Highly variable genomic methylation in the Beckwith-Wiedemann syndrome associated with Multi-Locus Imprinting Disturbances

Background The expression of imprinted genes, which depends on their gamete of origin, is regulated by DNA sequences characterized by differential methylation between the maternal and paternal alleles (also known as germline differentially methylated regions or gDMRs). The most common molecular defect associated with Beckwith-Wiedemann syndrome (BWS), a condition linked to overgrowth and tumors, is the loss of methylation of the KCNQ1OT1 -TSS gDMR located on chromosome 11p15.5 (also known as IC2 LoM). Approximately one-third of BWS patients with IC2 LoM exhibit multi-locus imprinting disturbances (MLID). While maternal-effect variants in proteins of the oocyte subcortical maternal complex (SCMC) have been linked to MLID, the underlying mechanisms and health impact of this epigenetic disturbance remain unclear. Results We used the Infinium EPIC methylation array to investigate whole-genome CpG methylation in 64 BWS patients with IC2 LoM and 37 control subjects. We distinguished two patient groups, one with a variable methylation level of 24 gDMRs and the other with single-locus IC2 LoM. We observed that the mothers of the former patient group carried more variants in maternal-effect genes than those of the latter group, and 50% of them, but none of the latter group had variants in the SCMC genes. Additionally, in the former group, the mothers were older at the time of pregnancy, and the patients showed higher variation in methylation levels of thousands of CpGs located in non-imprinted loci, including protochaderins and cancer-associated genes. We found no differences in clinical features or in the incidence of assisted reproductive technology between the two patient groups. However, multiple affected siblings and recurrent miscarriages were observed only among cases with biallelic maternal-effect SCMC gene variants. Conclusions This study demonstrates that the BWS patients with MLID exhibit highly variable methylation changes that affect both imprinted and non-imprinted loci in a seemingly stochastic manner throughout the genome. These findings support the hypothesis that MLID results from the interaction of maternal-effect genes and environmental factors in aged oocytes, leading to disordered DNA methylation in the whole genome. Future research should investigate whether and how these epimutations impact the health of affected individuals, particularly in adulthood.