Supplementary Tables S1-S12: Supplementary Table S1: Primer sequences used in this study. Supplementary Table S2: Clinical information of tumours analysed in the present study. Supplementary Table S3: Patients' characteristics. Supplementary Table S4: Likely causal mutations in mismatch repair genes detected in this study. Supplementary Table S5: List of Tier 2 mutations. Supplementary Table S6: Significantly mutated genes identified with MutSigCV. Supplementary Table S7: Genes differentially altered between Lynch syndrome-associated/Lynch-like tumours and MLH1 promoter-methylated tumours. Supplementary Table S8: Recurrent copy number alterations detected with allele-specific copy number analysis. Supplementary Table S9: Pathways detected from top 209 Tier 2 genes with The Database for Annotation, Visualization and Integrated Discovery. Supplementary Table S10: Pathways detected from significantly mutated genes with The Database for Annotation, Visualization and Integrated Discovery. Supplementary Table S11: Detected oncogenic alterations and associated mutations with uncertain significance. Supplementary Table S12: Complementary DNA sequences of fusion points confirmed by reverse-transcription polymerase chain reaction followed by Sanger sequencing.
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.
