Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Oncology Letters
      • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Biomedical Reports
      • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • Information for Authors
    • Information for Reviewers
    • Information for Librarians
    • Information for Advertisers
    • Conferences
  • Language Editing
Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • For Authors
    • For Reviewers
    • For Librarians
    • For Advertisers
    • Conferences
  • Language Editing
Login Register Submit
  • This site uses cookies
  • You can change your cookie settings at any time by following the instructions in our Cookie Policy. To find out more, you may read our Privacy Policy.

    I agree
Search articles by DOI, keyword, author or affiliation
Search
Advanced Search
presentation
Oncology Reports
Join Editorial Board Propose a Special Issue
Print ISSN: 1021-335X Online ISSN: 1791-2431
Journal Cover
March-2018 Volume 39 Issue 3

Full Size Image

Sign up for eToc alerts
Recommend to Library

Journals

International Journal of Molecular Medicine

International Journal of Molecular Medicine

International Journal of Molecular Medicine is an international journal devoted to molecular mechanisms of human disease.

International Journal of Oncology

International Journal of Oncology

International Journal of Oncology is an international journal devoted to oncology research and cancer treatment.

Molecular Medicine Reports

Molecular Medicine Reports

Covers molecular medicine topics such as pharmacology, pathology, genetics, neuroscience, infectious diseases, molecular cardiology, and molecular surgery.

Oncology Reports

Oncology Reports

Oncology Reports is an international journal devoted to fundamental and applied research in Oncology.

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine is an international journal devoted to laboratory and clinical medicine.

Oncology Letters

Oncology Letters

Oncology Letters is an international journal devoted to Experimental and Clinical Oncology.

Biomedical Reports

Biomedical Reports

Explores a wide range of biological and medical fields, including pharmacology, genetics, microbiology, neuroscience, and molecular cardiology.

Molecular and Clinical Oncology

Molecular and Clinical Oncology

International journal addressing all aspects of oncology research, from tumorigenesis and oncogenes to chemotherapy and metastasis.

World Academy of Sciences Journal

World Academy of Sciences Journal

Multidisciplinary open-access journal spanning biochemistry, genetics, neuroscience, environmental health, and synthetic biology.

International Journal of Functional Nutrition

International Journal of Functional Nutrition

Open-access journal combining biochemistry, pharmacology, immunology, and genetics to advance health through functional nutrition.

International Journal of Epigenetics

International Journal of Epigenetics

Publishes open-access research on using epigenetics to advance understanding and treatment of human disease.

Medicine International

Medicine International

An International Open Access Journal Devoted to General Medicine.

Journal Cover
March-2018 Volume 39 Issue 3

Full Size Image

Sign up for eToc alerts
Recommend to Library

  • Article
  • Citations
    • Cite This Article
    • Download Citation
    • Create Citation Alert
    • Remove Citation Alert
    • Cited By
  • Similar Articles
    • Related Articles (in Spandidos Publications)
    • Similar Articles (Google Scholar)
    • Similar Articles (PubMed)
  • Download PDF
  • Download XML
  • View XML
Article

Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer

  • Authors:
    • Yangjing Zhao
    • Hui Wang
    • Chengjiang Wu
    • Meina Yan
    • Haojie Wu
    • Jingzhe Wang
    • Xinxin Yang
    • Qixiang Shao
  • View Affiliations / Copyright

    Affiliations: Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
  • Pages: 1197-1206
    |
    Published online on: January 10, 2018
       https://doi.org/10.3892/or.2018.6207
  • Expand metrics +
Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )
Cited By (CrossRef): 0 citations Loading Articles...

This article is mentioned in:



