Profiling and Integrated Analysis of the ERCC6-regulated circRNA-miRNA-mRNA Network in Lens Epithelial Cells

References

• Pascolini D, Mariotti SP. Global estimates of visual impairment: 2010. Br J Ophthalmol. 2012;96:614–18.
   PubMed Web of Science ®Google Scholar
• Wei M, Xing KY, Fan YC, Libondi T, Lou MF. Loss of thiol repair systems in human cataractous lenses. Invest Ophthalmol Vis Sci. 2014;56:598–605.
   PubMed Web of Science ®Google Scholar
• Li WC, Kuszak JR, Dunn K, Wang RR, Ma W, Wang GM, Spector A, Leib M, Cotliar AM, Weiss M, et al. Lens epithelial cell apoptosis appears to be a common cellular basis for non-congenital cataract development in humans and animals. J Cell Biol. 1995;130(1):169–81.
   PubMed Web of Science ®Google Scholar
• Li WC, Kuszak JR, Wang GM, Wu ZQ, Spector A. Calcimycin-induced lens epithelial cell apoptosis contributes to cataract formation. Exp Eye Res. 1995;61:91–98.
   PubMed Web of Science ®Google Scholar
• Chang D, Zhang X, Rong S, Sha Q, Liu P, Han T, Pan H. Serum antioxidative enzymes levels and oxidative stress products in age-related cataract patients. Oxid Med Cell Longev. 2013;2013:587826.
   PubMed Web of Science ®Google Scholar
• Tu Y, Li L, Qin B, Wu J, Cheng T, Kang L, Guan H. Long noncoding RNA glutathione peroxidase 3-antisense inhibits lens epithelial cell apoptosis by upregulating glutathione peroxidase 3 expression in age-related cataract. Mol Vis. 2019;25:734–44.
   PubMed Web of Science ®Google Scholar
• Xiang J, Chen Q, Kang L, Zhang G, Wang Y, Qin B, Wu J, Zhou T, Han Y, Guan H. LncRNA PLCD3-OT1 functions as a CeRNA to prevent age-related cataract by sponging miR-224-5p and regulating PLCD3 expression. Invest Ophthalmol Vis Sci. 2019;60:4670–80.
   PubMed Web of Science ®Google Scholar
• Zhou W, Xu J, Wang C, Shi D, Yan Q. miR-23b-3p regulates apoptosis and autophagy via suppressing SIRT1 in lens epithelial cells. J Cell Biochem. 2019;120:19635–46.
   PubMed Web of Science ®Google Scholar
• Jin X, Jin H, Shi Y, Guo Y, Zhang H. Pyroptosis, a novel mechanism implicated in cataracts. Mol Med Rep. 2018;18:2277–85.
   PubMed Web of Science ®Google Scholar
• Jin X, Jin H, Shi Y, Guo Y, Zhang H. Long non-coding RNA KCNQ1OT1 promotes cataractogenesis via miR-214 and activation of the caspase-1 pathway. Cell Physiol Biochem. 2017;42:295–305.
   PubMedGoogle Scholar
• Chang JR, Koo E, Agron E, Hallak J, Clemons T, Azar D, Sperduto RD, Ferris FL 3rd, Chew EY. Age-related eye disease study G. Risk factors associated with incident cataracts and cataract surgery in the age-related eye disease study (AREDS): AREDS report number 32. Ophthalmology. 2011;118:2113–19.
   PubMed Web of Science ®Google Scholar
• Erol Tinaztepe O, Ay M, Eser E. Nuclear and mitochondrial DNA of age-related cataract patients are susceptible to oxidative damage. Curr Eye Res. 2017;42:583–88.
   PubMed Web of Science ®Google Scholar
• Maugeri-Sacca M, Bartucci M, De Maria R. DNA damage repair pathways in cancer stem cells. Mol Cancer Ther. 2012;11:1627–36.
   PubMed Web of Science ®Google Scholar
• Gaillard H, Santos-Pereira JM, Aguilera A. The Nup84 complex coordinates the DNA damage response to warrant genome integrity. Nucleic Acids Res. 2019;47:4054–67.
   PubMed Web of Science ®Google Scholar
• Ma H, Hu Z, Wang H, Jin G, Wang Y, Sun W, Chen D, Tian T, Jin L, Wei Q, et al. ERCC6/CSB gene polymorphisms and lung cancer risk. Cancer Lett. 2009;273(1):172–76.
