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Article Open Access

Identification of osteosarcoma driver genes using a network method

  • Authors:
    • Zebing Si
    • Konghe Hu
  • View Affiliations / Copyright

    Affiliations: Department of Orthopedics, The Affiliated Yuebei People's Hospital of Shantou University Medical College, Wujiang, Shaoguan 512026, P.R. China
    Copyright: © Si et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 1215-1222
    |
    Published online on: December 12, 2019
       https://doi.org/10.3892/ol.2019.11212
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Abstract

Osteosarcoma (OS) is a severe disease that is generally caused by genetic alterations. Systematic identification of driver genes may be used to increase the understanding of the mechanisms underlying the disease. The present study identified a framework to predict driver genes, with the hypothesis that driver genes operate through a number of connected functional genes. OS‑related genes were extracted from the Catalogue Of Somatic Mutations In Cancer and subsequently ranked by virtue of their effect on a set of functional genes using a network‑based algorithm. This revealed the driver genes associated with dysregulated networks. In addition, compared with the Mutations For Functional Impact on Network Neighbors algorithm, the results obtained using the aforementioned network‑based algorithm revealed that the proposed method is effective. Gene functional analysis demonstrated that the potential OS driver genes were involved in OS‑associated pathways. Through the validation of the 15 candidate OS driver genes, the classifier constructed in the present study revealed that the identified driver genes were able to distinguish 184 cancer samples from controls. Therefore, the present study provided insights into the identification of driver genes from a vast amount of sequencing data.
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1 

Ritter J and Bielack SS: Osteosarcoma. Ann Oncol. 21 (Suppl 7):vii320–vii325. 2010. View Article : Google Scholar : PubMed/NCBI

2 

Tumijan W, Khattak MN, Nadiah WA and Naing NN: Five-year survival of osteosarcoma patients in hospital universiti sains malaysia (Husm): An eleven year review. Res J Pharmacy Technol. 11:3534–3542. 2018. View Article : Google Scholar

3 

Chen X, Bahrami A, Pappo A, Easton J, Dalton J, Hedlund E, Ellison D, Shurtleff S, Wu G, Wei L, et al: Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. Cell Rep. 7:104–112. 2014. View Article : Google Scholar : PubMed/NCBI

4 

Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR and Campbell PJ: Universal patterns of selection in cancer and somatic tissues. Cell. 171:1029–1041.e21. 2017. View Article : Google Scholar : PubMed/NCBI

5 

Cheng F, Zhao J and Zhao Z: Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Brief Bioinform. 17:642–656. 2016. View Article : Google Scholar : PubMed/NCBI

6 

Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, et al: COSMIC: Exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43((Database Issue)): D805–D811. 2015. View Article : Google Scholar : PubMed/NCBI

7 

Rogers MF, Shihab HA, Gaunt TR and Campbell C: CScape: A tool for predicting oncogenic single-point mutations in the cancer genome. Sci Rep. 7:115972017. View Article : Google Scholar : PubMed/NCBI

8 

Shihab HA, Rogers MF, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR and Campbell C: An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics. 31:1536–1543. 2015. View Article : Google Scholar : PubMed/NCBI

9 

Dong C, Guo Y, Yang H, He Z, Liu X and Wang K: iCAGES: Integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes. Genome Med. 8:1352016. View Article : Google Scholar : PubMed/NCBI

10 

Cho A, Shim JE, Kim E, Supek F, Lehner B and Lee I: MUFFINN: Cancer gene discovery via network analysis of somatic mutation data. Genome Biol. 17:1292016. View Article : Google Scholar : PubMed/NCBI

11 

Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN and Gaunt TR: Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat. 34:57–65. 2013. View Article : Google Scholar : PubMed/NCBI

12 

Merid SK, Goranskaya D and Alexeyenko A: Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis. BMC Bioinformatics. 15:3082014. View Article : Google Scholar : PubMed/NCBI

