Author(s): Sanjay Bidichandani, University of Oklahoma Health Sciences Center; Layne N. Rodden, University of Oklahoma Health Sciences Center; Kaitlyn M. Gilliam, University of Oklahoma Health Sciences Center; Christina Lam, University of Oklahoma Health Sciences Center; David R. Lynch, The Children’s Hospital of Philadelphia //

ABSTRACT: Research objective: Friedreich ataxia (FRDA) is typically caused by homozygosity for an expanded GAA triplet-repeat in intron 1 of the FXN gene. The expanded repeat induces repressive histone changes and DNA hypermethylation, which result in epigenetic silencing and FXN transcriptional deficiency. A class I histone deacetylase inhibitor (HDACi-109) reactivates the silenced FXN gene, although with considerable inter-individual variability, which remains etiologically unexplained. Because HDAC inhibitors work by reversing epigenetic silencing, we hypothesized that epigenetic heterogeneity among patients may help to explain this inter-individual variability.  Methods: Fresh PBMCs were isolated from a prospective cohort of 50 FRDA patients. Somatic epigenetic heterogeneity was assessed via bisulfite deep sequencing, a highly quantitative measurement of DNA hypermethylation with single molecule resolution. Analysis of 1000 individual molecules per patient revealed the prevalence of unmethylated, partially methylated, and fully methylated FXN epialleles. PBMCs from this cohort were treated with HDACi-109, and gene reactivation was measured by RT-qPCR.  Results: HDACi-109 significantly increased FXN transcript to levels seen in asymptomatic heterozygous carriers, albeit with the expected inter-individual variability. Response to HDACi-109 correlated significantly with the prevalence of unmethylated and partially methylated FXN molecules, supporting the model that FXN reactivation involves a proportion of genes that are amenable to correction in non-dividing somatic cells, and that heavily methylated FXN molecules are relatively resistant to reactivation.   Conclusion: FXN reactivation is a promising therapeutic strategy in FRDA, and inter-individual variability in drug response is explained, at least in part, by somatic epigenetic heterogeneity.

Source of Funding: Muscular Dystrophy Association; Friedreich Ataxia Research Alliance