Abstract 5759: Molecular classification and risk stratification of colorectal cancer
Authors: Inoue Yoshikage , Kakiuchi Nobuyuki , Yoshida Kenichi , Nanya Yasuhito , Takeuchi Yasuhide , Fujii Yoichi , Shiraishi Yuichi , Chiba Kenichi , Nagayama Satoshi , Obama Kazutaka , Ogawa Seishi 
Published: June 2022

Abstract
Introduction: Currently, no widely accepted molecular classification of colorectal cancer (CRC) has been developed except for the distinction between hypermutated and nonhypermutated CRC. No reliable prognostication model has been available to optimize the effect of adjuvant chemotherapy either. To develop novel molecular classification and prognostication systems, we conducted large-scale studies of gene mutations and transcriptomes involving 3056 well-annotated CRC patients.
Methods: All patients were analyzed for mutations in 169 known/putative driver genes in CRC using targeted-capture sequencing, which also include1,630 SNPs sequenced to assess genome-wide copy numbers. RNA sequencing was also performed for gene expression profiling and comprehensive detection of gene fusions.
Results: Based on the strong mutually exclusive and co-occuring mutation patterns of mutations in Wnt pathway, non-hypermutated CRC patients (90%) were further classified into APC-mutated (81%) and unmutated (9%) case. The former was further divided into TP53-mutated (70%) and unmutated (11%), while the latter was into CTNNB1-mutated (2.7%), RNF43-mutated (1.7%), RSPO-fusion-positive (2%), and other cases (2.7%). Among these, TP53-unmutated CRC was characterized by significantly higher and lower numbers of mutations and copy number alterations, respectively, while accounting for 70% of all CRCs, the APC/TP53-double mutated ‘canonical CRC’ cases were classified into 13 unique subtypes having unique mutational profiles using non-negative matrix factorization consensus clustering. Next we modeled overall (OS) and relapse free (RFS) survival using Cox proportional hazard modeling with 1000 times cross validations using lasso. The final prediction model included gene mutations and copy number abnormalities, together with age, sex, stage, and tumor location, based on which we classified patients into groups having distinct OS and RFS in each stage. Importantly, adjuvant chemotherapy (ACT) was shown to have significantly different impacts on RFS between different risk groups within Stage2 and 3 CRC.
Conclusions: On the basis of comprehensive mutation analysis in a large cohort, we developed novel molecular classification of CRC. We further identified distinct risk groups showing different RFS and OS, which showed relationship to the efficacy of ACT, which could be used for risk stratification in Stage2 and Stage3 CRC for optimized use of ACT.
Citation Format: Yoshikage Inoue, Nobuyuki Kakiuchi, Kenichi Yoshida, Yasuhito Nanya, Yasuhide Takeuchi, Yoichi Fujii, Yuichi Shiraishi, Kenichi Chiba, Satoshi Nagayama, Kazutaka Obama, Seishi Ogawa. Molecular classification and risk stratification of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5759.