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ORIGINAL RESEARCH

Autophagy-Related Genes Predict the Progression of Periodontitis Through the ceRNA Network

, ORCID Icon, , , &
Pages 1811-1824 | Published online: 11 Mar 2022

References

  • Slots J. Periodontitis: facts, fallacies and the future. Periodontol 2000. 2017;75(1):7–23. doi:10.1111/prd.12221
  • Genco RJ, Sanz M. Clinical and public health implications of periodontal and systemic diseases: an overview. Periodontol 2000. 2020;83(1):7–13. doi:10.1111/prd.12344
  • Levine B, Mizushima N, Virgin HW. Autophagy in immunity and inflammation. Nature. 2011;469(7330):323–335. doi:10.1038/nature09782
  • Deretic V. Autophagy in immunity and cell-autonomous defense against intracellular microbes. Immunol Rev. 2011;240(1):92–104. doi:10.1111/j.1600-065X.2010.00995.x
  • Nixon RA. The role of autophagy in neurodegenerative disease. Nat Med. 2013;19(8):983–997. doi:10.1038/nm.3232
  • Amaravadi RK, Kimmelman AC, Debnath J. Targeting autophagy in cancer: recent advances and future directions. Cancer Discov. 2019;9(9):1167–1181. doi:10.1158/2159-8290.CD-19-0292
  • Kocak M, Ezazi Erdi S, Jorba G, et al. Targeting autophagy in disease: established and new strategies. Autophagy. 2021:1–23. doi:10.1080/15548627.2021.1936359.
  • Jiang M, Li Z, Zhu G. The role of autophagy in the pathogenesis of periodontal disease. Oral Dis. 2020;26(2):259–269. doi:10.1111/odi.13045
  • Yang Y, Huang Y, Li W. Autophagy and its significance in periodontal disease. J Periodontal Res. 2021;56(1):18–26. doi:10.1111/jre.12810
  • Li S, Liu X, Li H, et al. Integrated analysis of long noncoding RNA-associated competing endogenous RNA network in periodontitis. J Periodontal Res. 2018;53(4):495–505. doi:10.1111/jre.12539
  • Jin SH, Zhou JG, Guan XY, et al. Development of an miRNA-array-based diagnostic signature for periodontitis. Front Genet. 2020;11:577585. doi:10.3389/fgene.2020.577585
  • Salmena L, Poliseno L, Tay Y, et al. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011;146(3):353–358. doi:10.1016/j.cell.2011.07.014
  • Ala U. Competing endogenous RNAs, non-coding RNAs and diseases: an intertwined story. Cells. 2020;9(7):1574. doi:10.3390/cells9071574
  • Demmer RT, Behle JH, Wolf DL, et al. Transcriptomes in healthy and diseased gingival tissues. J Periodontol. 2008;79(11):2112–2124. doi:10.1902/jop.2008.080139
  • Kebschull M, Demmer RT, Grun B, et al. Gingival tissue transcriptomes identify distinct periodontitis phenotypes. J Dent Res. 2014;93(5):459–468. doi:10.1177/0022034514527288
  • Papapanou PN, Behle JH, Kebschull M, et al. Subgingival bacterial colonization profiles correlate with gingival tissue gene expression. BMC Microbiol. 2009;9(1):221. doi:10.1186/1471-2180-9-221
  • Stoecklin-Wasmer C, Guarnieri P, Celenti R, et al. MicroRNAs and their target genes in gingival tissues. J Dent Res. 2012;91(10):934–940. doi:10.1177/0022034512456551
  • Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57. doi:10.1038/nprot.2008.211
  • Xie C, Mao X, Huang J, et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011;39(suppl_2):W316–W322. doi:10.1093/nar/gkr483
  • Bindea G, Mlecnik B, Hackl H, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091–1093. doi:10.1093/bioinformatics/btp101
  • 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
  • Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2020;48(D1):D127–D131. doi:10.1093/nar/gkz757
  • Li JH, Liu S, Zhou H, et al. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42(D1):D92–D97. doi:10.1093/nar/gkt1248
  • Paraskevopoulou MD, Vlachos IS, Karagkouni D, et al. DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res. 2016;44(D1):D231–D238. doi:10.1093/nar/gkv1270
  • Mas-Ponte D, Carlevaro-Fita J, Palumbo E, et al. LncATLAS database for subcellular localization of long noncoding RNAs. RNA. 2017;23(7):1080–1087. doi:10.1261/rna.060814
  • Loos BG, Papantonopoulos G, Jepsen S, et al. What is the contribution of genetics to periodontal risk? Dent Clin North Am. 2015;59(4):761–780. doi:10.1016/j.cden.2015.06.005
  • Song L, Yao J, He Z, et al. Genes related to inflammation and bone loss process in periodontitis suggested by bioinformatics methods. BMC Oral Health. 2015;15(1):105. doi:10.1186/s12903-015-0086-7
  • Loos BG, Van Dyke TE. The role of inflammation and genetics in periodontal disease. Periodontol 2000. 2020;83(1):26–39. doi:10.1111/prd.12297
  • Suzuki A, Horie T, Numabe Y. Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO). BMC Oral Health. 2019;19(1):52. doi:10.1186/s12903-019-0738-0
  • Bullon P, Cordero MD, Quiles JL, et al. Autophagy in periodontitis patients and gingival fibroblasts: unraveling the link between chronic diseases and inflammation. BMC Med. 2012;10(1):122. doi:10.1186/1741-7015-10-122
