1,723
Views
2
CrossRef citations to date
0
Altmetric
Research Paper

Comprehensive analysis of transcriptome‐wide M6A methylation for hepatic ischaemia reperfusion injury in mice

, , , , , , , , , , & ORCID Icon show all
Article: 2201716 | Received 12 Oct 2022, Accepted 07 Apr 2023, Published online: 17 Apr 2023

References

  • Chen S, Li Y, Zhi S, et al. WTAP promotes osteosarcoma tumorigenesis by repressing HMBOX1 expression in an m(6)A-dependent manner. Cell Death Amp Dis. 2020;11(8):659.
  • Du J, Ji H, Ma S, et al., M6a regulator-mediated methylation modification patterns and characteristics of immunity and stemness in low-grade glioma. Briefings in bioinformatics 2021.
  • Song Y, Wang Q, Li L. Comprehensive epigenetic analysis of m6A modification in the hippocampal injury of diabetic rats. 2020;12(20):1811–16.
  • Wen J, Lv R, Ma H, et al. Zc3h13 regulates nuclear RNA m(6)A methylation and mouse embryonic stem cell self-renewal. Molecular Cell. 2018;69(6):1028–1038.e6.
  • Deng S, Zhang H, Zhu K, et al. M6a2target: a comprehensive database for targets of m6A writers, erasers and readers. Brief Bioinform. 2021;22:3.
  • Chen L, Wang P, Bahal R, et al. Ontogenic mRNA expression of RNA modification writers, erasers, and readers in mouse liver. PLoS ONE. 2019;14(12):e0227102.
  • Lan T, Li H, Zhang D, et al. KIAA1429 contributes to liver cancer progression through N6-methyladenosine-dependent post-transcriptional modification of GATA3. Mol Cancer. 2019;18(1):186. Molecular cancer 2019. 10.1186/s12943-019-1106-z.
  • Gu L, Wang L, Chen H, et al. CG14906 (mettl4) mediates m(6)A methylation of U2 snRNA in Drosophila. Cell Discov. 2020;6:44.
  • Chen Y, Zhao Y, Chen J, et al. ALKBH5 suppresses malignancy of hepatocellular carcinoma via m(6)A-guided epigenetic inhibition of LYPD1. Mol Cancer: BioMed Central. 2020;Vol. 191:p. 123.
  • Huang H, Weng H, Sun W, et al. Recognition of RNA N(6)-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nat Cell Biol. 2018;20(3):285–295.
  • Zaccara S, Jaffrey SR. A unified model for the function of YTHDF proteins in regulating m(6)A-Modified mRNA. Cell. 2020;181(7):1582–1595.e18.
  • Li Y, Gu J, Xu F, et al., Molecular characterization, biological function, tumor microenvironment association and clinical significance of m6A regulators in lung adenocarcinoma. Briefings in bioinformatics 2020.
  • Ye L, He S, Mao X, et al. Effect of hepatic macrophage polarization and apoptosis on liver ischemia and reperfusion injury during liver transplantation. Front Immunol. 2020;11:1193.
  • Bi J, Zhang J, Ren Y, et al. Irisin alleviates liver ischemia-reperfusion injury by inhibiting excessive mitochondrial fission, promoting mitochondrial biogenesis and decreasing oxidative stress. Redox Biol. 2019;20:296–306.
  • Jiménez-Castro MB, Cornide-Petronio ME, Gracia-Sancho J. Inflammasome-mediated inflammation in liver Ischemia-reperfusion injury. Cells. 2019;8:10.
  • Yao W, Han X, Ge M, et al. N(6)-methyladenosine (m(6)A) methylation in ischemia-reperfusion injury. Cell Death Amp Dis. 2020;11(6):478.
  • Zhang H, Shi X, Huang T, et al. Dynamic landscape and evolution of m6A methylation in human. Nucleic Acids Res. 2020;48(11):6251–6264.
  • Shi H, Wei J, He C. Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Molecular Cell. 2019;74(4):640–650.
  • 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.
  • 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.
