Abstract 2276: Genetic classification of colorectal cancer
Authors: Inoue Yoshikage , Kakiuchi Nobuyuki , Yoshida Kenichi , Nanya Yasuhito , Shiozawa Yusuke , Takeuchi Yasuhide , Fujii Yoichi , Shiraishi Yuichi , Chiba Kenichi , Yoshizato Tetsuichi , Nagayama Satoshi , Sakai Yoshiharu , Ogawa Seishi 
Published: July 2021

Abstract
Introduction: Comprehensive genetic research has classified colorectal cancer (CRC) into hypermutated CRC and non-hypermutated CRC. Among hypermutated CRC, microsatellite instable CRC (MSI-CRC) is reported as a distinct entity with good overall survival. However, there are still no widely accepted classification in non-hypermutated CRC. To classify CRC based on driver mutations and their association with clinical outcomes, we conducted targeted-capture sequencing of known driver mutations in over 3000 CRC samples.
Methods: We enrolled a total of 3056 CRC patients with varying stages, including stage I (n=653), II (n=894), III (n=994) and IV (n=653). All patients were treated at a single institute between 2004 and 2016 and clinically well-annotated. Targeted-capture sequencing was performed using RNA baits designed for detecting 169 driver genes in CRC. Additional baits for 1,630 SNPs were also included to assess genome-wide abnormalities (CNA).
Results: The median age at diagnosis was 64 (32-95) with a median observation period of 1,819 days. The average depth of the sequencing was 839 ×. Hypermutated CRC accounted for 9.6%, which included MSI-CRC, POLE mutated CRC and POLD1 mutated CRC (8%, 1,5%, 0.1%, respectively). As previously reported, they showed excellent overall survival. APC (88%), TP53 (79%), KRAS (45%), and PIK3CA (15%) represented the most frequent mutational targets among non-hypermutated CRC. We applied non-negative matrix factorization (NMF) consensus clustering to the identified driver mutations and discovered seven robust subsets of tumors with discrete genetic signatures (Cluster1-7) among non-hypermutated CRC. Clusters are characterized by APC/TP53 mutations (without other mutations, Cluster1), PI3K pathway gene alterations (Cluster2), TGF-beta pathway gene alterations (Cluster3), cell cycle pathway gene alterations (Cluster4), APC/TP53/KRAS mutations (without other mutations, Cluster5), SOX9/ARID1A mutations (Cluster6) and FBXW7mutation (Cluster7). Cluster1 and 5, which only harbor the basic genetic alterations in CRC carcinogenesis, showed moderate overall survival. Cluster7 showed improved overall survival, which indicates a protective role of FBXW7 mutation. In contrast, Cluster3, 4 and 6 have worse prognosis, which each cluster defining alterations are predicted to have additional effects on the aggressiveness of CRC. We constructed a multivariate model considering age, sex, stage and genetic clusters as variables, with stageI and Cluster1 as reference. Although stage showed the strongest contribution to overall survival, Cluster3, 4 and 6 had a hazard ratio of 1.51, 1.64 and 1.54. Thus, the genetic clusters captured outcome differences that were independent of stage.
Conclusions: We have revealed the genetic classification of non-hypermutated CRC in a large cohort. CRC are classified into 7 distinct genetic subtypes characterized by unique profiles of gene mutations and clinical outcomes.
Citation Format: Yoshikage Inoue, Nobuyuki Kakiuchi, Kenichi Yoshida, Yasuhito Nanya, Yusuke Shiozawa, Yasuhide Takeuchi, Yoichi Fujii, Yuichi Shiraishi, Kenichi Chiba, Tetsuichi Yoshizato, Satoshi Nagayama, Yoshiharu Sakai, Seishi Ogawa. Genetic classification of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2276.