Identification and validation of a five-lncRNA signature for predicting survival with targeted drug candidates in ovarian cancer

References

• Lheureux S, Gourley C, Vergote I, et al. Epithelial ovarian cancer. Lancet. 2019;393(10177):1240–1253.
   PubMed Web of Science ®Google Scholar
• Gadducci A, Guarneri V, Peccatori FA, et al. Current strategies for the targeted treatment of high-grade serous epithelial ovarian cancer and relevance of BRCA mutational status. J Ovarian Res. 2019;12(1):9.
   PubMed Web of Science ®Google Scholar
• Franzese E, Centonze S, Diana A, et al. PARP inhibitors in ovarian cancer. Cancer Treat Rev. 2019;73:1–9.
   PubMed Web of Science ®Google Scholar
• Pokhriyal R, Hariprasad R, Kumar L, et al. Chemotherapy resistance in advanced ovarian cancer patients. Biomark Cancer. 2019;11:1179299X19860815.
   PubMedGoogle Scholar
• Vasey PA. Resistance to chemotherapy in advanced ovarian cancer: mechanisms and current strategies. Br J Cancer. 2003;89(S3):S23–S8.
   PubMed Web of Science ®Google Scholar
• Anastasiadou E, Jacob LS, Slack FJ. Non-coding RNA networks in cancer. Nat Rev Cancer. 2017;18(1):5–18.
   PubMed Web of Science ®Google Scholar
• Yoon J-H, Abdelmohsen K, Gorospe M Functional interactions among microRNAs and long noncoding RNAs. Seminars in cell & developmental biology. 2014; 34:9–14.
   Google Scholar
• Poliseno L, Salmena L, Zhang J, et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 2010;465(7301):1033–1038.
   PubMed Web of Science ®Google Scholar
• Russo F, Fiscon G, Conte F, et al. Interplay between long noncoding RNAs and microRNAs in cancer. Methods Mol Biol. 2018;1819:75–92.
   PubMedGoogle Scholar
• Conte F, Fiscon G, Licursi V, et al. A paradigm shift in medicine: a comprehensive review of network-based approaches. Biochim Biophys Acta Gene Regul Mech. 2020;1863(6):194416.
   PubMed Web of Science ®Google Scholar
• Conte F, Fiscon G, Chiara M, et al. Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer. PLoS One. 2017;12(2):e0171661.
   PubMed Web of Science ®Google Scholar
• Wang L, Cho KB, Li Y, et al. Long Noncoding RNA (lncRNA)-mediated competing endogenous RNA networks provide novel potential biomarkers and therapeutic targets for colorectal cancer. Int J Mol Sci. 2019;20(22):5758.
   Web of Science ®Google Scholar
• Zhao L, Han T, Li Y, et al. The lncRNA SNHG5/miR-32 axis regulates gastric cancer cell proliferation and migration by targeting KLF4. The FASEB Journal. 2017;31(3):893–903.
   PubMed Web of Science ®Google Scholar
• Wright MW. A short guide to long non-coding RNA gene nomenclature. Hum Genomics. 2014;8(1):7.
   PubMed Web of Science ®Google 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–e.
   PubMed Web of Science ®Google Scholar
• Venables W, Ripley B. Modern applied statistics with S. New York: Springer-Verlag; 2002.
   Google Scholar
• Kuhn M. Building predictive models in R using the caret package. J Stat Softw. 2008;28(5):1–26.
   PubMed Web of Science ®Google Scholar
• Collett D. Modelling survival data in medical research, Third Edition, Bristol, UK: Chapman and Hall/CRC, 2015.
   Google Scholar
• Lin JZ, Lin N, Zhao WJ. Identification and validation of a six-lncRNA prognostic signature with its ceRNA networks and candidate drugs in lower-grade gliomas. Genomics. 2020;112(5):2990–3002.
   PubMed Web of Science ®Google Scholar
• Paraskevopoulou MD, Vlachos IS, Karagkouni D, et al. DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res. 2016;44(D1):D231–8.
   PubMed Web of Science ®Google Scholar
• Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2020;48(D1):D127–d31.
   PubMed Web of Science ®Google Scholar
• Hsu SD, Lin FM, Wu WY, et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 2011;39(suppl_1):D163–9.
   PubMed Web of Science ®Google Scholar
• Agarwal V, Bell GW, Nam JW, et al. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4. DOI:10.7554/eLife.05005
   Web of Science ®Google Scholar
• Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523.
   PubMed Web of Science ®Google Scholar
• Lamb J, Crawford ED, Peck D, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313(5795):1929–1935.
   PubMed Web of Science ®Google Scholar
• Ling H, Fabbri M, Calin GA. MicroRNAs and other non-coding RNAs as targets for anticancer drug development. Nat Rev Drug Discov. 2013;12(11):847–865.
