Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging

TBRS DNMT3A variants are associated with widespread DNA hypomethylation. (A) Simplified pedigree indicating the genotyping of individuals in the Amish family investigated: (+/−) heterozygous carriers of the DNMT3A c.2312G > A p.(Arg771Gln) variant; (+/− Mosaic) the DNMT3A c.2312G > A p.(Arg771Gln) mosaic father; (−/−) wild-type individuals. Black shading indicates individuals with a phenotype consistent with TBRS, gray shading, the father with macrocephaly and mild intellectual impairment; and white shading, unaffected individuals. Each of these samples was profiled on the Illumina 450K DNA methylation array. (B) Volcano plot showing site-specific DNA methylation differences (x-axis) and −log₁₀ P-values (y-axis) from an analysis comparing Amish DNMT3A c.2312G > A; p.(Arg771Gln) pathogenic variant carriers and wild-type family members using the Illumina 450K array. Red values indicate the 2606 differentially methylated positions (DMPs) detected at a Benjamini–Hochberg FDR < 0.05. (C) Top 20 Gene Ontology enrichment analysis categories associated with the 2606 DMPs identified in DNMT3A c.2312G > A; p.(Arg771Gln) pathogenic variant carriers versus wild-type family members. (D) Comparison of DNMT3A c.2312G > A; p.(Arg771Gln) identified DMPs (log₂ fold change) relative to other DNMT3A TBRS-associated variants assessed in this study (all variants grouped and measured relative to controls). Pearson correlation coefficient = 0.6620, P-value <2.2 × 10⁻¹⁶. (E) Boxplot illustrating the DNA methylation changes observed in association with the DNMT3A TBRS variants studied at the DMPs identified in the Amish DNMT3A c.2312G > A p.(Arg771Gln) carriers. The predicted protein consequence of each DNMT3A variant studied is indicated: Pink indicates in-frame deletion; yellow, single-nucleotide variant; cyan, duplications predicted to result in a frameshift; green, Amish c.2312G > A; p.(Arg771Gln) variant.