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A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis

  • Authors:
    • Lushun Yuan
    • Liang Chen
    • Kaiyu Qian
    • Gang Wang
    • Mengxin Lu
    • Guofeng Qian
    • Xinyue Cao
    • Wei Jiang
    • Yu Xiao
    • Xinghuan Wang
  • View Affiliations / Copyright

    Affiliations: Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, P.R. China, Department of Endocrinology, The First Affiliated Hospital of Zhejiang University, Hangzhou, P.R. China, Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, P.R. China
    Copyright: © Yuan et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 525-536
    |
    Published online on: December 4, 2017
       https://doi.org/10.3892/or.2017.6132
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Abstract

Clear cell renal cell carcinoma (ccRCC) is the most common solid lesion within kidneys, and its prognostic is influenced by the progression covering a complex network of gene interactions. In our study, a weighted gene co‑expression network was constructed to identify gene modules associated with the progression of ccRCC (n=35). In the significant module (R2 = -0.53), a total of 13 network hub genes were identified, and 2 of them were hub nodes in the protein-protein interaction network as well. In validation, ATP5A1 showed a higher correlation with the disease progression than any other hub gene in the hub module (P=0.001219). In the test set (n=202), ATP5A1 was also highly expressed in normal kidney than ccRCC tissues of each grade (P<0.001). Functional and pathway enrichment analysis demonstrated that ATP5A1 is overrepresented in pathway of oxidative phosphorylation, which associated with tumorigenesis and tumor progression. Gene set enrichment analysis (GSEA) also demonstrated that the gene set of ‘oxidative phosphorylation’ and metabolic pathways were enriched in ccRCC samples with ATP5A1 highly expressed (P<0.05). In conclusion, based on the co‑expression analysis, ATP5A1 was validated to be associated with progression of ccRCC, probably by regulating tumor-related phosphorylation.
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View References

1 

Cairns P: Renal cell carcinoma. Cancer Biomark. 9:461–473. 2010. View Article : Google Scholar : PubMed/NCBI

2 

Vera-Badillo FE, Templeton AJ, Duran I, Ocana A, de Gouveia P, Aneja P, Knox JJ, Tannock IF, Escudier B and Amir E: Systemic therapy for non-clear cell renal cell carcinomas: A systematic review and meta-analysis. Eur Urol. 67:740–749. 2015. View Article : Google Scholar : PubMed/NCBI

3 

Heng DY, Mackenzie MJ, Vaishampayan UN, Bjarnason GA, Knox JJ, Tan MH, Wood L, Wang Y, Kollmannsberger C, North S, et al: Primary anti-vascular endothelial growth factor (VEGF)-refractory metastatic renal cell carcinoma: Clinical characteristics, risk factors, and subsequent therapy. Ann Oncol. 23:1549–1555. 2012. View Article : Google Scholar : PubMed/NCBI

4 

Dahinden C, Ingold B, Wild P, Boysen G, Luu VD, Montani M, Kristiansen G, Sulser T, Bühlmann P, Moch H, et al: Mining tissue microarray data to uncover combinations of biomarker expression patterns that improve intermediate staging and grading of clear cell renal cell cancer. Clin Cancer Res. 16:88–98. 2010. View Article : Google Scholar : PubMed/NCBI

5 

Gerlinger M, Horswell S, Larkin J, Rowan AJ, Salm MP, Varela I, Fisher R, McGranahan N, Matthews N, Santos CR, et al: Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet. 46:225–233. 2014. View Article : Google Scholar : PubMed/NCBI

6 

Eckl J, Buchner A, Prinz PU, Riesenberg R, Siegert SI, Kammerer R, Nelson PJ and Noessner E: Transcript signature predicts tissue NK cell content and defines renal cell carcinoma subgroups independent of TNM staging. J Mol Med (Berl). 90:55–66. 2012. View Article : Google Scholar : PubMed/NCBI

7 

Tavazoie S, Hughes JD, Campbell MJ, Cho RJ and Church GM: Systematic determination of genetic network architecture. Nat Genet. 22:281–285. 1999. View Article : Google Scholar : PubMed/NCBI

