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Updated: May 12, 2025
Development of Compendium for Esophageal Squamous Cell Carcinoma
Published on: April 12, 2024
RNA-seq analysis reveals key genes associated with downregulation of APE1 in esophageal squamous cell carcinoma
Alan Chu1, Xiao Liu1, Shijia Liu1
1Department of Radiation Oncology, The Second Affiliated Hospital of Zhengzhou University, Henan, China.
Objective:
This study aims to explore the impact of APE1 gene knockout on the transcriptome of esophageal cancer cells and conduct a preliminary screening of APE1-regulated target genes to provide a basis for understanding APE1 target genes and finding new anti-esophageal cancer therapeutic targets.
Methods:
We collected 100 patients with esophageal squamous cell carcinoma (ESCC), analyzed the expression of APE1 in ESCC by immunohistochemical, and analyzed the overall survival. 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 conducted. Protein-protein interaction (PPI) network analysis was performed on the genes in the intersection of differential genes between the two sequencing datasets. The qRT-PCR and Western blotting experiments were employed to confirm the effect of APE1 knockdown on the expression levels of FN1, TNF, and IL-6 in esophageal cancer cells.
Results:
APE1 highly expressed in ESCC tissue, and its high expression leads the worse OS. The stable transfected TE-1 cell line with knockdown of the APE1 gene was successfully constructed, with a knockdown efficiency of 100%. RNA-seq analysis revealed that 2,060 differential genes were detected between APE1-KO stably transfected cells and their corresponding APE1-YD cells, with 1,063 upregulated genes and 997 downregulated genes. RNA-seq analysis found that differentially expressed genes after APE1 knockout in TE-1 cells were primarily enriched in pathways related to metabolism, extracellular matrix, inflammatory response, and angiogenesis. PPI network analysis demonstrated that FN1, TNF, and IL-6 may be essential target genes of APE1. The three core genes of FN1, TNF, and IL-6 were confirmed using qRT-PCR and Western blotting, and the results were consistent with the transcriptome sequencing results.
Conclusion:
Knocking out APE1 can affect the function, related pathways, and downstream target gene expression of ESCC cells. APE1 can promote the transcriptional expressions of FN1 and IL6 genes while inhibiting the TNF gene. FN1, TNF, and IL-6 may be potential target genes regulated by APE1 in esophageal cancer.
Insights
Apurinic/basic site eliminating 1 (APE1) gene knockout impacts esophageal squamous cell carcinoma (ESCC) cell transcriptome, identifying FN1, TNF, and IL-6 as potential therapeutic targets. This research offers new avenues for anti-ESCC therapies.
Area of Science:
- Molecular Oncology
- Cancer Genomics
- Gene Regulation
Background:
- Apurinic/basic site eliminating 1 (APE1) is implicated in DNA repair and is often overexpressed in various cancers.
- The specific role of APE1 in esophageal squamous cell carcinoma (ESCC) and its downstream targets remain incompletely understood.
- Identifying APE1-regulated genes is crucial for developing targeted therapies against ESCC.
Purpose of the Study:
- To investigate the transcriptomic changes in esophageal cancer cells following APE1 gene knockout.
- To perform a preliminary screening of APE1-regulated target genes in ESCC.
- To identify potential novel therapeutic targets for anti-esophageal cancer strategies.
Main Methods:
- Immunohistochemical analysis of APE1 expression and overall survival in 100 ESCC patients.
- Transcriptome sequencing (RNA-Seq) of TE-1 cells with APE1 knockout (APE1-KO).
- Gene Ontology (GO) and KEGG pathway enrichment analysis, Protein-Protein Interaction (PPI) network analysis, qRT-PCR, and Western blotting to validate target genes (FN1, TNF, IL-6).
Main Results:
- APE1 was highly expressed in ESCC tissues, correlating with worse overall survival.
- RNA-seq identified 2,060 differentially expressed genes in APE1-KO cells, enriched in metabolism, extracellular matrix, inflammatory response, and angiogenesis pathways.
- FN1, TNF, and IL-6 were identified as potential APE1 target genes, with their regulation confirmed by qRT-PCR and Western blotting.
Conclusions:
- APE1 knockout significantly alters the transcriptome, cellular functions, and downstream gene expression in ESCC cells.
- APE1 promotes FN1 and IL-6 transcription while inhibiting TNF transcription.
- FN1, TNF, and IL-6 represent potential APE1-regulated target genes for therapeutic intervention in esophageal cancer.
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