DNA Marks May Help Diagnose, Predict Prognosis in Fragile X, Study Suggests

Techniques that evaluate the pattern of DNA methylation — a chemical modification normally associated with gene silencing — in a portion of the FMR1 gene are feasible and highly sensitive methods to diagnose fragile X syndrome in newborns, a study suggests.

When used in newborn boys, and to a lesser extent in girls, these techniques can also be used to estimate the degree of intellectual impairments and autism features these children typically develop.

According to researchers, these methods have “the potential to open new avenues for detection of FXS [fragile X syndrome] … in newborn blood spots in both sexes and for prognostic testing in newborns and children as they develop.”

The study, “DNA Methylation at Birth Predicts Intellectual Functioning and Autism Features in Children with Fragile X Syndrome,” was published in the International Journal of Molecular Sciences.

Fragile X is caused by the excessive expansion of three nucleotides — one cytosine (C) and two guanines (G) — in a portion of the FMR1 gene. Nucleotides are the building blocks that make up the DNA sequence of all genes.

More than 200 CGG repeats in FMR1 is called a full mutation, which inactivates or silences the gene through epigenetic changes such as DNA methylation, and leads to a lack of FMRP — the protein encoded by FMR1 that is crucial for neurological development. Epigenetic changes are DNA modifications that affect gene expression — the process by which information within a gene gives rise to a functional product.

DNA methylation in a specific region of the FMR1 gene promoter, known as fragile X-related epigenetic element 2 (FREE2), has been associated with the presence of full mutations, and has been found to correlate with the degree of intellectual impairment and FMRP levels in patients of both sexes with fragile X. (A gene’s promoter is a region that controls its activity.)

Researchers in Australia investigated if different methods assessing the DNA methylation pattern of FREE2 might be useful to screen and diagnose newborns with fragile X, as well as in estimating their prognosis later in life.

They used two different techniques — methylation specific-quantitative melt analysis (MS-QMA) and EpiTYPER system — to evaluate FREE2 methylation in newborn blood spots (NBS) and dried blood spots (DBS) from 65 children and adolescents with fragile X, ages 1–16. NBS samples were collected at birth, while DBS samples were gathered during the study.

Both methods were also used to evaluate FREE2 DNA methylation in 168 NBS samples collected from infants from the general population, who served as controls. Neuropsychological assessments were done in 64 participants.

The investigators found that methylation analyses in NBS samples with both MS-QMA and EpiTYPER were able to distinguish patients with fragile X from controls with nearly 100% sensitivity and specificity. Sensitivity is a test’s ability to identify those who truly have a disease, while specificity refers to its ability to detect those who do not.

In addition, in NBS samples from boys, and in those from girls although to a lesser extent, increased DNA methylation in FREE2 correlated with greater intellectual disabilities and autism features during childhood.

FREE2 DNA methylation also correlated with levels of messenger RNA from FMR1 in NBS and DBS samples from children of both sexes. Messenger RNA is the molecule created from a gene that serves as the template for the production of a protein.

The investigators also found that DNA methylation was increased at birth and tended to decrease during childhood in girls. No significant differences in DNA methylation levels were found over time in boys.

“This study for the first time demonstrates that [FREE2 DNA methylation] analysis using both MS-QMA and the EpiTYPER system is a feasible approach for newborn screening,” the researchers wrote.

“The key novel findings were that [FREE2 DNA methylation] analysis in male, and to a lesser extent in female, infants was predictive of intellectual functioning and autism features,” they added.