Comprehensive analysis of m⁶A methylomes in idiopathic pulmonary arterial hypertension

References

• Thenappan T, Ormiston ML, Ryan JJ, et al. Pulmonary arterial hypertension: pathogenesis and clinical management. BMJ. 2018;360:j5492. doi: 10.1136/bmj.j5492
   PubMed Web of Science ®Google Scholar
• Thenappan T, Chan SY, Weir EK. Role of extracellular matrix in the pathogenesis of pulmonary arterial hypertension. Am J Physiol Heart Circ Physiol. 2018;315(5):H1322–H1331. doi: 10.1152/ajpheart.00136.2018
   PubMed Web of Science ®Google Scholar
• Galie N, Humbert M, Vachiery JL, et al. ESC/ERS Guidelines for the diagnosis and treatment of pulmonary hypertension: the joint task force for the diagnosis and treatment of pulmonary hypertension of the European society of cardiology (ESC) and the European respiratory society (ERS): endorsed by: association for European paediatric and congenital cardiology (AEPC), international society for heart and lung transplantation (ISHLT). Eur Heart J. 2016;37(1):67–22. doi: 10.1093/eurheartj/ehv317
   PubMed Web of Science ®Google Scholar
• Malekmohammad M, Folkerts G, Kashani BS, et al. Exhaled nitric oxide is not a biomarker for idiopathic pulmonary arterial hypertension or for treatment efficacy. BMC Pulm Med. 2019;19(1):188. doi: 10.1186/s12890-019-0954-z
   PubMed Web of Science ®Google Scholar
• Badagliacca R, Rischard F, Papa S, et al. Clinical implications of idiopathic pulmonary arterial hypertension phenotypes defined by cluster analysis. J Heart Lung Transplant. 2020;39(4):310–320. doi: 10.1016/j.healun.2019.12.012
   PubMed Web of Science ®Google Scholar
• Morena F, Argentati C, Bazzucchi M, et al. Above the epitranscriptome: RNA modifications and stem cell identity. Genes (Basel). 2018;9(7):329. doi: 10.3390/genes9070329
   PubMed Web of Science ®Google Scholar
• Vu LP, Cheng Y, Kharas MG. The biology of m6A RNA methylation in normal and malignant hematopoiesis. Cancer Discov. 2019;9(1):25–33. doi: 10.1158/2159-8290.CD-18-0959
   PubMed Web of Science ®Google Scholar
• Wang X, Zhao BS, Roundtree IA, et al. N(6)-methyladenosine modulates messenger RNA translation efficiency. Cell. 2015;161(6):1388–1399. doi: 10.1016/j.cell.2015.05.014
   PubMed Web of Science ®Google Scholar
• Zhao BS, Wang X, Beadell AV, et al. m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature. 2017;542(7642):475–478. doi: 10.1038/nature21355
   PubMed Web of Science ®Google Scholar
• 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. doi: 10.1038/s41556-018-0045-z
   PubMed Web of Science ®Google Scholar
• Wu Y, Xie L, Wang M, et al. Mettl3-mediated m6A RNA methylation regulates the fate of bone marrow mesenchymal stem cells and osteoporosis. Nat Commun. 2018;9(1):4772. doi: 10.1038/s41467-018-06898-4
   PubMedGoogle Scholar
• He L, Li J, Wang X, et al. The dual role of N6-methyladenosine modification of RNAs is involved in human cancers. J Cell Mol Med. 2018;22(10):4630–4639. doi: 10.1111/jcmm.13804
   PubMed Web of Science ®Google Scholar
• Spiekerkoetter E, Goncharova EA, Guignabert C, et al. Hot topics in the mechanisms of pulmonary arterial hypertension disease: cancer-like pathobiology, the role of the adventitia, systemic involvement, and right ventricular failure. Pulm Circ. 2019;9(4):2045894019889775. doi: 10.1177/2045894019889775
   Web of Science ®Google Scholar
• Su H, Wang G, Wu L, et al. Transcriptome-wide map of m6A circRnas identified in a rat model of hypoxia mediated pulmonary hypertension. BMC Genomics. 2020;21(1):39. doi: 10.1186/s12864-020-6462-y
   PubMed Web of Science ®Google Scholar
• Hu L, Wang J, Huang H, et al. YTHDF1 regulates pulmonary hypertension through translational control of MAGED1. Am J Respir Crit Care Med. 2021;203(9):1158–1172. doi: 10.1164/rccm.202009-3419OC
   PubMed Web of Science ®Google Scholar
• Zhang L, Zeng XX, YM L, et al. Keratin 1 attenuates hypoxic pulmonary artery hypertension by suppressing pulmonary artery media smooth muscle expansion. Acta Physiol (Oxf). 2021;231(2):e13558. doi: 10.1111/apha.13558
   PubMed Web of Science ®Google Scholar
• Yun X, Jiang H, Lai N, et al. Aquaporin 1-mediated changes in pulmonary arterial smooth muscle cell migration and proliferation involve beta-catenin. Am J Physiol Lung Cell Mol Physiol. 2017;313(5):L889–L898. doi: 10.1152/ajplung.00247.2016
