Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes

Abstract

Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the ''epigenetic machinery''). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery.

Genetics meets DNA methylation in rare diseases

“…Mutations in MLL2 (KMT2D), a SET domain‐containing H3K4me3 KMT, are the main cause of Kabuki syndrome characterized by ID and short stature. Methylome profiling in patients identified both gain and loss of DNAme, at CGI promoters and at enhancers . The gain in DNAme may well result from reduced deposition of the repulsive H3K4me3 mark at the onset of DNAme establishment.…”

“…It is deposited by EZH2 (Enhancer of zeste homolog 2; KMT6A), a SET domain‐containing KMT that belongs to the Polycomb Repressive Complex 2 (PRC2) . Mutations in EZH2 cause Weaver syndrome, an OGID syndrome with considerable phenotypic overlap with Sotos syndrome, whereas microdeletions in a H3K27me3 KDM, UTX (KDM6A), are found in certain patients with Kabuki symptoms . However, it remains unclear how EZH2 and NSD1 (or SETD2), which seemingly have opposite effects on chromatin state, could affect the same genomic regions and affect human growth.…”

“…A first step towards understanding whether and how these factors operate in common pathways is provided by a broad analysis of DNAme profiles in 14 Mendelian conditions that result from the disruption of epigenetic regulators, and the establishment of both specific and partially overlapping signatures. The latter may underlie neurological dysfunction and ID, which is a common feature of all these syndromes as a consequence of the disruption of epigenetic machineries …”

DNA methylation analysis of multiple imprinted DMRs in Sotos syndrome reveals IGF2 ‐DMR0 as a DNA methylation‐dependent, P0 promoter‐specific enhancer

“…12 Mutations in DNMT3A and SETD2 have been identified in patients with Sotos-like overgrowth syndromes, including Tatton-Brown-Rahman syndrome (TBRS; MIM: 615879). 16,17 In addition, NSD1 mutations were identified in patients with Beckwith-Wiedemann syndrome (BWS; MIM: 130650), a distinct overgrowth syndrome; further, anomalies at 11p15, a disease locus for BWS, were identified in patients with SoS. 15 As suggested by these findings, genome-wide DNA methylation analysis in SoS patients with NSD1 defects showed hypomethylation at thousands of CpG sites.…”

Genome‐wide DNA methylation and RNA analyses enable reclassification of two variants of uncertain significance in a patient with clinical Kabuki syndrome

“…We have previously reported that patients with Kabuki syndrome have a highly sensitive and specific DNA methylation episignature detectable in the peripheral blood (Aref‐Eshghi et al, ). The DNA methylation signature of Kabuki syndrome, along with those of several other congenital conditions, has been used to generate a computational functional assay for the concurrent detection of multiple neurodevelopmental syndromes in those presenting with uncertain clinical or molecular findings (Aref‐Eshghi, Rodenhiser, et al, ). This algorithm is a multiclass predictor, trained on the DNA methylation levels of ~900 informative CpG sites across the genome for 14 conditions with specific DNA methylation episignature in the blood (details in Supporting Information Methods; Aref‐Eshghi et al, ).…”