Transcriptome Analysis of Signaling Pathways Targeted by Ellagic Acid in Hepatocellular Carcinoma Cells

Ellagic acid (EA) possesses prominent inhibitory activities against various cancers, including hepatocellular carcinoma (HCC). Recent study showing EA's activities in suppressing HCC cell proliferation and tumor formation, we further demonstrate that EA reduces cell viability, and induces DNA damage and cell cycle arrest at G1 phase. Employing RNA-Seq, we identified 5765 differentially expressed genes (DEGs) encoding proteins with over 2.0-fold change in EA-treated HepG2 cells. Following Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, the DEGs caused by EA treatment showed significant enrichment in pathways regulating DNA replication and cell cycle progression. Consistently, integrative analyses of this RNA-seq dataset with a TCGA-LIHC dataset derived from HCC patients confirmed these two pathways as EA's primary targets. Furthermore, we identified p21 as a primary target gene of EA using the interaction network analysis of the DEGs regulating these pathways. Consistent with the results of our bioinformatic analyses, p21 knockdown desensitized four different liver cancer cell lines to EA treatment. Collectively, our study demonstrated that EA primarily targeted the G1/S phase checkpoint and DNA synthesis to inhibit HCC cell proliferation. Overall design: RNA-seq was constructed in HepG2 cells with Ellagic acid (EA) and cells with DMSO treatment