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Pathology & Oncology Research
Published in: Pathology & Oncology Research 2/2020

01-04-2020 | Esophageal Cancer | Original Article

Differential Analysis of lncRNA, miRNA and mRNA Expression Profiles and the Prognostic Value of lncRNA in Esophageal Cancer

Authors: Hongtao Liu, Qing Zhang, Qianqian Lou, Xin Zhang, Yunxia Cui, Panpan Wang, Fan Yang, Fan Wu, Jing Wang, Tianli Fan, Shenglei Li

Published in: Pathology & Oncology Research | Issue 2/2020

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Abstract

Integrative central axis of lncRNA-miRNA-mRNA plays pivotal roles in tumor development and progression. However, the regulatory role of lncRNA-miRNA-mRNA in esophageal cancer remains elusive. TCGA database was utilized to investigate the differential expression of lncRNA, miRNA and mRNA in esophageal cancer (ESCA) and normal esophageal tissues, and GEO database was used to further validate the expression profile of key genes. Differential lncRNAs in TCGA database were submitted to Starbase, and lncRNAs related to overall survival were analyzed using Kaplan-Meier and log-rank test. We found 145 lncRNAs, 112 miRNAs and 2000 protein coding mRNAs were differentially expressed in ESCA samples, which were tightly involved in chromosome segregation, extracellular matrix assembly by GO assay, and KEGG assay revealed the correlation of differentially expressed genes with cell cycle, apoptosis and cGMP-PKG signaling pathway. Furthermore, there were 291 nodes in ceRNA network, which consisted of 40 lncRNAs, 28 miRNAs and 233 mRNAs, and formed 677 relations. Furthermore, 6 of 10 lncRNAs in TCGA database were consistent with GEO database, and expressions of 10 mRNAs in TCGA database all exhibited the same tendency with GEO database. Notably, we found 8 lncRNAs (WDFY3-AS2, CASC8, UGDH-AS1, RAP2C-AS1, AC007128.1, AC016205.1, AC092803.2 and AC079949.2) were correlated with overall survival of the patients with ESCA. The key differentially expressed genes participate in the development and progression of ESCA, and thus the elucidation of functions of lncRNA-miRNA-mRNA will provide new novel therapeutic target for the patients with ESCA.
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Literature
1.
Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D (2011) Global cancer statistics. CA Cancer J Clin 61(2):69–90PubMedCrossRef
2.
Abnet CC, Arnold M, Wei WQ (2018) Epidemiology of esophageal squamous cell carcinoma. Gastroenterology 154(2):360–373PubMedCrossRef
3.
Arnold M, Soerjomataram I, Ferlay J, Forman D (2015) Global incidence of oesophageal cancer by histological subtype in 2012. Gut 64(3):381–387PubMedCrossRef
4.
Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A (2015) Global cancer statistics, 2012. CA Cancer J Clin 65(2):87–108PubMedCrossRef
5.
Ohashi S, Miyamoto S, Kikuchi O, Goto T, Amanuma Y, Muto M (2015) Recent advances from basic and clinical studies of esophageal squamous cell carcinoma. Gastroenterology 149(7):1700–1715PubMedCrossRef
6.
Song G, Shen Y, Ruan Z, Li X, Chen Y, Yuan W, Ding X, Zhu L, Qian L (2016) LncRNA-uc.167 influences cell proliferation, apoptosis and differentiation of P19 cells by regulating Mef2c. Gene 590(1):97–108PubMedCrossRef
7.
Zhao J, Liu Y, Zhang W, Zhou Z, Wu J, Cui P, Zhang Y, Huang G (2015) Long non-coding RNA Linc00152 is involved in cell cycle arrest, apoptosis, epithelial to mesenchymal transition, cell migration and invasion in gastric cancer. Cell Cycle 14(19):3112–3123PubMedPubMedCentralCrossRef
8.
Song R, Hou G, Yang J, Yuan J, Wang C, Chai T, Liu Z (2018) Effects of PLK1 on proliferation, invasion and metastasis of gastric cancer cells through epithelial-mesenchymal transition. Oncol Lett 16(5):5739–5744PubMedPubMedCentral