  • Xu Y, Li Z, Lu S, et al. Integrative analysis of the roles of lncRnas and mRnas in itaconate-mediated protection against liver Ischemia-reperfusion injury in mice. 2021;14:4519–4536. DOI:10.2147/JIR.S327467.
  • Wang C, Li Z, Zhao B. PGC-1α protects against hepatic Ischemia reperfusion injury by activating PPARα and PPARγ and regulating ROS production. 2021;2021:6677955. DOI:10.1155/2021/6677955.
  • Wang C, Yu H, Lu S, et al. LncRNA Hnf4αos exacerbates liver ischemia/reperfusion injury in mice via Hnf4αos/Hnf4α duplex-mediated PGC1α suppression. Redox Biol. 2022;57:102498.
  • Xu K, Mo Y, Li D, et al. N 6 -methyladenosine demethylases Alkbh5/Fto regulate cerebral ischemia-reperfusion injury. Ther Adv Chronic Dis. 2020;11:2040622320916024.
  • Xu K, Sun Y, Sheng B, et al. Role of identified RNA N6-methyladenosine methylation in liver. Anal Biochem. 2019;578:45–50.
  • Li Y, Zhang Q, Cui G, et al. M(6)a regulates liver metabolic disorders and hepatogenous diabetes. Genom Proteom Bioinformat. 2020;18(4):371–383.
  • Du YD, Guo WY, Han CH, et al. N6-methyladenosine demethylase FTO impairs hepatic ischemia–reperfusion injury via inhibiting Drp1-mediated mitochondrial fragmentation. Cell Death Amp Dis. 2021;12(5):442.
  • Huang Y, Chen S, Pang L, et al. Isovitexin protects against acute liver injury by targeting PTEN, PI3K and BiP via modification of m6A. Eur J Pharmacol. 2022;917:174749.
  • Liu T, Wei Q, Jin J, et al. The m6A reader YTHDF1 promotes ovarian cancer progression via augmenting EIF3C translation. Nucleic Acids Res. 2020;48(7):3816–3831.
  • He L, Li H, Wu A, et al. Functions of N6-methyladenosine and its role in cancer. Mol Cancer. 2019;18(1):176.
  • Yang Z, Yang S, Cui Y-H. METTL14 facilitates global genome repair and suppresses skin tumorigenesis. Proc Nat Acad Sci. 2021;118:35.
  • Luo Z, Zhang Z, Tai L, et al. Comprehensive analysis of differences of N(6)-methyladenosine RNA methylomes between high-fat-fed and normal mouse livers. Epigenomics. 2019;11(11):1267–1282.
  • Fry NJ, Law BA, Ilkayeva OR, et al. N 6 -methyladenosine is required for the hypoxic stabilization of specific mRnas. RNA. 2017;23(9):1444–1455.
  • Xu Y, Yuan XD, Wu JJ, et al. The N6-methyladenosine mRNA methylase METTL14 promotes renal ischemic reperfusion injury via suppressing YAP1. J Cell Biochem. 2020;121(1):524–533.
  • Song H, Feng X, Zhang H. METTL3 and ALKBH5 oppositely regulate m 6 a modification of TFEB mRNA, which dictates the fate of hypoxia/reoxygenation-treated cardiomyocytes. Autophagy. 2019;15(8):1419–1437.
  • Zhao W, Qi X, Liu L, et al. Epigenetic regulation of m(6)A modifications in human cancer. Mol Ther Nucl Acids. 2020;19:405–412.
  • Wang LJ, Xue Y, Li H, et al. Wilms’ tumour 1-associating protein inhibits endothelial cell angiogenesis by m6A-dependent epigenetic silencing of desmoplakin in brain arteriovenous malformation. J Cell Mol Med. 2020;24(9):4981–4991.
  • Chen Z, Zhao P, Li F, et al. Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. Brief Bioinform. 2020;21(5):1676–1696.
  • Wen K, Zhang Y, Li Y. Comprehensive analysis of transcriptome-wide m 6 a methylome in the anterior capsule of the lens of high myopia patients. Epigenetics. 2020;16:1–14.
