RBM47 functions as an anti-oncogene by regulating expression and alternative splicing of cell proliferation and apoptosis associated genes in colorectal cancer cells

Transcriptional and post-transcriptional regulation that are mediated by RNA binding proteins (RBPs) have essential influence on the development and progression of colorectal cancer (CRC), while the underlying mechanisms need to be clarified. In this study, we focused on RNA Binding Motif Protein 47 (RBM47) and overexpressed its expression in HCT116 cells to evaluate its influence on cellular phenotypes and performed transcriptome sequencing (RNA-seq) to identify the downstream targets, including the expression and splicing changed genes. After RBM47 overexpression (RBM47-OE), we found the proliferation level was decreased while apoptosis level was increased. Meanwhile, the invasion and migration ability of HCT116 was also significantly inhibited by RBM47-OE. To further decipher the molecular targets of RBM47, we identified 216 up and 97 down differentially expressed genes (DEGs) by RBM47-OE, and found they were significantly enriched in immune response, apoptosis, TNF signaling, and autophagy pathways. At the same time, RBM47-OE can also regulate the splicing pattern of 2541 alternative splicing (AS) events. The regulated AS genes (RASGs) were enriched in cell cycle, DNA damage and repair, mRNA splicing, and cell division associated pathways, indicating that the downstream targets of RBM47 were tightly associated its cellular functions. To validate the regulation on gene expression and AS, we selected several DEGs and AS events to perform RT-qPCR experiment. The results showed that the expression level of CASP3, CCN1, and ATF5, and the splicing pattern of CD44 and MDM2, were significantly regulated by RBM47-OE in HCT116 cells. In summary, our results demonstrated the anti-tumor function and the globally downstream targets of RBM47 in CRC cells. We extend the cellular and molecular cognition of RBM47 in tumor. The identified molecular targets can also be served as potential targets for CRC treatment in future.