Hemispheric asymmetry in the human brain and in Parkinson's disease is linked to divergent epigenetic patterns in neurons [Bisulfite_Seq_replication_cohort]

Background Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in isolated prefrontal cortex neurons from control and PD brain hemispheres. DNA methylation is fine-mapped at enhancers and promoters, genome-wide, by targeted bisulfite sequencing in two independent sample cohorts. Results We find that neurons of the human prefrontal cortex exhibit hemispheric differences in DNA methylation. Hemispheric asymmetry in neuronal DNA methylation patterns is largely mediated by differential CpH methylation, and chromatin conformation analysis finds that it targets thousands of genes. With aging, there is a loss of hemispheric asymmetry in neuronal epigenomes, such that hemispheres epigenetically converge in late life. In neurons of PD patients, hemispheric asymmetry in DNA methylation is greater than in controls and involves many PD risk genes. Epigenetic, transcriptomic, and proteomic differences between PD hemispheres correspond to the lateralization of PD symptoms, with abnormalities being most prevalent in the hemisphere matched to side of symptom predominance. Hemispheric asymmetry and symptom lateralization in PD is linked to genes affecting neurodevelopment, immune activation, and synaptic transmission. PD patients with a long disease course have greater hemispheric asymmetry in neuronal epigenomes than those with a short disease course. Conclusions Hemispheric differences in epigenetic gene regulation are prevalent in neurons and may affect the progression and symptoms of PD. Overall design: To determine whether DNA methylation could contribute to hemisphere differences in neuronal function in the healthy brain and PD, we comprehensively fine-mapped DNA methylation at enhancers and promoters, genome-wide, in neurons isolated from the left and right prefrontal cortex of PD patients and controls (57 individuals: 31 healthy controls (30 individuals with both left and right brain hemispheres, 1 with only left) and 26 PD patients (24 patients with both left and right brain hemispheres, 1 with only left, 1 with only right)). We first isolated neuronal nuclei using an established antibody (NeuN+) and flow cytometry-based approach. We then fine-mapped DNA methylation at enhancer elements using a targeted bisulfite sequencing strategy, known as bisulfite padlock probe sequencing.