  • Zheng L, Tang X, Lu M, et al. MicroRNA-421-3p prevents inflammatory response in cerebral ischemia/reperfusion injury through targeting m6A reader YTHDF1 to inhibit p65 mRNA translation. Int Immunopharmacol. 2020;88:106937.
  • Zuurbier CJ, Bertrand L, Beauloye CR, et al. Cardiac metabolism as a driver and therapeutic target of myocardial infarction. J Cell Mol Med. 2020;24(11):5937–5954.
  • Tani T, Okamoto K, Fujiwara M, et al. Metabolomics analysis elucidates unique influences on purine/pyrimidine metabolism by xanthine oxidoreductase inhibitors in a rat model of renal ischemia-reperfusion injury. Mol Med (Cambridge, MA). 2019;25(1):40.
  • Folch-Puy E, Panisello A, Oliva J, et al. Relevance of endoplasmic reticulum stress cell signaling in liver cold ischemia reperfusion injury. Int J Mol Sci. 2016;17:6.
  • Han Z, Li Y, Yang B, et al. Agmatine attenuates liver ischemia reperfusion injury by activating Wnt/β-catenin signaling in mice. Transplantation. 2020;104(9):1906–1916.
  • Hasumi H, Baba M, Hasumi Y, et al. Folliculin-interacting proteins Fnip1 and Fnip2 play critical roles in kidney tumor suppression in cooperation with Flcn. 2015;112(13):E1624–31.
  • Siggs OM, Stockenhuber A, Deobagkar-Lele M, et al. Mutation of Fnip1 is associated with B-cell deficiency, cardiomyopathy, and elevated AMPK activity. 2016;113(26):E3706–15.
  • Chen QS, Shen A, Dai JW, et al. IL37 overexpression inhibits autophagy and apoptosis induced by hepatic ischemia reperfusion injury via modulating AMPK/mTOR/ULLK1 signalling pathways. Life Sci. 2021;276:119424.
  • Hasumi H, Baba M, Hong SB, et al. Identification and characterization of a novel folliculin-interacting protein FNIP2. Gene. 2008;415(1–2):60–67.
  • Paranavitane V, Coadwell WJ, Eguinoa A, et al. Ll5beta is a phosphatidylinositol (3,4,5)-trisphosphate sensor that can bind the cytoskeletal adaptor, gamma-filamin. J Biol Chem. 2003;278(2):1328–1335.
  • Dowd GC, Bhalla M, Kean B, et al. Role of host type IA phosphoinositide 3-kinase pathway components in invasin-mediated internalization of yersinia enterocolitica. Infect Immun. 2016;84(6):1826–1841.
  • Lin ZY, Chuang WL. Genes responsible for the characteristics of primary cultured invasive phenotype hepatocellular carcinoma cells. Biomed Pharmacother = Biomed Pharmacother. 2012;66(6):454–458.
  • Chen G, Zhou T, Li Y, et al. P53 target miR-29c-3p suppresses colon cancer cell invasion and migration through inhibition of PHLDB2. Biochem Biophys Res Commun. 2017;487(1):90–95.
  • Wang R, Zheng D, Wei L, et al. Regulation of intronic polyadenylation by PCF11 impacts mRNA expression of long genes. Cell Rep. 2019;26(10):2766–2778.e6.
  • Moroz-Omori EV, Huang D, Kumar Bedi R, et al. METTL3 inhibitors for epitranscriptomic modulation of cellular processes. ChemMedchem. 2021;16(19):3035–3043.
  • Garbo S, Zwergel C, Battistelli C. M6a RNA methylation and beyond - the epigenetic machinery and potential treatment options. Drug Discovery Today. 2021;26(11):2559–2574.
  • Yankova E, Blackaby W, Albertella M, et al. Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature. 2021;593(7860):597–601.
  • Liu Y, Liang G, Xu H, et al. Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance. Cell Metab. 2021;33(6):1221–1233.e11.
  • Li N, Kang Y, Wang L, et al. ALKBH5 regulates anti-PD-1 therapy response by modulating lactate and suppressive immune cell accumulation in tumor microenvironment. 2020;117(33):20159–20170.