Background The variability of Huntington’s disease phenotype could be mostly explained through the number of CAG repeats in HTT gene. However, the remaining unexplained variations may be linked to the epigenetic landscape. DNA methylation influences gene expression, embryonic development and cell fate commitment. Human induced pluripotent stem cells (hiPS) constitute an appropriate cellular model that can be exploited to mimic and recapitulate brain development.

Aims The interplay between DNA methylation and neurodegenerative disorders still remains to be unravelled. Thus, we aim to test the influence of DNA methylation changes on the in vitrodifferentiation process of HD-hiPS toward post-mitotic medium sized spiny neurons, in order to check for potential modifications in the methylation patterns.

Methods hiPS from healthy and HD subjects were induced to differentiate toward DARPP32+ neurons through a dual SMAD inhibition step that drives neural induction, BMP/TGFβ inhibition and SHH/DKK1 treatment that generate ventral telencephalic specification. DNA was isolated from selected time-points reflecting undifferentiated status (day0), neural induction and patterning (day15) and terminal differentiation (day40). Genome-wide DNA methylation was performed through meDIP-chip protocol.

Results Global CpG methylation showed statistical significant differences in the methylation percentages of HD-iPS compared to control-iPS during the differentiation process. Moreover, pair-wise comparison of controls and HD iPS allowed to identify a panel of differentially methylated regions (DMRs) during the different phases of neuronal commitment. These DMRs could be considered as unique and specifically associated to HD phenotype.

Conclusions Epigenetic modifications could play an important role in striatal differentiation, probably by regulating developmental genes. Further studies will allow to elucidate the real contribution of DNA methylation in HD pathogenesis and phenotype.