Highly sensitive MLH1 methylation analysis in blood identifies a cancer patient with low-level mosaic MLH1 epimutation

Constitutional MLH1 methylation (epimutation) is a rare cause of Lynch syndrome. Low-level methylation (≤ 10%) has occasionally been described. This study aimed to identify low-level constitutional MLH1 epimutations and determine its causal role in patients with MLH1-hypermethylated colorectal cancer. Eighteen patients with MLH1-hypermethylated colorectal tumors in whom MLH1 methylation was previously undetected in blood by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) were screened for MLH1 methylation using highly sensitive MS-melting curve analysis (MS-MCA). Constitutional methylation was characterized by different approaches. MS-MCA identified one patient (5.6%) with low-level MLH1 methylation (~ 1%) in blood and other normal tissues, which was confirmed by clonal bisulfite sequencing in blood. The patient had developed three clonally related gastrointestinal MLH1-methylated tumor lesions at 22, 24, and 25 years of age. The methylated region in normal tissues overlapped with that reported for other carriers of constitutional MLH1 epimutations. Low-level MLH1 methylation and reduced allelic expression were linked to the same genetic haplotype, whereas the opposite allele was lost in patient’s tumors. Mutation screening of MLH1 and other hereditary cancer genes was negative. Herein, a highly sensitive MS-MCA-based approach has demonstrated its utility for the identification of low-level constitutional MLH1 epigenetic mosaicism. The eventual identification and characterization of additional cases will be critical to ascertain the cancer risks associated with constitutional MLH1 epigenetic mosaicism This work was funded by the Spanish Ministry of Economy and Competitiveness, which is part of Agencia Estatal de Investigación (AEI), and co-funded by FEDER funds—a way to build Europe—(grant SAF2012-33636 and SAF2015-68016-R), CIBERONC, the Spanish Association Against Cancer (080253), and the Government of Catalonia (grants 2014SGR338, 2017SGR1282, and PERIS SLT002/16/0037). ED was supported by a grant from the Spanish Ministry of Economy and Competitiveness. The Mexican National Council for Science and Technology (CONACyT) fellowship to GVP. JCH and FM were supported by CIBERONC, and AF was supported by a grant from the Catalonia Health Department (SLT002/16/00409). We thank CERCA Programme / Generalitat de Catalunya for institutional support