Matched short-read and long-read single-nucleus RNA-sequencing of substantia nigra / VTA and olfactory bulb from SNCA-GR humanized-knock-in mice

Parkinson's disease is a progressive neurodegenerative disorder often characterized by the accumulation of misfolded alpha-synuclein protein (aSyn) in the brain. While rare genetic variants in SNCA can cause neuronal aSyn accumulation and neurodegeneration in some cases of familial disease, the molecular mechanisms driving SNCA associated risk in idiopathic Parkinson's disease remain elusive. The canonical SNCA mRNA transcript contains a 5'UTR iron response element (IRE) that regulates translation based on cellular iron content. In this study we investigate an alternative transcript isoform lacking this element (dIRE) by evaluating SNCA transcript profiles across neuronal cell lines and post-mortem brain datasets. We show evidence that elevated dIRE expression correlates with increased disease risk in genome-wide association studies and is preferentially expressed in dopaminergic cells. Further, we show that dIRE expression may depend on transcription start site selection controlled by CpG methylation overlapping a known transcription factor binding site, where a PD associated risk haplotype exhibits lower methylation of this CpG site. To probe isoform function, we design and test isoform-specific antisense oligonucleotides (ASOs). With these ASO tools we demonstrate that the protective IRE isoform uniquely suppresses ATF4, an integrated stress response marker elevated in the substantia nigra of post-mortem Parkinson's disease brains. These analyses suggest that uncoupling aSyn translation from intracellular iron concentration may drive neurodegeneration in idiopathic Parkinson's disease. Importantly, non-isoform-selective SNCA-lowering strategies may trigger stress pathways and worsen disease progression, establishing isoform-specific ASOs as key stepping stones toward design of precision therapeutics for Parkinson's disease.