Construction and Comprehensive Analysis of a ceRNA Network to Reveal Potential Novel Biomarkers for Triple-Negative Breast Cancer

References

• Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68(6):394–424. doi:10.3322/caac.2149230207593
   PubMed Web of Science ®Google Scholar
• Venkitaraman R. Triple-negative/basal-like breast cancer: clinical, pathologic and molecular features. Expert Rev Anticancer Ther. 2010;10(2):199–207. doi:10.1586/ERA.09.18920131996
   PubMed Web of Science ®Google Scholar
• Bosch A, Eroles P, Zaragoza R, Viña JR, Lluch A. Triple-negative breast cancer: molecular features, pathogenesis, treatment and current lines of research. Cancer Treat Rev. 2010;36(3):206–215. doi:10.1016/j.ctrv.2009.12.00220060649
   PubMed Web of Science ®Google Scholar
• Li MX, Jin LT, Wang TJ, et al. Identification of potential core genes in triple negative breast cancer using bioinformatics analysis. Onco Targets Ther. 2018;11:4105–4112. doi:10.2147/OTT.S16656730140156
   PubMed Web of Science ®Google Scholar
• Foulkes WD, Smith IE, Reis-Filho JS. Triple-negative breast cancer. N Engl J Med. 2010;363(20):1938–1948. doi:10.1056/NEJMra100138921067385
   PubMed Web of Science ®Google Scholar
• Wein L, Loi S. Mechanisms of resistance of chemotherapy in early-stage triple negative breast cancer (TNBC). Breast. 2017;34:S27–S30. doi:10.1016/j.breast.2017.06.02328668293
   PubMed Web of Science ®Google Scholar
• Sardina DS, Alaimo S, Ferro A, Pulvirenti A, Giugno R. A novel computational method for inferring competing endogenous interactions. Brief Bioinform. 2017;18(6):1071–1081. doi:10.1093/bib/bbw08427677959
   PubMed Web of Science ®Google Scholar
• Cao Z, Pan X, Yang Y, Huang Y, Shen H-B, Hancock J. The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. Bioinformatics. 2018;34(13):2185–2194. doi:10.1093/bioinformatics/bty08529462250
   PubMed Web of Science ®Google Scholar
• Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014;505(7483):344–352. doi:10.1038/nature1298624429633
   PubMed Web of Science ®Google Scholar
• Thomson DW, Dinger ME. Endogenous microRNA sponges: evidence and controversy. Nat Rev Genet. 2016;17(5):272–283. doi:10.1038/nrg.2016.2027040487
   PubMed Web of Science ®Google Scholar
• Wang J, Liu X, Wu H, et al. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res. 2010;38(16):5366–5383. doi:10.1093/nar/gkq28520423907
   PubMed Web of Science ®Google Scholar
• Long J, Bai Y, Yang X, et al. Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for hepatocellular carcinoma. Cancer Cell Int. 2019;19(1):1–2. doi:10.1186/s12935-019-0817-y30622437
   PubMedGoogle Scholar
• Bai Y, Long J, Liu Z, et al. Comprehensive analysis of a ceRNA network reveals potential prognostic cytoplasmic lncRNAs involved in HCC progression. J Cell Physiol. 2019;234(10):18837–18848. doi:10.1002/jcp.2852230916406
   PubMed Web of Science ®Google Scholar
• Wang SH, Ma F, Tang ZH, et al. Long non-coding RNA H19 regulates FOXM1 expression by competitively binding endogenous miR-342-3p in gallbladder cancer. J Exp Clin Cancer Res. 2016;35(1):1–12. doi:10.1186/s13046-016-0436-626728266
   PubMedGoogle Scholar
• Jeong H, Mason SP, Barabási AL, Oltvai ZN. Lethality and centrality in protein networks. Nature. 2001;411(6833):41–42. doi:10.1038/3507513811333967
   PubMed Web of Science ®Google Scholar
• Goldman M, Craft B, Hastie M, et al. The UCSC Xena platform for public and private cancer genomics data visualization and interpretation. bioRxiv. 2018:326470. doi:10.1101/326470
   Google Scholar
• Lever J, Krzywinski M, Altman N. Points of significance: principal component analysis. Nat Methods. 2017;14(7):641–642. doi:10.1038/nmeth.4346
   Web of Science ®Google Scholar
• Komatsu M, Yoshimaru T, Matsuo T, et al. Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis. Int J Oncol. 2013;42(2):478–506. doi:10.3892/ijo.2012.174423254957
   PubMed Web of Science ®Google Scholar
• Gruosso T, Mieulet V, Cardon M, et al. Chronic oxidative stress promotes H2 AX protein degradation and enhances chemosensitivity in breast cancer patients. EMBO Mol Med. 2016;8(5):527–549. doi:10.15252/emmm.20150589127006338
   PubMed Web of Science ®Google Scholar
