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Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis

  • Authors:
    • Zhikui Wang
    • Zhaoxia Wang
    • Zhongqi Zhou
    • Yueqin Ren
  • View Affiliations / Copyright

    Affiliations: Department of Nephrology, Linyi People's Hospital, Linyi, Shandong 276003, P.R. China
    Copyright: © Wang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 953-958
    |
    Published online on: December 4, 2015
       https://doi.org/10.3892/ol.2015.4006
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Abstract

Despite clear cell sarcoma of the kidney (CCSK) being the second most common renal tumor in children, its mechanism has not yet been fully investigated. The aim of the present study was to investigate the potential role of vascular endothelial growth factor A (VEGFA) in CCSK development. Following preprocessing of the original GSE2712 data, the differentially‑expressed genes (DEGs) between 14 CCSK and 3 fetal kidney samples were identified through Significance Analysis of Microarrays, using the R package. Pathway enrichment analysis was then performed on the DEGs. A protein‑protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins database and the DEGs that were enriched in the most significant pathways. Following this, gene ontology analysis was performed on the VEGFA‑associated genes, whilst transcription factor binding site analysis was conducted on the hot genes. A total of 2,681 DEGs, including 543 upregulated and 2,138 downregulated genes, were identified, and these were significantly enriched in pathways associated with cancer and focal adhesion. Furthermore, VEGFA, integrin β1, integrin αV, v‑akt murine thymoma viral oncogene homolog 1 and endothelial growth factor receptor were identified as hot genes in the PPI network. In addition, the upregulated VEGFA‑associated genes, cyclin D1 and cyclin‑dependent kinase inhibitor 1B, affected kinase regulation, and the downregulated VEGFA‑associated genes, receptor tyrosine‑protein kinase erbB‑2, mesenchymal‑epithelial transition tyrosine kinase receptor and kinase insert domain receptor, were enriched in the protein tyrosine kinase process. It was identified that VEGFA was regulated by restorer of fertility, erythromycin resistance methylase, GA binding protein subunit α, norepinephrine transporter, nuclear factor κB and Sp2 transcription factor genes. Overall, VEGFA and its associated genes serve important roles during CCSK development, and alongside transcription factors, they may function as novel therapeutic targets for disease treatment.
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1 

Hartman RJ Jr, Welchons DR, Teot L, Chow J and Cendron M: Incidental capture of rarely diagnosed pediatric tumor, An infant boy with clear cell sarcoma of the kidney. Urology. 82:1416–1418. 2013. View Article : Google Scholar : PubMed/NCBI

2 

Argani P, Perlman EJ, Breslow NE, Browning NG, Green DM, D'Angio GJ and Beckwith JB: Clear cell sarcoma of the kidney, A review of 351 cases from the National Wilms Tumor Study Group Pathology Center. Am J Surg Pathol. 24:4–18. 2000. View Article : Google Scholar : PubMed/NCBI

3 

Seibel NL, Li S, Breslow NE, Beckwith JB, Green DM, Haase GM, Ritchey ML, Thomas PR, Grundy PE, Finklestein JZ, et al: Effect of duration of treatment on treatment outcome for patients with clear-cell sarcoma of the kidney: A report from the National Wilms' Tumor Study Group. J Clin Oncol. 22:468–473. 2004. View Article : Google Scholar : PubMed/NCBI

4 

Cutcliffe C, Kersey D, Huang CC, Zeng Y, Walterhouse D and Perlman EJ: Renal Tumor Committee of the Children's Oncology Group: Clear cell sarcoma of the kidney. Up-regulation of neural markers with activation of the sonic hedgehog and Akt pathways. Clin Cancer Res. 11:7986–7994. 2005. View Article : Google Scholar : PubMed/NCBI

5 

Dhamne S, Brown RE, Covinsky M, Dhamne C, Eldin K and Tatevian N: Clear cell sarcoma of kidney, Morphoproteomic analysis reveals genomic correlates and therapeutic options. Pediatr Dev Pathol. 16:20–27. 2013. View Article : Google Scholar : PubMed/NCBI

6 

Karlsson J, Mengelbier Holmquist L, Ciornei CD, Naranjo A, O'Sullivan MJ and Gisselsson D: Clear cell sarcoma of the kidney demonstrates an embryonic signature indicative of a primitive nephrogenic origin. Genes Chromosomes Cancer. 53:381–391. 2014. View Article : Google Scholar : PubMed/NCBI

