Epigenomic analysis of Parkinson’s disease neurons identifies TET2 loss as neuroprotective [TET2i_Bisulfite_Padlock_seq]

Epigenetic control of enhancers is centrally involved in modifying neuronal functions and may contribute to Parkinson's disease (PD) pathogenesis. Here, we comprehensively profile DNA methylation at enhancers genome-wide in neurons of 57 PD patients and 48 healthy individuals. There is a widespread increase in cytosine modifications at enhancers in PD neurons, which is partly due to elevated hydroxymethylation levels. Epigenetic dysregulation of enhancers in PD converge on transcriptional abnormalities affecting neuronal signaling and immune activation pathways. In particular, PD patients exhibit an epigenetic and transcriptional upregulation of TET2, a master-regulator of cytosine modification status. TET2 inactivation in a neuronal cell line enriches for cytosine modification changes that are reciprocal to those observed in PD neurons. Furthermore, Tet2 inactivation in mice fully prevents dopaminergic neuronal loss in the substantia nigra induced by prior inflammation. Tet2 loss in mice also attenuates transcriptional immune responses to an inflammatory trigger. Thus, widespread epigenetic dysregulation of enhancers in PD neurons may, in part, be mediated by increased TET2 expression. Decreased Tet2 activity is neuroprotective, in vivo, and may be a novel therapeutic target for PD. To explore the capacity for TET2 to induce epigenetic changes at cytosine sites associated with PD in neurons, we depleted TET2 mRNA levels by siRNA in an in vitro neuronal cell model, SH-SY5Y cells. DNA isolated from TET2 inhibited and non-targeting control were then used for targeted bisulfite deep sequencing (16 samples: 8 TET2 siRNA, 8 non-targeting control).