Somatic copy number gains of α-synuclein (SNCA) in Parkinson’s disease and multiple system atrophy brains

Abstract

The α-synuclein protein, encoded by SNCA, has a key role in the pathogenesis of Parkinson's disease and other synucleinopathies. Although usually sporadic, Parkinson's disease can result from inherited copy number variants in SNCA and other genes. We have hypothesized a role of somatic SNCA mutations, leading to mosaicism, in sporadic synucleinopathies. The evidence for mosaicism in healthy and diseased brain is increasing rapidly, with somatic copy number gains of APP reported in Alzheimer's brain. Here we demonstrate somatic SNCA copy number gains in synucleinopathies (Parkinson's disease and multiple system atrophy), focusing on substantia nigra. We selected sporadic cases with relatively young onset or short disease duration, and first excluded high level copy number variant mosaicism by DNA analysis using digital PCR for SNCA, and/or customized array comparative genomic hybridization. To detect low level SNCA copy number variant mosaicism, we used fluorescent in situ hybridization with oligonucleotide custom-designed probes for SNCA, validated on brain and fibroblasts with known copy number variants. We determined SNCA copy number in nigral dopaminergic neurons and other cells in frozen nigra sections from 40 cases with Parkinson's disease and five with multiple system atrophy, and 25 controls, in a blinded fashion. Parkinson's disease cases were significantly more likely than controls to have any SNCA gains in dopaminergic neurons (P = 0.0036), and overall (P = 0.0052). The average proportion of dopaminergic neurons with gains in each nigra was significantly higher in Parkinson's disease than controls (0.78% versus 0.45%; P = 0.017). There was a negative correlation between the proportion of dopaminergic neurons with gains and onset age in Parkinson's disease (P = 0.013), but not with disease duration, or age of death in cases or controls. Cases with tremor at onset were less likely to have gains (P = 0.035). All multiple system atrophy cases had gains, and the highest levels in dopaminergic neurons were in two of these cases (2.76%, 2.48%). We performed selective validation with different probes after dye swapping. All three control probes used showed minimal or no gains (≤0.1% in dopaminergic neurons). We also found occasional SNCA gains in frontal neurons of cases with Parkinson's disease, and the putamen of one multiple system atrophy case. We present evidence of somatic SNCA gains in brain, more commonly in nigral dopaminergic neurons of Parkinson's disease than controls, negatively correlated with onset age, and possibly commonest in some multiple system atrophy cases. Somatic SNCA gains may be a risk factor for sporadic synucleinopathies, or a result of the disease process.

Seeded propagation of α‐synuclein aggregation in mouse brain using protein misfolding cyclic amplification

“…Most cases of these diseases are considered as sporadic, but some cases can be genetically triggered by duplication or triplication of the a-syn-encoding (SNCA) gene, leading to constitutive overexpression of the protein, or by mutations in the N-terminal region of the protein, which favor its oligomerization and aggregation (A30P, E46K, or A53T, for instance) (1). Evidence of somatic SNCA gains in brain, more commonly in nigral dopaminergic neurons of PD than in controls, and possibly commonest in some MSA cases, was also recently described by Mokretar et al (2), suggesting that this may be a risk factor for sporadic synucleinopathies or, alternatively, a result of the disease process.…”

The Role of Lipids in the Initiation of α-Synuclein Misfolding

“…This simplified scenario for initial aggregate formation determined by a low lipid/α-syn ratio as well as altered concentrations of α-syn lipid−bound and α-syn free could explain several PD-associated findings, like the α-syn-dosage effect for the development of PD. Increased α-syn expression levels by genetic locus duplication/triplication, variabilities in SNCA-promoter region REP1 or somatic copy number gains of α-syn all demonstrate the close relation of α-syn concentration and PD age of onset (Singleton et al, 2003;Chartier-Harlin et al, 2004;Maraganore et al, 2006;Fuchs et al, 2008;Mokretar et al, 2018). The lipid/α-syn ratio is likely to be lowered by elevated levels of α-syn at the synapse, thereby increasing the chance for lipid-induced spontaneous aggregation events.…”

Newest Methods for Detecting Structural Variations

“…Since epigenetic information is simultaneously obtained with native long-read sequencing, the preferred DNA source in the context of neurodegenerative diseases would be affected brain tissue, if available, as demonstrated for the diagnosis of brain tumors [86]. Using brain tissue would also inform us about the presence and potential impact of mosaicism [12]. This initial SVdiscovery phase would be followed by genotyping larger cohorts using (existing) short-read data, as such generating a comprehensive SV catalog.…”

“…Unexplained heritability in complex diseases such as AD might be partially attributed to unnoticed SVs. In addition, somatic and de novo SVs can potentially explain a proportion of genetically unexplained sporadic patients [11,12].…”