SNCA transcript diversity in human dopaminergic neurons informs antisense oligonucleotide targeting

Parkinson’s disease (PD) is a prevalent neurodegenerative disorder with no curative or diseasemodifying therapies, representing a major unmet clinical need. Rare and common variation at the SNCA locus, which encodes α-synuclein, is well recognised as a driver of disease, yet the transcriptional diversity of SNCA in vulnerable cell types remains poorly defined. We performed targeted long-read RNA sequencing of SNCA in human induced pluripotent stem cell-derived midbrain dopaminergic neurons to resolve its transcript repertoire and assess implications for antisense oligonucleotide targeting. Transcripts fully represented in current annotation accounted for only 5% of total SNCA expression, whereas 75% arose from transcripts with alternative 5′ and 3′ untranslated regions and 10% from transcripts containing previously unannotated open reading frames. Six of seven newly identified open reading frames were also detected across human central nervous system regions, and isoform-specific peptides supported translation of three novel α-synuclein isoforms in human postmortem brain. Mapping antisense oligonucleotide target sites onto the expressed transcript repertoire revealed marked differences in predicted transcript coverage. An oligonucleotide targeting the predominant neuronal transcripts produced sustained SNCA reduction and decreased αsynuclein aggregation, mitochondrial dysfunction and toxicity. These findings show how resolving SNCA transcript diversity can inform RNA-targeting strategies in PD.