Somatic SNCA Gene Gains in Glia Drive Multiple System Atrophy

Multiple system atrophy is one of the most ruthless disorders in neurology, a rare and rapidly progressive condition that strips away autonomic control, movement and balance, typically claiming life within a decade of the first symptom. Unlike Parkinson’s disease and dementia with Lewy bodies, which are dominated by neuronal protein aggregates, multiple system atrophy carries a unique signature: glial cytoplasmic inclusions, dense clumps of alpha-synuclein protein that accumulate inside oligodendrocytes, the myelin-producing support cells of the brain. Despite decades of study, the root cause of the disease has remained stubbornly obscure. It shows no clear familial clustering, heritability is estimated below seven percent, and no major reproducible inherited risk factors have been confirmed. Now a team at UCL Queen Square Institute of Neurology has uncovered a compelling clue hiding not in the inherited genome, but in the somatic genomes of individual brain cells.

The researchers, led by Caoimhe Morley and Christos Proukakis, built on their earlier finding that somatic copy number gains of SNCA, the gene encoding alpha-synuclein, occur in the brains of people with synucleinopathies. In their new study, published in Acta Neuropathologica, they asked whether these gains arise specifically in oligodendrocytes, whether they cluster in the brain regions most damaged by the disease, and whether they correlate with the pathological inclusions that define it. Their strategy hinged on a technically demanding hybrid method that combines fluorescent in situ hybridisation, or FISH, with immunofluorescence, applied not to tissue sections but to suspensions of individual nuclei isolated from fresh-frozen post-mortem brain tissue.

The methodological choice matters. Working on sections makes it nearly impossible to reliably detect copy number losses, because slicing the tissue can truncate FISH signals and mimic a missing gene copy. Isolating nuclei eliminates this artefact while preserving alpha-synuclein inclusions, which in multiple system atrophy often sit in perinuclear or nuclear positions and remain attached to the nuclei during preparation. Each nucleus could therefore be interrogated on several axes simultaneously: the number of SNCA copies it carried, whether it belonged to the oligodendrocyte lineage as marked by the transcription factor SOX10, and whether it harboured an alpha-synuclein inclusion. The team analysed tissue from the putamen, cerebellum and substantia nigra of 13 cases with the striatonigral degeneration subtype, 12 cases with the olivopontocerebellar atrophy subtype, and 15 controls from the Queen Square Brain Bank.

The results were striking. Somatic SNCA copy number variants, both gains and losses, were significantly more frequent in multiple system atrophy oligodendrocytes than in controls. Gains were enriched more than threefold, appearing in 6.3 percent of SOX10-positive oligodendrocytes compared with 2.0 percent in controls, while losses were present in 12.5 percent versus 7.4 percent, with both differences highly significant. Crucially, the gains were not randomly distributed. They concentrated in the regions preferentially devastated by each disease subtype: the putamen in striatonigral degeneration and the cerebellum in olivopontocerebellar atrophy, along with the substantia nigra in both. The analysis also showed that CNVs were preferentially enriched at the SNCA locus itself; a chromosome 7 reference probe displayed relative genomic stability, indicating a locus-specific phenomenon rather than wholesale genomic chaos.

The single-cell correlations provide the study’s most provocative evidence. In the preferentially affected region of each subtype, oligodendrocytes carrying a somatic SNCA gain were more than twice as likely to contain an alpha-synuclein inclusion as their neighbours with a normal copy number, an effect that vanished in less affected regions. At the regional level, the frequency of oligodendrocyte gains correlated significantly with the overall burden of glial inclusions. This dovetails with established biology: people who inherit extra copies of SNCA develop parkinsonism driven by chronic alpha-synuclein overproduction, with duplications causing later-onset disease and triplications causing aggressive early-onset forms. Mouse models engineered to overexpress human alpha-synuclein specifically in oligodendrocytes develop inclusion-like pathology, demyelination and neuroinflammation. The new data suggest that the same dosage logic operates cell by cell in the human disease brain, with gains locally pushing intracellular alpha-synuclein toward the aggregation threshold.

