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Article

Prediction of key genes in ovarian cancer treated with decitabine based on network strategy

  • Authors:
    • Yu-Zhen Wang
    • Sheng-Chun Qiu
  • View Affiliations / Copyright

    Affiliations: Department of Pharmacy, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China, Department of Nursing, Zhejiang Provincial People's Hospital, Xiacheng, Hangzhou, Zhejiang 310014, P.R. China
  • Pages: 3548-3558
    |
    Published online on: March 23, 2016
       https://doi.org/10.3892/or.2016.4697
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Abstract

The objective of the present study was to predict key genes in ovarian cancer before and after treatment with decitabine utilizing a network approach and to reveal the molecular mechanism. Pathogenic networks of ovarian cancer before and after treatment were identified based on known pathogenic genes (seed genes) and differentially expressed genes (DEGs) detected by Significance Analysis of Microarrays (SAM) method. A weight was assigned to each gene in the pathogenic network and then candidate genes were evaluated. Topological properties (degree, betweenness, closeness and stress) of candidate genes were analyzed to investigate more confident pathogenic genes. Pathway enrichment analysis for candidate and seed genes were conducted. Validation of candidate gene expression in ovarian cancer was performed by reverse transcriptase-polymerase chain reaction (RT-PCR) assays. There were 73 nodes and 147 interactions in the pathogenic network before treatment, while 47 nodes and 66 interactions after treatment. A total of 32 candidate genes were identified in the before treatment group of ovarian cancer, of which 16 were rightly candidate genes after treatment and the others were silenced. We obtained 5 key genes (PIK3R2, CCNB1, IL2, IL1B and CDC6) for decitabine treatment that were validated by RT-PCR. In conclusion, we successfully identified 5 key genes (PIK3R2, CCNB1, IL2, IL1B and CDC6) and validated them, which provides insight into the molecular mechanisms of decitabine treatment and may be potential pathogenic biomarkers for the therapy of ovarian cancer.
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1 

Madathil KC, Greenstein JS, Juang KA, Neyens DM and Gramopadhye AK: An investigation of the informational needs of ovarian cancer patients and their supporters. In: Proceedings of the Human Factors and Ergonomics Society Annual Meeting. SAGE Journals. 57:748–752. 2013. View Article : Google Scholar

2 

Network CGAR; Cancer Genome Atlas Research Network: Integrated genomic analyses of ovarian carcinoma. Nature. 474:609–615. 2011. View Article : Google Scholar : PubMed/NCBI

3 

Siegel R, Naishadham D and Jemal A: Cancer statistics, 2012. CA Cancer J Clin. 62:10–29. 2012. View Article : Google Scholar : PubMed/NCBI

4 

Holohan C, Van Schaeybroeck S, Longley DB and Johnston PG: Cancer drug resistance: An evolving paradigm. Nat Rev Cancer. 13:714–726. 2013. View Article : Google Scholar : PubMed/NCBI

5 

Khaider NG, Lane D, Matte I, Rancourt C and Piché A: Targeted ovarian cancer treatment: The TRAILs of resistance. Am J Cancer Res. 2:75–92. 2012.

6 

Liu X, Tang WH, Zhao XM and Chen L: A network approach to predict pathogenic genes for Fusarium graminearum. PLoS One. 5:e130212010. View Article : Google Scholar : PubMed/NCBI

7 

Göhre V and Robatzek S: Breaking the barriers: Microbial effector molecules subvert plant immunity. Annu Rev Phytopathol. 46:189–215. 2008. View Article : Google Scholar : PubMed/NCBI

8 

Ein-Dor L, Kela I, Getz G, Givol D and Domany E: Outcome signature genes in breast cancer: Is there a unique set? Bioinformatics. 21:171–178. 2005. View Article : Google Scholar

9 

Zhang L, Li S, Hao C, Hong G, Zou J, Zhang Y, Li P and Guo Z: Extracting a few functionally reproducible biomarkers to build robust subnetwork-based classifiers for the diagnosis of cancer. Gene. 526:232–238. 2013. View Article : Google Scholar : PubMed/NCBI

10 

Rodríguez-Paredes M and Esteller M: Cancer epigenetics reaches mainstream oncology. Nat Med. 17:330–339. 2011. View Article : Google Scholar : PubMed/NCBI

11 

Ballestar E and Esteller M: Epigenetic gene regulation in cancer. Adv Genet. 61:247–267. 2008. View Article : Google Scholar : PubMed/NCBI

12 

Xiang Y, Ma N, Wang D, Zhang Y, Zhou J, Wu G, Zhao R, Huang H, Wang X, Qiao Y, et al: MiR-152 and miR-185 co-contribute to ovarian cancer cells cisplatin sensitivity by targeting DNMT1 directly: A novel epigenetic therapy independent of decitabine. Oncogene. 33:378–386. 2014. View Article : Google Scholar

