Quantifying ‘just-right’ APC inactivation for colorectal cancer initiation

Abstract

Dysregulation of the tumour suppressor gene Adenomatous Polyposis Coli (APC)is a canonical step in colorectal cancer development. Curiously, most colorectal tumours carry biallelic mutations that result in only partial loss of APC function, suggesting that a ‘just-right’ level of APC inactivation, and hence Wnt signalling, provides the optimal conditions for tumorigenesis. Mutational processes act variably across theAPCgene, which could contribute to the bias against complete APC inactivation. Thus the selective consequences of partial APC loss are unclear. Here we propose a mathematical model to quantify the tumorigenic effect of biallelicAPCgenotypes, controlling for somatic mutational processes. Analysing sequence data from >2500 colorectal cancers, we find thatAPCgenotypes resulting in partial protein function confer about 50 times higher probability of progressing to cancer compared to complete APC inactivation. The optimal inactivation level varies with anatomical location and additional mutations of Wnt pathway regulators. We use this context dependency to assess the regulatory effect of secondary Wnt drivers in combination with APCin vivo, and provide evidence that mutantAMER1combines withAPCgenotypes that lead to relatively low Wnt. The fitness landscape of APC inactivation is consistent across microsatellite unstable andPOLE-deficient colorectal cancers and tumours in patients with Familial Adenomatous Polyposis suggesting a general ‘just-right’ optimum, and pointing to Wnt hyperactivation as a potential cancer vulnerability.