The m7G Modification Level and Immune Infiltration Characteristics in Patients with COVID-19

References

• Fung SY, Yuen KS, Ye ZW, Chan CP, Jin DY. A tug-of-war between severe acute respiratory syndrome coronavirus 2 and host antiviral defence: lessons from other pathogenic viruses. Emerg Microbes Infect. 2020;9(1):558–570. doi:10.1080/22221751.2020.1736644
   PubMed Web of Science ®Google Scholar
• Muniyappa R, Gubbi S. COVID-19 pandemic, coronaviruses, and diabetes mellitus. Am J Physiol Endocrinol Metab. 2020;318(5):E736–e741. doi:10.1152/ajpendo.00124.2020
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. 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
• Roundtree IA, Evans ME, Pan T, He C. Dynamic RNA modifications in gene expression regulation. Cell. 2017;169(7):1187–1200. doi:10.1016/j.cell.2017.05.045
   PubMed Web of Science ®Google Scholar
• Thapar R, Bacolla A, Oyeniran C, et al. RNA modifications: reversal mechanisms and cancer. Biochemistry. 2019;58(5):312–329. doi:10.1021/acs.biochem.8b00949
   PubMed Web of Science ®Google Scholar
• Barbieri I, Kouzarides T. Role of RNA modifications in cancer. Nat Rev Cancer. 2020;20(6):303–322. doi:10.1038/s41568-020-0253-2
   PubMed Web of Science ®Google Scholar
• Muthukrishnan S, Both GW, Furuichi Y, Shatkin AJ. 5’-Terminal 7-methylguanosine in eukaryotic mRNA is required for translation. Nature. 1975;255(5503):33–37. doi:10.1038/255033a0
   PubMed Web of Science ®Google Scholar
• Malbec L, Zhang T, Chen YS, et al. Dynamic methylome of internal mRNA N(7)-methylguanosine and its regulatory role in translation. Cell Res. 2019;29(11):927–941. doi:10.1038/s41422-019-0230-z
   PubMed Web of Science ®Google Scholar
• Furuichi Y. Discovery of m(7) G-capin eukaryotic mRNAs. Proc Jpn Acad Ser B Phys Biol Sci. 2015;91(8):394–409. doi:10.2183/pjab.91.394
   PubMed Web of Science ®Google Scholar
• Chu JM, Ye TT, Ma CJ, et al. Existence of internal N7-methylguanosine modification in mRNA determined by differential enzyme treatment coupled with mass spectrometry analysis. ACS Chem Biol. 2018;13(12):3243–3250. doi:10.1021/acschembio.7b00906
   PubMed Web of Science ®Google Scholar
• Zhang LS, Liu C, Ma H, et al. Transcriptome-wide mapping of internal N(7)-methylguanosine methylome in mammalian mRNA. Mol Cell. 2019;74(6):1304–1316.e8. doi:10.1016/j.molcel.2019.03.036
   PubMed Web of Science ®Google Scholar
• Song B, Tang Y, Chen K, et al. m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Bioinformatics. 2020;36(11):3528–3536. doi:10.1093/bioinformatics/btaa178
   PubMed Web of Science ®Google Scholar
• Tan B, Gao SJ. RNA epitranscriptomics: regulation of infection of RNA and DNA viruses by N(6) -methyladenosine (m(6) A). Rev Med Virol. 2018;28(4):e1983. doi:10.1002/rmv.1983
   PubMed Web of Science ®Google Scholar
• Tan B, Gao SJ. The RNA epitranscriptome of DNA viruses. J Virol. 2018;92(22). doi:10.1128/jvi.00696-18
   Web of Science ®Google Scholar
• Courtney DG, Tsai K, Bogerd HP, et al. Epitranscriptomic addition of m(5) C to HIV-1 transcripts regulates viral gene expression. Cell Host Microbe. 2019;26(2):217–227.e6. doi:10.1016/j.chom.2019.07.005
   PubMed Web of Science ®Google Scholar
• Tsai K, Cullen BR. Epigenetic and epitranscriptomic regulation of viral replication. Nat Rev Microbiol. 2020;18(10):559–570. doi:10.1038/s41579-020-0382-3
   PubMed Web of Science ®Google Scholar
• Aouadi W, Eydoux C, Coutard B, et al. Toward the identification of viral cap-methyltransferase inhibitors by fluorescence screening assay. Antiviral Res. 2017;144:330–339. doi:10.1016/j.antiviral.2017.06.021
   PubMed Web of Science ®Google Scholar
• Sevajol M, Subissi L, Decroly E, Canard B, Imbert I. Insights into RNA synthesis, capping, and proofreading mechanisms of SARS-coronavirus. Virus Res. 2014;194:90–99. doi:10.1016/j.virusres.2014.10.008
   PubMed Web of Science ®Google Scholar
• Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res. 2016;44(16):7511–7526. doi:10.1093/nar/gkw551
   PubMed Web of Science ®Google Scholar
• Furuse Y. RNA modifications in genomic RNA of influenza A virus and the relationship between RNA modifications and viral infection. Int J Mol Sci. 2021;22(17):9127. doi:10.3390/ijms22179127
   PubMed Web of Science ®Google Scholar
• Meng Y, Zhang Q, Wang K, et al. RBM15-mediated N6-methyladenosine modification affects COVID-19 severity by regulating the expression of multitarget genes. Cell Death Dis. 2021;12(8):732. doi:10.1038/s41419-021-04012-z
   PubMed Web of Science ®Google Scholar
