DNA methylation in neurodevelopmental disorders Epigenetics as a paradigm shift in genome diagnostics and beyond

Neurodevelopmental disorders (NDDs), including intellectual disability, autism spectrum disorder, and epilepsy, are a diverse group of conditions affecting central nervous system development. Despite advances in next-generation sequencing, many patients remain without a molecular diagnosis or receive variants of uncertain significance (VUS), highlighting the need for complementary diagnostic approaches.
This thesis investigates the role of DNA methylation (DNAm), an epigenetic modification that regulates gene activity without altering the DNA sequence, in improving the diagnosis and understanding of NDDs. Disease-specific DNAm patterns, known as episignatures, can serve as biomarkers for pathogenic variants and provide insight into underlying disease mechanisms.
We studied episignatures in disorders affecting the ubiquitination pathway (including TRIP12 and USP7), copy number variations (CNVs), and fetal alcohol syndrome (FAS). Distinct and reproducible episignatures were identified across these conditions, supporting their diagnostic utility. Importantly, episignatures were also detected in FAS, a non-genetic condition, suggesting that environmental exposures can also leave stable epigenetic marks.
In addition, we explored long-read Nanopore sequencing as a method to simultaneously detect genetic variants and DNAm changes, confirming its potential for integrated molecular diagnostics. Finally, patient-derived induced pluripotent stem cells (iPSCs) were generated to model disease mechanisms at the cellular level and to provide a platform for future therapeutic research.
Together, these findings demonstrate that DNA methylation profiling is a powerful tool for improving diagnosis and deepening our understanding of the molecular basis of neurodevelopmental disorders.