13 

Kuijjer ML, Peterse EF, van den Akker BE, Briaire-de Bruijn IH, Serra M, Meza-Zepeda LA, Myklebost O, Hassan AB, Hogendoorn PC and Cleton-Jansen AM: IR/IGF1R signaling as potential target for treatment of high-grade osteosarcoma. BMC Cancer. 13:2452013. View Article : Google Scholar : PubMed/NCBI

14 

Zhang T and Zhang D: Integrating omics data and protein interaction networks to prioritize driver genes in cancer. Oncotarget. 8:58050–58060. 2017.PubMed/NCBI

15 

Breiman L: Random forests. Machine Learning. 45:5–32. 2001. View Article : Google Scholar

16 

Wen Z, Liu ZP, Liu Z, Zhang Y and Chen L: An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. J Am Med Inform Assoc. 20:659–667. 2013. View Article : Google Scholar : PubMed/NCBI

17 

Zheng S and Zhao Z: GenRev: Exploring functional relevance of genes in molecular networks. Genomics. 99:183–188. 2012. View Article : Google Scholar : PubMed/NCBI

18 

Dupont P, Callut J, Dooms G, Monette JN and Deville Y: Relevant subgraph extraction from random walks in a graph. Research Report UCL/FSA/INGI RR 2006-07. 2006.

19 

Miao YR, Liu W, Zhang Q and Guo AY: lncRNASNP2: An updated database of functional SNPs and mutations in human and mouse lncRNAs. Nucleic Acids Res. 46:D276–D280. 2018. View Article : Google Scholar : PubMed/NCBI

20 

Bashashati A, Haffari G, Ding J, Ha G, Lui K, Rosner J, Huntsman DG, Caldas C, Aparicio SA and Shah SP: DriverNet: Uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol. 13:R1242012. View Article : Google Scholar : PubMed/NCBI

21 

Hou JP and Ma J: DawnRank: Discovering personalized driver genes in cancer. Genome Med. 6:562014. View Article : Google Scholar : PubMed/NCBI

22 

Liu Y, Zhang X, Han C, Wan G, Huang X, Ivan C, Jiang D, Rodriguez-Aguayo C, Lopez-Berestein G, Rao PH, et al: TP53 loss creates therapeutic vulnerability in colorectal cancer. Nature. 520:697–701. 2015. View Article : Google Scholar : PubMed/NCBI

23 

Li G, Zhang W, Zeng H, Chen L, Wang W, Liu J, Zhang Z and Cai Z: An integrative multi-platform analysis for discovering biomarkers of osteosarcoma. BMC Cancer. 9:1502009. View Article : Google Scholar : PubMed/NCBI

24 

Behjati S and Tarpey PS: What is next generation sequencing. Arch Dis Child Educ Pract Ed. 98:236–238. 2013. View Article : Google Scholar : PubMed/NCBI

25 

Ma M, Wang C, Glicksberg BS, Schadt EE, Li SD and Chen R: Identify cancer driver genes through shared Mendelian disease pathogenic variants and cancer somatic mutations. Pac Symp Biocomput. 22:473–484. 2017.PubMed/NCBI

26 

Do SI, Jung WW, Kim HS and Park YK: The expression of epidermal growth factor receptor and its downstream signaling molecules in osteosarcoma. Int J Oncol. 34:797–803. 2009.PubMed/NCBI

27 

Fu HL, Shao L, Wang Q, Jia T, Li M and Yang DP: A systematic review of p53 as a biomarker of survival in patients with osteosarcoma. Tumour Biol. 34:3817–3821. 2013. View Article : Google Scholar : PubMed/NCBI

28 

Henson E, Chen Y and Gibson S: EGFR family Members' regulation of autophagy is at a crossroads of cell survival and death in cancer. Cancers (Basel). 9:E272017. View Article : Google Scholar : PubMed/NCBI

29 

Lamora A, Talbot J, Mullard M, Brounais-Le Royer B, Redini F and Verrecchia F: TGF-β signaling in bone remodeling and osteosarcoma progression. J Clin Med. 5:E962016. View Article : Google Scholar : PubMed/NCBI