   PubMed Web of Science ®Google Scholar
• Wang Y, Li F, Zhang G, Kang L, Guan H. Ultraviolet-B induces ERCC6 repression in lens epithelium cells of age-related nuclear cataract through coordinated DNA hypermethylation and histone deacetylation. Clin Epigenetics. 2016;8:62.
   PubMed Web of Science ®Google Scholar
• Cheng T, Xu M, Qin B, Wu J, Tu Y, Kang L, Wang Y, Guan H. lncRNA H19 contributes to oxidative damage repair in the early age-related cataract by regulating miR-29a/TDG axis. J Cell Mol Med. 2019;23:6131–39.
   PubMed Web of Science ®Google Scholar
• Fan F, Zhuang J, Zhou P, Liu X, Luo Y. MicroRNA-34a promotes mitochondrial dysfunction-induced apoptosis in human lens epithelial cells by targeting Notch2. Oncotarget. 2017;8:110209–20.
   PubMedGoogle Scholar
• Shen Y, Dong LF, Zhou RM, Yao J, Song YC, Yang H, Jiang Q, Yan B. Role of long non-coding RNA MIAT in proliferation, apoptosis and migration of lens epithelial cells: a clinical and in vitro study. J Cell Mol Med. 2016;20:537–48.
   PubMed Web of Science ®Google Scholar
• Zhang F, Meng W, Tong B. Down-regulation of MicroRNA-133b suppresses apoptosis of lens epithelial cell by up-regulating BCL2L2 in age-related cataracts. Med Sci Monit. 2016;22:4139–45.
   PubMed Web of Science ®Google Scholar
• Zhu J, Gong L, Zhao B. MicroRNA-4328 promotes lens epithelial cell apoptosis by targeting NLR family, apoptosis inhibitory protein in age-related cataract. Cell Biochem Funct. 2020;38:149–57.
   PubMed Web of Science ®Google Scholar
• Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs. Nat Biotechnol. 2014;32:453–61.
   PubMed Web of Science ®Google Scholar
• Chen LL. The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol. 2016;17:205–11.
   PubMed Web of Science ®Google Scholar
• Liu X, Liu B, Zhou M, Fan F, Yu M, Gao C, Lu Y, Luo Y. Circular RNA HIPK3 regulates human lens epithelial cells proliferation and apoptosis by targeting the miR-193a/CRYAA axis. Biochem Biophys Res Commun. 2018;503:2277–85.
   PubMed Web of Science ®Google Scholar
• Fan C, Liu X, Li W, Wang H, Teng Y, Ren J, Huang Y. Circular RNA circ KMT2E is up-regulated in diabetic cataract lenses and is associated with miR-204-5p sponge function. Gene. 2019;710:170–77.
   PubMed Web of Science ®Google Scholar
• Wang FW, Cao CH, Han K, Zhao YX, Cai MY, Xiang ZC, Zhang JX, Chen JW, Zhong LP, Huang Y, et al. APC-activated long noncoding RNA inhibits colorectal carcinoma pathogenesis through reduction of exosome production. J Clin Invest. 2019;129(2):727–43.
   PubMed Web of Science ®Google Scholar
• Gao Y, Zhang J, Zhao F. Circular RNA identification based on multiple seed matching. Brief Bioinform. 2018;19:803–10.
   PubMed Web of Science ®Google Scholar
• Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016;26:1277–87.
   PubMed Web of Science ®Google Scholar
• Feng J, Meyer CA, Wang Q, Liu JS, Shirley Liu X, Zhang Y. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics. 2012;28:2782–88.
   PubMed Web of Science ®Google Scholar
• Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012;8:e1002375.
   PubMed Web of Science ®Google Scholar
• Zhong Y, Du Y, Yang X, Mo Y, Fan C, Xiong F, Ren D, Ye X, Li C, Wang Y, et al. Circular RNAs function as ceRNAs to regulate and control human cancer progression. Mol Cancer. 2018;17(1):79.
   PubMed Web of Science ®Google Scholar
• Du WW, Zhang C, Yang W, Yong T, Awan FM, Yang BB. Identifying and characterizing circRNA-protein interaction. Theranostics. 2017;7:4183–91.
