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Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks

  • Authors:
    • Jia Zhou
    • Chao Chen
    • Hua‑Feng Li
    • Yu‑Jie Hu
    • Hong‑Ling Xie
  • View Affiliations / Copyright

    Affiliations: Department of Geratology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China, Department of Radiotherapy, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310006, P.R. China
    Copyright: © Zhou et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 696-702
    |
    Published online on: May 29, 2017
       https://doi.org/10.3892/mmr.2017.6641
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Abstract

The progression of glioblastoma (GBM) is driven by dynamic alterations in the activity and connectivity of gene pathways. Revealing these dynamic events is necessary in order to understand the pathological mechanisms of, and develop effective treatments for, GBM. The present study aimed to investigate dynamic alterations in pathway activity and connectivity across radiotherapy and chemoradiation conditions in GBM, and to give system‑level insights into molecular mechanisms for GBM therapy. A total of two differential co‑expression networks (DCNs) were constructed using Pearson correlation coefficient analysis and one sided t‑tests, based on gene expression profiles and protein‑protein interaction networks, one for each condition. Subsequently, shared differential modules across DCNs were detected via significance analysis for candidate modules, which were obtained according to seed selection, module search by seed expansion and refinement of searched modules. As condition‑specific differential modules mediate differential biological processes, the module connectivity dynamic score (MCDS) was implemented to explore dynamic alterations among them. Based on DCNs with 287 nodes and 1,052 edges, a total of 28 seed genes and seven candidate modules were identified. Following significance analysis, five shared differential modules were identified in total. Dynamic alterations among these differential modules were identified using the MCDS, and one module with significant dynamic alterations was identified, termed the dynamic module. The present study revealed the dynamic alterations of shared differential modules, identified one dynamic module between the radiotherapy and chemoradiation conditions, and demonstrated that pathway dynamics may applied to the study of the pathogenesis and therapy of GBM.
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1 

Omuro A and DeAngelis LM: Glioblastoma and other malignant gliomas: A clinical review. JAMA. 310:1842–1850. 2013. View Article : Google Scholar : PubMed/NCBI

2 

Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C and Tavaré S: Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci USA. 110:4009–4014. 2013. View Article : Google Scholar : PubMed/NCBI

3 

Stupp R, Mason WP, Van Den Bent MJ, Weller M, Fisher B, Taphoorn MJ, Belanger K, Brandes AA, Marosi C, Bogdahn U, et al: Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N Engl J Med. 352:987–996. 2005. View Article : Google Scholar : PubMed/NCBI

4 

Lambiv WL, Vassallo I, Delorenzi M, Shay T, Diserens AC, Misra A, Feuerstein B, Murat A, Migliavacca E, Hamou MF, et al: The Wnt inhibitory factor 1 (WIF1) is targeted in glioblastoma and has a tumor suppressing function potentially by induction of senescence. Neuro Oncol. 13:736–747. 2011. View Article : Google Scholar : PubMed/NCBI

5 

Werner T: Target gene identification from expression array data by promoter analysis. Biomol Eng. 17:87–94. 2001. View Article : Google Scholar : PubMed/NCBI

6 

Liu T, Reinhart BJ, Magnani E, Huang T, Kerstetter R and Barton M: Of blades and branches: Understanding and expanding the Arabidopsis Ad/Abaxial regulatory network through target gene identification. Cold Spring Harb Symp Quant Biol. 77:31–45. 2012. View Article : Google Scholar : PubMed/NCBI

7 

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, et al: The STRING database in: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39:(Database issue). D561–D568. 2011. View Article : Google Scholar : PubMed/NCBI

8 

Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q and Wrana JL: Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol. 27:199–204. 2009. View Article : Google Scholar : PubMed/NCBI

9 

Lee MJ, Ye AS, Gardino AK, Heijink AM, Sorger PK, MacBeath G and Yaffe MB: Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell. 149:780–794. 2012. View Article : Google Scholar : PubMed/NCBI

10 

Murat A, Migliavacca E, Gorlia T, Lambiv WL, Shay T, Hamou MF, de Tribolet N, Regli L, Wick W, Kouwenhoven MC, et al: Stem cell-related ‘self-renewal’ signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma. J Clin Oncol. 26:3015–3024. 2008. View Article : Google Scholar : PubMed/NCBI

11 

Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B and Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31:e152003. View Article : Google Scholar : PubMed/NCBI

12 

Bolstad BM, Irizarry RA, Astrand M and Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 19:185–193. 2003. View Article : Google Scholar : PubMed/NCBI

13 

Bolstad B: Affy: Built-in Processing Methods. 2015.http://120.52.72.36/www.bioconductor.org/c3pr90ntcsf0/packages/release/bioc/vignettes/affy/inst/doc/builtinMethods.pdf

14 

Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS and Green MR: ChIPpeakAnno: A Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 11:2372010. View Article : Google Scholar : PubMed/NCBI

15 

Gentleman R, Carey V, Huber W and Hahne F: Genefilter: Methods for filtering genes from microarray experiments. R package. 2011.http://www.bioconductor.org/packages/2.3/bioc/html/genefilter.html

