Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for hepatocellular carcinoma

Galun D, Bogdanovic A, Djokic Kovac J, Bulajic P, Loncar Z, Zuvela M. Preoperative neutrophil-to-lymphocyte ratio as a prognostic predictor after curative-intent surgery for hepatocellular carcinoma: experience from a developing country. Cancer Manag Res. 2018;10:977–88.

Llovet JM, Zucman-Rossi J, Pikarsky E, et al. Hepatocellular carcinoma. Nat Rev Dis Primers. 2016;2:16018.

Luo CL, Xu ZG, Chen H, et al. LncRNAs and EGFRvIII sequestered in TEPs enable blood-based NSCLC diagnosis. Cancer Manag Res. 2018;10:1449–59.

Ye X, Wang X, Shang L, et al. Genetic variants of ALDH2-rs671 and CYP2E1-rs2031920 contributed to risk of hepatocellular carcinoma susceptibility in a Chinese population. Cancer Manag Res. 2018;10:1037–50.

Mittal S, El-Serag HB. Epidemiology of hepatocellular carcinoma: consider the population. J Clin Gastroenterol. 2013;47(Suppl):S2–6.

Yamamura S, Imai-Sumida M, Tanaka Y, Dahiya R. Interaction and cross-talk between non-coding RNAs. Cell Mol Life Sci. 2018;75(3):467–84.

Sana J, Faltejskova P, Svoboda M, Slaby O. Novel classes of non-coding RNAs and cancer. J Transl Med. 2012;10:103.

Takahashi K, Yan I, Haga H, Patel T. Long noncoding RNA in liver diseases. Hepatology (Baltimore, MD). 2014;60(2):744–53.

Ba Z, Gu L, Hao S, Wang X, Cheng Z, Nie G. Downregulation of lncRNA CASC2 facilitates osteosarcoma growth and invasion through miR-181a. Cell Prolif. 2018;51(1):e12409.

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):353–8.

Tan JY, Sirey T, Honti F, et al. Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells. Genome Res. 2015;25(5):655–66.

Karreth FA, Pandolfi PP. ceRNA cross-talk in cancer: when ce-bling rivalries go awry. Cancer Dis. 2013;3(10):1113–21.

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):5366–83.

Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 2010;465(7301):1033–8.

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):160.

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (Oxford, England). 2010;26(1):139–40.

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.

Rosvall M, Bergstrom CT. Mapping change in large networks. PLoS ONE. 2010;5(1):e8694.

Jeggari A, Marks DS, Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics (Oxford, England). 2012;28(15):2062–3.

Wong N, Wang X. MiRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Res. 2015;43(Database issue):D146–52.

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):D296–302.

Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. eLife. 2015;4:e05005.

Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102(43):15545–50.

Siegel RL, Miller KD, Jemal A. Cancer statistics, 2017. Cancer J Clin. 2017;67(1):7–30.

Chen D, Zhang C, Lin J, Song X, Wang H. Screening differential circular RNA expression profiles reveal that hsa_circ_0128298 is a biomarker in the diagnosis and prognosis of hepatocellular carcinoma. Cancer Manag Res. 2018;10:1275–83.

Muers M. RNA: genome-wide views of long non-coding RNAs. Nat Rev Genet. 2011;12(11):742.

Caley DP, Pink RC, Trujillano D, Carter DR. Long noncoding RNAs, chromatin, and development. Sci World J. 2010;10:90–102.

Augoff K, McCue B, Plow EF, Sossey-Alaoui K. miR-31 and its host gene lncRNA LOC554202 are regulated by promoter hypermethylation in triple-negative breast cancer. Mol Cancer. 2012;11:5.

Robinson JM, Henderson WA. Modelling the structure of a ceRNA-theoretical, bipartite microRNA-mRNA interaction network regulating intestinal epithelial cellular pathways using R programming. BMC Res Notes. 2018;11(1):19.

Russell MR, Penikis A, Oldridge DA, et al. CASC15-S is a tumor suppressor lncRNA at the 6p22 neuroblastoma susceptibility locus. Cancer Res. 2015;75(15):3155–66.

Fan CN, Ma L, Liu N. Systematic analysis of lncRNA–miRNA–mRNA competing endogenous RNA network identifies four-lncRNA signature as a prognostic biomarker for breast cancer. J Transl Med. 2018;16(1):264.

He W, Zhang D, Li X, et al. TCGA datasetbased construction and integrated analysis of aberrantly expressed long noncoding RNA mediated competing endogenous RNA network in gastric cancer. Oncol Rep. 2018;40(6):3511–22.

Zhang Y, Li H, Zhang W, Che Y, Bai W, Huang G. LASSObased CoxPH model identifies an 11lncRNA signature for prognosis prediction in gastric cancer. Mol Med Rep. 2018;18(6):5579–93.

Wang H, Niu L, Jiang S, et al. Comprehensive analysis of aberrantly expressed profiles of lncRNAs and miRNAs with associated ceRNA network in muscle-invasive bladder cancer. Oncotarget. 2016;7(52):86174–85.

Patel N, Garikapati KR, Makani VKK, et al. Regulating BMI1 expression via miRNAs promote mesenchymal to epithelial transition (MET) and sensitizes breast cancer cell to chemotherapeutic drug. PLoS ONE. 2018;13(2):e0190245.

Arya D, Sachithanandan SP, Ross C, Palakodeti D, Li S, Krishna S. MiRNA182 regulates percentage of myeloid and erythroid cells in chronic myeloid leukemia. Cell Death Dis. 2017;8(1):e2547.

Liu L, Zhang X, Nan C, et al. MicroRNA-182 targets protein phosphatase 1 regulatory inhibitor subunit 1C in glioblastoma. Oncotarget. 2017;8(70):114677–84.

