Background: Treatment of castration-resistant prostate cancer (CRPC) is an enormous challenge. As E2F transcription factor 1 (E2F1) is an essential factor in CRPC, this study investigated the genes and pathways controlled by E2F1 and their effects on cellular behavior in CRPC.
Methods: In vitro assays were used to evaluate cellular proliferation, apoptosis, and behavior. Cellular expression was quantified by RNA sequencing (RNA-seq). Gene co-expression was assessed using the GeneMANIA database, and correlations were analyzed with the GEPIA server. Altered pathways of differentially expressed genes (DEGs) were revealed by functional annotation. Module analysis was performed using the STRING database and hub genes were filtered with the Cytoscape software. Some DEGs were validated by real-time quantitative PCR (RT-qPCR).
Results: Knockdown of E2F1 significantly inhibited proliferation and accelerated apoptosis in PC3 cells but not in DU145 cells. Invasion and migration were reduced for both cell lines. A total of 1811 DEGs were identified in PC3 cells and 27 DEGs in DU145 cells exhibiting E2F1 knockdown. Ten overlapping DEGs, including TMOD2  and AIF1L , were identified in both knockdown cell lines and were significantly enriched for association with actin filament organization pathways. TMOD2  and KREMEN2  were genes co-expressed with E2F1 ; six overlapping DEGs were positively correlated with transcription factor E2F1. DEGs of the PC3 and DU145 groups were associated with multiple pathways. Five DEGs that overlapped between the two cell lines and three hub DEGs from PC3 cells were validated by RT-qPCR.
Conclusion: The results of this study suggest that E2F1 has a critical role in regulating actin filaments, as indicated by the change in expression level of several genes, including TMOD2  and AIF1L , in CRPC. This extends our understanding of the cellular responses affected by E2F1 in CRPC.
Keywords: CRPC, E2F1, transcriptome, RNA-seq