DNA Methylation at Birth Predicts Intellectual Functioning and Autism Features in Children with Fragile X Syndrome

Abstract

Fragile X syndrome (FXS) is a leading single-gene cause of intellectual disability (ID) with autism features. This study analysed diagnostic and prognostic utility of the Fragile X-Related Epigenetic Element 2 DNA methylation (FREE2m) assessed by Methylation Specific-Quantitative Melt Analysis and the EpiTYPER system, in retrospectively retrieved newborn blood spots (NBS) and newly created dried blood spots (DBS) from 65 children with FXS (~2–17 years). A further 168 NBS from infants from the general population were used to establish control reference ranges, in both sexes. FREE2m analysis showed sensitivity and specificity approaching 100%. In FXS males, NBS FREE2m strongly correlated with intellectual functioning and autism features, however associations were not as strong for FXS females. Fragile X mental retardation 1 gene (FMR1) mRNA levels in blood were correlated with FREE2m in both NBS and DBS, for both sexes. In females, DNAm was significantly increased at birth with a decrease in childhood. The findings support the use of FREE2m analysis in newborns for screening, diagnostic and prognostic testing in FXS.

Parental Reports on Early Autism Behaviors in Their Children with Fragile X Syndrome as a Function of Infant Feeding

“…The methylation silencing and mosaicism status of the FMR1 gene in the FXS participants in this study are not known. DNA methylation status of the CGG repeats in the FMR1 gene promoter at birth is predictive of later intellectual function and autism features [ 45 ]. The majority of males with FXS express some FMR1 mRNA and this incomplete silencing of the promoter is associated with increased autistic features [ 46 , 47 , 48 , 49 ], In males, full mutation FXS with complete or incomplete methylation silencing of the FMR1 gene is associated with increased inappropriate speech on the ABC-C sub-scale compared to the FXS group mosaic for pre- and full mutation alleles, and mosaicism in either sex is associated with less maladaptive behaviors [ 50 , 51 ].…”

Variable Expressivity in Fragile X Syndrome: Towards the Identification of Molecular Characteristics That Modify the Phenotype

“…Hypermethylation of the CpG island generates transcriptional silencing of the FMR1 gene. 23 As a consequence, the Fragile Mental Retardation Protein (FMRP), codified by the FMR1 gene, is not produced 24 and in turn, the absence or low expression of FMRP causes FXS. CGG tract repetition expansion in the untranslated region (UTR) of exon 1 in the FMR1 gene generates instability of that region during the replication process, inducing size mosaicism, which is defined as the presence of premutation and mutation alleles in several cells.…”

“…Hypermethylation of the CpG island generates transcriptional silencing of the FMR1 gene. 23 As a consequence, the Fragile Mental Retardation Protein (FMRP), codified by the FMR1 gene, is not produced 24 and in turn, the absence or low expression of FMRP causes FXS.…”

“… 26 Furthermore, longitudinal studies in women with FXS have shown that levels of mRNA transcribed from FMR1 decrease significantly with age. 23 Complicating even more the behavior of mDNA and FXS, it has been found that in premutation alleles, a considerable number of cells have mDNA. 27 The variation between methylation states of the CpG island and nearby regions among different cells and tissue of the same person is known as methylation mosaicism.…”

Paternal retraction of a fragile X allele to normal size, showing normal function over two generations

“…The clinical and molecular assessments were completed at the Murdoch Children's Research Institute, and the DNA methylation and FMR1 mRNA analysis reference data were analyzed previously as part of the FREE FX study (Kraan et al, 2020), with approval from The Royal-Children's Hospital Human Research Ethics Committee (Reference numbers: HREC 34227, HREC 33066, and HREC/13/RCHM/24).…”