8 

Chou WC, Cheng AL, Brotto M and Chuang CY: Visual gene-network analysis reveals the cancer gene co-expression in human endometrial cancer. BMC Genomics. 15:3002014. View Article : Google Scholar : PubMed/NCBI

9 

Wang F, Chang Y, Li J, Wang H, Zhou R, Qi J, Liu J and Zhao Q: Strong correlation between ASPM gene expression and HCV cirrhosis progression identified by co-expression analysis. Dig Liver Dis. 49:70–76. 2017. View Article : Google Scholar : PubMed/NCBI

10 

Clarke C, Madden SF, Doolan P, Aherne ST, Joyce H, O'Driscoll L, Gallagher WM, Hennessy BT, Moriarty M, Crown J, et al: Correlating transcriptional networks to breast cancer survival: A large-scale coexpression analysis. Carcinogenesis. 34:2300–2308. 2013. View Article : Google Scholar : PubMed/NCBI

11 

Horvath S and Dong J: Geometric interpretation of gene coexpression network analysis. PLOS Comput Biol. 4:e10001172008. View Article : Google Scholar : PubMed/NCBI

12 

Mason MJ, Fan G, Plath K, Zhou Q and Horvath S: Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics. 10:3272009. View Article : Google Scholar : PubMed/NCBI

13 

Yip AM and Horvath S: Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics. 8:222007. View Article : Google Scholar : PubMed/NCBI

14 

Ravasz E, Somera AL, Mongru DA, Oltvai ZN and Barabási AL: Hierarchical organization of modularity in metabolic networks. Science. 297:1551–1555. 2002. View Article : Google Scholar : PubMed/NCBI

15 

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(D1): D447–D452. 2015. View Article : Google Scholar : PubMed/NCBI

16 

Franceschini A, Lin J, von Mering C and Jensen LJ: SVD-phy: Improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics. 32:1085–1087. 2016. View Article : Google Scholar : PubMed/NCBI

17 

Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, et al: Proteomics. Tissue-based map of the human proteome. Science. 347:12604192015. View Article : Google Scholar : PubMed/NCBI

18 

Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC and Lempicki RA: DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4:32003. View Article : Google Scholar

19 

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

20 

Xu G and Li JY: ATP5A1 and ATP5B are highly expressed in glioblastoma tumor cells and endothelial cells of microvascular proliferation. J Neurooncol. 126:405–413. 2016. View Article : Google Scholar : PubMed/NCBI

21 

Seth R, Keeley J, Abu-Ali G, Crook S, Jackson D and Ilyas M: The putative tumour modifier gene ATP5A1 is not mutated in human colorectal cancer cell lines but expression levels correlate with TP53 mutations and chromosomal instability. J Clin Pathol. 62:598–603. 2009. View Article : Google Scholar : PubMed/NCBI

22 

Jonckheere AI, Renkema GH, Bras M, Van den Heuvel LP, Hoischen A, Gilissen C, Nabuurs SB, Huynen MA, de Vries MC, Smeitink JA, et al: A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy. Brain. 136:1544–1554. 2013. View Article : Google Scholar : PubMed/NCBI

23 

Bata P, Gyebnar J, Tarnoki DL, Tarnoki AD, Kekesi D, Szendroi A, Fejer B, Szasz AM, Nyirady P, Karlinger K, et al: Clear cell renal cell carcinoma and papillary renal cell carcinoma: Differentiation of distinct histological types with multiphase CT. Diagn Interv Radiol. 19:387–392. 2013.PubMed/NCBI

24 

Arnold RS, Fedewa SA, Goodman M, Osunkoya AO, Kissick HT, Morrissey C, True LD and Petros JA: Bone metastasis in prostate cancer: Recurring mitochondrial DNA mutation reveals selective pressure exerted by the bone microenvironment. Bone. 78:81–86. 2015. View Article : Google Scholar : PubMed/NCBI

