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Identification of Pathogenic Genes and Transcription Factors in Osteosarcoma

  • Original Article
  • Published:
Pathology & Oncology Research

Abstract

Osteosarcoma (OS) is an aggressive malignant tumor of the bones. Our study intended to identify and analyze potential pathogenic genes and upstream regulators for OS. We performed an integrated analysis to identify candidate pathogenic genes of OS by using three Gene Expression Omnibus (GEO) databases (GSE66673, GSE49003 and GSE37552). GO and KEGG enrichment analysis were utilized to predict the functional annotation and potential pathways of differentially expressed genes (DEGs). The OS-specific transcriptional regulatory network was established to study the crucial transcriptional factors (TFs) which target the DEGs in OS. From the three GEO datasets, we identified 759 DEGs between metastasis OS samples and non-metastasis OS samples. After GO and KEGG analysis, ‘cell adhesion’ (FDR = 1.27E-08), ‘protein binding’ (FDR = 1.13E-22), ‘cytoplasm’ (FDR = 5.63E-32) and ‘osteoclast differentiation’ (FDR = 0.000992221) were significantly enriched pathways for DEGs. HSP90AA1 exhibited a highest degree (degree = 32) and was enriched in ‘pathways in cancer’ and ‘signal transduction’. BMP6, regulated by Pax-6, was enriched in the ‘TGF-beta signaling pathway’. We indicated that BMP6 may be downregulated by Pax-6 in the non-metastasis OS samples. The up-regulated HSP90AA1 and down-regulated BMP6 and ‘pathways in cancer’ and ‘signal transduction’ were deduced to be involved in the pathogenesis of OS. The identified biomarkers and biological process in OS may provide foundation for further study.

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Authors and Affiliations

  1. Gu’an Bojian Bio-Technology Co., LTD, Langfang, China

    Chenggang Yang, Di Huang, Cui Ma & Xiaofeng Shi

  2. Department of BigData, Beijing Medintell Bioinformatic Technology Co., LTD, No. 1, Shanyuan Street, Haidian District, Beijing, 100081, China

    Chenggang Yang, Di Huang, Cui Ma, Jing Ren, Lina Fu, Cheng Cheng & Xiaofeng Shi

  3. School of biotechnology, Jiangnan University, Wuxi, China

    Bangling Li

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  1. Chenggang Yang
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  2. Di Huang
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  5. Lina Fu
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  7. Bangling Li
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  8. Xiaofeng Shi
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Contributions

CY and XS designed and performed the train of thought, DH and CM analyzed the resulting data, JR, LF, CC and BL contributed the analysis tools. All authors read and approved the final manuscript.

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Correspondence to Xiaofeng Shi.

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Yang, C., Huang, D., Ma, C. et al. Identification of Pathogenic Genes and Transcription Factors in Osteosarcoma. Pathol. Oncol. Res. 26, 1041–1048 (2020). https://doi.org/10.1007/s12253-019-00645-w

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  • DOI: https://doi.org/10.1007/s12253-019-00645-w

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