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

Alpha-synuclein (α-Syn) is the primary component of Lewy bodies, the pathological hallmark of neurodegenerative synucleinopathies, including Parkinson’s disease (PD) and dementia with Lewy bodies (DLB). Dysregulated expression of encoding gene SNCA has been associated with both disorders in short-read sequencing studies. However, such studies do not capture transcript isoform variation. Here, we combine SNCA -targeted long-read multiplexed arrays isoform sequencing (MAS-Iso-seq) with unbiased short-read single nucleus (sn) RNA-seq to simultaneously characterize the SNCA transcript isoform landscape and map isoform expression to specific cell subtypes in PD, DLB, and control tissues. This approach identified 327 SNCA transcript isoforms grouped into 50 unique splicing classes. We further identified an abundant class of transcript isoforms predicted to encode a novel α-Syn protein variant (α-Syn-115) and displaying increased proportional detection in excitatory neurons of PD and DLB, especially within several glutamatergic neuron subtypes. In silico structural modeling predicted greater aggregative propensity for α-Syn-115 than canonical α-Syn-140, suggesting that increased cytosolic α-Syn-115 could induce aggregation between heterogeneous α-Syn isoforms, potentially driving fibril formation and disease progression. Together, these findings provide new insight into α-Syn biology in synucleinopathies and suggest directions for potential treatment strategies targeting specific transcript and protein isoforms and disease-associated cell subtypes.