Integrative analysis of the lncRNA-associated ceRNA network reveals lncRNAs as potential prognostic biomarkers in human muscle-invasive bladder cancer

References

• Chen W, Zheng R, Baade PD, et al. Cancer statistics in China, 2015. CA Cancer J Clin. 2016;66(2):115–132. doi:10.3322/caac.2133826808342
   PubMed Web of Science ®Google Scholar
• Kaufman DS, Shipley WU, Feldman AS. Bladder cancer. Lancet. 2009;374(9685):239–249. doi:10.1016/S0140-6736(09)60491-819520422
   PubMed Web of Science ®Google Scholar
• Chou R, Selph SS, Buckley DI, et al. Treatment of muscle-invasive bladder cancer: a systematic review. Cancer. 2016;122(6):842–851. doi:10.1002/cncr.2984326773572
   PubMed Web of Science ®Google Scholar
• Seiler R, Ashab HAD, Erho N, et al. Impact of molecular subtypes in muscle-invasive bladder cancer on predictingresponse and survival after neoadjuvant chemotherapy. Eur Urol. 2017;72(4):544–554. doi:10.1016/j.eururo.2017.03.03028390739
   PubMed Web of Science ®Google Scholar
• Bartonicek N, Maag JL, Dinger ME. Long noncoding RNAs in cancer: mechanisms of action and technological advancements. Mol Cancer. 2016;15(1):43. doi:10.1186/s12943-016-0530-627233618
   PubMed Web of Science ®Google Scholar
• Dykes IM, Emanueli C. Transcriptional and post-transcriptional gene regulation by long non-coding RNA. Genomics Proteomics Bioinformatics. 2017;15(3):177–186. doi:10.1016/j.gpb.2016.12.00528529100
   PubMed Web of Science ®Google Scholar
• Nie FQ, Sun M, Yang JS, et al. Long noncoding RNA ANRIL promotes non-small cell lung cancer cell proliferation and inhibits apoptosis by silencing KLF2 and P21 expression. Mol Cancer Ther. 2015;14(1):268–277. doi:10.1158/1535-7163.MCT-14-049225504755
   PubMed Web of Science ®Google Scholar
• Peng F, Shi X, Meng Y, et al. Long non-coding RNA HOTTIP is upregulated in renal cell carcinoma and regulates cell growth and apoptosis by epigenetically silencing of LATS2. Biomed Pharmacother. 2018;105:1133–1140. doi:10.1016/j.biopha.2018.06.08130021349
   PubMed Web of Science ®Google Scholar
• Han YJ, Boatman SM, Zhang J, et al. LncRNA BLAT1 is upregulated in basal-like breast cancer through epigenetic modifications. Sci Rep. 2018;8(1):15572. doi:10.1038/s41598-018-33629-y30349062
   PubMedGoogle Scholar
• Pastori C, Kapranov P, Penas C, et al. The bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation. Proc Natl Acad Sci USA. 2015;112(27):8326–8331. doi:10.1073/pnas.142422011226111795
   PubMed Web of Science ®Google Scholar
• Pan J, Li X, Wu W, et al. Long non-coding RNA UCA1 promotes cisplatin/gemcitabine resistance through CREB modulating miR-196a-5p in bladder cancer cells. Cancer Lett. 2016;382(1):64–76. doi:10.1016/j.canlet.2016.08.01527591936
   PubMed Web of Science ®Google Scholar
• Hu XY, Hou PF, Li TT, et al. The roles of Wnt/beta-catenin signaling pathway related lncRNAs in cancer. Int J Biol Sci. 2018;14(14):2003–2011. doi:10.7150/ijbs.2797730585264
   PubMed Web of Science ®Google Scholar
• Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011;146(3):353–358. doi:10.1016/j.cell.2011.07.01421802130
   PubMed Web of Science ®Google Scholar
• Zheng P, Yin Z, Wu Y, Xu Y, Luo Y, Zhang TC. LncRNA HOTAIR promotes cell migration and invasion by regulating MKL1 via inhibition miR206 expression in HeLa cells. Cell Commun Signal. 2018;16(1):5. doi:10.1186/s12964-018-0216-329391067
   PubMedGoogle Scholar
• Wu M, Huang Y, Chen T, et al. LncRNA MEG3 inhibits the progression of prostate cancer by modulating miR-9-5p/QKI-5 axis. J Cell Mol Med. 2019;23(1):29–38. doi:10.1111/jcmm.1365830565858
