Next-generation sequencing reveals heterogeneous genetic alterations in key signaling pathways of mismatch repair deficient colorectal carcinomas

Colorectal carcinoma (CRC) with deficient mismatch repair (dMMR) is an etiologically heterogeneous molecular entity. We investigated the genetic profile, focusing on key signaling pathways and molecular diversity of dMMR CRCs. In this study, next-generation sequencing was applied to 156 consecutive dMMR CRCs and 225 randomly selected proficient MMR (pMMR) CRCs diagnosed between July 2015 and December 2019 at Peking Union Medical College Hospital. Genetic alterations andMLH1promoter hypermethylation (MLH1(me+)) were analyzed. Among the most frequently mutated genes,RNF43, ARID1A, PIK3CA, ATM, andBRCA2mutants were enriched in dMMR CRCs, whereasAPCandTP53mutations were enriched in pMMR CRCs. In dMMR group,RNF43, APC, ARID1A, andBRCA2mutations were largely microsatellite instability events. WNT pathway was commonly altered regardless of MMR status. Compared to pMMR CRCs, dMMR CRCs had remarkably more prevalent PI3K, RTK-RAS, TGF beta, and DNA damage repair pathway alterations and more multiple mutations in WNT and PI3K pathways. Within dMMR tumors, mutual exclusivity occurred betweenCTNNB1mutation andAPCorRNF43mutation, while coexistence existed betweenBRAFandRNF43mutation, as well asRASandAPCmutation. MLH1(me+)dMMR CRCs had significantly more frequentRNF43mutations but less frequentKRAS, APC, andCTNNB1mutations comparing toMLH1-unmethylated dMMR CRCs.RNF43/BRAFcomutations were detected inMLH1(me+)dMMR CRCs, whereasRAS/APCcomutations were largely detected in Lynch syndrome-associated cases.RNF43mutation was independently associated withMLH1(me+)rather thanBRAFmutations. dMMR CRCs bearing receptor tyrosine kinase fusion demonstrated no additional RTK-RAS mutations, significantly fewer PI3K alterations and moreTGFBR2mutations than other dMMR tumors. Our study revealed that dMMR CRCs had distinctive gene mutation spectra and signaling pathway interaction patterns compared to proficient mismatch repair (pMMR) CRCs, and molecular heterogeneity was evident for these divergent oncogenic pathways. These findings justify the use of individualized therapy targeted to dMMR CRC subgroups.