The RNA-binding protein LARP6 regulates the alternative splicing of related genes in MDA-MB-231 cells

Triple-negative breast cancer (TNBC) has the highest mortality rate of all breast cancer subtypes and currently lacks effective targeted therapies. LARP6 is an RNA-binding protein associated with cancer promotion, but its mechanism of action in TNBC remains unclear. We conducted RNA sequencing (RNA-seq) and improved RNA immunoprecipitation and sequencing (iRIP-seq) to identify the differentially expressed genes (DEGs) and alternative splice sites bound and regulated by LARP6 in MDA-MB-231 cells. Finally, both RT-qPCR and RIP-qPCR were employed for verification. Our study revealed that LARP6 overexpression altered the expression levels of 171 genes and that the number of regulated alternative splicing events (RASEs) exceeded 1000. The regulated alternative splicing genes (RASGs) corresponding to RASEs were enriched in biological processes such as DNA repair, the cell cycle, and the cellular response to DNA damage stimulus. In addition, we found that LARP6 tends to bind the CGACGAG motif. The intersection of peak-related genes with RASGs suggested that LARP6 can bind to 16 genes and regulate their alternative splicing (AS), thus playing an important role in TNBC progression. Our research indicated that LARP6 may promote the proliferation and invasion of TNBC cells by directly regulating the AS of related genes, providing new clues for targeted therapy for TNBC.