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| Background Ewing sarcoma is a highly malignant tumor. It is of great significance to identify new biomarkers or therapeutic targets. This study aimed to analyze the differentially expressed genes between Ewing sarcoma ERG type cell line cado-es1 tumor stem cell like cells, non-tumor stem cell like cells and mesenchymal stem cells (MSC) derived from Ewing sarcoma patients, and study the key genes related to Ewing sarcoma ERG type.
Methods The NCBI SRA database data ERP104460 was retrieved, and three groups of MSC cells, tumor stem cell like cells (SP group) and non-tumor stem cell like cells (nsp group) obtained from different Ewing sarcoma patients were selected. The RNA-seq data of 9 samples in each group were analyzed to screen the significantly differentially expressed genes. Pathway enrichment analysis and the protein-protein interaction network was performed, and the hub genes were screened.
Results Compared with MSC group, 8286 differentially expressed genes were obtained, including 3638 up-regulated genes and 4648 down-regulated genes. There were 9097 differentially expressed genes in nsp group compared with msc group, including 4800 up-regulated genes and 4297 down regulated genes. Compared with nsp group, four differentially expressed genes were obtained, including three up-regulated genes, U2, SNORA45b and RNU2-1. One down regulated gene was MTND1P27. These differentially expressed genes are mainly involved in biological processes and biological pathways such as cell division, cell cycle and DNA replication. By GO, KEGG and protein interaction network, 10 hub genes including THBS1, POSTN, COL1A1, COL1A2, MMP2, MMP14, SPARC, DCN, SPP1 and COL3A1 were screened in sp vs msc group; 10 hub genes including THBS1, MMP2, LOX, POSTN, COL1A1, COL1A2, MMP14, SPARC, DCN and SPP1 were obtained in nsp vs msc group. The key differential genes of PPI network between sp vs msc group and nsp vs msc group were COL3A1 and LOX.
Conclusion THBS1, POSTN, COL1A1, COL1A2, MMP2, MMP14, SPARC, DCN, SPP1 and COL3A1 are key hub genes in Ewing sarcoma tumor stem cell like cells; THBS1, MMP2, LOX, POSTN, COL1A1, COL1A2, MMP14, SPARC, DCN and SPP1 are key hub genes in non-tumor stem cell like cells of Ewing sarcoma. |
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| Keywords:Ewing sarcoma(ES), Tumor stem cells, Differentially expressed genes (DEGs), Hub gene |
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