  • An Y, Liu W, Xue P, et al. Increased autophagy is required to protect periodontal ligament stem cells from apoptosis in inflammatory microenvironment. J Clin Periodontol. 2016;43(7):618–625. doi:10.1111/jcpe.12549
  • Hasturk H, Kantarci A. Activation and resolution of periodontal inflammation and its systemic impact. Periodontol 2000. 2015;69(1):255–273. doi:10.1111/prd.12105
  • Li RF, Chen G, Ren JG, et al. The adaptor protein p62 is involved in RANKL-induced autophagy and osteoclastogenesis. J Histochem Cytochem. 2014;62(12):879–888. doi:10.1369/0022155414551367
  • Whitehouse CA, Waters S, Marchbank K, et al. Neighbor of Brca1 gene (Nbr1) functions as a negative regulator of postnatal osteoblastic bone formation and p38 MAPK activity. Proc Natl Acad Sci U S A. 2010;107(29):12913–12918. doi:10.1073/pnas.0913058107
  • Tanaka Y, Guhde G, Suter A, et al. Accumulation of autophagic vacuoles and cardiomyopathy in LAMP-2-deficient mice. Nature. 2000;406(6798):902–906. doi:10.1038/35022595
  • Beertsen W, Willenborg M, Everts V, et al. Impaired phagosomal maturation in neutrophils leads to periodontitis in lysosomal-associated membrane protein-2 knockout mice. J Immunol. 2008;180(1):475–482. doi:10.4049/jimmunol.180.1.475
  • Pajares M, Rojo AI, Arias E, et al. Transcription factor NFE2L2/NRF2 modulates chaperone-mediated autophagy through the regulation of LAMP2A. Autophagy. 2018;14(8):1310–1322. doi:10.1080/15548627.2018.1474992
  • Zhang X, Jin Y, Wang Q, et al. Autophagy-mediated regulation patterns contribute to the alterations of the immune microenvironment in periodontitis. Aging. 2021;13(1):555–577. doi:10.18632/aging.202165
  • Chunhui Y, Wenjun C, Hui W, et al. Pilose antler peptide protects osteoblasts from inflammatory and oxidative injury through EGF/EGFR signaling. Int J Biol Macromol. 2017;99::15–20. doi:10.1016/j.ijbiomac.2017.02.056
  • Kim EN, Kaygusuz O, Lee HS, et al. Simultaneous quantitative analysis of ginsenosides isolated from the fruit of panax ginseng C.A. Meyer and regulation of HO-1 expression through EGFR signaling has anti-inflammatory and osteogenic induction effects in HPDL cells. Molecules. 2021;26(7):2092. doi:10.3390/molecules26072092
  • Ntoumou E, Tzetis M, Braoudaki M, et al. Serum microRNA array analysis identifies miR-140-3p, miR-33b-3p and miR-671-3p as potential osteoarthritis biomarkers involved in metabolic processes. Clin Epigenetics. 2017;9(1):127. doi:10.1186/s13148-017-0428-1
  • Ramirez-Salazar EG, Carrillo-Patino S, Hidalgo-Bravo A, et al. Serum miRNAs miR-140-3p and miR-23b-3p as potential biomarkers for osteoporosis and osteoporotic fracture in postmenopausal Mexican-Mestizo women. Gene. 2018;679::19–27. doi:10.1016/j.gene.2018.08.074
  • Ren T, Wei P, Song Q, et al. MiR-140-3p ameliorates the progression of osteoarthritis via targeting CXCR4. Biol Pharm Bull. 2020;43(5):810–816. doi:10.1248/bpb.b19-00959
  • Mao JH, Sui YX, Ao S, et al. miR-140-3p exhibits repressive functions on preosteoblast viability and differentiation by downregulating MCF2L in osteoporosis. In Vitro Cell Dev Biol Anim. 2020;56(1):49–58. doi:10.1007/s11626-019-00405-9
  • Lou Z, Peng Z, Wang B, et al. miR-142-5p promotes the osteoclast differentiation of bone marrow-derived macrophages via PTEN/PI3K/AKT/FoxO1 pathway. J Bone Miner Metab. 2019;37(5):815–824. doi:10.1007/s00774-019-00997-y
  • Sun P, Wu Y, Li X, et al. miR-142-5p protects against osteoarthritis through competing with lncRNA XIST. J Gene Med. 2020;22(4):e3158. doi:10.1002/jgm.3158
  • Ma C, Nie ZK, Guo HM, et al. MiR-671-5p plays a promising role in restraining osteosarcoma cell characteristics through targeting TUFT1. J Biochem Mol Toxicol. 2020;34(7):e22490. doi:10.1002/jbt.22490
  • Loda A, Heard E. Xist RNA in action: past, present, and future. PLoS Genet. 2019;15(9):e1008333. doi:10.1371/journal.pgen.1008333
  • Wang W, Min L, Qiu X, et al. Biological function of long non-coding RNA (LncRNA) Xist. Front Cell Dev Biol. 2021;9:645647. doi:10.3389/fcell.2021.645647
  • Lipsky MS, Su S, Crespo CJ, et al. Men and oral health: a review of sex and gender differences. Am J Mens Health. 2021;15(3):15579883211016361. doi:10.1177/15579883211016361
  • Chen X, Yang L, Ge D, et al. Long non-coding RNA XIST promotes osteoporosis through inhibiting bone marrow mesenchymal stem cell differentiation. Exp Ther Med. 2019;17(1):803–811. doi:10.3892/etm.2018.7033
  • Feng Y, Wan P, Yin L. Long noncoding RNA X-inactive specific transcript (XIST) promotes osteogenic differentiation of periodontal ligament stem cells by sponging microRNA-214-3p. Med Sci Monit. 2020;26:e918932. doi:10.12659/MSM.918932