13 

Stephan L and Momparler R: Combination chemotherapy of cancer using the inhibitor of DNA methylation 5-aza-2′-deoxy-cytidine (decitabine). J Cancer Res Ther. 3:56–65. 2015. View Article : Google Scholar

14 

Chen MY, Liao WS, Lu Z, Bornmann WG, Hennessey V, Washington MN, Rosner GL, Yu Y, Ahmed AA and Bast RC Jr: Decitabine and suberoylanilide hydroxamic acid (SAHA) inhibit growth of ovarian cancer cell lines and xenografts while inducing expression of imprinted tumor suppressor genes, apoptosis, G2/M arrest, and autophagy. Cancer. 117:4424–4438. 2011. View Article : Google Scholar : PubMed/NCBI

15 

Matsumura N, Huang Z, Mori S, Baba T, Fujii S, Konishi I, Iversen ES, Berchuck A and Murphy SK: Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer. Genome Res. 21:74–82. 2011. View Article : Google Scholar :

16 

Li J and Tibshirani R: Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data. Stat Methods Med Res. 22:519–536. 2013. View Article : Google Scholar

17 

Amberger JS, Bocchini CA, Schiettecatte F, Scott AF and Hamosh A: OMIM org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 43:D789–D798. 2015. View Article : Google Scholar

18 

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, Von Mering C, et al: STRING v9.1: Protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41:D808–D815. 2013. View Article : Google Scholar :

19 

Benesty J, Chen J, Huang Y and Cohen I: Pearson correlation coefficient. Noise Reduction in Speech Processing. Springer; pp. 1–4. 2009, View Article : Google Scholar

20 

Haythornthwaite C: Social network analysis: An approach and technique for the study of information exchange. Libr Inf Sci Res. 18:323–342. 1996. View Article : Google Scholar

21 

Barthelemy M: Betweenness centrality in large complex networks. Eur Phys J b Cond Matter Complex Syst. 38:163–168. 2004. View Article : Google Scholar

22 

Wasserman S: Social network analysis: Methods and Applications. Cambridge University Press; 1994, http://dx.doi.org/10.1017/Cbo9780511815478. View Article : Google Scholar

23 

Fekete SP, Kaufmann M, Kröller A and Lehmann K: A new approach for boundary recognition in geometric sensor networks. Proc. 17th Canadian Conference on Computational Geometry; pp. 82–85. 2005

24 

Huang W, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57. 2009. View Article : Google Scholar

25 

Wang X and Simon R: Microarray-based cancer prediction using single genes. BMC Bioinformatics. 12:3912011. View Article : Google Scholar : PubMed/NCBI

26 

Vogt PK, Hart JR, Gymnopoulos M, Jiang H, Kang S, Bader AG, Zhao L and Denley A: Phosphatidylinositol 3-kinase: The oncoprotein. Phosphoinositide 3-kinase in Health and Disease. Springer; pp. 79–104. 2010, View Article : Google Scholar

27 

Herrero-Gonzalez S and Di Cristofano A: New routes to old places: PIK3R1 and PIK3R2 join PIK3CA and PTEN as endometrial cancer genes. Cancer Discov. 1:106–107. 2011. View Article : Google Scholar

28 

Fayard E, Xue G, Parcellier A, Bozulic L and Hemmings BA: Protein kinase B (PKB/Akt), a key mediator of the Pi3k signaling pathway. Phosphoinositide 3-kinase in Health and Disease. Springer; pp. 31–56. 2011

29 

Wu R, Hu TC, Rehemtulla A, Fearon ER and Cho KR: Preclinical testing of PI3K/AKT/mTOR signaling inhibitors in a mouse model of ovarian endometrioid adenocarcinoma. Clin Cancer Res. 17:7359–7372. 2011. View Article : Google Scholar : PubMed/NCBI

30 

De Graeff P, Crijns AP, Ten Hoor KA, Klip HG, Hollema H, Oien K, Bartlett JM, Wisman GB, de Bock GH, de Vries EG, et al: The ErbB signalling pathway: Protein expression and prognostic value in epithelial ovarian cancer. Br J Cancer. 99:341–349. 2008. View Article : Google Scholar : PubMed/NCBI

31 

Thiele CJ, Li Z and Mckee AE: On Trk - the Trkb signal transduction pathway is an increasingly important target in cancer biology. Clin Cancer Res. 15:5962–5967. 2009. View Article : Google Scholar : PubMed/NCBI

