Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing

Abstract

Synucleinopathies are mostly sporadic neurodegenerative disorders of partly unexplained aetiology, and include Parkinson’s disease (PD) and multiple system atrophy (MSA). We have further investigated our recent finding of somatic SNCA (α-synuclein) copy number variants (CNVs, specifically gains) in synucleinopathies, using Fluorescent in-situ Hybridisation for SNCA, and single-cell whole genome sequencing for the first time in a synucleinopathy. In the cingulate cortex, mosaicism levels for SNCA gains were higher in MSA and PD than controls in neurons (> 2% in both diseases), and for MSA also in non-neurons. In MSA substantia nigra (SN), we noted SNCA gains in > 3% of dopaminergic (DA) neurons (identified by neuromelanin) and neuromelanin-negative cells, including olig2-positive oligodendroglia. Cells with CNVs were more likely to have α-synuclein inclusions, in a pattern corresponding to cell categories mostly relevant to the disease: DA neurons in Lewy-body cases, and other cells in the striatonigral degeneration-dominant MSA variant (MSA-SND). Higher mosaicism levels in SN neuromelanin-negative cells may correlate with younger onset in typical MSA-SND, and in cingulate neurons with younger death in PD. Larger sample sizes will, however, be required to confirm these putative findings. We obtained genome-wide somatic CNV profiles from 169 cells from the substantia nigra of two MSA cases, and pons and putamen of one. These showed somatic CNVs in ~ 30% of cells, with clonality and origins in segmental duplications for some. CNVs had distinct profiles based on cell type, with neurons having a mix of gains and losses, and other cells having almost exclusively gains, although control data sets will be required to determine possible disease relevance. We propose that somatic SNCA CNVs may contribute to the aetiology and pathogenesis of synucleinopathies, and that genome-wide somatic CNVs in MSA brain merit further study.

Neurophysiological Biomarkers of Parkinson’s Disease

“…There is also evidence at the genetic level that the cingulate cortex is an important region in PD. Perez-Rodriguez et al [35] found somatic copy number variant gains (gene duplicates or triplicates) of SNCA, the gene encoding alpha-synuclein, in the cingulate cortex. These post-zygotic mutations were >2% higher in neurons in the cingulate cortex of patients diagnosed with alpha-synucleinopathies than healthy controls.…”

Patient-Derived Midbrain Organoids to Explore the Molecular Basis of Parkinson's Disease

“…Recent population studies have yielded PD heritability rates ranging between 0.22 and 0.27 ( 32 , 35 ), suggesting that a majority of cases may be due to the interaction of genetic and environmental factors [rural living and pesticide exposure are well-known risk factors, while tobacco, coffee, and moderate alcohol consumption may be protective, see review ( 36 )], and to stochastic processes. Mosaicism may for instance be a non-negligible contributor to the pathogenesis of sporadic PD ( 37 ), as changes in copy numbers of the SCNA gene have been observed in patient SN DA neurons ( 38 ). Nevertheless, only a minor fraction of the disease's heritability (16–36% depending on its prevalence) can be explained by the most recently identified risk loci ( 32 ), indicating that much of the “missing heritability” remains yet to be uncovered.…”

Network Analysis and Human Single Cell Brain Transcriptomics Reveal Novel Aspects of Alpha-Synuclein (SNCA) Biology

“…The role and contributions of SNCA in different neurodegenerative disorders remains partially understood. SNCA mutations are only identified in a minority of PD and other synucleinopathy patients (39), with most synucleinopathy cases occurring in the absence of defined mutations or in the context of interacting polygenetic, epigenetic, and environmental contributions to synucleinopathy risk (6,7). In this study, single-cell analysis reveals clear variations in SNCA expression by cell type in human ACC and MTG samples, with striking differences in SNCA expression by excitatory versus inhibitory neurons and other cell types.…”