EBNA1 inhibitors reveal CDC7 and POU2F1 as direct functional targets in EBV+ epithelial cancers [RNA-Seq]

Epstein-Barr virus (EBV) latent infection is ubiquitously associated with nasopharyngeal carcinoma and gastric cancer, expressing very few viral protein components (EBNA1 and LMP1/2A). We previously showed that EBNA1 inhibitor VK1727 blocked cell cycle progression and growth of EBV+ tumors in vivo. However, the underlying molecular mechanism requires more evidence. In this study, we employed VK1727 to remove EBNA1 binding to viral and cellular genomes in three EBV+ epithelial tumors (PDX C15, C666-1 and SNU719). Then we integrated EBNA1 ChIP-seq and transcriptomic analysis to identify direct gene targets of VK1727, which involve in cell cycle progression and cell proliferation. Our analysis characterized a cell cycle dependent kinase CDC7 and a stem cell transcription factor POU2F1. Further analysis illustrated that EBNA1 binding to CDC7 promoter and POU2F1 intron promotes RNA Pol II-pS5 to initiate transcription of these two genes. Moreover, our results revealed CDC7 inhibitor Simurosertib is epistatic with VK1727 in reduction of EBV copy number, induction of cell cycle arrest, and inhibition of cell proliferation in EBV+ epithelial cancer. While POU2F1 knockdown reduced copy number of EBV, decreased expression of viral genes and inhibited proliferation of SNU719 cells. Our study revealed two functional gene targets of VK1727 in EBV+ epithelial cancers, which provides two potential biomarkers for following therapeutical research.