Perhaps the most clinically resonant finding is a correlation between copy number gain burden and disease onset. Cases carrying a higher average proportion of oligodendrocyte SNCA gains developed symptoms significantly earlier, with a Spearman correlation coefficient of minus 0.45 and a p-value of 0.03. No such relationship existed for gains in non-oligodendroglial cells or for losses. Moreover, within individual cases, the level of gains correlated across brain regions and between oligodendrocytes and other cell populations, hinting that some patients carry an intrinsic, case-wide propensity for SNCA mosaicism. This raises the possibility of an early clonal event, arising during development, that seeds descendant cells across multiple regions and predisposes the brain to alpha-synuclein aggregation decades later. Distinguishing this from a generalised susceptibility to SNCA instability will require deep single-cell whole-genome sequencing, which is only now approaching the necessary resolution.

The study also reported, for the first time in multiple system atrophy, somatic SNCA losses. These were elevated in both oligodendrocytes and other cells but told a different story. They showed no clear regional predilection matching each subtype’s pathology, associated with inclusions only in the substantia nigra, and showed no correlation with age of onset or disease duration. That pattern argues against a primary causal role. Unlike gains, germline losses of SNCA have never been linked to synucleinopathies, and mice lacking alpha-synuclein do not develop relevant neurodegenerative phenotypes. The authors instead propose that losses may arise secondarily as the disease progresses, through the mis-repair of DNA damage.

That hypothesis gains weight from the study’s final arm, an examination of DNA double-strand breaks using immunofluorescence for gamma H2AX, the phosphorylated histone that marks sites of breakage and repair. Across the sampled regions, the proportion of gamma H2AX-positive cells was significantly higher in multiple system atrophy than in controls, 4.9 versus 2.5 percent overall, and nearly fourfold higher within oligodendrocytes. The signal was stronger in the preferentially affected regions and, strikingly, present in 22.2 percent of inclusion-bearing cells versus 14.9 percent of inclusion-free ones. This mirrors recent reports in Lewy body diseases linking DNA damage to alpha-synuclein pathology. Because post-mitotic brain cells repair double-strand breaks through the error-prone non-homologous end joining pathway, unrepaired or mis-repaired breaks can generate deletions, potentially including SNCA itself. Yet the authors caution that more than three-quarters of inclusion-positive cells showed no evidence of breaks, and the temporal sequence of damage, aggregation and copy number change remains unresolved.

The findings do not paint copy number variation as a sole cause. Most inclusion-bearing oligodendrocytes carried a normal SNCA copy number, and individuals with inherited SNCA multiplications typically develop a Parkinson-like picture rather than full multiple system atrophy, suggesting that somatic gains act as one influential contributor among many, a first hit or modifier that lowers the threshold for aggregation within vulnerable glia. Cell-type-specific stress, environmental exposures, unidentified inherited variants and other somatic mutations, possibly including age-related clonal haematopoiesis recently associated with the disease, are likely to complete the picture. Even so, the work reframes the search for multiple system atrophy’s origins. The culprit may not lie in the genome everyone inherits, but in the mosaic of genomes that individual brain cells acquire across a lifetime, and in oligodendrocytes silently accumulating extra copies of the very gene whose protein will one day fill them with inclusions.

Subject of Research: Somatic SNCA copy number variation in oligodendrocytes and its role in multiple system atrophy pathogenesis

Article Title: Oligodendroglial somatic SNCA copy number gains are associated with inclusions and disease onset in multiple system atrophy

Article References: Oligodendroglial somatic SNCA copy number gains are associated with inclusions and disease onset in multiple system atrophy. (n.d.). https://doi.org/10.1007/s00401-026-03077-4

Image Credits: AI Generated

DOI: 10.1007/s00401-026-03077-4

Keywords: multiple system atrophy, SNCA, alpha-synuclein, oligodendrocytes, somatic copy number variants, glial cytoplasmic inclusions, DNA double-strand breaks, gamma H2AX, fluorescent in situ hybridisation, genetic mosaicism, synucleinopathy, neurodegeneration