Abstract

Increasing evidence has experimentally proved the competitive endogenous RNA (ceRNA) hypothesis that long non-coding RNA (lncRNA) can affect the expression of RNA targets by competitively combining microRNA (miRNA) via miRNA response elements. However, an extensive ceRNA network of thyroid carcinoma in a large cohort has not been evaluated. We analyzed the RNAseq and miRNAseq data of 348 cases of primary papillary thyroid cancer (PTC) patients with clinical information downloaded from The Cancer Genome Atlas (TCGA) project to search for potential biomarkers or therapeutic targets. A computational approach was applied to build an lncRNA-miRNA-mRNA regulatory network of PTC. In total, 780 lncRNAs were detected as collectively dysregulated lncRNAs in all 3 PTC variants compared with normal tissues (fold change >2 and false discovery rate <0.05). The interactions among 45 lncRNAs, 13 miRNAs and 86 mRNAs constituted a ceRNA network of PTC. Nine out of the 45 aberrantly expressed lncRNAs were related to the clinical features of PTC patients. However, the expression levels of 3 lncRNAs (LINC00284, RBMS3-AS1 and ZFX-AS1) were identified to be tightly correlated with the patients overall survival (log-rank, P<0.05). The present study identified a list of specific lncRNAs associated with PTC progression and prognosis. This complex ceRNA interaction network in PTC may provide guidance for better understanding the molecular mechanisms underlying PTC.
View Figures

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

View References

1 

Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, Parkin DM, Forman D and Bray F: Cancer incidence and mortality worldwide: Sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer. 136:E359–E386. 2015. View Article : Google Scholar : PubMed/NCBI

2 

Siegel RL, Miller KD and Jemal A: Cancer statistics, 2016. CA Cancer J Clin. 66:7–30. 2016. View Article : Google Scholar : PubMed/NCBI

3 

Pellegriti G, Frasca F, Regalbuto C, Squatrito S and Vigneri R: Worldwide increasing incidence of thyroid cancer: Update on epidemiology and risk factors. J Cancer Epidemiol. 2013:9652122013. View Article : Google Scholar : PubMed/NCBI

4 

Schneider DF and Chen H: New developments in the diagnosis and treatment of thyroid cancer. CA Cancer J Clin. 63:374–394. 2013. View Article : Google Scholar : PubMed/NCBI

5 

Rosenbaum MA and McHenry CR: Contemporary management of papillary carcinoma of the thyroid gland. Expert Rev Anticancer Ther. 9:317–329. 2009. View Article : Google Scholar : PubMed/NCBI

6 

Brosnan CA and Voinnet O: The long and the short of noncoding RNAs. Curr Opin Cell Biol. 21:416–425. 2009. View Article : Google Scholar : PubMed/NCBI

7 

Calin GA and Croce CM: MicroRNA signatures in human cancers. Nat Rev Cancer. 6:857–866. 2006. View Article : Google Scholar : PubMed/NCBI

8 

Fatica A and Bozzoni I: Long non-coding RNAs: New players in cell differentiation and development. Nat Rev Genet. 15:7–21. 2014. View Article : Google Scholar : PubMed/NCBI

9 

Gibb EA, Brown CJ and Lam WL: The functional role of long non-coding RNA in human carcinomas. Mol Cancer. 10:382011. View Article : Google Scholar : PubMed/NCBI

10 

Salmena L, Poliseno L, Tay Y, Kats L and Pandolfi PP: A ceRNA hypothesis: The Rosetta stone of a hidden RNA language? Cell. 146:353–358. 2011. View Article : Google Scholar : PubMed/NCBI

11 

Xia T, Liao Q, Jiang X, Shao Y, Xiao B, Xi Y and Guo J: Long noncoding RNA associated-competing endogenous RNAs in gastric cancer. Sci Rep. 4:60882014. View Article : Google Scholar : PubMed/NCBI

12 

Zhang J, Fan D, Jian Z, Chen GG and Lai P: Cancer specific long noncoding RNAs show differential expression patterns and competing endogenous RNA potential in hepatocellular carcinoma. PLoS One. 10:e01410422015. View Article : Google Scholar : PubMed/NCBI

13 

Zhang K, Li Q, Kang X, Wang Y and Wang S: Identification and functional characterization of lncRNAs acting as ceRNA involved in the malignant progression of glioblastoma multiforme. Oncol Rep. 36:2911–2925. 2016. View Article : Google Scholar : PubMed/NCBI

14 

Sui J, Li YH, Zhang YQ, Li CY, Shen X, Yao WZ, Peng H, Hong WW, Yin LH, Pu YP, et al: Integrated analysis of long non-coding RNA-associated ceRNA network reveals potential lncRNA biomarkers in human lung adenocarcinoma. Int J Oncol. 49:2023–2036. 2016. View Article : Google Scholar : PubMed/NCBI

