ALDH18A1 has carcinogenic functions and regulates alternative splicing events of DNA repair-related genes in esophageal carcinoma cells.

Esophageal carcinoma (ESCA) is a common tumor in the digestive system, resulting in approximately 300,000 death worldwide every year. ALDH18A1, a potential RNA binding protein (RBP), is significantly overexpressed as in ESCA, while its functions and mechanism is unclear. In this study, we silenced ALDH18A1 in KYSE150 cells using small interfering RNA (siALDH18A1), and evaluated its effect on cell characteristics. Finally, we conducted whole transcriptome sequencing (RNA-seq) and RNA immunoprecipitation (iRIP-seq) experiments to explore the downstream targets of ALDH18A1, and verified their change patterns using quantitative polymerase chain reaction. We found that ALDH18A1 exhibited a high expression level in ESCA patients using online database. The proliferation, invasion, and migration abilities of KYSE150 cells were significantly inhibited in siALDH18A1 samples. Through the investigation of RNA-seq data, we found that ALDH18A1 globally regulates the expression and alternative splicing profiles of KYSE150 cells by identifying 437 differentially expressed genes (DEGs) and 1071 ALDH18A1-regulated AS events (RASEs), respectively. The functions of RASE genes (RASGs) were enriched in pathways such as DNA repair and gene expression. In addition, through the integration analysis of iRIP-seq data and DEGs, we found that ALDH18A1 bound to and regulated the expression of 59 DEGs, including LAMB3 and IL1B, which were verified by RT-qPCR experiment. In addition, we performed an overlap analysis between the genes bound by ALDH18A1 and RASGs and found 339 bound RASGs. The functional enrichment of these genes revealed pathways such as DNA repair, cell proliferation, and DNA damage response. Among them, we found significant alternative splicing events of MTA1, which were confirmed by PCR experiments. In summary, our study comprehensively explored the functions and downstream targets of ALDH18A1 in ESCA cells, highlighting the molecular mechanism of ALDH18A1 on the carcinogenic characteristics of ESCA. The identified molecular targets, especially DNA repair-related genes, can serve as potential therapeutic targets for future ESCA treatment.