Hypomethylation of the MEG8:Int2-DMR in patients with pathogenic PLAG1 variants suggests new role of the chr14q32 imprinting cluster in Silver-Russell syndrome

Abstract

BACKGROUND: Silver-Russell syndrome (SRS) is a clinically and genetically heterogeneous imprinting disorder. The most common molecular defects are loss of methylation of the H19/IGF2:IG-DMR on chromosome 11p15.5, followed by maternal uniparental disomy of chromosome 7. Further molecular lesions are genetic variants in the PLAG1 oncogene, as well as in the transcription factor HMGA2 and the fetal growth factor IGF2. A phenotypic overlap exists between SRS and Temple syndrome (TS14) that is also characterized by growth restriction but associated with abnormalities in the imprinted chromosome 14q32 gene cluster. In TS14 patients, the germline MEG3/DLK1: IG-DMR is hypomethylated and the MEG8:Int2-DMR gains methylation probably as consequence of transcriptional readthrough from the MEG3 promoter on the paternal chromosome. However, the functional role of the MEG8 DMR remains unknown. RESULTS: We analysed the DNA methylation of 11-12 imprinted regions in 17 cases with clinical SRS features and heterozygous for a PLAG1 variant. We observed a specific loss of methylation of the MEG8:Int2-DMR in the ten cases carrying pathogenic PLAG1 variants that result in stable aberrant proteins. Normal MEG8 methylation was observed in the cases carrying variants of uncertain pathogenicity or gene deletions. Most of the PLAG1 cases are familial and both epigenetic and genetic defects co-segregated within the families. Additionally, we assessed the methylation status of the MEG8:Int2-DMR in several SRS patients with HMGA2 or IGF2 variants, H19/IGF2:IG-DMR-LoM and upd(7)mat and all of them showed normal methylation. CONCLUSIONS: Our results indicate that pathogenic PLAG1 variants leading to stable aberrant PLAG1 proteins and possibly acting in a dominant-negative manner influence methylation of the MEG8 locus. This study suggests a new pathogenetic mechanism of the PLAG1 gene in SRS, involving imprinted genes in the chr14q32 cluster through deregulation of the MEG8:Int2-DMR and provides an epigenetic signature that may be used to assess the damaging potential of the PLAG1 variants.