   PubMed Web of Science ®Google Scholar
• Meyer KD, Saletore Y, Zumbo P, et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3’ UTRs and near stop codons. Cell. 2012;149(7):1635–1646. doi: 10.1016/j.cell.2012.05.003
   PubMed Web of Science ®Google Scholar
• Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–515. doi: 10.1038/nbt.1621
   PubMed Web of Science ®Google Scholar
• Zhou XL, Liu ZB, Zhu RR, et al. NSD2 silencing alleviates pulmonary arterial hypertension by inhibiting trehalose metabolism and autophagy. Clin Sci. 2019;133(9):1085–1096. doi: 10.1042/CS20190142
   Web of Science ®Google Scholar
• Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10–12. doi: 10.14806/ej.17.1.200
   Google Scholar
• Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357–360. doi: 10.1038/nmeth.3317
   PubMed Web of Science ®Google Scholar
• Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137
   PubMed Web of Science ®Google Scholar
• Shen L, Shao NY, Liu X, et al. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. Plos One. 2013;8(6):e65598. doi: 10.1371/journal.pone.0065598
   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. doi: 10.1093/nar/28.1.27
   PubMed Web of Science ®Google Scholar
• Kanehisa M. Toward understanding the origin and evolution of cellularorganisms. Protein Sci. 2019;28(11):1947–1951. doi: 10.1002/pro.3715
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Furumichi M, Sato Y, et al. KEGG: integrating viruses and cellular organisms. Nucleic Acids Res. 2021;49(D1):D545–D551. doi: 10.1093/nar/gkaa970
   PubMed Web of Science ®Google Scholar
• Zhong X, Yu J, Frazier K, et al. Circadian clock regulation of hepatic lipid metabolism by modulation of m6A mRNA methylation. Cell Rep. 2018;25(7):1816–1828. doi: 10.1016/j.celrep.2018.10.068
   PubMed Web of Science ®Google Scholar
• Chen T, Hao YJ, Zhang Y, et al. m6A RNA methylation is regulated by microRnas and promotes reprogramming to pluripotency. Cell Stem Cell. 2015;16(3):289–301. doi: 10.1016/j.stem.2015.01.016
   PubMed Web of Science ®Google Scholar
• Zhang S, Zhao BS, Zhou A, et al. m6A demethylase ALKBH5 maintains tumorigenicity of glioblastoma stem-like cells by sustaining FOXM1 expression and cell proliferation program. Cancer Cell. 2017;31(4):591–606. doi: 10.1016/j.ccell.2017.02.013
   PubMed Web of Science ®Google Scholar
• Song H, Feng X, Zhang H, et al. METTL3 and ALKBH5 oppositely regulate m6A modification of TFEB mRNA, which dictates the fate of hypoxia/reoxygenation-treated cardiomyocytes. Autophagy. 2019;15(8):1419–1437. doi: 10.1080/15548627.2019.1586246
   PubMed Web of Science ®Google Scholar
• Dorn LE, Lasman L, Chen J, et al. The N(6)-methyladenosine mRNA methylase METTL3 controls cardiac homeostasis and hypertrophy. Circulation. 2019;139(4):533–545. doi: 10.1161/CIRCULATIONAHA.118.036146
   PubMed Web of Science ®Google Scholar
• Mathiyalagan P, Adamiak M, Mayourian J, et al. FTO-dependent N(6)-methyladenosine regulates cardiac function during remodeling and repair. Circulation. 2019;139(4):518–532. doi: 10.1161/CIRCULATIONAHA.118.033794
   PubMed Web of Science ®Google Scholar
• Qin Y, Qiao Y, Li L, et al. The m6A methyltransferase METTL3 promotes hypoxic pulmonary arterial hypertension. Life Sci. 2021;274:119366. doi: 10.1016/j.lfs.2021.119366
   PubMed Web of Science ®Google Scholar
• Zeng Y, Huang T, Zuo W, et al. Integrated analysis of m6A mRNA methylation in rats with monocrotaline-induced pulmonary arterial hypertension. Aging. 2021;13(14):18238–18256. doi: 10.18632/aging.203230
   PubMedGoogle Scholar
• de Jesus Perez V, Yuan K, Alastalo TP, et al. Targeting the Wnt signaling pathways in pulmonary arterial hypertension. Drug Discov Today. 2014;19(8):1270–1276. doi: 10.1016/j.drudis.2014.06.014
   PubMed Web of Science ®Google Scholar
• Chen F, Wang H, Zhao J, et al. Grape seed proanthocyanidin inhibits monocrotaline-induced pulmonary arterial hypertension via attenuating inflammation: in vivo and in vitro studies. J Nutr Biochem. 2019;67:72–77. doi: 10.1016/j.jnutbio.2019.01.013
   PubMed Web of Science ®Google Scholar