9.
10.
11.
12.
13.
14.
Li DY, Chen WJ, Luo L, Wang YK, Shang J, Zhang Y, Chen G, Li SK (2017) Prospective lncRNA-miRNA-mRNA regulatory network of long non-coding RNA LINC00968 in non-small cell lung cancer A549 cells: a miRNA microarray and bioinformatics investigation. Int J Mol Med 40(6):1895–1906PubMed
15.
Yao K, Wang Q, Jia J, Zhao H (2017) A competing endogenous RNA network identifies novel mRNA, miRNA and lncRNA markers for the prognosis of diabetic pancreatic cancer. Tumour Biol 39(6):1010428317707882PubMed
16.
Ye S, Yang L, Zhao X, Song W, Wang W, Zheng S (2014) Bioinformatics method to predict two regulation mechanism: TF-miRNA-mRNA and lncRNA-miRNA-mRNA in pancreatic cancer. Cell Biochem Biophys 70(3):1849–1858PubMedCrossRef
17.
Liu Y, Zhu J, Ma X, Han S, Xiao D, Jia Y, Wang Y (2018) ceRNA network construction and comparison of gastric cancer with or without Helicobacter pylori infection. J Cell Physiol
18.
Li R, Qu H, Wang S, Wei J, Zhang L, Ma R, Lu J, Zhu J, Zhong WD, Jia Z (2018) GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC. Bioinformatics 34(14):2515–2517PubMedCrossRef
19.
Anders S, Pyl PT, Huber W (2015) HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31(2):166–169PubMedCrossRef
20.
Lun AT, Chen Y, Smyth GK (2016) It's DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR. Methods Mol Biol 1418:391–416PubMedCrossRef
21.
Li JH, Liu S, Zhou H, Qu LH, Yang JH (2014) starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 42(Database issue):D92–D97PubMedCrossRef
22.
Jeggari A, Marks DS, Larsson E (2012) miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics 28(15):2062–2063PubMedPubMedCentralCrossRef
23.
Chou CH, Shrestha S, Yang CD, Chang NW, Lin YL, Liao KW, Huang WC, Sun TH, Tu SJ, Lee WH et al (2018) miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res 46(D1):D296–D302PubMedCrossRef
24.
Furio-Tari P, Tarazona S, Gabaldon T, Enright AJ, Conesa A (2016) spongeScan: a web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Res 44(W1):W176–W180PubMedPubMedCentralCrossRef
25.
26.
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43(7):e47PubMedPubMedCentralCrossRef
27.
Zhu H, Lu J, Zhao H, Chen Z, Cui Q, Lin Z, Wang X, Wang J, Dong H, Wang S et al (2018) Functional long noncoding RNAs (lncRNAs) in clear cell kidney carcinoma revealed by reconstruction and comprehensive analysis of the lncRNA-miRNA-mRNA regulatory network. Med Sci Monit 24:8250–8263PubMedPubMedCentralCrossRef
28.
Fan CN, Ma L, Liu N (2018) Systematic analysis of lncRNA-miRNA-mRNA competing endogenous RNA network identifies four-lncRNA signature as a prognostic biomarker for breast cancer. J Transl Med 16(1):264PubMedPubMedCentralCrossRef
29.
Lin P, Wen DY, Li Q, He Y, Yang H, Chen G (2018) Genome-wide analysis of prognostic lncRNAs, miRNAs, and mRNAs forming a competing endogenous RNA network in hepatocellular carcinoma. Cell Physiol Biochem 48(5):1953–1967PubMedCrossRef
30.
Zhao J, Cheng W, He X, Liu Y, Li J, Sun J, Li J, Wang F, Gao Y (2018) Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. Onco Targets Ther 11:3129–3140PubMedPubMedCentralCrossRef
31.
Chen X, Han H, Li Y, Zhang Q, Mo K, Chen S (2016) Upregulation of long noncoding RNA HOTTIP promotes metastasis of esophageal squamous cell carcinoma via induction of EMT. Oncotarget 7(51):84480–84485PubMedPubMedCentralCrossRef
32.
Song W, Zou SB (2016) Prognostic role of lncRNA HOTAIR in esophageal squamous cell carcinoma. Clin Chim Acta 463:169–173PubMedCrossRef
33.