16 

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, et al: STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43:(Database issue). D447–D452. 2015. View Article : Google Scholar : PubMed/NCBI

17 

Benesty J, Chen J, Huang Y and Cohen I: Pearson correlation coefficient. Noise reduction in speech processing Berlin Heidelberg: Springer; pp. 1–4. 2009, View Article : Google Scholar

18 

Cohen J, Cohen P, West SG and Aiken LS: Applied multiple regression/correlation analysis for the behavioral sciences. 3rd. Hoboken: Taylor and Francis; 2013

19 

Ma X, Gao L and Tan K: Modeling disease progression using dynamics of pathway connectivity. Bioinformatics. 30:2343–2350. 2014. View Article : Google Scholar : PubMed/NCBI

20 

Vanunu O, Magger O, Ruppin E, Shlomi T and Sharan R: Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol. 6:e10006412010. View Article : Google Scholar : PubMed/NCBI

21 

Zhou D, Bousquet O, Lal TN, Weston J and Schölkopf B: Learning with local and global consistency. Adv Neural Inform Pro Systems. 16:321–328. 2004.

22 

Fortunato S and Barthélemy M: Resolution limit in community detection. Proc Natl Acad Sci USA. 104:36–41. 2007. View Article : Google Scholar : PubMed/NCBI

23 

Bouchard M, Jousselme A-L and Doré P-E: A proof for the positive definiteness of the Jaccard index matrix. Int J Approximate Reasoning. 54:615–626. 2013. View Article : Google Scholar

24 

Benjamini Y and Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Stat Soc Series B (Methodological). 57:289–300. 1995.

25 

Ma X, Gao L, Karamanlidis G, Gao P, Lee CF, Garcia-Menendez L, Tian R and Tan K: Revealing pathway dynamics in heart diseases by analyzing multiple differential networks. PLoS Comput Biol. 11:e10043322015. View Article : Google Scholar : PubMed/NCBI

26 

Nibbe RK, Chowdhury SA, Koyutürk M, Ewing R and Chance MR: Protein-protein interaction networks and subnetworks in the biology of disease. Wiley Interdiscip Rev Syst Biol Med. 3:357–367. 2011. View Article : Google Scholar : PubMed/NCBI

27 

Wu Y, Jing R, Jiang L, Jiang Y, Kuang Q, Ye L, Yang L, Li Y and Li M: Combination use of protein-protein interaction network topological features improves the predictive scores of deleterious non-synonymous single-nucleotide polymorphisms. Amino Acids. 46:2025–2035. 2014. View Article : Google Scholar : PubMed/NCBI

28 

Hesson LB, Cooper WN and Latif F: Evaluation of the 3p21. 3 tumour-suppressor gene cluster. Oncogene. 26:7283–7301. 2007. View Article : Google Scholar : PubMed/NCBI

29 

Zariwala MA, Gee HY, Kurkowiak M, Al-Mutairi DA, Leigh MW, Hurd TW, Hjeij R, Dell SD, Chaki M, Dougherty GW, et al: ZMYND10 is mutated in primary ciliary dyskinesia and interacts with LRRC6. Am J Hum Genet. 93:336–345. 2013. View Article : Google Scholar : PubMed/NCBI

30 

Zhang X, Liu H, Li B, Huang P, Shao J and He Z: Tumor suppressor BLU inhibits proliferation of nasopharyngeal carcinoma cells by regulation of cell cycle, c-Jun N-terminal kinase and the cyclin D1 promoter. BMC Cancer. 12:2672012. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Zhou J, Chen C, Li HF, Hu YJ and Xie HL: Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks. Mol Med Rep 16: 696-702, 2017.
APA
Zhou, J., Chen, C., Li, H., Hu, Y., & Xie, H. (2017). Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks. Molecular Medicine Reports, 16, 696-702. https://doi.org/10.3892/mmr.2017.6641
MLA
Zhou, J., Chen, C., Li, H., Hu, Y., Xie, H."Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks". Molecular Medicine Reports 16.1 (2017): 696-702.
Chicago
Zhou, J., Chen, C., Li, H., Hu, Y., Xie, H."Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks". Molecular Medicine Reports 16, no. 1 (2017): 696-702. https://doi.org/10.3892/mmr.2017.6641
Copy and paste a formatted citation
x
Spandidos Publications style
Zhou J, Chen C, Li HF, Hu YJ and Xie HL: Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks. Mol Med Rep 16: 696-702, 2017.
APA
Zhou, J., Chen, C., Li, H., Hu, Y., & Xie, H. (2017). Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks. Molecular Medicine Reports, 16, 696-702. https://doi.org/10.3892/mmr.2017.6641
MLA
Zhou, J., Chen, C., Li, H., Hu, Y., Xie, H."Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks". Molecular Medicine Reports 16.1 (2017): 696-702.
Chicago
Zhou, J., Chen, C., Li, H., Hu, Y., Xie, H."Revealing radiotherapy- and chemoradiation-induced pathway dynamics in glioblastoma by analyzing multiple differential networks". Molecular Medicine Reports 16, no. 1 (2017): 696-702. https://doi.org/10.3892/mmr.2017.6641
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