Gene expression profile analysis of U251 glioma cells with shRNA-mediated SOX9 knockdown.

Purpose: In glioma, the sex-determining region Y-box 9 gene (SOX9) is overexpressed and its downregulation leads to inhibition of cell proliferation, invasion and increased cell apoptosis. To further evaluate the molecular and signal pathways associated with the function of SOX9 and SOX9 target genes, a global gene expression profile of the established SOX9-knockdown U251 cells was investigated.

Methods: The molecular function and biological pathways of differentially expressed genes (DEGs) were identified by gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The interactome networks of DEGs were constructed using the STRING online tool. The genes were further validated by RT-qPCR.

Results: GO analysis revealed that a set of 194 DEGs was shared in both the SOX9 KD-1 and SOX9 KD-2 U251 cells. GO analysis and KEGG pathway analysis showed that the DEGs were associated with biological processes involving cellular responses to hypoxia, osteoblast differentiation and angiogenesis, and special biological pathways, such as a TGF-beta signaling pathway and a HIF-1 signaling pathway. In addition, computational network of novel identified potential target genes linked to SOX9, including TGFB2, VEGFA, EGLN3 (PHD3), CA9 and HIF-1a. All of these genes were downregulated in the SOX9 knockdown U251 cells.

Conclusions: SOX9 may be a key regulator impacting the glioma cellular processes by influencing the cellular response to hypoxia and HIF-1 signaling pathway. TGFB2, VEGFA, EGLN3 (PHD3), CA9, and HIF-1a may be the target genes of SOX9.