15 

Liu L, Yang J, Zhu X, Li D, Lv Z and Zhang X: Long noncoding RNA H19 competitively binds miR-17-5p to regulate YES1 expression in thyroid cancer. FEBS J. 283:2326–2339. 2016. View Article : Google Scholar : PubMed/NCBI

16 

Arancio W, Carina V, Pizzolanti G, Tomasello L, Pitrone M, Baiamonte C, Amato MC and Giordano C: Anaplastic thyroid carcinoma: A ceRNA analysis pointed to a crosstalk between SOX2, TP53, and microRNA biogenesis. Int J Endocrinol. 2015:4393702015. View Article : Google Scholar : PubMed/NCBI

17 

Huang CT, Oyang YJ, Huang HC and Juan HF: MicroRNA-mediated networks underlie immune response regulation in papillary thyroid carcinoma. Sci Rep. 4:64952015. View Article : Google Scholar

18 

Lan X, Zhang H, Wang Z, Dong W, Sun W, Shao L, Zhang T and Zhang D: Genome-wide analysis of long noncoding RNA expression profile in papillary thyroid carcinoma. Gene. 569:109–117. 2015. View Article : Google Scholar : PubMed/NCBI

19 

Robinson MD, McCarthy DJ and Smyth GK: edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 26:139–140. 2010. View Article : Google Scholar : PubMed/NCBI

20 

Jeggari A, Marks DS and Larsson E: miRcode: A map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics. 28:2062–2063. 2012. View Article : Google Scholar : PubMed/NCBI

21 

Riffo-Campos ÁL, Riquelme I and Brebi-Mieville P: Tools for sequence-based miRNA target prediction: What to choose? Int J Mol Sci. 17(pii): E19872016. View Article : Google Scholar : PubMed/NCBI

22 

Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, et al: miRTarBase: A database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 39:D163–D169. 2011. View Article : Google Scholar : PubMed/NCBI

23 

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B and Ideker T: Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498–2504. 2003. View Article : Google Scholar : PubMed/NCBI

24 

LiVolsi VA: Papillary thyroid carcinoma: An update. Mod Pathol. 24 Suppl 2:S1–S9. 2011. View Article : Google Scholar : PubMed/NCBI

25 

Tunca F, Sormaz IC, Iscan Y, Senyurek YG and Terzioglu T: Comparison of histopathological features and prognosis of classical and follicular variant papillary thyroid carcinoma. J Endocrinol Invest. 38:1327–1334. 2015. View Article : Google Scholar : PubMed/NCBI

26 

Xing M: Molecular pathogenesis and mechanisms of thyroid cancer. Nat Rev Cancer. 13:184–199. 2013. View Article : Google Scholar : PubMed/NCBI

27 

Aragon Han P, Weng CH, Khawaja HT, Nagarajan N, Schneider EB, Umbricht CB, Witwer KW and Zeiger MA: MicroRNA expression and association with clinicopathologic features in papillary thyroid cancer: A systematic review. Thyroid. 25:1322–1329. 2015. View Article : Google Scholar : PubMed/NCBI

28 

Li Q, Li H, Zhang L, Zhang C, Yan W and Wang C: Identification of novel long non-coding RNA biomarkers for prognosis prediction of papillary thyroid cancer. Oncotarget. 8:46136–46144. 2017.PubMed/NCBI

29 

Ergun S and Oztuzcu S: Oncocers: ceRNA-mediated cross-talk by sponging miRNAs in oncogenic pathways. Tumor Biol. 36:3129–3136. 2015. View Article : Google Scholar

30 

Yang M, Tian J, Guo X, Yang Y, Guan R, Qiu M, Li Y, Sun X, Zhen Y, Zhang Y, et al: Long noncoding RNA are aberrantly expressed in human papillary thyroid carcinoma. Oncol Lett. 12:544–552. 2016. View Article : Google Scholar : PubMed/NCBI

31 

Xie J, Guo B, Ding Z, Kang J, Deng X, Wu B and Fan Y: Microarray analysis of lncRNAs and mRNAs co-expression network and lncRNA function as ceRNA in papillary thyroid carcinoma. J Biomater Tiss Eng. 5:872–880. 2015. View Article : Google Scholar

32 

Chen Z, Li J, Lin S, Cao C, Gimbrone NT, Yang R, Fu DA, Carper MB, Haura EB, Schabath MB, et al: cAMP/CREB-regulated LINC00473 marks LKB1-inactivated lung cancer and mediates tumor growth. J Clin Invest. 126:2267–2279. 2016. View Article : Google Scholar : PubMed/NCBI

33 

Zhang Y, Tao Y and Liao Q: Long noncoding RNA: A crosslink in biological regulatory network. Brief Bioinform. Apr 24–2017.(Epub ahead of print).

