedGoogle Scholar
• Chen Q, Meng X, Liao Q, Chen M. Versatile interactions and bioinformatics analysis of noncoding RNAs. Brief Bioinform. 2019;20(5):1781–1794.
   PubMed Web of Science ®Google Scholar
• Chen Z, Luo Y, Yang W, et al. Comparison analysis of dysregulated LncRNA profile in mouse plasma and liver after hepatic ischemia/reperfusion injury. PLoS One. 2015;10(7):e0133462.
   PubMed Web of Science ®Google Scholar
• ElAzzouny M, Tom CT, Evans CR, et al. Dimethyl itaconate is not metabolized into itaconate intracellularly. J Biol Chem. 2017;292(12):4766–4769.
   PubMed Web of Science ®Google Scholar
• Wang D, Ma Y, Li Z, et al. The role of AKT1 and autophagy in the protective effect of hydrogen sulphide against hepatic ischemia/reperfusion injury in mice. Autophagy. 2012;8(6):954–962.
   PubMed Web of Science ®Google Scholar
• Pan S, Liu L, Pan H, et al. Protective effects of hydroxytyrosol on liver ischemia/reperfusion injury in mice. Mol Nutr Food Res. 2013;57(7):1218–1227.
   PubMed Web of Science ®Google Scholar
• Wang C, Li Z, Zhao B, et al. PGC-1α protects against hepatic ischemia reperfusion injury by Activating PPARα and PPARγ and regulating ROS production. Oxid Med Cell Longev. 2021;2021:6677955.
   PubMed Web of Science ®Google Scholar
• Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25–29.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30.
   PubMed Web of Science ®Google Scholar
• Dennis G Jr, Sherman BT, Hosack DA, et al. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 2003;4(5):P3.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Franceschini A, Kuhn M, et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011;39(Databaseissue):D561–D568.
   PubMedGoogle 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.
   PubMed Web of Science ®Google Scholar
• Chen C, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–1202.
   PubMed Web of Science ®Google Scholar
• Alkan F, Wenzel A, Palasca O, et al. RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. Nucleic Acids Res. 2017;45(8):e60.
   PubMed Web of Science ®Google Scholar
• Caldwell CC, Tschoep J, Lentsch AB. Lymphocyte function during hepatic ischemia/reperfusion injury. J Leukoc Biol. 2007;82(3):457–464.
   PubMed Web of Science ®Google Scholar
• Mukhopadhyay P, Horváth B, Zsengellėr Z, et al. Mitochondrial reactive oxygen species generation triggers inflammatory response and tissue injury associated with hepatic ischemia-reperfusion: therapeutic potential of mitochondrially targeted antioxidants. Free Radic Biol Med. 2012;53(5):1123–1138.
   PubMed Web of Science ®Google Scholar
• Kim SJ, Eum HA, Billiar TR, Lee SM. Role of heme oxygenase 1 in TNF/TNF receptor-mediated apoptosis after hepatic ischemia/reperfusion in rats. Shock. 2013;39(4):380–388.
   PubMed Web of Science ®Google Scholar
• Li SP, Wang FF, Zhang WK, et al. Characteristics of changes in inflammatory cytokines as a function of hepatic ischemia-reperfusion injury stage in mice. Inflammation. 2019;42(6):2139–2147.
   PubMed Web of Science ®Google Scholar
• Xu T, Du Y, Fang XB, et al. New insights into Nod-like receptors (NLRs) in liver diseases. Int J Physiol Pathophysiol Pharmacol. 2018;10(1):1–16.
   PubMedGoogle Scholar
• Zheng J, Li H, He L, et al. Preconditioning of umbilical cord-derived mesenchymal stem cells by rapamycin increases cell migration and ameliorates liver ischaemia/reperfusion injury in mice via the CXCR4/CXCL12 axis. Cell Prolif. 2019;52(2):e12546.
   PubMed Web of Science ®Google Scholar
• Chang WJ, Toledo-Pereyra LH. Toll-like receptor signaling in liver ischemia and reperfusion. J Invest Surg. 2012;25(4):271–277.
