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Original Research

Transcriptome-Wide High-Throughput m6A Sequencing of Differential m6A Methylation Patterns in the Human Rheumatoid Arthritis Fibroblast-Like Synoviocytes Cell Line MH7A

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Pages 575-586 | Published online: 25 Feb 2021

References

  • Fu Y, Dominissini D, Rechavi G, He C. Gene expression regulation mediated through reversible m6A RNA methylation. Nat Rev Genet. 2014;15(5):293–306. doi:10.1038/nrg3724
  • Burgess A, David R, Searle IR. Deciphering the epitranscriptome: a green perspective. J Integr Plant Biol. 2016;58(10):822–835. doi:10.1111/jipb.12483
  • Zhang X-Z, Liu H, Chen S-R. Mechanisms of long non-coding RNAs in cancers and their dynamic regulations. Cancers. 2020;12(5):5. doi:10.3390/cancers12051245
  • Li D, Cai L, Meng R, Feng Z, Xu Q. METTL3 Modulates Osteoclast Differentiation and Function by Controlling RNA Stability and Nuclear Export. Int J Mol Sci. 2020;21:5.
  • Li E, Wei B, Wang X, Kang R. METTL3 enhances cell adhesion through stabilizing integrin β1 mRNA via an m6A-HuR-dependent mechanism in prostatic carcinoma.. Am J Cancer Res. 2020;10(3):1012–1025.
  • Qin Y, Li L, Luo E, et al. Role of m6A RNA methylation in cardiovascular disease (Review). Int J Mol Med. 2020;46(6):1958–1972. doi:10.3892/ijmm.2020.4746
  • Reichel M, Köster T, Staiger D. Marking RNA: m6A writers, readers, and functions in Arabidopsis. Journal of Molecular Cell Biology. 2019;11(10):899–910. doi:10.1093/jmcb/mjz085
  • Xu S, Li Y, Chen J-P, et al. Oxygen glucose deprivation/re-oxygenation-induced neuronal cell death is associated with Lnc-D63785 m6A methylation and miR-422a accumulation. Cell Death Dis. 2020;2020(9):816. doi:10.1038/s41419-020-03021-8
  • Fei Q, Zou Z, Roundtree IA, Sun HL, He C. YTHDF2 promotes mitotic entry and is regulated by cell cycle mediators. PLoS Biol. 2020;18(4):e3000664.
  • Hazra D, Chapat C, Graille M. m6A mRNA Destiny: chained to the rhYTHm by the YTH-Containing Proteins. Genes. 2019;10(1):1. doi:10.3390/genes10010049
  • Sparks JA. Rheumatoid Arthritis. Ann Intern Med. 2019;170(1):Itc1–itc16. doi:10.7326/AITC201901010
  • Adawi M, Firas S, Blum A. Rheumatoid Arthritis and Atherosclerosis.. Isr Med Assoc J. 2019;21(7):460–463.
  • Liu T, Wang X, He YL, et al. In Vivo and In Vitro Anti-Arthritic Effects of Cardenolide-Rich and Caffeoylquinic Acid-Rich Fractions of Periploca forrestii. Molecules. 2018;23:8.
  • Fan S, Li C, Ai R, Wang M, Firestein GS, Wang W. Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis. Bioinformatics. 2016;32(12):1773–1778. doi:10.1093/bioinformatics/btw089
  • Luo Q, Gao Y, Zhang L, et al. Decreased ALKBH5, FTO, and YTHDF2 in Peripheral Blood Are as Risk Factors for Rheumatoid Arthritis. Biomed Res Int. 2020;2020:5735279. doi:10.1155/2020/5735279
  • Zheng J, Zeng P, Zhang H, et al. Long noncoding RNA ZFAS1 silencing alleviates rheumatoid arthritis via blocking miR-296-5p-mediated down-regulation of MMP-15. Int Immunopharmacol. 2020;107061.
