19th Annual Child Health Research Days

RBC Convention Center

Oct. 24 & 26, 2023


#36 Genome-wide DNA methylation analysis of the brain in Rett Synrdome patients

Daniel Kroft, University of Manitoba; Kimia Sheikholeslami, University of Toronto; Shayan Amiri, University of Manitoba; Carl Olson, University of Manitoba; Marc Del Bigio, Unviersity of Manitoba; Victoria Siu, Western University; Trevor Pemberton, University of Manitoba; Mojgan Rastegar, University of Manitoba


Rett Syndrome (RTT) is an X-linked neurodevelopment disorder that typically presents in the first two years of life, and is one of the most common causes of intellectual disability in females. Methyl-CpG-binding protein 2 (MECP2) has emerged as the gene responsible for this phenotype, with several hundred unique mutations currently known. The MeCP2 protein functions as a reader of DNA methylation, and contributes to the process of gene silencing. Due to its relationship with DNA methylation, we studied whether RTT was accompanied by a change in DNA methylation patterns in the brain.


Tissue samples from four brain regions (cortex, hippocampus, amygdala, and cerebellum) were collected from three RTT patients with different mutations and three age-/sex-matched control participants. DNA was extracted from each sample and DNA methylation was measured using Illumina’s Infinium MethylationEPIC BeadChip. The resultant data was analyzed using the RnBeads package for the R statistical software, which performs data normalization as well as multi-dimensional scaling, cluster, and differential methylation analyses.


Our results show a small but highly significant trend of hypomethylation of CpG sites in patients compared to controls (p < 0.001). A clear difference was also seen between methylation patterns in promoter regions of patients and controls across brain regions. However, permutation testing revealed several marginally significant (p < 0.10) differential methylation regions within the cortex, amygdala, and cerebellum.


The clear separation of patients and controls observed in the differential methylation analysis suggests that mutations in MeCP2 affect not only the reading of methylation, but also DNA methylation itself. Further studies with larger sample sizes will be required to validate and expand upon these findings. This work is supported by funding from International Rett Syndrome Foundation (IRSF), Ontario Rett Syndrome Association (ORSA), and Children’s Research Institute of Manitoba (CHRIM) to MR.