Genes Such as IRS2 Differ from Ewing Sarcoma and Normal Tissue-specific Expression for Osteosarcoma
DOI:
https://doi.org/10.54097/ijbls.v4i2.02Keywords:
Osteosarcoma, Ewing Sarcoma, GEO Database, Enrichment, Tumor Staging, Survival AnalysisAbstract
Objective: To screen and validate the expression of other key genes specific to osteosarcoma that distinguish normal tissue from Ewing sarcoma using a bioinformatics approach. Methods: GSE73166 for osteosarcoma associated with Ewing sarcoma and GSE42352 for osteosarcoma associated with normal tissue were obtained from the GEO database, and these two datasets were screened for differential genes (DEGs) and subjected to corresponding GO enrichment and KEGG enrichment with GSEA validation, and then correlation analysis, PCA and immuno-infiltration analysis were performed on the two datasets, and the These two datasets were intersected to derive 28 differential genes, and the corresponding heat map analysis and protein interaction network analysis were performed for these 28 genes, and then the expression statistics of these 28 genes in GSE21257 for different graded genes and survival analysis in R2 for osteosarcoma in TARGET. Results: TNFRSF11B, COL12A1, PLOD2, PTGES, MEF2C, IRS2 and MMP13 were found to have an effect on the staging of osteosarcoma, while CCND1 (P=0.021), IRS2 (P=0.015), OLFML2B (P=0.035), CPE (P=0.037), MAMDC2 (P=0.044) and MMP13 (P=0.013) had an impact on the survival prognosis of osteosarcoma. Conclusions: IRS2 and 11 other genes differ from Ewing sarcoma and normal tissues, producing a specific expression on the staging or survival prognosis of osteosarcoma.
Downloads
References
G. Sheng, Y. Gao, Y. Yang, H. Wu, Osteosarcoma and Metastasis, Front Oncol 11 (2021) 780264.
T.A. Damron, W.G. Ward, A. Stewart, Osteosarcoma, chondrosarcoma, and Ewing's sarcoma: National Cancer Data Base Report, Clin Orthop Relat Res 459 (2007) 40-47.
A.J. Mutsaers, C.R. Walkley, Cells of origin in osteosarcoma: mesenchymal stem cells or osteoblast committed cells?, Bone 62 (2014) 56-63.
B. Tang, C. Liu, Q.M. Zhang, M. Ni, Decreased expression of miR-490-3p in osteosarcoma and its clinical significance, Eur Rev Med Pharmacol Sci 21(2) (2017) 246-251.
R. Rathore, B.A. Van Tine, Pathogenesis and Current Treatment of Osteosarcoma: Perspectives for Future Therapies, J Clin Med 10(6) (2021).
A. Blum, P. Wang, J.C. Zenklusen, SnapShot: TCGA-Analyzed Tumors, Cell 173(2) (2018) 530.
K. Horibe, [Characteristics of Adolescent and Young Adult Cancer], Gan To Kagaku Ryoho 44(1) (2017).
E. Schaafsma, C.M. Fugle, X. Wang, C. Cheng, Pan-cancer association of HLA gene expression with cancer prognosis and immunotherapy efficacy, Br J Cancer 125(3) (2021) 422-432.
T. Barrett, S.E. Wilhite, P. Ledoux, C. Evangelista, I.F. Kim, M. Tomashevsky, K.A. Marshall, K.H. Phillippy, P.M. Sherman, M. Holko, A. Yefanov, H. Lee, N. Zhang, C.L. Robertson, N. Serova, S. Davis, A. Soboleva, NCBI GEO: archive for functional genomics data sets--update, Nucleic Acids Res 41(Database issue) (2013) D991-D995.
M.E. Ritchie, B. Phipson, D. Wu, Y. Hu, C.W. Law, W. Shi, G.K. Smyth, limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res 43(7) (2015) e47.