32 

Cheung LW, Hennessy BT, Li J, Yu S, Myers AP, Djordjevic B, Lu Y, Stemke-Hale K, Dyer MD, Zhang F, et al: High frequency of PIK3R1 and PIK3R2 mutations in endometrial cancer elucidates a novel mechanism for regulation of PTEN protein stability. Cancer Discov. 1:170–185. 2011. View Article : Google Scholar : PubMed/NCBI

33 

Egloff AM, Vella LA and Finn OJ: Cyclin B1 and other cyclins as tumor antigens in immunosurveillance and immunotherapy of cancer. Cancer Res. 66:6–9. 2006. View Article : Google Scholar : PubMed/NCBI

34 

Ding K, Li W, Zou Z, Zou X and Wang C: CCNB1 is a prognostic biomarker for ER+ breast cancer. Med Hypotheses. 83:359–364. 2014. View Article : Google Scholar : PubMed/NCBI

35 

Liao W, Lin JX and Leonard WJ: Interleukin-2 at the crossroads of effector responses, tolerance, and immunotherapy. Immunity. 38:13–25. 2013. View Article : Google Scholar : PubMed/NCBI

36 

Wilke CM, Kryczek I and Zou W: Antigen-presenting cell (APC) subsets in ovarian cancer. Int Rev Immunol. 30:120–126. 2011. View Article : Google Scholar : PubMed/NCBI

37 

Duraiswamy J, Freeman GJ and Coukos G: Therapeutic PD-1 pathway blockade augments with other modalities of immunotherapy T-cell function to prevent immune decline in ovarian cancer. Cancer Res. 73:6900–6912. 2013. View Article : Google Scholar : PubMed/NCBI

38 

Zhang X, Xiao D, Wang Z, Zou Y, Huang L, Lin W, Deng Q, Pan H, Zhou J, Liang C, et al: MicroRNA-26a/b regulate DNA replication licensing, tumorigenesis, and prognosis by targeting CDC6 in lung cancer. Mol Cancer Res. 12:1535–1546. 2014. View Article : Google Scholar : PubMed/NCBI

39 

Blow JJ and Gillespie PJ: Replication licensing and cancer - a fatal entanglement? Nat Rev Cancer. 8:799–806. 2008. View Article : Google Scholar : PubMed/NCBI

40 

Booher K, Lin DW, Borrego SL and Kaiser P: Downregulation of Cdc6 and pre-replication complexes in response to methionine stress in breast cancer cells. Cell Cycle. 11:4414–4423. 2012. View Article : Google Scholar : PubMed/NCBI

41 

Deng Y, Jiang L, Wang Y, Xi Q, Zhong J, Liu J, Yang S, Liu R, Wang J, Huang M, et al: High expression of CDC6 is associated with accelerated cell proliferation and poor prognosis of epithelial ovarian cancer. Pathol Res Pract. Sep 18–2015.(Epub ahead of print). pii: S0344-0338(15)30014-5. View Article : Google Scholar

42 

Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Du Y, Zhang Y, Larsson E, Sheridan R, et al Cancer Genome Atlas Research Network: Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One. 7:e345462012. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Wang Y and Qiu S: Prediction of key genes in ovarian cancer treated with decitabine based on network strategy. Oncol Rep 35: 3548-3558, 2016.
APA
Wang, Y., & Qiu, S. (2016). Prediction of key genes in ovarian cancer treated with decitabine based on network strategy. Oncology Reports, 35, 3548-3558. https://doi.org/10.3892/or.2016.4697
MLA
Wang, Y., Qiu, S."Prediction of key genes in ovarian cancer treated with decitabine based on network strategy". Oncology Reports 35.6 (2016): 3548-3558.
Chicago
Wang, Y., Qiu, S."Prediction of key genes in ovarian cancer treated with decitabine based on network strategy". Oncology Reports 35, no. 6 (2016): 3548-3558. https://doi.org/10.3892/or.2016.4697
Copy and paste a formatted citation
x
Spandidos Publications style
Wang Y and Qiu S: Prediction of key genes in ovarian cancer treated with decitabine based on network strategy. Oncol Rep 35: 3548-3558, 2016.
APA
Wang, Y., & Qiu, S. (2016). Prediction of key genes in ovarian cancer treated with decitabine based on network strategy. Oncology Reports, 35, 3548-3558. https://doi.org/10.3892/or.2016.4697
MLA
Wang, Y., Qiu, S."Prediction of key genes in ovarian cancer treated with decitabine based on network strategy". Oncology Reports 35.6 (2016): 3548-3558.
Chicago
Wang, Y., Qiu, S."Prediction of key genes in ovarian cancer treated with decitabine based on network strategy". Oncology Reports 35, no. 6 (2016): 3548-3558. https://doi.org/10.3892/or.2016.4697
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