Abstract 3394: Actionable fusion kinases in microsatellite instability-high colorectal cancers

Abstract

Abstract Colorectal cancer (CRC) patients who are microsatellite instability-high (MSI-H) due to mismatch repair (MMR) deficiency have poor prognosis after relapse by consensus molecular subtyping. In response to reports of some MSI-H CRC resistance to immune checkpoint blockade and immune-related adverse events, we sought to identify a new therapeutic target. MSI testing was done on ~2,800 resected colorectal tumors; next-generation sequencing was done on 149 MSI-H tumors showing MSI in both BAT25 and BAT26 loci. MSI-H CRCs are conventionally divided into hereditary and sporadic categories; in this study whole-exome sequencing, transcriptome sequencing, and methylation array revealed that sporadic MSI-H CRCs are further classifiable into somatic MMR gene mutation (Lynch-like) or MLH1 promoter methylated (MM) types. Methylation of other MMR genes (MSH2/MSH6/PMS2) was not detected. The mutational properties of sporadic MSI-H CRCs harboring somatic MMR gene mutations more closely resembled those of Lynch syndrome-associated MSI-H CRCs than those of MM CRCs, which were more likely to develop in the right-sided colon and harbor more insertions/deletions, more recurrent mutations of BRAF/RNF43, and fewer recurrent mutations of KRAS/APC than Lynch syndrome-associated/Lynch-like CRCs (P < 0.001, Fisher's exact test). Loss of heterozygosity of the locus encompassing TGFBR2, MLH1, and CTNNB1 was specific to Lynch syndrome-associated/Lynch-like MSI-H CRCs; this loss appears to be instrumental in the inactivation of TGFBR2/MLH1. Pathway-level analyses of MSI-H CRCs identified DNA damage-sensing and histone H3 methylation-associated pathways as well as Wnt signaling and RAS/RAF/mitogen-activated protein kinase pathways. One mutational signature, Mutational Signature A, accounted for a median percentage 2.3 times larger of mutations in tumors with mutated PMS2 than in tumors with intact PMS2 (P = 1.5 × 10-5, Mann-Whitney U test). Although it is believed that fusion kinases are found in less than 1% of all CRCs, clinically actionable fusion kinases were detected in 11/19 (58%) MM MSI-H CRCs lacking KRAS/BRAF oncogenes. A 3T3 transformation assay confirmed the tumorigenicity of identified fusion kinases; small-molecule inhibitors that suppress the activity of the kinases identified in fusion products significantly attenuated malignant transformation of 3T3 cells in a concentration-dependent manner. Patients with MSI-H CRCs harboring fusion kinases had worse post-relapse prognoses than did patients with MSI-H CRCs harboring KRAS oncogenes. These findings promise to advance MSI-H CRC precision medicine. Citation Format: Kazuhito Sato, Masahito Kawazu, Yoko Yamamoto, Toshihide Ueno, Shinya Kojima, Genta Nagae, Manabu Soda, Takafumi Oga, Shinji Kohsaka, Eirin Sai, Yoshihiro Yamashita, Shoichi Hazama, Hisae Iinuma, Hiroyuki Aburatani, Hiroyuki Mano. Actionable fusion kinases in microsatellite instability-high colorectal cancers [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 3394.