Screening and Functional Analysis of Differentially Expressed of shAPE1 in esophageal cancer cells based on RNA-seq

Abstract

Abstract Purpose To explore the impact of APE1 knockout on the transcriptome of esophageal cancer cells, and conduct a preliminary screening of target genes regulated by APE1, in order to provide a basis for clarifying APE1 target genes and finding new anti-esophageal cancer therapeutic targets. Methods TE-1 cells with APE1 knockout were used for transcriptome sequencing (RNA sequencing, RNA-Seq) detection, and GO and KEGG enrichment analysis of differentially expressed genes was performed. protein network interaction (PPI) analysis was performed on the differential genes, and qRT-PCR and Western blot experiments were used to verify the effect of knocking down APE1 on the expression levels of FN1, TNF and IL-6. Results RNA-seq analysis found that a total of 2060 differential genes were detected, including 1063 up-regulated genes and 997 down-regulated genes. GO and KEGG analysis revealed that the main enrichment pathway were metabolism, extracellular matrix, inflammatory response, and angiogenesis. PPI protein network analysis found that FN1, TNF and IL-6 may be important target genes of APE1. The three core genes were verified using qRT-PCR and Western blot. Conclusion The gene functions affected by APE1 gene knockout in esophageal cancer cells are mainly concentrated in pathways such as metabolism, extracellular matrix, inflammatory response, and angiogenesis. APE1 can promote the transcriptional expression of FN1 and IL6 genes and inhibit the TNF gene. FN1, TNF and IL-6 may be potential target genes regulated by APE1 in esophageal cancer.