Sharifi M, Moridnia A. Apoptosis-inducing and antiproliferative effect by inhibition of miR-182-5p through the regulation of CASP9 expression in human breast cancer. Cancer Gene Ther. 2017;24(2):75–82.

Xue J, Zhou A, Wu Y, et al. miR-182-5p induced by STAT3 activation promotes glioma tumorigenesis. Cancer Res. 2016;76(14):4293–304.

Tang T, Wong HK, Gu W, et al. MicroRNA-182 plays an onco-miRNA role in cervical cancer. Gynecol Oncol. 2013;129(1):199–208.

Wang Y, Lee AT, Ma JZ, et al. Profiling microRNA expression in hepatocellular carcinoma reveals microRNA-224 up-regulation and apoptosis inhibitor-5 as a microRNA-224-specific target. J Biol Chem. 2008;283(19):13205–15.

Rossi S, Shimizu M, Barbarotto E, et al. microRNA fingerprinting of CLL patients with chromosome 17p deletion identify a miR-21 score that stratifies early survival. Blood. 2010;116(6):945–52.

Segura MF, Hanniford D, Menendez S, et al. Aberrant miR-182 expression promotes melanoma metastasis by repressing FOXO3 and microphthalmia-associated transcription factor. Proc Natl Acad Sci USA. 2009;106(6):1814–9.

Zhu H, Fang J, Zhang J, et al. miR-182 targets CHL1 and controls tumor growth and invasion in papillary thyroid carcinoma. Biochem Biophys Res Commun. 2014;450(1):857–62.

Kouri FM, Hurley LA, Daniel WL, et al. miR-182 integrates apoptosis, growth, and differentiation programs in glioblastoma. Genes Dev. 2015;29(7):732–45.

Xu C, Luo L, Yu Y, et al. Screening therapeutic targets of ribavirin in hepatocellular carcinoma. Oncol Lett. 2018;15(6):9625–32.

Allemani C, Weir HK, Carreira H, et al. Global surveillance of cancer survival 1995-2009: analysis of individual data for 25,676,887 patients from 279 population-based registries in 67 countries (CONCORD-2). Lancet (London, England). 2015;385(9972):977–1010.

Morgan DO. Principles of CDK regulation. Nature. 1995;374(6518):131–4.

Yoshida T, Tanaka S, Mogi A, Shitara Y, Kuwano H. The clinical significance of Cyclin B1 and Wee1 expression in non-small-cell lung cancer. Ann Oncol. 2004;15(2):252–6.

Nozoe T, Korenaga D, Kabashima A, Ohga T, Saeki H, Sugimachi K. Significance of cyclin B1 expression as an independent prognostic indicator of patients with squamous cell carcinoma of the esophagus. Clin Cancer Res. 2002;8(3):817–22.

Androic I, Kramer A, Yan R, et al. Targeting cyclin B1 inhibits proliferation and sensitizes breast cancer cells to taxol. BMC Cancer. 2008;8:391.

Ding K, Li W, Zou Z, Zou X, Wang C. CCNB1 is a prognostic biomarker for ER+ breast cancer. Med Hypotheses. 2014;83(3):359–64.

Weng L, Du J, Zhou Q, et al. Identification of cyclin B1 and Sec62 as biomarkers for recurrence in patients with HBV-related hepatocellular carcinoma after surgical resection. Mol Cancer. 2012;11:39.

Liu W, Ouyang S, Zhou Z, et al. Identification of genes associated with cancer progression and prognosis in lung adenocarcinoma: analyses based on microarray from Oncomine and The Cancer Genome Atlas databases. Mol Genet Genomic Med. 2018;7:e0052.

Gu J, Liu X, Li J, He Y. MicroRNA-144 inhibits cell proliferation, migration and invasion in human hepatocellular carcinoma by targeting CCNB1. Cancer Cell Int. 2019;19:15.

Schmandt R, Liu SK, McGlade CJ. Cloning and characterization of mPAL, a novel Shc SH2 domain-binding protein expressed in proliferating cells. Oncogene. 1999;18(10):1867–79.

Feng W, Li HC, Xu K, et al. SHCBP1 is over-expressed in breast cancer and is important in the proliferation and apoptosis of the human malignant breast cancer cell line. Gene. 2016;587(1):91–7.

Zhou Y, Tan Z, Chen K, et al. Overexpression of SHCBP1 promotes migration and invasion in gliomas by activating the NF-kappaB signaling pathway. Mol Carcinog. 2018;57(9):1181–90.

Tao HC, Wang HX, Dai M, et al. Targeting SHCBP1 inhibits cell proliferation in human hepatocellular carcinoma cells. Asian Pac J Cancer Prev. 2013;14(10):5645–50.

Figliuzzi M, Marinari E, De Martino A. MicroRNAs as a selective channel of communication between competing RNAs: a steady-state theory. Biophys J. 2013;104(5):1203–13.

Jens M, Rajewsky N. Competition between target sites of regulators shapes post-transcriptional gene regulation. Nat Rev Genet. 2015;16(2):113–26.

Martirosyan A, Figliuzzi M, Marinari E, De Martino A. Probing the limits to microRNA-mediated control of gene expression. PLoS Comput Biol. 2016;12(1):e1004715.

Bosson AD, Zamudio JR, Sharp PA. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol Cell. 2014;56(3):347–59.

Denzler R, Agarwal V, Stefano J, Bartel DP, Stoffel M. Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell. 2014;54(5):766–76.

Figliuzzi M, De Martino A, Marinari E. RNA-based regulation: dynamics and response to perturbations of competing RNAs. Biophys J. 2014;107(4):1011–22.