7 

Little SE, Bax DA, Rodriguez-Pinilla M, Natrajan R, Messahel B, Pritchard-Jones K, Vujanic GM, Reis-Filho JS and Jones C: Multifaceted dysregulation of the epidermal growth factor receptor pathway in clear cell sarcoma of the kidney. Clin Cancer Res. 13:4360–4364. 2007. View Article : Google Scholar : PubMed/NCBI

8 

Boo YJ, Fisher JC, Haley MJ, Cowles RA, Kandel JJ and Yamashiro DJ: Vascular characterization of clear cell sarcoma of the kidney in a child, A case report and review. J Pediatr Surg. 44:2031–2036. 2009. View Article : Google Scholar : PubMed/NCBI

9 

Short SS, Zmora O, Hunter CJ, Wang L, Siegel S and Ford HR: Large clear cell sarcoma of the kidney mistaken as Wilms' tumor. J Pediatr Surg Rep. 1:235–238. 2013. View Article : Google Scholar

10 

Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, et al: NCBI GEO: Archive for functional genomics data sets - update. Nucleic Acids Res. 41:D991–D995. 2013. View Article : Google Scholar : PubMed/NCBI

11 

Gautier L, Cope L and Bolstad BM: andI rizarry RA: affy - analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 20:307–315. 2004. View Article : Google Scholar : PubMed/NCBI

12 

Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U and Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 4:249–264. 2003. View Article : Google Scholar : PubMed/NCBI

13 

Tiengo A, Barbarini N, Troiani S, Rusconi L and Magni P: A Perl procedure for protein identification by peptide mass fingerprinting. BMC Bioinformatics. 10(Suppl 12): S112009. View Article : Google Scholar : PubMed/NCBI

14 

Efron B, Tibshirani R, Storey JD and Tusher V: Empirical Bayes analysis of a microarray experiment. J Am Stat Assoc. 96:1151–1160. 2001. View Article : Google Scholar

15 

Efron B and Tibshirani R: Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol. 23:70–86. 2002. View Article : Google Scholar : PubMed/NCBI

16 

Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC and Lempicki RA: The DAVID Gene Functional Classification Tool, A novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 8:R1832007. View Article : Google Scholar : PubMed/NCBI

17 

Kanehisa M and Goto S: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27–30. 2000. View Article : Google Scholar : PubMed/NCBI

18 

Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P and Bork P: vonM ering C and Jensen LJ: STRING v9. Histopathology. Nucleic Acids Res. 41:D808–D815. 2013.PubMed/NCBI

19 

Saito R, Smoot ME, Ono K, Ruscheinski J, Wang P-L, Lotia S, Pico AR, Bader GD and Ideker T: A travel guide to Cytoscape plugins. Nat Methods. 9:1069–1076. 2012. View Article : Google Scholar : PubMed/NCBI

20 

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al: Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25–29. 2000. View Article : Google Scholar : PubMed/NCBI

21 

Lenhard B and Wasserman WW: TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics. 18:1135–1136. 2002. View Article : Google Scholar : PubMed/NCBI

22 

Loots GG, Ovcharenko I, Pachter L, Dubchak I and Rubin EM: rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 12:832–839. 2002. View Article : Google Scholar : PubMed/NCBI

23 

Kidd JM: Exclusion of certain renal neoplasms from the category of Wilms tumor. Am J Pathol. 59:16a1970.

24 

McLean GW, Carragher NO, Avizienyte E, Evans J, Brunton VG and Frame MC: The role of focal-adhesion kinase in cancer - a new therapeutic opportunity. Nat Rev Cancer. 5:505–515. 2005. View Article : Google Scholar : PubMed/NCBI

25 

Rodriguez-Gonzalez A, Lin T, Ikeda AK, Simms-Waldrip T, Fu C and Sakamoto KM: Role of the aggresome pathway in cancer, Targeting histone deacetylase 6-dependent protein degradation. Cancer Res. 68:2557–2560. 2008. View Article : Google Scholar : PubMed/NCBI

26 

Hanrahan V, Currie MJ, Gunningham SP, Morrin HR, Scott PA, Robinson BA and Fox SB: The angiogenic switch for vascular endothelial growth factor (VEGF)-A, VEGF-B, VEGF-C, and VEGF-D in the adenoma-carcinoma sequence during colorectal cancer progression. J Pathol. 200:183–194. 2003. View Article : Google Scholar : PubMed/NCBI