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559. doi:10.1186/1471-2105-9-55919114008
   PubMed Web of Science ®Google Scholar
• Sun M, Nie F, Wang Y, et al. LncRNA HOXA11-AS promotes proliferation and invasion of gastric cancer by scaffolding the chromatin modification factors PRC2, LSD1, and DNMT1. Cancer Res. 2016;76(21):6299–6310. doi:10.1158/0008-5472.CAN-16-035627651312
   PubMed Web of Science ®Google Scholar
• Misawa A, Takayama KI, Fujimura T, Homma Y, Suzuki Y, Inoue S. Androgen-induced lncRNA POTEF-AS1 regulates apoptosis-related pathway to facilitate cell survival in prostate cancer cells. Cancer Sci. 2017;108(3):373–379. doi:10.1111/cas.1315128032932
   PubMed Web of Science ®Google Scholar
• Battistelli C, Cicchini C, Santangelo L, et al. The Snail repressor recruits EZH2 to specific genomic sites through the enrollment of the lncRNA HOTAIR in epithelial-to-mesenchymal transition. Oncogene. 2017;36(7):942–955. doi:10.1038/onc.2016.26027452518
   PubMed Web of Science ®Google Scholar
• Imamura K, Akimitsu N. Long non-coding RNAs involved in immune responses. Front Immunol. 2014;5:573. doi:10.3389/fimmu.2014.0057325431574
   PubMed Web of Science ®Google Scholar
• Liu G, Ye Z, Zhao X, Ji Z. SP1-induced up-regulation of lncRNA SNHG14 as a ceRNA promotes migration and invasion of clear cell renal cell carcinoma by regulating N-WASP. Am J Cancer Res. 2017;7(12):2515–2525. PMID: 29312804 Available from: https://www.ncbi.nlm.nih.gov/pubmed/2931280429312804
   PubMed Web of Science ®Google Scholar
• Tang RX, Chen WJ, He RQ, et al. Identification of a RNA-Seq based prognostic signature with five lncRNAs for lung squamous cell carcinoma. Oncotarget. 2017;8(31):50761–50773. doi:10.18632/oncotarget.1709828881601
   PubMedGoogle Scholar
• Yue C, Ren Y, Ge H, et al. Comprehensive analysis of potential prognostic genes for the construction of a competing endogenous RNA regulatory network in hepatocellular carcinoma. Onco Targets Ther. 2019;12:561–576. doi:10.2147/OTT.S18891330679912
   PubMed Web of Science ®Google Scholar
• Huang B, Song JH, Cheng Y, et al. Long non-coding antisense RNA KRT7-AS is activated in gastric cancers and supports cancer cell progression by increasing KRT7 expression. Oncogene. 2016;35(37):4927–4936. doi:10.1038/onc.2016.2526876208
   PubMed Web of Science ®Google Scholar
• Zhang Z, Qian W, Wang S, et al. Analysis of lncRNA-associated ceRNA network reveals potential lncRNA biomarkers in human colon adenocarcinoma. Cell Physiol Biochem. 2018;49(5):1778–1791. doi:10.1159/00049362330231249
   PubMedGoogle Scholar
• Sui J, Li YH, Zhang YQ, et al. Integrated analysis of long non-coding RNAassociated ceRNA network reveals potential lncRNA biomarkers in human lung adenocarcinoma. Int J Oncol. 2016;49(5):2023–2036. doi:10.3892/ijo.2016.371627826625
   PubMed Web of Science ®Google Scholar
• Jin Z, Hamilton JP, Yang J, et al. Hypermethylation of the AKAP12 promoter is a biomarker of Barrett’s-associated esophageal neoplastic progression. Cancer Epidemiol Biomarkers Prev. 2008;17(1):111–117. doi:10.1158/1055-9965.EPI-07-040718199717
   PubMed Web of Science ®Google Scholar
• Wu X, Wu T, Li K, et al. The mechanism and influence of AKAP12 in different cancers. Biomed Environ Sci. 2018;31(12):927–932. doi:10.3967/bes2018.12730636667
   PubMed Web of Science ®Google Scholar
• Prost G, Braun S, Hertwig F, et al. The putative tumor suppressor gene EphA7 is a novel BMI-1 target. Oncotarget. 2016;7(36):58203–58217. doi:10.18632/oncotarget.1127927533460
   PubMedGoogle Scholar
