Investigating resistance to beta-catenin degradation in a colorectal cancer cell line

Oncogenic mutations to the Wnt pathway are present in approximately 80% of colorectal cancer (CRC) patients. In mouse CRC models, Beta-Catenin (BC) loss inhibits tumour growth reinforcing BC as a promising anticancer target. Small molecules or peptides targeting BC have been reported but these generally lack features of high-quality chemical probes. To date there are no reports of these tool compounds progressing to chemical series with more drug-like physiochemical and pharmaceutical characteristics, yet interest in developing BC inhibitors or degraders remains. To explore potential fragment-binding pockets on BC we established a BC-degron model for genetic rescue experiments using the dTAG system to degrade FKBP12 F36V -tagged BC. Based on literature and in-house date we selected the APC-mutant, BC-dependent SW480 human CRC cell line as our model of choice. During the characterisation of multiple dTAG single cell clones we identified two resistant SW480 cell clones which proliferated despite BC degradation. One line (Res1) contained no detectable BC protein following treatment with the dTAG V -1 heterobifunctional degrader molecule. Whereas the other, Res2, retained expression of an internally truncated species of BC,that was sufficient to rescue WT-BC function. Genetic and proteomic profiling were used to define the response of resistant populations to BC degradation. Res2 exhibited a similar molecular profile to cells expressing full length BC. Res1 exhibited a proteomic profile distinct from sensitive cells after BC degradation. BC-driven oncogenic gene expression profile was degraded in resistant cells, similarly to sensitive cells. But metabolic pathways, including autophagy, were markedly altered in resistant cells. Additionally, we found a region of chromosome 19 lost only in Res1. Res1 exhibited distinct morphological features to sensitive cells and an increased migratory capacity. Multiple patient-like cancer stem cell subtypes have been classified within the SW480 CRC cell line population, with different invasive and Wnt signalling capacities. But their responses to BC inhibition or loss are unknown. Molecular and cellular characterisation of Res-1 is on-going to identify key SW480 subtype features and mechanism of resistance to BC loss as potential biomarkers to predict patients with resistance to BC inhibition and suggest novel pathway dependencies which can be exploited for combination therapies alongside BC inhibition or degradation.