Lewy body neuropathologies and SNCA gene: variants expression and splicing

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ABSTRACT Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and Lewy bodies variant of Alzheimer disease (LBV/AD) are common synucleinopathies, a group of neurodegenerative disorders that share a pathological hallmark composed of a-synuclein protein, termed Lewy bodies (LBs); however, each disease presents distinct characteristics. Genetic association studies have implicated SNCA gene in the etiology of synucleinopathies. Interestingly, SNCA variants defining the PD GWA hits are distinct from those that were significantly associated with DLB. However, the precise causal variants and the molecular mechanisms through which they exert their pathogenic effects are yet to be explored. Our overarching goal is to identify the common and distinct causal variants underlying the etiology and the heterogeneity of synucleinopathies, and to uncover the underpinning mechanisms that mediate their effects. It has been well-known that SNCA expression levels play a key role in the development of these diseases, supporting the premise for this study that impaired regulation of SNCA gene expression is a major pathogenic mechanism of synucleinopathies. We hypothesize that noncoding genetic variants in SNCA locus exert common and/or neuronal type-specific effects on the dysregulation of SNCA expression via multiple mechanisms such as, epigenetic, transcriptional and post transcriptional, which in turn plays a role in the genetic etiology and heterogeneity of synucleionopathies. To investigate the SNCA genome, epigenome and expression in the context of synucleinopathies, we will combine discovery analyses in single neurons isolated from brain tissues of the same subjects for all three aims, and validation approaches using hiPSC-derived neuronal models. Aim 1 will define neuronal regulatory elements in SNCA region that are common and specific to the different synucleinopathies, brain regions, and neuronal types. We’ll use NeuN+/- nuclei from affected and unaffected human brain tissues to determine chromatin accessibility, integrate with publicly available human epigenome datasets, and validate using isogenic hiPSC- derived neurons in which the putative regulatory elements will be systematically deleted. Aim 2 will discover noncoding regulatory variants and haplotypes in SNCA locus using SMRT-seq (PacBio) and evaluate their associations with SNCA-mRNA in neuronal nuclei measured by nCounter (NanoString). The strongest candidate variants will be validated using isogenic hiPSC-derived neuronal models edited by CRISPR/Cas9. In Aim 3 we’ll characterize differences in neuronal DNA-methylation profiles within SNCA promoter/intron 1 region, and their effects on SNCA-mRNA levels. The role of DNA-methylation in regulating SNCA expression and the consequences on reversing disease related cellular perturbations will be validated by DNA-methylation editing using CRISPR/dCas9-based tool in isogenic hiPSC-derived neurons. Our study will decipher mechanisms of SNCA dysregulation that mediate the susceptibility to the different synucleinopathies. The results are translational for both new genetic biomarkers and therapeutic targets for fine-tuning SNCA expression to normal physiological levels.