30 

Sulzmaier FJ, Jean C and Schlaepfer DD: FAK in cancer: Mechanistic findings and clinical applications. Nat Rev Cancer. 14:598–610. 2014. View Article : Google Scholar : PubMed/NCBI

31 

Starczynowski DT, Lockwood WW, Deléhouzée S, Chari R, Wegrzyn J, Fuller M, Tsao MS, Lam S, Gazdar AF, Lam WL and Karsan A: TRAF6 is an amplified oncogene bridging the RAS and NF-κB pathways in human lung cancer. J Clin Invest. 121:4095–4105. 2011. View Article : Google Scholar : PubMed/NCBI

32 

Meng Q, Zheng M, Liu H, Song C, Zhang W, Yan J, Qin L and Liu X: TRAF6 regulates proliferation, apoptosis, and invasion of osteosarcoma cell. Mol Cell Biochem. 371:177–186. 2012. View Article : Google Scholar : PubMed/NCBI

33 

Krisenko MO and Geahlen RL: Calling in SYK: SYK's dual role as a tumor promoter and tumor suppressor in cancer. Biochim Biophys Acta. 1853:254–263. 2015. View Article : Google Scholar : PubMed/NCBI

34 

Sun L, Li J and Yan B: Gene expression profiling analysis of osteosarcoma cell lines. Mol Med Rep. 12:4266–4272. 2015. View Article : Google Scholar : PubMed/NCBI

35 

Chen MJ, Wu DW, Wang YC, Chen CY and Lee H: PAK1 confers chemoresistance and poor outcome in non-small cell lung cancer via β-catenin-mediated stemness. Sci Rep. 6:349332016. View Article : Google Scholar : PubMed/NCBI

36 

Chen YL, Huang WC, Yao HL, Chen PM, Lin PY, Feng FY and Chu PY: Down-regulation of RASA1 is associated with poor prognosis in human hepatocellular carcinoma. Anticancer Res. 37:781–785. 2017. View Article : Google Scholar : PubMed/NCBI

37 

Wolf M, El-Rifai W, Tarkkanen M, Kononen J, Serra M, Eriksen EF, Elomaa I, Kallioniemi A, Kallioniemi OP and Knuutila S: Novel findings in gene expression detected in human osteosarcoma by cDNA microarray. Cancer Genet Cytogenet. 123:128–132. 2000. View Article : Google Scholar : PubMed/NCBI

38 

Supek F, Miñana B, Valcárcel J, Gabaldón T and Lehner B: Synonymous mutations frequently act as driver mutations in human cancers. Cell. 156:1324–1335. 2014. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Si Z and Hu K: Identification of osteosarcoma driver genes using a network method. Oncol Lett 19: 1215-1222, 2020.
APA
Si , Z., & Hu, K. (2020). Identification of osteosarcoma driver genes using a network method. Oncology Letters, 19, 1215-1222. https://doi.org/10.3892/ol.2019.11212
MLA
Si , Z., Hu, K."Identification of osteosarcoma driver genes using a network method". Oncology Letters 19.2 (2020): 1215-1222.
Chicago
Si , Z., Hu, K."Identification of osteosarcoma driver genes using a network method". Oncology Letters 19, no. 2 (2020): 1215-1222. https://doi.org/10.3892/ol.2019.11212
Copy and paste a formatted citation
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Spandidos Publications style
Si Z and Hu K: Identification of osteosarcoma driver genes using a network method. Oncol Lett 19: 1215-1222, 2020.
APA
Si , Z., & Hu, K. (2020). Identification of osteosarcoma driver genes using a network method. Oncology Letters, 19, 1215-1222. https://doi.org/10.3892/ol.2019.11212
MLA
Si , Z., Hu, K."Identification of osteosarcoma driver genes using a network method". Oncology Letters 19.2 (2020): 1215-1222.
Chicago
Si , Z., Hu, K."Identification of osteosarcoma driver genes using a network method". Oncology Letters 19, no. 2 (2020): 1215-1222. https://doi.org/10.3892/ol.2019.11212
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