  • Jiang H, Liu J, Wang T, et al. Urinary metabolite profiling provides potential differentiation to explore the mechanisms of adjuvant-induced arthritis in rats. Biomed Chromatography. 2016;30(9):1397–1405. doi:10.1002/bmc.3697
  • Brown J, Pirrung M, McCue LA, Dashboard: FQC, Wren J. FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics. 2017;33(19):3137–3139. doi:10.1093/bioinformatics/btx373
  • 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, 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
  • Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016;11(9):1650–1667. doi:10.1038/nprot.2016.095
  • Oshlack A, Robinson MD, Young MD. From RNA-seq reads to differential expression results. Genome Biol. 2010;11(12):220. doi:10.1186/gb-2010-11-12-220
  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621–628. doi:10.1038/nmeth.1226
  • Nikolayeva O, Robinson MD. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods Mol Biol. 2014;1150:45–79.
  • Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. Controlling the false discovery rate in behavior genetics research. Behav Brain Res. 2001;125(1–2):279–284. doi:10.1016/S0166-4328(01)00297-2
  • 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. doi:10.1038/75556
  • Szklarczyk D, Morris JH, Cook H, et al. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45(D1):D362–d368. doi:10.1093/nar/gkw937
  • Wang X, Liu X, Liu N, Chen H. Prediction of crucial epigenetically‑associated, differentially expressed genes by integrated bioinformatics analysis and the identification of S100A9 as a novel biomarker in psoriasis.. Int J Mol Med. 2020;45(1):93–102. doi:10.3892/ijmm.2019.4392
  • Zhou KI, Shi H, Lyu R, et al. Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG. Mol Cell. 2019;76(1):70–81.e79. doi:10.1016/j.molcel.2019.07.005
  • Zheng H, Li S, Zhang X, Sui N. Functional Implications of Active N6-Methyladenosine in Plants. Front Cell Dev Biol. 2020;8:291. doi:10.3389/fcell.2020.00291
  • Zhang B, Wu Q, Li B, Wang D, Wang L, Zhou YL. m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in gastric cancer. Mol Cancer. 2020;19(1):53. doi:10.1186/s12943-020-01170-0
  • Qu N, Qin S, Zhang X, et al. Multiple m6A RNA methylation modulators promote the malignant progression of hepatocellular carcinoma and affect its clinical prognosis. BMC Cancer. 2020;20(1):165. doi:10.1186/s12885-020-6638-5
  • Dominissini D, Moshitch-Moshkovitz S, Schwartz S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012;485(7397):201–206. doi:10.1038/nature11112
  • Guo C, Fu R, Wang S, et al. NLRP3 inflammasome activation contributes to the pathogenesis of rheumatoid arthritis. Clin Exp Immunol. 2018;194(2):231–243. doi:10.1111/cei.13167
  • Roman-Blas JA, Jimenez SA. NF-κB as a potential therapeutic target in osteoarthritis and rheumatoid arthritis. Osteoarthritis Cartilage. 2006;14(9):839–848. doi:10.1016/j.joca.2006.04.008
  • Zhao S-Y, Liao L-X, Tu P-F, Li -W-W, Zeng K-W. Icariin Inhibits AGE-Induced Injury in PC12 cells by directly targeting apoptosis regulator bax. Oxid Med Cell Longev. 2019;2019:7940808. doi:10.1155/2019/7940808
  • Guan X, Lu J, Sun F, Li Q, Pang Y. The molecular evolution and functional divergence of lamprey programmed cell death genes. Front Immunol. 2019;10:1382. doi:10.3389/fimmu.2019.01382
  • Garg NK, Tyagi RK, Singh B, et al. Nanostructured lipid carrier mediates effective delivery of methotrexate to induce apoptosis of rheumatoid arthritis via NF-κB and FOXO1. Int J Pharm. 2016;499(1–2):301–320. doi:10.1016/j.ijpharm.2015.12.061
  • Hellvard A, Zeitlmann L, Heiser U, et al. Inhibition of CDK9 as a therapeutic strategy for inflammatory arthritis. Sci Rep. 2016;6(1):31441. doi:10.1038/srep31441