34 

Cao W, Liu JN, Liu Z, Wang X, Han ZG, Ji T, Chen WT and Zou X: A three-lncRNA signature derived from the Atlas of ncRNA in cancer (TANRIC) database predicts the survival of patients with head and neck squamous cell carcinoma. Oral Oncol. 65:94–101. 2017. View Article : Google Scholar : PubMed/NCBI

35 

Onda M, Nagai H, Yoshida A, Miyamoto S, Asaka S, Akaishi J, Takatsu K, Nagahama M, Ito K, Shimizu K and Emi M: Up-regulation of transcriptional factor E2F1 in papillary and anaplastic thyroid cancers. J Hum Genet. 49:312–318. 2004. View Article : Google Scholar : PubMed/NCBI

36 

Hallstrom TC, Mori S and Nevins JR: An E2F1-dependent gene expression program that determines the balance between proliferation and cell death. Cancer Cell. 13:11–22. 2008. View Article : Google Scholar : PubMed/NCBI

37 

Tian W, Cui F and Esteban MA: E2F1 in renal cancer: Mr Hyde disguised as Dr Jekyll? J Pathol. 231:143–146. 2013. View Article : Google Scholar : PubMed/NCBI

38 

Zhan L, Zhang Y, Wang W, Song E, Fan Y and Wei B: E2F1: A promising regulator in ovarian carcinoma. Tumour Biol. 37:2823–2831. 2016. View Article : Google Scholar : PubMed/NCBI

39 

Dar AA, Majid S, de Semir D, Nosrati M, Bezrookove V and Kashani-Sabet M: miRNA-205 suppresses melanoma cell proliferation and induces senescence via regulation of E2F1 protein. J Biol Chem. 286:16606–16614. 2011. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Zhao Y, Wang H, Wu C, Yan M, Wu H, Wang J, Yang X and Shao Q: Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer. Oncol Rep 39: 1197-1206, 2018.
APA
Zhao, Y., Wang, H., Wu, C., Yan, M., Wu, H., Wang, J. ... Shao, Q. (2018). Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer. Oncology Reports, 39, 1197-1206. https://doi.org/10.3892/or.2018.6207
MLA
Zhao, Y., Wang, H., Wu, C., Yan, M., Wu, H., Wang, J., Yang, X., Shao, Q."Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer". Oncology Reports 39.3 (2018): 1197-1206.
Chicago
Zhao, Y., Wang, H., Wu, C., Yan, M., Wu, H., Wang, J., Yang, X., Shao, Q."Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer". Oncology Reports 39, no. 3 (2018): 1197-1206. https://doi.org/10.3892/or.2018.6207
Copy and paste a formatted citation
x
Spandidos Publications style
Zhao Y, Wang H, Wu C, Yan M, Wu H, Wang J, Yang X and Shao Q: Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer. Oncol Rep 39: 1197-1206, 2018.
APA
Zhao, Y., Wang, H., Wu, C., Yan, M., Wu, H., Wang, J. ... Shao, Q. (2018). Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer. Oncology Reports, 39, 1197-1206. https://doi.org/10.3892/or.2018.6207
MLA
Zhao, Y., Wang, H., Wu, C., Yan, M., Wu, H., Wang, J., Yang, X., Shao, Q."Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer". Oncology Reports 39.3 (2018): 1197-1206.
Chicago
Zhao, Y., Wang, H., Wu, C., Yan, M., Wu, H., Wang, J., Yang, X., Shao, Q."Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer". Oncology Reports 39, no. 3 (2018): 1197-1206. https://doi.org/10.3892/or.2018.6207
Follow us
  • Twitter
  • LinkedIn
  • Facebook
About
  • Spandidos Publications
  • Careers
  • Cookie Policy
  • Privacy Policy
How can we help?
  • Help
  • Live Chat
  • Contact
  • Email to our Support Team