The genetic defect in
Friedreich's ataxia (FRDA) is the hyperexpansion of a GAA•TTC triplet in the first intron of the FXN gene, encoding the essential
mitochondrial protein frataxin.
Histone post-translational modifications near the expanded repeats are consistent with
heterochromatin formation and consequent FXN gene silencing. Using a newly developed human neuronal cell model, derived from patient-induced pluripotent stem cells, we find that
2-aminobenzamide histone deacetylase (
HDAC) inhibitors increase FXN
mRNA levels and
frataxin protein in FRDA neuronal cells. However, only compounds targeting the class I HDACs 1 and 3 are active in increasing FXN
mRNA in these cells. Structural analogs of the active
HDAC inhibitors that selectively target either HDAC1 or HDAC3 do not show similar increases in FXN
mRNA levels. To understand the mechanism of action of these compounds, we probed the kinetic properties of the active and inactive inhibitors, and found that only compounds that target HDACs 1 and 3 exhibited a slow-on/slow-off mechanism of action for the HDAC
enzymes. HDAC1- and HDAC3-selective compounds did not show this activity. Using
siRNA methods in the FRDA neuronal cells, we show increases in FXN
mRNA upon silencing of either HDACs 1 or 3, suggesting the possibility that inhibition of each of these class I HDACs is necessary for activation of FXN
mRNA synthesis, as there appears to be redundancy in the silencing mechanism caused by the GAA•TTC repeats. Moreover, inhibitors must have a long residence time on their target
enzymes for this activity. By interrogating microarray data from neuronal cells treated with inhibitors of different specificity, we selected two genes encoding
histone macroH2A (H2AFY2) and Polycomb group ring finger 2 (PCGF2) that were specifically down-regulated by the inhibitors targeting HDACs1 and 3 versus the more selective inhibitors for further investigation. Both genes are involved in transcriptional repression and we speculate their involvement in FXN gene silencing. Our results shed light on the mechanism whereby
HDAC inhibitors increase FXN
mRNA levels in FRDA neuronal cells.