Liu B, Pan CF, Yao GL, Wei K, Xia Y, Chen YJ (2018) The long non-coding RNA AK001796 contributes to tumor growth via regulating expression of p53 in esophageal squamous cell carcinoma. Cancer Cell Int 18:38PubMedPubMedCentralCrossRef
34.
Wang W, Zhu Y, Li S, Chen X, Jiang G, Shen Z, Qiao Y, Wang L, Zheng P, Zhang Y (2016) Long noncoding RNA MALAT1 promotes malignant development of esophageal squamous cell carcinoma by targeting beta-catenin via Ezh2. Oncotarget 7(18):25668–25682PubMedPubMedCentralCrossRef
35.
Yao J, Huang JX, Lin M, Wu ZD, Yu H, Wang PC, Ye J, Chen P, Wu J, Zhao GJ (2016) Microarray expression profile analysis of aberrant long non-coding RNAs in esophageal squamous cell carcinoma. Int J Oncol 48(6):2543–2557PubMedCrossRef
36.
Cao W, Wu W, Shi F, Chen X, Wu L, Yang K, Tian F, Zhu M, Chen G, Wang W et al (2013) Integrated analysis of long noncoding RNA and coding RNA expression in esophageal squamous cell carcinoma. Int J Genomics 2013:480534PubMedPubMedCentralCrossRef
37.
Wang W, Wei C, Li P, Wang L, Li W, Chen K, Zhang J, Zhang W, Jiang G (2018) Integrative analysis of mRNA and lncRNA profiles identified pathogenetic lncRNAs in esophageal squamous cell carcinoma. Gene 661:169–175PubMedCrossRef
38.
Dong X, Kong C, Liu X, Bi J, Li Z, Li Z, Zhu Y, Zhang Z (2018) GAS5 functions as a ceRNA to regulate hZIP1 expression by sponging miR-223 in clear cell renal cell carcinoma. Am J Cancer Res 8(8):1414–1426PubMedPubMedCentral
39.
40.
Chi H, Yang R, Zheng X, Zhang L, Jiang R, Chen J (2018) LncRNA RP11-79H23.3 Functions as a Competing Endogenous RNA to Regulate PTEN Expression through Sponging hsa-miR-107 in the Development of Bladder Cancer. Int J Mol Sci 19(9)PubMedCentralCrossRef
41.
Wang P, Li J, Zhao W, Shang C, Jiang X, Wang Y, Zhou B, Bao F, Qiao H (2018) A novel LncRNA-miRNA-mRNA triple network identifies LncRNA RP11-363E7.4 as an important regulator of miRNA and gene expression in gastric Cancer. Cell Physiol Biochem 47(3):1025–1041PubMedCrossRef
42.
Botti G, Marra L, Malzone MG, Anniciello A, Botti C, Franco R, Cantile M (2017) LncRNA HOTAIR as prognostic circulating marker and potential therapeutic target in patients with tumor diseases. Curr Drug Targets 18(1):27–34PubMedCrossRef
43.
Wang Y, Li Y, Song HQ, Sun GW (2018) Long non-coding RNA LINC00899 as a novel serum biomarker for diagnosis and prognosis prediction of acute myeloid leukemia. Eur Rev Med Pharmacol Sci 22(21):7364–7370PubMed
44.
Yang L, Zhou JD, Zhang TJ, Ma JC, Xiao GF, Chen Q, Deng ZQ, Lin J, Qian J, Yao DM (2018) Overexpression of lncRNA PANDAR predicts adverse prognosis in acute myeloid leukemia. Cancer Manag Res 10:4999–5007PubMedPubMedCentralCrossRef
45.
Kiran M, Chatrath A, Tang X, Keenan DM, Dutta A (2018) A prognostic signature for lower grade gliomas based on expression of long non-coding RNAs. Mol Neurobiol
46.
Mao Y, Fu Z, Zhang Y, Dong L, Zhang Y, Zhang Q, Li X, Liu J (2018) A seven-lncRNA signature predicts overall survival in esophageal squamous cell carcinoma. Sci Rep 8(1):8823PubMedPubMedCentralCrossRef
47.
Bao J, Zhou C, Zhang J, Mo J, Ye Q, He J, Diao J (2018) Upregulation of the long noncoding RNA FOXD2-AS1 predicts poor prognosis in esophageal squamous cell carcinoma. Cancer Biomark 21(3):527–533PubMedCrossRef
Metadata
Title
Differential Analysis of lncRNA, miRNA and mRNA Expression Profiles and the Prognostic Value of lncRNA in Esophageal Cancer
Authors
Hongtao Liu
Qing Zhang
Qianqian Lou
Xin Zhang
Yunxia Cui
Panpan Wang
Fan Yang
Fan Wu
Jing Wang
Tianli Fan
Shenglei Li
Publication date
01-04-2020
Publisher
Springer Netherlands
Published in
Pathology & Oncology Research / Issue 2/2020
Print ISSN: 1219-4956
Electronic ISSN: 1532-2807
DOI
https://doi.org/10.1007/s12253-019-00655-8

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