A. Jia, L. Xu, Y. Wang, Venn diagrams in bioinformatics, Brief Bioinform 22(5) (2021).
R. Kindt, an R package to predict and visualize population-level changes in allele frequencies in response to climate change, PeerJ 9 (2021) e11534.
G. Dennis, B.T. Sherman, D.A. Hosack, J. Yang, W. Gao, H.C. Lane, R.A. Lempicki, DAVID: Database for Annotation, Visualization, and Integrated Discovery, Genome Biol 4(5) (2003) P3.
C. Xie, X. Mao, J. Huang, Y. Ding, J. Wu, S. Dong, L. Kong, G. Gao, C.-Y. Li, L. Wei, KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases, Nucleic Acids Res 39(Web Server issue) (2011) W316-W322.
S. Guo, J. Wu, W. Zhou, X. Liu, Y. Liu, J. Zhang, S. Jia, J. Li, H. Wang, Identification and analysis of key genes associated with acute myocardial infarction by integrated bioinformatics methods, Medicine (Baltimore) 100(15) (2021) e25553.
W. Liu, J. Liu, J.C. Rajapakse, Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes, Sci Rep 8(1) (2018) 12100.
M. Kanehisa, M. Furumichi, Y. Sato, M. Ishiguro-Watanabe, M. Tanabe, KEGG: integrating viruses and cellular organisms, Nucleic Acids Res 49(D1) (2021) D545-D551.
D. Szklarczyk, A.L. Gable, K.C. Nastou, D. Lyon, R. Kirsch, S. Pyysalo, N.T. Doncheva, M. Legeay, T. Fang, P. Bork, L.J. Jensen, C. von Mering, The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets, Nucleic Acids Res 49(D1) (2021) D605-D612.
J. Zhou, W. Xiong, Y. Wang, J. Guan, Protein Function Prediction Based on PPI Networks: Network Reconstruction vs Edge Enrichment, Front Genet 12 (2021) 758131.
K. Ono, B. Demchak, T. Ideker, Cytoscape tools for the web age: D3.js and Cytoscape.js exporters, F1000Res 3 (2014) 143.
Y. Zhang, X. Lei, R. He, L. Mao, P. Jiang, C. Ni, X. Zhong, Z. Yin, X. Wu, D. Li, Q. Zheng, Identification and preliminary validation of a four-gene signature to predict metastasis and survival in osteosarcoma, Am J Transl Res 13(11) (2021) 12264-12284.
I. Corre, F. Verrecchia, V. Crenn, F. Redini, V. Trichet, The Osteosarcoma Microenvironment: A Complex But Targetable Ecosystem, Cells 9(4) (2020).
F. Cersosimo, S. Lonardi, G. Bernardini, B. Telfer, G.E. Mandelli, A. Santucci, W. Vermi, E. Giurisato, Tumor-Associated Macrophages in Osteosarcoma: From Mechanisms to Therapy, Int J Mol Sci 21(15) (2020).
C. Zheng, F. Tang, L. Min, F. Hornicek, Z. Duan, C. Tu, PTEN in osteosarcoma: Recent advances and the therapeutic potential, Biochim Biophys Acta Rev Cancer 1874(2) (2020) 188405.
J. Niu, T. Yan, W. Guo, W. Wang, Z. Zhao, T. Ren, Y. Huang, H. Zhang, Y. Yu, X. Liang, Identification of Potential Therapeutic Targets and Immune Cell Infiltration Characteristics in Osteosarcoma Using Bioinformatics Strategy, Front Oncol 10 (2020) 1628.
K.M. Skubitz, D.R. D'Adamo, Sarcoma, Mayo Clin Proc 82(11) (2007) 1409-1432.
N.J. Balamuth, R.B. Womer, Ewing's sarcoma, Lancet Oncol 11(2) (2010) 184-192.
Z. Dai, H. Tang, Y. Pan, J. Chen, Y. Li, J. Zhu, Gene expression profiles and pathway enrichment analysis of human osteosarcoma cells exposed to sorafenib, FEBS Open Bio 8(5) (2018) 860-867.