• Li N, Hui H, Bray B, et al. METTL3 regulates viral m6A RNA modification and host cell innate immune responses during SARS-CoV-2 infection. Cell Rep. 2021;35(6):109091. doi:10.1016/j.celrep.2021.109091
   PubMed Web of Science ®Google Scholar
• Zhang X, Hao H, Ma L, et al. Methyltransferase-like 3 modulates severe acute respiratory syndrome coronavirus-2 RNA N6-methyladenosine modification and replication. mBio. 2021;12(4):e0106721. doi:10.1128/mBio.01067-21
   PubMed Web of Science ®Google Scholar
• Overmyer KA, Shishkova E, Miller IJ, et al. Large-scale multi-omic analysis of COVID-19 severity. Cell sys. 2021;12(1):23–40.e7. doi:10.1016/j.cels.2020.10.003
   PubMed Web of Science ®Google Scholar
• Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30(1):207–210. doi:10.1093/nar/30.1.207
   PubMed Web of Science ®Google Scholar
• Wang F, Nie J, Wang H, et al. Characteristics of peripheral lymphocyte subset alteration in COVID-19 pneumonia. J Infect Dis. 2020;221(11):1762–1769. doi:10.1093/infdis/jiaa150
   PubMed Web of Science ®Google Scholar
• Silberstein M. Correlation between premorbid IL-6 levels and COVID-19 mortality: potential role for Vitamin D. Int Immunopharmacol. 2020;88:106995. doi:10.1016/j.intimp.2020.106995
   PubMed Web of Science ®Google Scholar
• Kloc M, Ghobrial RM, Lipińska-Opałka A, et al. Effects of vitamin D on macrophages and myeloid-derived suppressor cells (MDSCs) hyperinflammatory response in the lungs of COVID-19 patients. Cell Immunol. 2021;360:104259. doi:10.1016/j.cellimm.2020.104259
   PubMed Web of Science ®Google Scholar
• Grifoni A, Weiskopf D, Ramirez SI, et al. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell. 2020;181(7):1489–1501.e15. doi:10.1016/j.cell.2020.05.015
   PubMed Web of Science ®Google Scholar
• Krammer F. SARS-CoV-2 vaccines in development. Nature. 2020;586(7830):516–527. doi:10.1038/s41586-020-2798-3
   PubMed Web of Science ®Google Scholar
• Rydyznski Moderbacher C, Ramirez SI, Dan JM, et al. Antigen-specific adaptive immunity to SARS-CoV-2 in acute COVID-19 and associations with age and disease severity. Cell. 2020;183(4):996–1012.e19. doi:10.1016/j.cell.2020.09.038
   PubMed Web of Science ®Google Scholar
• Braun J, Loyal L, Frentsch M, et al. SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19. Nature. 2020;587(7833):270–274. doi:10.1038/s41586-020-2598-9
   PubMed Web of Science ®Google Scholar
• Chen P, Nirula A, Heller B, et al. SARS-CoV-2 neutralizing antibody LY-CoV555 in outpatients with Covid-19. N Engl J Med. 2021;384(3):229–237. doi:10.1056/NEJMoa2029849
   PubMed Web of Science ®Google Scholar
• Devarkar SC, Wang C, Miller MT, et al. Structural basis for m7G recognition and 2’-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc Natl Acad Sci USA. 2016;113(3):596–601. doi:10.1073/pnas.1515152113
   PubMed Web of Science ®Google Scholar
• Ivanov KA, Thiel V, Dobbe JC, van der Meer Y, Snijder EJ, Ziebuhr J. Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase. J Virol. 2004;78(11):5619–5632. doi:10.1128/jvi.78.11.5619-5632.2004
   PubMed Web of Science ®Google Scholar
• Yan L, Ge J, Zheng L, et al. Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex reveals an intermediate state in cap synthesis. Cell. 2021;184(1):184–193.e10. doi:10.1016/j.cell.2020.11.016
   PubMed Web of Science ®Google Scholar
• Montero H, García-Román R, Mora SI. eIF4E as a control target for viruses. Viruses. 2015;7(2):739–750. doi:10.3390/v7020739
   PubMed Web of Science ®Google Scholar
• Kumar R, Afsar M, Khandelwal N, et al. Emetine suppresses SARS-CoV-2 replication by inhibiting interaction of viral mRNA with eIF4E. Antiviral Res. 2021;189:105056. doi:10.1016/j.antiviral.2021.105056
   PubMed Web of Science ®Google Scholar
• Schmidt N, Lareau CA, Keshishian H, et al. The SARS-CoV-2 RNA-protein interactome in infected human cells. Nat Microbiol. 2021;6(3):339–353. doi:10.1038/s41564-020-00846-z
   PubMed Web of Science ®Google Scholar
• Dong Y, Yang J, Ye W, et al. LSm1 binds to the Dengue virus RNA 3’ UTR and is a positive regulator of Dengue virus replication. Int J Mol Med. 2015;35(6):1683–1689. doi:10.3892/ijmm.2015.2169
   PubMed Web of Science ®Google Scholar
• Scheller N, Mina LB, Galão RP, et al. Translation and replication of hepatitis C virus genomic RNA depends on ancient cellular proteins that control mRNA fates. Proc Natl Acad Sci USA. 2009;106(32):13517–13522. doi:10.1073/pnas.0906413106
   PubMed Web of Science ®Google Scholar
• Zhang B, Liu X, Chen W, Chen L. IFIT5 potentiates anti-viral response through enhancing innate immune signaling pathways. Acta Biochim Biophys Sin. 2013;45(10):867–874. doi:10.1093/abbs/gmt088
   Google Scholar