Abstract 3753: Differential roles of Wnt pathway mutations in colorectal cancer

Abstract Colorectal cancer (CRC) is one of the most prevalent cancers in the developed countries and is classified into hypermutated and non-hypermutated (NHM) subtypes based on their mutational burden. The complex co-occurrence patterns of major driver gene mutations have hindered the development of a genetic classification for NHM, which could advance our understanding of CRC pathogenesis. In this study, we analyzed 4, 434 CRC cases using targeted-capture sequencing to evaluate somatic mutations and copy number alterations (CNAs) in 169 driver genes and 1, 660 polymorphic sites. RNA sequencing of 2, 833 cases was also performed. Of the 4, 434 cases, 3, 986 were classified as NHM. These cases were further stratified into APC-mutated (APCmut) and APC-unmutated (APCwt) subtypes based on the mutually exclusive relationship between APC mutations and other Wnt pathway alterations. The APCwt subtype was further divided into three subgroups characterized by CTNNB1 (2.4%), RNF43 (1.8%) mutations, and RSPO fusions (1.7%). These alterations, including APC mutations, tended to occur in a mutually exclusive manner. In contrast, mutations in other Wnt-related genes, such as AMER1, ZNRF3, AXIN1/2, TCF7L2, BCL9L, FBXW7, and SOX9, co-occurred with other Wnt pathway mutations in >90% of cases. Notably, all APCwt subtypes, including the Wnt-negative group (∼1.5%) that had no evidence of any Wnt-pathway gene mutations even using whole-genome sequencing, had significantly worse prognoses compared to APCmut cases. Each APCwt subtype also displayed distinct clinical, expression, and mutational profiles. For APC-mut cases, which accounted for ∼80% of all CRCs, we examined the degree of fitness conferred by mutations based on their location within the APC gene. This analysis identified four distinct regions within the APC gene, enabling the subclassification of APCmut cases into four subgroups. Importantly, these subgroups exhibited significant differences in Wnt pathway activation, as assessed by GSVA analysis and AXIN2 expression. Subgroups with low Wnt-activation were frequently accompanied by AMER1 mutations, which could facilitate Wnt activation. Additionally, these subgroups, together with other Wnt-mutated subgroups, exhibited distinct features of chromosomal copy numbers, mutations in additional drivers in p53, PI3K, RAS, and TGF-β, tumor location, and clinical outcomes. Our findings demonstrate that the type of founder Wnt lesion dictate the evolutionary trajectory of CRCs and determine their genetic and clinical features. This study provides a refined framework for our understanding of the molecular heterogeneity of CRC and offers new insights into its pathogenesis. Citation Format: Yoshikage Inoue, Nobuyuki Kakiuchi, Yasuhito Nanya, Kenichi Yoshida, Koichi Watanabe, Yasuhide Takeuchi, Yoichi Fujii, Yuichi Shiraishi, Kenichi Chiba, Tetsuichi Yoshizato, Satoshi Miyano, Satoshi Nagayama, Kazutaka Obama, Seishi Ogawa. Differential roles of Wnt pathway mutations in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3753.