25 

Fang Y, Huang J, Zhang J, Wang J, Qiao F, Chen HM and Hong ZP: Detecting the somatic mutations spectrum of Chinese lung cancer by analyzing the whole mitochondrial DNA genomes. Mitochondrial DNA. 26:56–60. 2015. View Article : Google Scholar : PubMed/NCBI

26 

Li LH, Kang T, Chen L, Zhang W, Liao Y, Chen J and Shi Y: Detection of mitochondrial DNA mutations by high-throughput sequencing in the blood of breast cancer patients. Int J Mol Med. 33:77–82. 2014. View Article : Google Scholar : PubMed/NCBI

27 

Hashimoto M, Bacman SR, Peralta S, Falk MJ, Chomyn A, Chan DC, Williams SL and Moraes CT: MitoTALEN: A general approach to reduce mutant mtDNA loads and restore oxidative phosphorylation function in mitochondrial dseases. Mol Ther. 23:1592–1599. 2015. View Article : Google Scholar : PubMed/NCBI

28 

Bonora E, Porcelli AM, Gasparre G, Biondi A, Ghelli A, Carelli V, Baracca A, Tallini G, Martinuzzi A, Lenaz G, et al: Defective oxidative phosphorylation in thyroid oncocytic carcinoma is associated with pathogenic mitochondrial DNA mutations affecting complexes I and III. Cancer Res. 66:6087–6096. 2006. View Article : Google Scholar : PubMed/NCBI

29 

Cheng L, Lin H, Hu Y, Wang J and Yang Z: Gene function prediction based on the Gene Ontology hierarchical structure. PLoS One. 9:e1071872014. View Article : Google Scholar : PubMed/NCBI

30 

Du J, Yuan Z, Ma Z, Song J, Xie X and Chen Y: KEGG-PATH: Kyoto encyclopedia of genes and genomes-based pathway analysis using a path analysis model. Mol Biosyst. 10:2441–2447. 2014. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Yuan L, Chen L, Qian K, Wang G, Lu M, Qian G, Cao X, Jiang W, Xiao Y, Wang X, Wang X, et al: A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis. Oncol Rep 39: 525-536, 2018.
APA
Yuan, L., Chen, L., Qian, K., Wang, G., Lu, M., Qian, G. ... Wang, X. (2018). A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis. Oncology Reports, 39, 525-536. https://doi.org/10.3892/or.2017.6132
MLA
Yuan, L., Chen, L., Qian, K., Wang, G., Lu, M., Qian, G., Cao, X., Jiang, W., Xiao, Y., Wang, X."A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis". Oncology Reports 39.2 (2018): 525-536.
Chicago
Yuan, L., Chen, L., Qian, K., Wang, G., Lu, M., Qian, G., Cao, X., Jiang, W., Xiao, Y., Wang, X."A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis". Oncology Reports 39, no. 2 (2018): 525-536. https://doi.org/10.3892/or.2017.6132
Copy and paste a formatted citation
x
Spandidos Publications style
Yuan L, Chen L, Qian K, Wang G, Lu M, Qian G, Cao X, Jiang W, Xiao Y, Wang X, Wang X, et al: A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis. Oncol Rep 39: 525-536, 2018.
APA
Yuan, L., Chen, L., Qian, K., Wang, G., Lu, M., Qian, G. ... Wang, X. (2018). A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis. Oncology Reports, 39, 525-536. https://doi.org/10.3892/or.2017.6132
MLA
Yuan, L., Chen, L., Qian, K., Wang, G., Lu, M., Qian, G., Cao, X., Jiang, W., Xiao, Y., Wang, X."A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis". Oncology Reports 39.2 (2018): 525-536.
Chicago
Yuan, L., Chen, L., Qian, K., Wang, G., Lu, M., Qian, G., Cao, X., Jiang, W., Xiao, Y., Wang, X."A novel correlation between ATP5A1 gene expression and progression of human clear cell renal cell carcinoma identified by co‑expression analysis". Oncology Reports 39, no. 2 (2018): 525-536. https://doi.org/10.3892/or.2017.6132
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