Germline hypermethylation of MLH1 and EPCAM deletions are a frequent cause of Lynch syndrome

Abstract

It was shown that Lynch syndrome can be caused by germline hypermethylation of the MLH1 and MSH2 promoters. Furthermore, it has been demonstrated very recently that germline deletions of the 3' region of EPCAM cause transcriptional read-through which results in silencing of MSH2 by hypermethylation. We wanted to determine the prevalence of germline MLH1 promoter hypermethylation and of germline and somatic MSH2 promoter hypermethylation in a large group of Lynch syndrome-suspected patients. From a group of 331 Lynch Syndrome-suspected patients we selected cases, who had no germline MLH1, MSH2, or MSH6 mutation and whose tumors showed loss of MLH1 or MSH2, or, if staining was unavailable, had a tumor with microsatellite instability. Methylation assays were performed to test these patients for germline MLH1 and/or MSH2 promoter hypermethylation. Two patients with germline MLH1 promoter hypermethylation and no patients with germline MSH2 promoter hypermethylation were identified. In the subgroup screened for germline MSH2 promoter hypermethylation, we identified 3 patients with somatic MSH2 promoter hypermethylation in their tumors, which was caused by a germline EPCAM deletion. In the group of 331 Lynch Syndrome-suspected patients, the frequencies of germline MLH1 promoter hypermethylation and somatic MSH2 promoter hypermethylation caused by germline EPCAM deletions are 0.6 and 0.9%, respectively. These mutations, therefore, seem to be rather infrequent. However, the contribution of germline MLH1 hypermethylation and EPCAM deletions to the genetically proven Lynch syndrome cases in this cohort is very high. Previously 27 pathogenic mutations were identified; the newly identified mutations now represent 16% of all mutations.

Frequency of Deletions of EPCAM (TACSTD1) in MSH2-Associated Lynch Syndrome Cases

“…Heritable DNA methylation abnormalities have been identified in two Lynch syndrome-associated genes, MLH1 [33][34][35][36][37][38][39][40] and MSH2. 22,31,32,41,42 Heritable MLH1 promoter hypermethylation appears to be a relatively rare event, and the mechanism for this alteration has not yet been determined. Evidence presented in the literature 22 proposes that the hypermethylation of the MSH2 promoter region results from the production of an abnormal EPCAM/TACSTD1 RNA; specifically, a deletion of the EPCAM/TACSTD1 transcriptional termination signal results in a fusion transcript that includes at least part of MSH2.…”

Gene discovery in familial cancer syndromes by exome sequencing: prospects for the elucidation of familial colorectal cancer type X

“…[70][71][72] EPCAM (also known as TACSTD1) deletion leading to MSH2 promoter methylation is another common genetic aberration causing Lynch syndrome. [73][74][75] Therefore, it is evident that only a proportion of hereditary non-polyposis colorectal cancer cases which fulfill the Amsterdam Criteria have germline mutations in mismatch-repair genes, which by 'definition' constitutes Lynch syndrome. As a result, families with a strong family history of colorectal cancer that do not have Lynch syndrome have been grouped as 'familial colorectal cancer-type X'; alternatively, some studies have referred to them as mismatch-repair gene mutation-positive and -negative families for Lynch syndrome and familial colorectal cancer type X, respectively.…”

Germline Genetics in Colorectal Cancer Susceptibility and Prognosis

“…The most commonly mutated genes in LS are MLH1 and MSH2. Recently, deletions of the 3'end of EPCAM, a gene mapping 5' of the MSH2 gene, have been found to give rise to LS by causing methylation of the MSH2 gene in about 6% of LS cases (Niessen et al, 2009a). Criteria based on family history, Amsterdam I, Amsterdam II and Bethesda criteria, were developed in order to identify families for further evaluation of Lynch syndrome.…”