APC Mutation Marks an Aggressive Subtype of BRAF Mutant Colorectal Cancers

Abstract

Background: WNT activation is a hallmark of colorectal cancer. BRAF mutation is present in 15% of colorectal cancers, and the role of mutations in WNT signaling regulators in this context is unclear. Here, we evaluate the mutational landscape of WNT signaling regulators in BRAF mutant cancers.

Methods: we performed exome-sequencing on 24 BRAF mutant colorectal cancers and analyzed these data in combination with 175 publicly available BRAF mutant colorectal cancer exomes. We assessed the somatic mutational landscape of WNT signaling regulators, and performed hotspot and driver mutation analyses to identify potential drivers of WNT signaling. The effects of Apc and Braf mutation were modelled, in vivo, using the Apc^min/+ and Braf^V637/Villin-Cre^ERT2/+ mouse, respectively.

Results: RNF43 was the most frequently mutated WNT signaling regulator (41%). Mutations in the beta-catenin destruction complex occurred in 48% of cancers. Hotspot analyses identified potential cancer driver genes in the WNT signaling cascade, including MEN1, GNG12 and WNT16. Truncating APC mutation was identified in 20.8% of cancers. Truncating APC mutation was associated with early age at diagnosis (p < 2 × 10^-5), advanced stage (p < 0.01), and poor survival (p = 0.026). Apc^min/+/Braf^V637 animals had more numerous and larger SI and colonic lesions (p < 0.0001 and p < 0.05, respectively), and a markedly reduced survival (median survival: 3.2 months, p = 8.8 × 10^-21), compared to animals with Apc or Braf mutation alone.

Conclusions: the WNT signaling axis is frequently mutated in BRAF mutant colorectal cancers. WNT16 and MEN1 may be novel drivers of aberrant WNT signaling in colorectal cancer. Co-mutation of BRAF and APC generates an extremely aggressive neoplastic phenotype that is associated with poor patient outcome.

Keywords: APC; BRAF; WNT signaling; colorectal cancer; driver mutations; genomics; serrated neoplasia.

Figure 1

The somatic mutation landscape of WNT signaling regulators in BRAF mutant colorectal cancers. The 30 most frequently mutated genes in the WNT pathway are depicted. Each column corresponds to a single cancer. The colors of bars are indicative of the type of mutation, with grey = wild-type. The barplot at the top of the figure represents the number of mutations in the WNT pathway a sample has. The vertical plot on the right of the figure represents the number of mutations in each gene, color coded by mutation type. Microsatellite instability status is indicated below the mutation plot.

Figure 2

Mutations in the Beta-Catenin destruction complex. Each column corresponds to a single cancer, and each row, a single gene.

Figure 3

Somatic interaction analysis reveals mutually exclusive mutations between gene pairs, and significant co-occurring mutations. Co-occurring mutations are indicated by green squares and mutually exclusive mutations between gene pairs in purple. The intensity of the color is proportionate the –log10 (p-value). p-values were determined using Fisher’s exact test.

Figure 4

The mutational landscape of WNT signaling regulators by microsatellite instability status. Note that this analysis is limited to cancers with microsatellite instability status available (n = 167).

Figure 5

The mutational landscape of WNT signaling regulators in BRAF wild type cancers.

Figure 6

Survival analysis of (A) BRAF mutant human cancers by the presence or absence of truncating APC mutation. (B) Apc, Braf, and Apc/Braf mutant murine models. p-values are univariate and derived from the log-rank test. (C–E) Assessment of the number and size of lesions in Apc, Braf, and Apc/Braf mutant mouse models. (C) Total lesions in the small intestine. (D) Total number of lesions in the colon and caecum. E: Mean size of lesions in the colon and caecum.