Investigation of methylation profiles in Silver-Russell syndrome to explore episignatures

Episignatures are disease-specific, genome-wide DNA methylation patterns identified in more than 100 genetic syndromes caused by mutation of genes related to epigenetic modifiers. The utility of episignatures as a disease diagnostic tool has been demonstrated in recent years. However, studies evaluating episignatures in imprinting disorders (IDs) are very limited. We hypothesized that identifying episignatures in Silver-Russell syndrome (SRS), one of the representative IDs, could lead to the development of a new diagnostic tool for SRS. We investigated methylation profiles in patients with different molecular etiologies to clarify the presence or absence of DNA methylation episignatures in SRS.

We conducted genome-wide methylation analysis (GWMA) using the HumanMethylationEPIC array in 27 patients consisting of five groups based on molecular etiologies satisfying clinical diagnostic criteria: hypomethylation of H19-differentially methylated region (DMR) (n = 9), maternal uniparental disomy chromosome 7 (n = 11), IGF2 variant (n = 3), PLAG1 variant (n = 2), and deletions including KCNQ1OT1:TSS-DMR (n = 2). We compared the methylation levels of CpGs (β values) between each group and control group (94 pediatric samples) and extracted aberrantly methylated CpGs satisfying the following criteria: (1) Bonferroni-corrected p value < 0.05, and (2) the absolute value of ∆β (|∆β|), the difference between the average β value of each ID group and controls at each probe, was above 0.1. Based on the extracted aberrantly methylated CpGs, we examined (1) aberrantly methylated patterns, (2) aberrantly methylated regions, and 3) CpG-enriched genes and their functions, shared by multiple groups. Although several CpGs were commonly hypermethylated or hypomethylated in two of the five groups, the number of CpGs was too small to form characteristic methylation patterns. Several aberrantly methylated regions, including disease-responsible DMRs of SRS, were identified in each group, but no regions common in multiple groups were identified. Previously reported aberrantly methylated regions other than disease-responsible DMRs were not identified. In addition, we found no CpG-enriched genes or their functions common in multiple groups.

GWMA in SRS patients with different molecular etiologies identified no characteristic episignatures. Only methylation changes of CpGs within disease-responsible DMRs, not genome-wide methylation changes, occur in some SRS etiologies.