   PubMed Web of Science ®Google Scholar
• Xiang J, Chen Q, Kang L, Zhang G, Wang Y, Qin B, Wu J, Zhou T, Han Y, LncRNA GH. PLCD3-OT1 functions as a CeRNA to prevent age-related cataract by sponging miR-224-5p and regulating PLCD3 expression. Invest Opthalmol Visual Sci. 2019;60(14):4670–80.
   Web of Science ®Google Scholar
• Caiment F, Gaj S, Claessen S, Kleinjans J. High-throughput data integration of RNA-miRNA-circRNA reveals novel insights into mechanisms of benzo[a]pyrene-induced carcinogenicity. Nucleic Acids Res. 2015;43:2525–34.
   PubMed Web of Science ®Google Scholar
• Xu X, Zhang J, Tian Y, Gao Y, Dong X, Chen W, Yuan X, Yin W, Xu J, Chen K, et al. CircRNA inhibits DNA damage repair by interacting with host gene. Mol Cancer. 2020;19(1):128.
   PubMed Web of Science ®Google Scholar
• Conn VM, Hugouvieux V, Nayak A, Conos SA, Capovilla G, Cildir G, Jourdain A, Tergaonkar V, Schmid M, Zubieta C, et al. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat Plants. 2017;3:17053.
   PubMed Web of Science ®Google Scholar
• Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol. 2015;22(3):256–64.
   PubMed Web of Science ®Google Scholar
• Li X, Liu CX, Xue W, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L, Chen LL. Coordinated circRNA biogenesis and function with NF90/NF110 in viral infection. Mol Cell. 2017;67:214–227 e217.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Zhang XO, Chen T, Xiang JF, Yin QF, Xing YH, Zhu S, Yang L, Chen LL. Circular intronic long noncoding RNAs. Mol Cell. 2013;51:792–806.
   PubMed Web of Science ®Google Scholar
• Zhong C, Yu S, Han M, Chen J, Ning K. Heterogeneous circRNA expression profiles and regulatory functions among HEK293T single cells. Sci Rep. 2017;7:14393.
   PubMed Web of Science ®Google Scholar
• Li Y, Liu S, Zhang F, Jiang P, Wu X, Liang Y. Expression of the microRNAs hsa-miR-15a and hsa-miR-16-1 in lens epithelial cells of patients with age-related cataract. Int J Clin Exp Med. 2015;8:2405–10.
   PubMed Web of Science ®Google Scholar
• Levine AJ. p53, the cellular gatekeeper for growth and division. Cell. 1997;88:323–31.
   PubMed Web of Science ®Google Scholar
• Galichanin K. Exposure to subthreshold dose of UVR-B induces apoptosis in the lens epithelial cells and does not in the lens cortical fibre cells. Acta Ophthalmol. 2017;95:834–38.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Li X, Zhu S. rs78378222 polymorphism in the 3ʹ-untranslated region of TP53 contributes to development of age-associated cataracts by modifying microRNA-125b-induced apoptosis of lens epithelial cells. Mol Med Rep. 2016;14:2305–10.
   PubMed Web of Science ®Google Scholar
• Boccone L, Dessi V, Serra G, Zibordi F, Loudianos G. Bannayan-Riley-Ruvalcaba syndrome with posterior subcapsular congenital cataract and a consensus sequence splicing PTEN mutation. Am J Med Genet A. 2008;146A(2:257–60.
   Web of Science ®Google Scholar
• Sellitto C, Li L, Gao J, Robinson ML, Lin RZ, Mathias RT, White TW. AKT activation promotes PTEN hamartoma tumor syndrome-associated cataract development. J Clin Invest. 2013;123:5401–09.
   PubMed Web of Science ®Google Scholar
• Wang Y, Zhang J, Wu J, Guan H. Expression of DNA repair genes in lens cortex of age-related cortical cataract. Exp Mol Pathol. 2017;102:219–23.
   PubMed Web of Science ®Google Scholar
• Zhao W, Zhao W, Zhao J, Wang D, Li J. Screening of potential target genes for cataract by analyzing mRNA expression profile of mouse Hsf4-null lens. BMC Ophthalmol. 2015;15:76.
   PubMed Web of Science ®Google Scholar