GSE185932
Gene expression changes associated with reducing Sox2 expression in ovarian cancer cell line PA1 under anchorage independence
Sex-determining region Y- box 2 (Sox2) is a single-exon transcription factor essential for development and in cancer that has been shown to be overexpressed broadly in many cancers including multiple ovarian cancer subtypes. The objective of this study is to examine the effect of changing Sox2 expression under the conditions of anchorage independent growth that is known to drive the expression of survival genes. We compared genome wide gene expression profiles of the ovarian tumor cell line PA1 upon transient knockdown of Sox2 expression using siRNA and compared to negative silencer control siRNA cells. Cells grown in biological triplicates were transfected under steady state 2D growth conditions and then transferred to poly-hema coated plates to prevent attachment. After 72 hrs, RNA was collected from siSox2 and sicontrol cells followed by verification of reduction in Sox2 levels at the protein and RNA levels . Our analysis of the RNA seq results revealed 59 differentially expressed genes (DEG) between sicontrol and siSox2 cells (p-value = 0.05) of which 52 were protein coding. Of the 59, 35 genes were upregulated in siSox2 and 24 genes were downregulated in the siSox2 cells .  Gene set enrichment analysis of all the differentially expressed genes from the RNA-seq data revealed enrichment of 8 gene sets based on an FDR value <25% and included 'hallmark of Apoptosis', 'TGF-ß signaling', and 'Epithelial-Mesenchymal transition' in siSox2 cells and hallmark interferon alpha response and interferon gamma response in sicontrol cells. Several transcription factors with prior established relationships to Sox2 including several PARP family members and TRIM family members were present in these gene sets. Overall design: mRNA sequencing of human ovarian ovarian teratocarcinoma (PA1) cells, control and Sox2 reduction with siRNA Two siRNAs to human Sox2 or negative silencer control obtained from Ambion used to transfect PA1 cells grown in 2D. After 24 hrs, cells were transferred to poly hema coated non adherent plates for 3D growth for an additional 72 hrs followed by RNA extraction.