27 

Nicholson RI and Gee JM: andH arper ME: EGFR and cancer prognosis. Eur J Cancer. 37((Suppl 4)): S9–S15. 2001. View Article : Google Scholar : PubMed/NCBI

28 

Liu H, Radisky DC, Nelson CM, Zhang H, Fata JE, Roth RA and Bissell MJ: Mechanism of Akt1 inhibition of breast cancer cell invasion reveals a protumorigenic role for TSC2. Proc Natl Acad Sci USA. 103:4134–4139. 2006. View Article : Google Scholar : PubMed/NCBI

29 

Hunt S, Jones AV, Hinsley EE, Whawell SA and Lambert DW: MicroRNA-124 suppresses oral squamous cell carcinoma motility by targeting ITGB1. FEBS Lett. 585:187–192. 2011. View Article : Google Scholar : PubMed/NCBI

30 

Daemen A, Gevaert O, De Bie T, Debucquoy A, Machiels J-P, De Moor B and Haustermans K: Integrating microarray and proteomics data to predict the response on cetuximab in patients with rectal cancer. Pac Symp Biocomput. 13:166–177. 2008.

31 

Porter TR, Richards FM, Houlston RS, Evans DG, Jankowski JA, Macdonald F, Norbury G, Payne SJ, Fisher SA, Tomlinson I and Maher ER: Contribution of cyclin d1 (CCND1) and E-cadherin (CDH1) polymorphisms to familial and sporadic colorectal cancer. Oncogene. 21:1928–1933. 2002. View Article : Google Scholar : PubMed/NCBI

32 

Fornari F, Gramantieri L, Ferracin M, Veronese A, Sabbioni S, Calin GA, Grazi GL, Giovannini C, Croce CM, Bolondi L and Negrini M: MiR-221 controls CDKN1C/p57 and CDKN1B/p27 expression in human hepatocellular carcinoma. Oncogene. 27:5651–5661. 2008. View Article : Google Scholar : PubMed/NCBI

33 

Harari D and Yarden Y: Molecular mechanisms underlying ErbB2/HER2 action in breast cancer. Oncogene. 19:6102–6114. 2000. View Article : Google Scholar : PubMed/NCBI

34 

Trusolino L, Bertotti A and Comoglio PM: MET signalling, Principles and functions in development, organ regeneration and cancer. Nat Rev Mol Cell Biol. 11:834–848. 2010. View Article : Google Scholar : PubMed/NCBI

35 

Jang MJ, Jeon YJ, Kim JW, Cho YK, Lee SK, Hwang SG, Oh D and Kim NK: Association of VEGF and KDR single nucleotide polymorphisms with colorectal cancer susceptibility in Koreans. Mol Carcinog. 52((Suppl 1)): E60–E69. 2013. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Wang Z, Wang Z, Zhou Z and Ren Y: Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis. Oncol Lett 11: 953-958, 2016.
APA
Wang, Z., Wang, Z., Zhou, Z., & Ren, Y. (2016). Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis. Oncology Letters, 11, 953-958. https://doi.org/10.3892/ol.2015.4006
MLA
Wang, Z., Wang, Z., Zhou, Z., Ren, Y."Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis". Oncology Letters 11.2 (2016): 953-958.
Chicago
Wang, Z., Wang, Z., Zhou, Z., Ren, Y."Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis". Oncology Letters 11, no. 2 (2016): 953-958. https://doi.org/10.3892/ol.2015.4006
Copy and paste a formatted citation
x
Spandidos Publications style
Wang Z, Wang Z, Zhou Z and Ren Y: Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis. Oncol Lett 11: 953-958, 2016.
APA
Wang, Z., Wang, Z., Zhou, Z., & Ren, Y. (2016). Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis. Oncology Letters, 11, 953-958. https://doi.org/10.3892/ol.2015.4006
MLA
Wang, Z., Wang, Z., Zhou, Z., Ren, Y."Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis". Oncology Letters 11.2 (2016): 953-958.
Chicago
Wang, Z., Wang, Z., Zhou, Z., Ren, Y."Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis". Oncology Letters 11, no. 2 (2016): 953-958. https://doi.org/10.3892/ol.2015.4006
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