#IARC2017 – Epigenetic ‘Off Switch’ May Be Reason Frataxin Levels Low in Cells of FA Patients

New research, presented at IARC 2017, showed that the frataxin gene in cells taken from Friedreich’s ataxia patients produces very little of the frataxin protein in part due to epigenetic marks that essentially tell the gene to switch off.

These findings suggest that targeting the epigenetic remodeling of frataxin gene is a potential way of treating Friedreich’s ataxia.

Sanjay Bidichandani with the University of Oklahoma Health Sciences Center presented the study, “Epigenetic silencing in Friedreich ataxia is caused by hypermethylation of the FXN CpG island shore,” Wednesday at IARC, the International Ataxia Research Conference, taking place in Pisa, Italy, through Sept. 30.

Friedreich’s ataxia is caused by an abnormal repeat of a sequence — GAA — in the frataxin gene. This mutation decreases production of the frataxin protein, a key protein of mitochondria, the energy-producing organelles of the cell.

But how do excessive repeats impair the normal expression of the frataxin gene, and subsequently the production of the frataxin protein?

An abnormal number of repeats change the structure of the DNA molecule where the frataxin gene is located, potentially affecting gene expression in a number of ways.

One of these ways is called epigenetic silencing, in which the DNA sequence itself is not changed, but marks are added to it — epigenetic marks — that switch a gene on or off, inducing either its activation or its repression.

The researchers investigated the presence of epigenetic repressive marks by analyzing the DNA sequence of the frataxin gene and neighboring regions multiple times.

DNA regions flanking the frataxin gene were found to be highly enriched in repressive epigenetic marks — one of which is called methylation, and occurs in genetic regions known as CpG islands. Methylation is the addition of methyl groups (a chemical) to the DNA molecule, affecting the gene’s activity.

“There is a day and night difference in the methylation pattern,” Bidichandani said in his presentation, referring to a disease state and a non-disease state. “If you take out methylation you can improve frataxin levels.”

Notably, CpG islands were free of methylation in a non-disease state, and reverted from methylated to un-methylated when the frataxin gene was manipulated to move from an abnormal repeat sequence to a normal number of repeats.

This suggests that CpG islands within the frataxin gene and their methylation status are specific factors linked to Friedreich’s ataxia development.

But, Bidichandani wondered, is this finding “functionally relevant?”

To address this question, researchers analyzed this genetic region in several cell types derived from patients, and in tissues from a humanized mouse model of Friedreich’s ataxia.

All cells and tissues showed increased methylation in this CpG region.

Moreover, the magnitude and extent of methylation within the CpG islands correlated with the number of GAA repeats in the frataxin gene. Said Bidichandani, “we know that the hypermethylation is related to the repeat length.”

Researchers then targeted one of the molecular players required for DNA methylation, called DNMT3A. Decreasing the levels of DNMT3A in patient-derived cells both lowered methylation in the frataxin gene and increased the levels of frataxin protein. These same results were obtained when researchers used a chemical inhibitor of DNA methylation.

Overall, this study supports the hypothesis that methylation of the frataxin gene plays a role in the epigenetic silencing of the gene in Friedreich’s ataxia, and the potential of focusing on methylation as a possible way of treating the disease.