Single cell transcriptomics reveals enrichment of aggregation-prone alpha-synuclein isoforms across synucleinopathies

Shwab, E. K.; Pierson, W.; Gingerich, D. C.; Man, Z.; Margalit, S.; Yona, D.; Sivan, A.; Gamache, J.; Serrano, G. E. E.; Beach, T.; Ebenstein, Y.; Beck, R.; Chiba-Falek, O.

doi:10.1101/2025.10.13.682119

bioRxiv · 10.1101/2025.10.13.682119

Single cell transcriptomics reveals enrichment of aggregation-prone alpha-synuclein isoforms across synucleinopathies

Shwab, E. K.·Pierson, W.·Gingerich, D. C.·Man, Z.·Margalit, S.·Yona, D.·Sivan, A.·Gamache, J.·Serrano, G. E. E.·Beach, T.·Ebenstein, Y.·Beck, R.·Chiba-Falek, O.

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Abstract

Alpha-synuclein (-Syn) is the primary component of Lewy bodies, the pathological hallmark of neurodegenerative synucleinopathies, including Parkinsons disease (PD) and dementia with Lewy bodies (DLB). Dysregulated expression of its encoding gene, SNCA, has been identified in association with both PD and DLB in short-read sequencing studies. However, such studies do not capture variation in transcript isoforms expressed. Here we combine for the first time SNCA-targeted long-read multiplexed arrays isoform sequencing (MAS-Iso-seq) with unbiased short-read single nucleus (sn) RNA-seq for simultaneous characterization of the SNCA transcript isoform landscape and mapping of isoform expression to specific cell types and subtypes in PD, DLB, and control sample cortical tissues. This approach enabled discovery of numerous SNCA transcript isoforms displaying novel splicing patterns and incorporating novel exons. We further identified an abundant class of transcript isoforms encoding a previously unreported -Syn protein variant (-Syn-115) and displaying increased proportional detection in excitatory neurons of PD and DLB tissues in comparison to controls. The proportion of these isoforms was found to be especially high within several specific glutamatergic neuron subtypes. In-depth characterization of the predicted structural and biochemical properties of -Syn-115 using an in silico modeling approach revealed a greater aggregative affinity compared with canonical -Syn-140, suggesting the potential for increased cytosolic -Syn-115 abundance to induce aggregation between heterogeneous -Syn isoforms, potentially driving fibril formation and disease progression. Together, our findings provide new insights into the molecular mechanisms underlying -Syn involvement in multiple synucleinopathies and have translational implications for the development of new precision medicine strategies to combat these diseases, indicating the potential for treatments targeting both specific transcript and protein isoforms, as well as disease-driving cell subtypes.

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Shwab, E. K., Pierson, W., Gingerich, D. C., Man, Z., Margalit, S., Yona, D., Sivan, A., Gamache, J., Serrano, G. E. E., Beach, T., Ebenstein, Y., Beck, R., Chiba-Falek, O.. 2025-10-14. Single cell transcriptomics reveals enrichment of aggregation-prone alpha-synuclein isoforms across synucleinopathies. https://doi.org/10.1101/2025.10.13.682119

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