Convergence of miRNA Expression Profiling, α-Synuclein Interacton and GWAS in Parkinson's Disease

miRNAs were recently implicated in the pathogenesis of numerous diseases, including neurological disorders such as Parkinson's disease (PD). miRNAs are abundant in the nervous system, essential for efficient brain function and play important roles in neuronal patterning and cell specification. To further investigate their involvement in the etiology of PD, we conducted miRNA expression profiling in peripheral blood mononuclear cells (PBMCs) of 19 patients and 13 controls using microarrays. We found 18 miRNAs differentially expressed, and pathway analysis of 662 predicted target genes of 11 of these miRNAs revealed an over-representation in pathways previously linked to PD as well as novel pathways. To narrow down the genes for further investigations, we undertook a parallel approach using chromatin immunoprecipitation-sequencing (ChIP-seq) analysis to uncover genome-wide interactions of α-synuclein, a molecule with a central role in both monogenic and idiopathic PD. Convergence of ChIP-seq and miRNomics data highlighted the glycosphingolipid biosynthesis and the ubiquitin proteasome system as key players in PD. We then tested the association of target genes belonging to these pathways with PD risk, and identified nine SNPs in USP37 consistently associated with PD susceptibility in three genome-wide association studies (GWAS) datasets (0.46≤OR≤0.63) and highly significant in the meta-dataset (3.36×10−4<p<1.94×10−3). A SNP in ST8SIA4 was also highly associated with PD (p = 6.15×10−3) in the meta-dataset. These findings suggest that several miRNAs may act as regulators of both known and novel biological processes leading to idiopathic PD

Genetic variants in RBFOX3 are associated with sleep latency

Time to fall asleep (sleep latency) is a major determinant of sleep quality. Chronic, long sleep latency is a major characteristic of sleep-onset insomnia and/or delayed sleep phase syndrome. In this study we aimed to discover common polymorphisms that contribute to the genetics of sleep latency. We performed a meta-analysis of genome-wide association studies (GWAS) including 2 572 737 single nucleotide polymorphisms (SNPs) established in seven European cohorts including 4242 individuals. We found a cluster of three highly correlated variants (rs9900428, rs9907432 and rs7211029) in the RNA-binding protein fox-1 homolog 3 gene (RBFOX3) associated with sleep latency (P-values=5.77 × 10-08, 6.59 × 10- 08 and 9.17 × 10- 08). These SNPs were replicated in up to 12 independent populations including 30 377 individuals (P-values=1.5 × 10- 02, 7.0 × 10- 03 and 2.5 × 10- 03; combined meta-analysis P-values=5.5 × 10-07, 5.4 × 10-07 and 1.0 × 10-07). A functional prediction of RBFOX3 based on co-expression with other genes shows that this gene is predominantly expressed in brain (P-value=1.4 × 10-316) and the central nervous system (P-value=7.5 × 10- 321). The predicted function of RBFOX3 based on co-expression analysis with other genes shows that this gene is significantly involved in the release cycle of neurotransmitte

Correction: Gene Expression Differences in Peripheral Blood of Parkinson's Disease Patients with Distinct Progression Profiles.

[This corrects the article DOI: 10.1371/journal.pone.0157852.]

Selected genes investigated by qPCR in PD patients-derived samples.

<p>-ΔCts plotted for 10 genes chosen for qPCR validation in cDNA obtained from 16 patients with either slow or rapid progression of the disease. Data is expressed as means ± SD of triplicates. T-test was used for statistical analysis with significance level of p<0.05. *p<0.05; **p<0.01; ***p<0.0005.</p

Nuclear localization and phosphorylation modulate pathological effects of α-synuclein

Alpha-synuclein (aSyn) is a central player in Parkinson's disease (PD) but the precise molecular mechanisms underlying its pathogenicity remain unclear. It has recently been suggested that nuclear aSyn may modulate gene expression, possibly via interactions with DNA. However, the biological behavior of aSyn in the nucleus and the factors affecting its transcriptional role are not known. Here, we investigated the mechanisms underlying aSyn-mediated transcription deregulation by assessing its effects in the nucleus and the impact of phosphorylation in these dynamics. We found that aSyn induced severe transcriptional deregulation, including the downregulation of important cell cycle-related genes. Importantly, transcriptional deregulation was concomitant with reduced binding of aSyn to DNA. By forcing the nuclear presence of aSyn in the nucleus (aSyn-NLS), we found the accumulation of high molecular weight aSyn species altered gene expression and reduced toxicity when compared to the wild-type or exclusively cytosolic protein. Interestingly, nuclear localization of aSyn, and the effect on gene expression and cytotoxicity, was also modulated by phosphorylation on serine 129. Thus, we hypothesize that the role of aSyn on gene expression and, ultimately, toxicity, may be modulated by the phosphorylation status and nuclear presence of different aSyn species. Our findings shed new light onto the subcellular dynamics of aSyn and unveil an intricate interplay between subcellular location, phosphorylation, and toxicity, opening novel avenues for the design of future strategies for therapeutic intervention in PD and other synucleinopathies

Clinical characterization of the cohort.

<p>Clinical characterization of the cohort.</p

Selected genes investigated in a LUHMES/MPP⁺ cell model of PD.

<p><b>(A)</b> LUHMES cells treated with solvent (DMSO) or 2.5μM MPP⁺ stained for Tyrosine Hydroxylase (TH), TUJ1 and nucleus or <b>(B)</b> observed in bright field, showed robust loss of neurite integrity upon MPP⁺ treatment. <b>(C)</b> Cell viability analysis assessed by ToxiLigh assay revealed a significant increase of adenylate kinase content in the supernatants of MPP⁺ treated cells. <b>(D)</b> -Δcts plotted for seven genes chosen for validation using D8 differentiated LUHMES cells exposed to 2.5μm MPP⁺. <b>(E)</b> Correlation between fold-change expression values obtained in LUHMES/MPP⁺ model and PD patients. Data is expressed as means ± SD of triplicate samples. T-test was used for statistical analysis with significance level of p<0.05. *p<0.05; **p<0.01. Scale bar 100 μm.</p

Hierarchical clustering of genes detected as differentially expressed in rapid <i>versus</i> slow progression PD patients.

<p>Classification based on expression signals of the bootstrapping t-test-detected genes resulted in only five mis-classified slow and 11 mis-classified rapid progression patients. The color bar denotes z-score adjusted expression values, green used for lower expression and purple for higher expression levels. Eucledian distance and average linkage methods were used.</p

Selected genes investigated by qPCR in PD patients-derived samples.

<p>-ΔCts plotted for 10 genes chosen for qPCR validation in cDNA obtained from 16 patients with either slow or rapid progression of the disease. Data is expressed as means ± SD of triplicates. T-test was used for statistical analysis with significance level of p<0.05. *p<0.05; **p<0.01; ***p<0.0005.</p