• Maubant S, Tesson B, Maire V, et al. Transcriptome analysis of wnt3a-treated triple-negative breast cancer cells. PLoS One. 2015;10(4):e0122333. doi:10.1371/journal.pone.012233325848952
   PubMed Web of Science ®Google Scholar
• Maire V, Baldeyron C, Richardson M, et al. TTK/hMPS1 is an attractive therapeutic target for triple-negative breast cancer. PLoS One. 2013;8(5):e63712. doi:10.1371/journal.pone.006371223700430
   PubMed Web of Science ®Google Scholar
• Maire V, Némati F, Richardson M, et al. Polo-like kinase 1: a potential therapeutic option in combination with conventional chemotherapy for the management of patients with triple-negative breast cancer. Cancer Res. 2013;73(2):813–823. doi:10.1158/0008-5472.CAN-12-263323144294
   PubMed Web of Science ®Google Scholar
• Aken BL, Ayling S, Barrell D, et al. The Ensembl gene annotation system. Database. 2016;2016:baw093. doi:10.1093/database/baw09327337980
   PubMedGoogle Scholar
• Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv00725605792
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57(1):289–300. doi:10.1111/j.2517-6161.1995.tb02031.x
   Google Scholar
• Li R, Qu H, Wang S, et al. GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC. Bioinformatics. 2018;34(14):2515–2517. doi:10.1093/bioinformatics/bty12429509844
   PubMed Web of Science ®Google Scholar
• Paci P, Colombo T, Farina L. Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer. BMC Syst Biol. 2014;8(1):83. doi:10.1186/1752-0509-8-8325033876
   PubMedGoogle Scholar
• Jeggari A, Marks DS, Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics. 2012;28(15):2062–2063. doi:10.1093/bioinformatics/bts34422718787
   PubMed Web of Science ®Google Scholar
• Li JH, Liu S, Zhou H, Qu LH, Yang JH. 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/gkt124824297251
   PubMed Web of Science ®Google Scholar
• Chou CH, Shrestha S, Yang CD, et al. MiRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res. 2018;46(D1):D296–D302. doi:10.1093/nar/gkx106729126174
   PubMed Web of Science ®Google Scholar
• Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A. spongeScan: a web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Res. 2016;44(W1):W176–W180. doi:10.1093/nar/gkw44327198221
   PubMed Web of Science ®Google Scholar
• Li Y, Gu J, Xu F, Zhu Q, Ge D, Lu C. Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data. Sci Rep. 2018;8(1):15834. doi:10.1038/s41598-018-34160-w30367091
   PubMedGoogle Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software Environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi:10.1101/gr.123930314597658
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, He QY. ClusterProfiler: an R package for comparing biological themes among gene clusters. Omi a J Integr Biol. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Yan GR, He Q-Y. DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics. 2015;31(4):608–609. doi:10.1093/bioinformatics/btu68425677125
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–D613. doi:10.1093/nar/gky113130476243
   PubMed Web of Science ®Google Scholar
• Royston P, Choodari-Oskooei B, Parmar MKB, Rogers JK. Combined test versus logrank/Cox test in 50 randomised trials. Trials. 2019;20(1). doi:10.1186/s13063-019-3251-5
   PubMed Web of Science ®Google Scholar
• Mu J, Li M, Wang T, et al. Myelin damage in diffuse axonal injury. Front Neurosci. 2019;13:217. doi:10.3389/fnins.2019.0021730941005
   PubMed Web of Science ®Google Scholar
• Fatima I, El-Ayachi I, Taotao L, et al. The natural compound Jatrophone interferes with Wnt/β-catenin signaling and inhibits proliferation and EMT in human triple-negative breast cancer. PLoS One. 2017;12(12):e0189864. doi:10.1371/journal.pone.018986429281678
   PubMed Web of Science ®Google Scholar
• Zamberi NR, Abu N, Mohamed NE, et al. The antimetastatic and antiangiogenesis effects of kefir water on murine breast cancer cells. Integr Cancer Ther. 2016;15(4):NP53–NP66. doi:10.1177/153473541664286227230756
   PubMed Web of Science ®Google Scholar
• Wang S, Wang W, Wang W, et al. Context-specific coordinately regulatory network prioritize breast cancer genetic risk factors. Front Genet. 2020;11:255. doi:10.3389/fgene.2020.0025532273883
   PubMed Web of Science ®Google Scholar
• Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012;482(7385):339–346. doi:10.1038/nature1088722337053
   PubMed Web of Science ®Google Scholar
• Schmitt AM, Chang HY. Long noncoding RNAs in cancer pathways. Cancer Cell. 2016;29(4):452–463. doi:10.1016/j.ccell.2016.03.01027070700
   PubMed Web of Science ®Google Scholar
• Beermann J, Piccoli MT, Viereck J, Thum T. Non-coding RNAs in development and disease: background, mechanisms, and therapeutic approaches. Physiol Rev. 2016;96(4):1297–1325. doi:10.1152/physrev.00041.201527535639
   PubMed Web of Science ®Google Scholar
• Zhang G, Li S, Lu J, et al. LncRNA MT1JP functions as a ceRNA in regulating FBXW7 through competitively binding to miR-92a-3p in gastric cancer. Mol Cancer. 2018;17(1):1–11. doi:10.1186/s12943-018-0829-629304823
   PubMedGoogle Scholar
• Wu DD, Chen X, Sun KX, Wang LL, Chen S, Zhao Y. Role of the lncRNA ABHD11-AS1 in the tumorigenesis and progression of epithelial ovarian cancer through targeted regulation of RhoC. Mol Cancer. 2017;16(1):138. doi:10.1186/s12943-017-0709-528818073
   PubMedGoogle Scholar
• Shi SJ, Wang LJ, Yu B, Li YH, Jin Y, Bai XZ. LncRNA-ATB promotes trastuzumab resistance and invasion-metastasis cascade in breast cancer. Oncotarget. 2015;6(13):11652–11663. doi:10.18632/oncotarget.345725871474
   PubMedGoogle Scholar
• Gu P, Chen X, Xie R, et al. lncRNA HOXD-AS1 regulates proliferation and chemo-resistance of castration-resistant prostate cancer via recruiting WDR5. Mol Ther. 2017;25(8):1959–1973. doi:10.1016/j.ymthe.2017.04.01628487115
   PubMed Web of Science ®Google Scholar
• Liu RS, Jin GH, Xiao DR, Li HM, Bai FW, Tang YJ. Screening of the key volatile organic compounds of Tuber melanosporum fermentation by aroma sensory evaluation combination with principle component analysis. Sci Rep. 2015;5. doi:10.1038/srep17954
   Web of Science ®Google Scholar
• Ko MA, Rosario CO, Hudson JW, et al. Plk4 haploinsufficiency causes mitotic infidelity and carcinogenesis. Nat Genet. 2005;37(8):883–888. doi:10.1038/ng160516025114
   PubMed Web of Science ®Google Scholar
• Broggini-Tenzer A, Sharma A, Nytko KJ, et al. Combined treatment strategies for microtubule stabilizing agent-resistant tumors. J Natl Cancer Inst. 2015;107(4). doi:10.1093/jnci/dju504
   PubMedGoogle Scholar
• Muramatsu T, Muramatsu H. Glycosaminoglycan-binding cytokines as tumor markers. Proteomics. 2008;8(16):3350–3359. doi:10.1002/pmic.20080004218651707
   PubMed Web of Science ®Google Scholar
• Christianson HC, Menard JA, Chandran VI, et al. Tumor antigen glycosaminoglycan modification regulates antibody-drug conjugate delivery and cytotoxicity. Oncotarget. 2017;8(40):66960–66974. doi:10.18632/oncotarget.1692128978009
   PubMedGoogle Scholar
• Dong P, Yu B, Pan L, Tian X, Liu F. Identification of key genes and pathways in triple-negative breast cancer by integrated bioinformatics analysis. Biomed Res Int. 2018;2018:1–10. doi:10.1155/2018/2760918
   Web of Science ®Google Scholar
• Yang F, Liu YH, Dong SY, et al. Co-expression networks revealed potential core lncRNAs in the triple-negative breast cancer. Gene. 2016;591(2):471–477. doi:10.1016/j.gene.2016.07.00227380926
   PubMed Web of Science ®Google Scholar
• Iorns E, Ward TM, Dean S, et al. Whole genome in vivo RNAi screening identifies the leukemia inhibitory factor receptor as a novel breast tumor suppressor. Breast Cancer Res Treat. 2012;135(1):79–91. doi:10.1007/s10549-012-2068-722535017
   PubMed Web of Science ®Google Scholar
• Wang M, Wang M, Wang Z, et al. Long non-coding RNA-CTD-2108O9.1 represses breast cancer metastasis by influencing leukemia inhibitory factor receptor. Cancer Sci. 2018;109(6):1764–1774. doi:10.1111/cas.1359229603493
   PubMed Web of Science ®Google Scholar
• Ma D, Jing X, Shen B, et al. Leukemia inhibitory factor receptor negatively regulates the metastasis of pancreatic cancer cells in vitro and in vivo. Oncol Rep. 2016;36(2):827–836. doi:10.3892/or.2016.486527375070
   PubMed Web of Science ®Google Scholar
• Hergovich A. YAP-Hippo signalling downstream of leukemia inhibitory factor receptor: implications for breast cancer. Breast Cancer Res. 2012;14(6):326. doi:10.1186/bcr334923216692
   PubMed Web of Science ®Google Scholar