• Pang Y, Liang MT, Gong Y, et al. HGF reduces disease severity and inflammation by attenuating the NF-kappaB signaling in a rat model of pulmonary artery hypertension. Inflammation. 2018;41(3):924–931. doi: 10.1007/s10753-018-0747-1
   PubMed Web of Science ®Google Scholar
• Jing X, Jiang T, Dai L, et al. Hypoxia-induced autophagy activation through NF-kappaB pathway regulates cell proliferation and migration to induce pulmonary vascular remodeling. Exp Cell Res. 2018;368(2):174–183. doi: 10.1016/j.yexcr.2018.04.026
   PubMed Web of Science ®Google Scholar
• Parpaleix A, Amsellem V, Houssaini A, et al. Role of interleukin-1 receptor 1/MyD88 signalling in the development and progression of pulmonary hypertension. Eur Respir J. 2016;48(2):470–483. doi: 10.1183/13993003.01448-2015
   PubMed Web of Science ®Google Scholar
• Budas GR, Boehm M, Kojonazarov B, et al. ASK1 inhibition halts disease progression in preclinical models of pulmonary arterial hypertension. Am J Respir Crit Care Med. 2018;197(3):373–385. doi: 10.1164/rccm.201703-0502OC
   PubMed Web of Science ®Google Scholar
• Leong ZP, Hikasa Y. Effects of masitinib compared with tadalafil for the treatment of monocrotaline-induced pulmonary arterial hypertension in rats. Vasc Pharmacol. 2019;122-123:106599. doi: 10.1016/j.vph.2019.106599
   PubMed Web of Science ®Google Scholar
• Church AC, Martin DH, Wadsworth R, et al. The reversal of pulmonary vascular remodeling through inhibition of p38 MAPK-alpha: a potential novel anti-inflammatory strategy in pulmonary hypertension. Am J Physiol Lung Cell Mol Physiol. 2015;309(4):L333–347. doi: 10.1152/ajplung.00038.2015
   PubMed Web of Science ®Google Scholar
• Nasim MT, Ogo T, Chowdhury HM, et al. BMPR-II deficiency elicits pro-proliferative and anti-apoptotic responses through the activation of TGFβ-TAK1-MAPK pathways in PAH. Human Molecular Genetics. 2012;21(11):2548–2558. doi: 10.1093/hmg/dds073
   PubMed Web of Science ®Google Scholar
• Savai R, Al-Tamari HM, Sedding D, et al. Pro-proliferative and inflammatory signaling converge on FoxO1 transcription factor in pulmonary hypertension. Nat Med. 2014;20(11):1289–1300. doi: 10.1038/nm.3695
   PubMed Web of Science ®Google Scholar
• Xu F, Lin H, He P, et al. A TP53-associated gene signature for prediction of prognosis and therapeutic responses in lung squamous cell carcinoma. Oncoimmunology. 2020;9(1):1731943. doi: 10.1080/2162402X.2020.1731943
   PubMed Web of Science ®Google Scholar
• Mizuno S, Bogaard HJ, Kraskauskas D, et al. P53 Gene deficiency promotes hypoxia-induced pulmonary hypertension and vascular remodeling in mice. Am J Physiol Lung Cell Mol Physiol. 2011;300(5):L753–761. doi: 10.1152/ajplung.00286.2010
   PubMed Web of Science ®Google Scholar
• Wang Y, Zhong B, Wu Q, et al. Effect of aldosterone on senescence and proliferation inhibition of endothelial progenitor cells induced by sirtuin 1 (SIRT1) in pulmonary arterial hypertension. Med Sci Monit. 2020;18(26):e920678. doi: 10.12659/MSM.920678
   Google Scholar
• Zabini D, Granton E, Hu Y, et al. Loss of SMAD3 promotes vascular remodeling in pulmonary arterial hypertension via MRTF disinhibition. Am J Respir Crit Care Med. 2018;197(2):244–260. doi: 10.1164/rccm.201702-0386OC
   PubMed Web of Science ®Google Scholar
• Zhao M, Chen N, Li X, et al. MiR-629 regulates hypoxic pulmonary vascular remodelling by targeting FOXO3 and PERP. J Cell Mol Med. 2019;23(8):5165–5175. doi: 10.1111/jcmm.14385
   PubMed Web of Science ®Google Scholar
• Sankhe S, Manousakidi S, Antigny F, et al. T-type Ca(2+) channels elicit pro-proliferative and anti-apoptotic responses through impaired PP2A/Akt1 signaling in PASMCs from patients with pulmonary arterial hypertension. Biochim Biophys Acta, Mol Cell Res. 2017;1864(10):1631–1641. doi: 10.1016/j.bbamcr.2017.06.018
   PubMed Web of Science ®Google Scholar
• Wang H, Xie B, Kong Y, et al. Overexpression of RPS27a contributes to enhanced chemoresistance of CML cells to imatinib by the transactivated STAT3. Oncotarget. 2016;7(14):18638–18650. doi: 10.18632/oncotarget.7888
   PubMedGoogle Scholar
• Niu Y, Lin Z, Wan A, et al. Loss-of-function genetic screening identifies ALDOA as an essential driver for liver cancer cell growth under hypoxia. Hepatology. 2021Apr 4;74(3):1461–1479. doi: 10.1002/hep.31846
   PubMed Web of Science ®Google Scholar