A novel cause of Lynch syndrome: heritable somatic methylation of MSH2 due to deletion of the 30 exons of the upstream gene

Abstract

Lynch syndrome patients are susceptible to colorectal, endometrial and a range of other cancers due to heterozygous inactivating mutations in one of the mismatch repair genes, MLH1, PMS2, MSH2 or MSH6. During routine diagnostics for germline mismatch repair gene mutations, multiple patients with an MSH2-deficient tumor presented an aberrant MLPA result of a probe, which is located 16 kb upstream of MSH2. All these patients carried an heterozygous germline deletion of 4.9 kb encompassing the last exons of EPCAM (formerly known as TACSTD1), a gene directly upstream of MSH2 encoding the epithelial cell adhesion molecule Ep-CAM. Due to the deletion the transcription termination signal is lost and transcription of EPCAM was shown to extend into MSH2. As antisense transcription of CpG islands may lead to methylation, we tested whether the transcription of the MSH2 promoter would lead to methylation of its CpG dinucleotides. Indeed, the MSH2 promoter in cis with the deletion is methylated in Ep-CAM positive, but not in Ep-CAM negative, normal tissues, thus revealing a correlation between transcriptional read-through of the mutated EPCAM allele and epigenetic inactivation of the corresponding MSH2 allele. This mechanism explains the mosaic pattern of epigenetic inactivation of MSH2, that we observed in successive generations (Ligtenberg et al., Nature Genetics, 41: 112–117 (2009)). Because EPCAM is expressed in the target tissues of Lynch syndrome, subjects with a 30 end deletion of EPCAM are offered the standard Lynch syndrome surveillance protocol. To optimize patient care clinical data of subjects with such a deletion that leads to loss of one functional EPCAM allele and mosaic inactivation of MSH2 are being collected.