Elucidating the molecular basis of MSH2‐deficient tumors by combined germline and somatic analysis

Abstract

In a proportion of patients presenting mismatch repair (MMR)-deficient tumors, no germline MMR mutations are identified, the so-called Lynch-like syndrome (LLS). Recently, MMR-deficient tumors have been associated with germline mutations in POLE and MUTYH or double somatic MMR events. Our aim was to elucidate the molecular basis of MSH2-deficient LS-suspected cases using a comprehensive analysis of colorectal cancer (CRC)-associated genes at germline and somatic level. Fifty-eight probands harboring MSH2-deficient tumors were included. Germline mutational analysis of MSH2 (including EPCAM deletions) and MSH6 was performed. Pathogenicity of MSH2 variants was assessed by RNA analysis and multifactorial likelihood calculations. MSH2 cDNA and methylation of MSH2 and MSH6 promoters were studied. Matched blood and tumor DNA were analyzed using a customized next generation sequencing panel. Thirty-five individuals were carriers of pathogenic or probably pathogenic variants in MSH2 and EPCAM. Five patients harbored 4 different MSH2 variants of unknown significance (VUS) and one had 2 novel MSH6 promoter VUS. Pathogenicity assessment allowed the reclassification of the 4 MSH2 VUS and 6 probably pathogenic variants as pathogenic mutations, enabling a total of 40 LS diagnostics. Predicted pathogenic germline variants in BUB1, SETD2, FAN1 and MUTYH were identified in 5 cases. Three patients had double somatic hits in MSH2 or MSH6, and another 2 had somatic alterations in other MMR genes and/or proofreading polymerases. In conclusion, our comprehensive strategy combining germline and somatic mutational status of CRC-associated genes by means of a subexome panel allows the elucidation of up to 86% of MSH2-deficient suspected LS tumors.

Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes

“…Nevertheless, two pathogenic somatic variants affecting the two alleles of one MMR gene generally have the same effect. Several recent publications have shown that this is not uncommon in MSH2 and MSH6 negative tumors, particularly in the presence of an additional POLE or POLD1 variant or biallelic MUTYH variants . No two clearly pathogenic somatic MMR variants were found in any of the 11 tumors available for analysis in the present study.…”

Unique genomic and neoepitope landscapes across tumors: a study across time, tissues, and space within a single lynch syndrome patient

“…Strikingly there was a somatic MSH6 M875I variant in the TNBC samples. The lack of MSH6 IHC staining is consistent with the presence of this likely pathogenic variant giving rise to a double negative MSI + tumor 13,14 . In contrast to MSH2 this variant was heterozygous suggesting that additional events such as epigenetic silencing may have contributed to the lack of MSH6 expression.…”

Comparison of Molecular, Clinicopathological, and Pedigree Differences Between Lynch-like and Lynch Syndromes

“…In addition to MMR genes, most of the other PVs and likely PVs were detected in the MUTYH and GJB2 genes. Biallelic MUTYH variants have been detected in 1.8-3.1% of patients with LLS [20,21]. MUTYHassociated polyposis is extremely variable, ranging from severe polyposis coli to attenuated forms with a late age of onset or few adenomas, or CRC, which creates a phenotypic overlap with LS [20,22].…”