Supplementary Figures S1-S10: Supplementary Figure S1: Clustering of microsatellite instability-high colorectal cancers with promoter DNA methylation analysis. Supplementary Figure S2: Methylation status of CpG dinucleotides in each patient, as assessed by bisulphite sequencing. Supplementary Figure S3: Allele-specific copy number status of mismatch repair genes. Supplementary Figure S4: Summary of mutations in microsatellite instability-high colorectal tumours. Supplementary Figure S5: Transforming capacities of oncogenes detected in this study. Supplementary Figure S6: Sanger sequences of genomic fusion points. Supplementary Figure S7: Confirmation of somatic fusion by identification of genomic breakpoints. Supplementary Figure S8: Effects of kinase inhibitor therapy in in vivo mouse model. Supplementary Figure S9: Establishment of cost-effective fusion kinase detection. Supplementary Figure S10: Survival curves among patients with microsatellite instability-high colorectal cancers harbouring each mutation were estimated by the Kaplan-Meier method and compared using Bonferroni-adjusted log-rank tests.
ARTICLE ABSTRACT
Colorectal cancers with microsatellite instability–high (MSI-H) status, due to mismatch repair deficiency, are associated with poor patient outcomes after relapse. We aimed to identify novel therapeutic targets for them.
We performed MSI analyses of over 2,800 surgically resected colorectal tumors obtained from consecutive patients treated in Japan from 1998 through June 2016. Whole-exome sequencing, transcriptome sequencing, and methylation analyses were performed on 149 of 162 tumors showing MSI in BAT25 and BAT26 loci. We analyzed patient survival times using Bonferroni-adjusted log-rank tests.
Sporadic MSI-H colorectal cancers with promoter methylation of MLH1 (called MM) had a clinicopathological profile that was distinct from that of colorectal cancers of patients with germline mutations (Lynch syndrome, LS-associated) or somatic, Lynch-like mutations in mismatch repair genes. MM tumors had more insertions and deletions and more recurrent mutations in BRAF and RNF43 than LS-associated or Lynch-like MSI-H tumors. Eleven fusion kinases were exclusively detected in MM MSI-H colorectal cancers lacking oncogenic KRAS/BRAF missense mutations and were associated with worse post-relapse prognosis. We developed a simple method to identify MM tumors and applied it to a validation cohort of 28 MSI-H colorectal cancers, identifying 16 MM tumors and 2 fusion kinases.
We discovered that fusion kinases are frequently observed among sporadic MM MSI-H colorectal cancers. The new method to identify MM tumors enables us to straightforwardly group MSI-H patients into candidates of LS or fusion kinase carriers.