   PubMed Web of Science ®Google Scholar
• Jia L, Song Y. Long noncoding RNA TPT1-AS1 downregulates the microRNA-770-5p expression to inhibit glioma cell autophagy and promote proliferation through STMN1 upregulation. Cancer Sci. 2020;235:3679–3689.
   Google Scholar
• Zhang Y, Sun J, Qi Y, et al. Long non-coding RNA TPT1-AS1 promotes angiogenesis and metastasis of colorectal cancer through TPT1-AS1/NF90/VEGFA signaling pathway. Aging (Albany NY). 2020;12(7):6191–6205.
   Google Scholar
• Wu W, Gao H, Li X, et al. LncRNA TPT1-AS1 promotes tumorigenesis and metastasis in epithelial ovarian cancer by inducing TPT1 expression. Cancer Sci. 2019;110(5):1587–1598.
   Google Scholar
• Wang H, Fu Z, Dai C, et al. LncRNAs expression profiling in normal ovary, benign ovarian cyst and malignant epithelial ovarian cancer. Sci Rep. 2016;6:38983.
   PubMed Web of Science ®Google Scholar
• Wu X, Sharp PA. Divergent transcription: a driving force for new gene origination? Cell. 2013;155(5):990–996.
   PubMed Web of Science ®Google Scholar
• Gibbons HR, Shaginurova G, Kim LC, et al. Divergent lncRNA GATA3-AS1 Regulates GATA3 Transcription in T-Helper 2 Cells. Front Immunol. 2018;9:2512.
   PubMed Web of Science ®Google Scholar
• Basal E, Ayeni T, Zhang Q, et al. Patterns of Mullerian inhibiting substance type II and candidate type I receptors in epithelial ovarian cancer. Curr Mol Med. 2016;16(3):222–231.
   PubMed Web of Science ®Google Scholar
• Zhu D, Shi C, Jiang Y, et al. Cisatracurium inhibits the growth and induces apoptosis of ovarian cancer cells by promoting lincRNA-p21. Bioengineered. 2021;12:1505–1516.
   PubMed Web of Science ®Google Scholar
• Park MS, Dong SM, Kim B-R, et al. Thioridazine inhibits angiogenesis and tumor growth by targeting the VEGFR-2/PI3K/mTOR pathway in ovarian cancer xenografts. Oncotarget. 2014;5(13):4929–4934.
   PubMedGoogle Scholar
• Marques LO, Lima MS, Soares BGO Trifluoperazine for schizophrenia. The Cochrane database of systematic reviews. 2004: CD003545.
   Google Scholar
• Perez RP, Handel LM, Hamilton TC. Potentiation of cisplatin cytotoxicity in human ovarian carcinoma cell lines by trifluoperazine, a calmodulin inhibitor. Gynecol Oncol. 1992;46(1):82–87.
   PubMed Web of Science ®Google Scholar
• Regan RC, Gogal RM, Barber JP, et al. Cytotoxic effects of loperamide hydrochloride on canine cancer cells. J Vet Med Sci. 2014;76(12):1563–1568.
   PubMed Web of Science ®Google Scholar
• Gong XW, Xu YH, Chen XL, et al. Loperamide, an antidiarrhea drug, has antitumor activity by inducing cell apoptosis. Pharmacol Res. 2012;65(3):372–378.
   PubMed Web of Science ®Google Scholar
• Hu L, Zaloudek C, Mills GB, et al. In vivo and in vitro ovarian carcinoma growth inhibition by a phosphatidylinositol 3-kinase inhibitor (LY294002). Clin Cancer Res. 2000;6(3):880–886.
   PubMed Web of Science ®Google Scholar
• Giegé R, Frugier M, Rudinger J. tRNA mimics. Curr Opin Struct Biol. 1998;8(3):286–293.
   PubMed Web of Science ®Google Scholar
• Söderlund G, Haarhaus M, Chisalita S, et al. Inhibition of puromycin-induced apoptosis in breast cancer cells by IGF-I occurs simultaneously with increased protein synthesis. Neoplasma. 2004;51(1):1–11.
   PubMed Web of Science ®Google Scholar
• Beauchamp M-C, Yasmeen A, Knafo A, et al. Targeting insulin and insulin-like growth factor pathways in epithelial ovarian cancer. J Oncol. 2010;2010:257058.
   PubMedGoogle Scholar
• Zhou M, Wang X, Shi H, et al. Characterization of long non-coding RNA-associated ceRNA network to reveal potential prognostic lncRNA biomarkers in human ovarian cancer. Oncotarget. 2016;7(11):12598–12611.
   PubMed Web of Science ®Google Scholar
• The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013;45(6):580–585.
   PubMed Web of Science ®Google Scholar
• Paik ES, Lee J-W, Park J-Y, et al. Prediction of survival outcomes in patients with epithelial ovarian cancer using machine learning methods. J Gynecol Oncol. 2019;30(4):30.
   Web of Science ®Google Scholar