Expression profiles of lncRNAs and mRNAs in KGN/shPWRN2 cell lines

In this study, to identify the target genes of PWRN2, we first constructed lentivirus shRNA vectors to infect the KGN cell lines to gain three KGN/shPWRN2 cell lines with down-regulated PWRN2 expression levels. Then, the expression profiles of mRNAs and lncRNAs in KGN/shPWRN2 cells were determined by microarray. The results revealed thousands of lncRNAs and mRNAs expressed in KGN/shPWRN2. The expression of 176 lncRNAs significantly changed in KGN/shPWRN2 cell lines relative to control NC cell lines. Among these, 118 were up-regulated, whereas 58 were down-regulated. A total of 131 mRNAs significantly changed in expression: 84 were upregulated, and 47 were downregulated (fold change≥2.0, P value<0.05). We further do some bioinformatic analysis for the data. Our results will provide some new information to help us understand the molecular roles of PWRN2. (1) For the lncRNA and mRNA expression profiles in KGN/shPWRN2 cell lines, three KGN cell lines treated with LV-PWRN2-homo-502, LV-PWRN2-homo-1574, LV-PWRN2-homo-1261, respectively, were as test group, while three KGN cell lines treated with LV-NC were as control group. (2) For microarray analysis, KGN/shPWRN2 with down-regulated (FC< 0.5) PWRN2 mRNA levels was selected as test group (3 KGN/shPWRN2 cell lines) and the corresponding NC cells (3 KGN cell lines with negative control) were as control groups. (3) The GO and KEGG pathways analyses were performed to predict the molecular function of the differentially expressed genes. (4) Combined to our two previously microarray data of PCOS (miRNAs array, lncRNA+mRNA array), we searched the candidate mRNA and miRNAs which related with PWRN2 and construct of PWRN2-mediated lncRNA-mRNA ceRNA network. (5) qRT-PCR validation of components of the PWRN2-mediated lncRNA-mRNA ceRNA network.