Effect of activating Wnt signalling on expression of 3' UTR spliced transcripts in colorectal carcinoma cell line HCT116

The Wnt signalling pathway is commonly mutated or dysregulated in colorectal cancer, including approximately 93% of solid tumour samples from The Cancer Genome Atlas. Such dysregulation commonly leads to overactivation of CTNNB1, a transcription factor central to Wnt signalling. We have previously observed an increase in splicing of the 3'UTR of CTNNB1 in colon cancer samples compared to healthy samples. Additionally, we have observed isoform-specific regulation of CTNNB1 3'UTR spliced and retained isoforms in response culturing HCT116 cells with increasing concentrations of Wnt activator CHIR99021, and the opposite upon incubation with Wnt inhibitor IWR-1. By treating HCT116 cells with a high concentration of Wnt activator CHIR99021 and performing RNA sequencing, we assessed the global impact of Wnt signalling on expression of transcripts with spliced 3'UTRs. Interestingly, we observe an enrichment of alternative splicing events relating to components of the canonical Wnt signalling pathway itself, highlighting potential autoregulatory functions. Overall design: To investigate the role that Wnt signalling has on expression of 3'UTR spliced transcripts, HCT116 cells were treated with CHIR99021, a small molecule inhibitor of GSK3B, to activate the Wnt signalling pathway. Following RNAseq, we conducted differential transcript usage and differential splicing analyses.