Introduction

Extensive genetic studies of recent years using next generation sequencing have clarified a comprehensive registry of genetic alteration in colorectal cancer (CRC). However, the clinical impacts of these genetic alterations have not fully been investigated, except for a better response to immune checkpoint blockade and favorable prognosis in patients with microsatellite instability (MSI) cancer. In this study, we investigated the effects of common genetic alterations on survival in CRC patients using large-scale mutation profiling.

Methods

We performed targeted-capture sequencing to common driver genes (n=128) in CRC in a total of 544 patients with stage I (n = 36), II (n = 236) and III (n = 272) CRC. All patients were treated at a single institute between 2004 and 2016 and clinically well-annotated. Genome-wide copy numbers, fusion genes and MSI were also interrogated using baits for 1,605 SNPs, 7 introns and 18 microsatellites, respectively. RT-PCR was performed for the detection of PTPRK-RSPO3 fusion gene.

Results

The median age at diagnosis was 65 (32-95) with a median observation period of 1250 days. Of the 156 patients with recurrence, 15, 61 and 80 patients had stage I, II and III diseases, respectively. APC, TP53, KRAS, and PIK3CA represented the most frequently mutated, while common focal copy number alterations involved PTEN, SMAD4, SMAD2, FGFR1 and IGF2. Novel fusion genes including PTPRK-RSPO3 were detected in only 7 (1.5%) samples. Fifty-five patients had more than 20 mutations, comprising a group of hypermutated CRC. Among these, 44 were thought to have MSI based on the microsatellite analysis, while the remaining 11 were explained by POLE mutations affecting the proof reading domain. CRCs with POLE mutations were diagnosed earlier in life, with the median age of 49 (35-66). The frequency of CRCs with MSI was significantly lower than previous reports from the western population. In contrast to mutation frequency, copy number alterations were infrequent, which most hypermutated tumors showed Genomic Instability Index (GII) below 0.2. FBXW7 mutation positively affected tumor free survival. BRAF mutation, SMAD4 mutation, or existence of fusion genes did not have any effect on prognosis. In accordance with previous reports, only 4 patients (9.1%) with MSI had recurrence, confirming a better prognosis of MSI-positive patients. Similarly, only one of the 11 patients (9.1%) with POLE mutation had recurrence. The low relapse rate was also observed among an additional cohort of 819 patients, which included 6 POLE mutated cases, none of whom had recurrence, suggesting that POLE mutation was associated with a favorable prognosis.

Conclusions

We revealed the landscape of driver mutations in patients with stage I, II and III CRC with their implication in clinical outcomes. In addition to FBXW7 mutations, the MSI status and somatic POLE mutations are significantly associated with a better prognosis.

Citation Format: Yoshikage Inoue, Nobuyuki Kakiuchi, Kenichi Yoshida, Yusuke Shiozawa, Kenichi Chiba, Tetsuichi Yoshizato, Yuichi Shiraishi, Satoru Miyano, Satoshi Nagayama, Yoshiharu Sakai, Seishi Ogawa. Targeted sequencing of colorectal cancer in search for prognostic biomarkers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1426.