  • Sorci M, Ianniello Z, Cruciani S, et al. METTL3 regulates WTAP protein homeostasis. Cell Death Dis. 2018;9(8):796. doi:10.1038/s41419-018-0843-z
  • Ping X-L, Sun B-F, Wang L, et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 2014;24(2):177–189. doi:10.1038/cr.2014.3
  • Li H, Su Q, Li B, et al. High expression of WTAP leads to poor prognosis of gastric cancer by influencing tumour-associated T lymphocyte infiltration. J Cell Mol Med. 2020;24(8):4452–4465. doi:10.1111/jcmm.15104
  • Wang L-J, 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. doi:10.1111/jcmm.15101
  • Tong J, Cao G, Zhang T, et al. m6A mRNA methylation sustains Treg suppressive functions. Cell Res. 2018;28(2):253–256. doi:10.1038/cr.2018.7
  • Chen L, Qiu Y, Hao Z, et al. A novel humanized anti-tumor necrosis factor-related apoptosis-inducing ligand-R2 monoclonal antibody induces apoptotic and autophagic cell death. IUBMB Life. 2017;69(9):735–744. doi:10.1002/iub.1659
  • Duiker EW, Dijkers EC, Lambers Heerspink H, et al. Development of a radioiodinated apoptosis-inducing ligand, rhTRAIL, and a radiolabelled agonist TRAIL receptor antibody for clinical imaging studies. Br J Pharmacol. 2012;165(7):2203–2212. doi:10.1111/j.1476-5381.2011.01718.x
  • Bi R, Deng Y, Tang C, et al. Andrographolide sensitizes human renal carcinoma cells to TRAIL‑induced apoptosis through upregulation of death receptor 4. Oncol Rep. 2020;44(5):1939–1948. doi:10.3892/or.2020.7737
  • Dai X, Zhang J, Arfuso F, et al. Targeting TNF-related apoptosis-inducing ligand (TRAIL) receptor by natural products as a potential therapeutic approach for cancer therapy. Exp Biol Med (Maywood). 2015;240(6):760–773. doi:10.1177/1535370215579167
  • Li T, Su L, Lei Y, Liu X, Zhang Y, Liu X. DDIT3 and KAT2A Proteins Regulate TNFRSF10A and TNFRSF10B expression in endoplasmic reticulum stress-mediated apoptosis in human lung cancer cells. J Biol Chem. 2015;290(17):11108–11118. doi:10.1074/jbc.M115.645333
  • Kapoor A, Fan Y-H, Arav-Boger R. Bacterial Muramyl Dipeptide (MDP) restricts human cytomegalovirus replication via an IFN-β-Dependent Pathway. Sci Rep. 2016;6(1):20295. doi:10.1038/srep20295
  • Duggan BM, Foley KP, Henriksbo BD, Cavallari JF, Tamrakar AK, Schertzer JD. Tyrosine kinase inhibitors of Ripk2 attenuate bacterial cell wall-mediated lipolysis, inflammation and dysglycemia. Sci Rep. 2017;7(1):1578. doi:10.1038/s41598-017-01822-0
  • Usluoglu N, Pavlovic J, Moelling K, Radziwill G. RIP2 mediates LPS-induced p38 and IκBα signaling including IL-12 p40 expression in human monocyte-derived dendritic cells. Eur J Immunol. 2007;37(8):2317–2325. doi:10.1002/eji.200636388
  • Krieg A, Le Negrate G, Reed JC. RIP2-β: a novel alternative mRNA splice variant of the receptor interacting protein kinase RIP2. Mol Immunol. 2009;46(6):1163–1170. doi:10.1016/j.molimm.2008.11.002
  • Santos J, Hubert T, Milthorpe BK. Valproic acid promotes early neural differentiation in adult mesenchymal stem cells through protein signalling pathways. Cells. 2020;9(3):3. doi:10.3390/cells9030619
  • Rokosz LL, Beasley JR, Carroll CD, et al. Kinase inhibitors as drugs for chronic inflammatory and immunological diseases: progress and challenges. Expert Opin Ther Targets. 2008;12(7):883–903. doi:10.1517/14728222.12.7.883
  • Pei H, He L, Shao M, et al. Discovery of a highly selective JAK3 inhibitor for the treatment of rheumatoid arthritis. Sci Rep. 2018;8(1):5273. doi:10.1038/s41598-018-23569-y
  • Kim B-H, Kim M, Yin C-H, et al. Inhibition of the signalling kinase JAK3 alleviates inflammation in monoarthritic rats. Br J Pharmacol. 2011;164(1):106–118. doi:10.1111/j.1476-5381.2011.01353.x