Genome-Wide Allelic Methylation Analysis Reveals Disease-Specific Susceptibility to Multiple Methylation Defects in Imprinting Syndromes

Abstract

Genomic imprinting is the parent-of-origin-specific allelic transcriptional silencing observed in mammals, which is governed by DNA methylation established in the gametes and maintained throughout the development. The frequency and extent of epimutations associated with the nine reported imprinting syndromes varies because it is evident that aberrant preimplantation maintenance of imprinted differentially methylated regions (DMRs) may affect multiple loci. Using a custom Illumina GoldenGate array targeting 27 imprinted DMRs, we profiled allelic methylation in 65 imprinting defect patients. We identify multilocus hypomethylation in numerous Beckwith-Wiedemann syndrome, transient neonatal diabetes mellitus (TNDM), and pseudohypoparathyroidism 1B patients, and an individual with Silver-Russell syndrome. Our data reveal a broad range of epimutations exist in certain imprinting syndromes, with the exception of Prader-Willi syndrome and Angelman syndrome patients that are associated with solitary SNRPN-DMR defects. A mutation analysis identified a 1 bp deletion in the ZFP57 gene in a TNDM patient with methylation defects at multiple maternal DMRs. In addition, we observe missense variants in ZFP57, NLRP2, and NLRP7 that are not consistent with maternal effect and aberrant establishment or methylation maintenance, and are likely benign. This work illustrates that further extensive molecular characterization of these rare patients is required to fully understand the mechanism underlying the etiology of imprint establishment and maintenance.

Characterization of multi-locus imprinting disturbances and underlying genetic defects in patients with chromosome 11p15.5 related imprinting disorders

“…The frequency of MLID appears to vary depending on the sensitivity of the technology used for analyses and the iDMRs investigated [6–8,15,19]. In this study, we set up a panel of 12 iDMRs by MassARRAY technology and applied it to a cohort of patients with BWS, presenting with primary GOM at ICR1 or LOM at ICR2, and with SRS, showing LOM at ICR1.…”

“…The phenotypic heterogeneity of BWS/SRS and the presence of clinical features overlapping with other IDs [6–8], have prompted the investigation of methylation defects at additional imprinted genes in patients with epimutations at the disease-specific locus, leading to the identification of a subset of patients with aberrant methylation affecting other imprinted differentially methylated regions (iDMRs), a condition described as multi-locus imprinting disturbance (MLID). MLID has been identified in BWS patients at frequencies of up to 30% in patients with LOM at ICR2 [6–14], while it is very rare among cases with GOM at ICR1 [15].…”

“…MLID has been identified in BWS patients at frequencies of up to 30% in patients with LOM at ICR2 [6–14], while it is very rare among cases with GOM at ICR1 [15]. Some BWS patients with MLID show LOM or GOM at both maternal and paternal DMRs [8,15], while others have a hypomethylation syndrome restricted to maternally imprinted genes [16–18]. MLID has less frequently been described in patients with SRS (~ 15%) [8].…”

“…Some BWS patients with MLID show LOM or GOM at both maternal and paternal DMRs [8,15], while others have a hypomethylation syndrome restricted to maternally imprinted genes [16–18]. MLID has less frequently been described in patients with SRS (~ 15%) [8]. …”

“…Indeed, in NLRP mutated MLID cases, the affected iDMRs appear to vary, and intermediate levels of LOM suggest a post-zygotic effect. In addition, both homozygous and heterozygous causative mutations in the NLRP genes have been reported in BWS patients, suggesting a variable pattern of inheritance [8,21,22,25]. Furthermore, incomplete penetrance may account for the variability observed among patients with the same pathogenic mutations [21].…”