• Li S, Wu Z, Ma P, et al. Ligand-dependent EphA7 signaling inhibits prostate tumor growth and progression. Cell Death Dis. 2017;8(10):e3122. doi:10.1038/cddis.2017.50729022918
   PubMedGoogle Scholar
• Moon EH, Kim MJ, Ko KS, et al. Generation of mice with a conditional and reporter allele for Tmem100. Genesis. 2010;48(11):673–678. doi:10.1002/dvg.2067420848592
   PubMed Web of Science ®Google Scholar
• Ou D, Yang H, Hua D, Xiao S, Yang L. Novel roles of TMEM100: inhibition metastasis and proliferation of hepatocellular carcinoma. Oncotarget. 2015;6(19):17379–17390. doi:10.18632/oncotarget.395425978032
   PubMedGoogle Scholar
• Han Z, Wang T, Han S, et al. Low-expression of TMEM100 is associated with poor prognosis in non-small-cell lung cancer. Am J Transl Res. 2017;9(5):2567–2578. PMID:28560005.28560005
   PubMed Web of Science ®Google Scholar
• Wang F, Liang S, Liu X, Han L, Wang J, Du Q. LINC00460 modulates KDM2A to promote cell proliferation and migration by targeting miR-342-3p in gastric cancer. Onco Targets Ther. 2018;11:6383–6394. doi:10.2147/OTT.S16930730323616
   PubMed Web of Science ®Google Scholar
• Chang L, Hu Z, Zhou Z, Zhang H. Linc00518 contributes to multidrug resistance through regulating the MiR-199a/MRP1 axis in breast cancer. Cell Physiol Biochem. 2018;48(1):16–28. doi:10.1159/00049165930001527
   PubMedGoogle Scholar
• Wright C, Gupta CN, Chen J, et al. Polymorphisms in MIR137HG and microRNA-137-regulated genes influence gray matter structure in schizophrenia. Transl Psychiatry. 2016;6:e724. doi:10.1038/tp.2015.21126836412
   PubMed Web of Science ®Google Scholar
• Lv C, Li F, Li X, et al. MiR-31 promotes mammary stem cell expansion and breast tumorigenesis by suppressing Wnt signaling antagonists. Nat Commun. 2017;8(1):1036. doi:10.1038/s41467-017-01059-529051494
   PubMedGoogle Scholar
• Creighton CJ, Fountain MD, Yu Z, et al. Molecular profiling uncovers a p53-associated role for microRNA-31 in inhibiting the proliferation of serous ovarian carcinomas and other cancers. Cancer Res. 2010;70(5):1906–1915. doi:10.1158/0008-5472.CAN-09-387520179198
   PubMed Web of Science ®Google Scholar
• Kasiri S, Ansari KI, Hussain I, Bhan A, Mandal SS. Antisense oligonucleotide mediated knockdown of HOXC13 affects cell growth and induces apoptosis in tumor cells and over expression of HOXC13 induces 3D-colony formation. RSC Adv. 2013;3(10):3260–3269. doi:10.1039/C2RA22006G23495364
   PubMed Web of Science ®Google Scholar
• Luo J, Wang Z, Huang J, et al. HOXC13 promotes proliferation of esophageal squamous cell carcinoma via repressing transcription of CASP3. Cancer Sci. 2018;109(2):317–329. doi:10.1111/cas.1345329168599
   PubMed Web of Science ®Google Scholar
• Battistella M, Carlson JA, Osio A, Langbein L, Cribier B. Skin tumors with matrical differentiation: lessons from hair keratins, beta-catenin and PHLDA-1 expression. J Cutan Pathol. 2014;41(5):427–436. doi:10.1111/cup.1231324673383
   PubMed Web of Science ®Google Scholar
• Saha SS, Chowdhury RR, Mondal NR, Roy S, Sengupta S. Expression signatures of HOX cluster genes in cervical cancer pathogenesis: impact of human papillomavirus type 16 oncoprotein E7. Oncotarget. 2017;8(22):36591–36602. doi:10.18632/oncotarget.1661928402266
   PubMedGoogle Scholar
• Molino Y, Jabès F, Bonnet A, et al. Gene expression comparison reveals distinct basal expression of HOX members and differential TNF-induced response between brain- and spinal cord-derived microvascular endothelial cells. J Neuroinflammation. 2016;13(1):290. doi:10.1186/s12974-016-0749-627832801
   PubMed Web of Science ®Google Scholar