   PubMed Web of Science ®Google Scholar
• Mahmoud MF, Gamal S, El-Fayoumi HM. Limonin attenuates hepatocellular injury following liver ischemia and reperfusion in rats via toll-like receptor dependent pathway. Eur J Pharmacol. 2014;740:676–682.
   PubMed Web of Science ®Google Scholar
• Ke B, Shen XD, Ji H, et al. HO-1-STAT3 axis in mouse liver ischemia/reperfusion injury: regulation of TLR4 innate responses through PI3K/PTEN signaling. J Hepatol. 2012;56(2):359–366.
   PubMed Web of Science ®Google Scholar
• Li Z, Zhao F, Cao Y, et al. DHA attenuates hepatic ischemia reperfusion injury by inhibiting pyroptosis and activating PI3K/Akt pathway. Eur J Pharmacol. 2018;835:1–10.
   PubMed Web of Science ®Google Scholar
• Thc DO, Marques PE, Poosti F, et al. Intravital microscopic evaluation of the effects of a CXCR2 antagonist in a model of liver ischemia reperfusion injury in mice. Front Immunol. 2017;8:1917.
   PubMed Web of Science ®Google Scholar
• Yue S, Zhu J, Zhang M, et al. The myeloid heat shock transcription factor 1/β-catenin axis regulates NLR family, pyrin domain-containing 3 inflammasome activation in mouse liver ischemia/reperfusion injury. Hepatology. 2016;64(5):1683–1698.
   PubMed Web of Science ®Google Scholar
• Hamada T, Tsuchihashi S, Avanesyan A, et al. Cyclooxygenase-2 deficiency enhances Th2 immune responses and impairs neutrophil recruitment in hepatic ischemia/reperfusion injury. J Immunol. 2008;180(3):1843–1853.
   PubMed Web of Science ®Google Scholar
• Takasu C, Vaziri ND, Li S, et al. Treatment with dimethyl fumarate ameliorates liver ischemia/reperfusion injury. World J Gastroenterol. 2017;23(25):4508–4516.
   PubMed Web of Science ®Google Scholar
• George J, Tsutsumi M, Tsuchishima M. MMP-13 deletion decreases profibrogenic molecules and attenuates N-nitrosodimethylamine-induced liver injury and fibrosis in mice. J Cell Mol Med. 2017;21(12):3821–3835.
   PubMed Web of Science ®Google Scholar
• Chen X, Patra A, Sadowska GB, Stonestreet BS. Ischemic-reperfusion injury increases matrix metalloproteinases and tissue metalloproteinase inhibitors in fetal sheep brain. Dev Neurosci. 2018;40(3):234–245.
   PubMed Web of Science ®Google Scholar
• Adams DH, Hubscher S, Fear J, Johnston J, Shaw S, Afford S. Hepatic expression of macrophage inflammatory protein-1 alpha and macrophage inflammatory protein-1 beta after liver transplantation. Transplantation. 1996;61(5):817–825.
   PubMed Web of Science ®Google Scholar
• Kopp F, Mendell JT. Functional classification and experimental dissection of long noncoding RNAs. Cell. 2018;172(3):393–407.
   PubMed Web of Science ®Google Scholar
• Sigfridsson E, Marangoni M, Hardingham GE, Horsburgh K, Fowler JH. Deficiency of Nrf2 exacerbates white matter damage and microglia/macrophage levels in a mouse model of vascular cognitive impairment. J Neuroinflammation. 2020;17(1):367.
   PubMed Web of Science ®Google Scholar
• Fowler JH, McQueen J, Holland PR, et al. Dimethyl fumarate improves white matter function following severe hypoperfusion: involvement of microglia/macrophages and inflammatory mediators. J Cereb Blood Flow Metab. 2018;38(8):1354–1370.
   PubMed Web of Science ®Google Scholar
• Li B, Abdalrahman A, Lai Y, et al. Dihydro-CDDO-trifluoroethyl amide suppresses inflammatory responses in macrophages via activation of Nrf2. Biochem Biophys Res Commun. 2014;444(4):555–561.
   PubMed Web of Science ®Google Scholar