Spatial Multi-Omics Identifies Early Synaptic Pruning and Context-Specific Dopaminergic Vulnerability in Synucleinopathies

The molecular events that precede overt neurodegeneration in Parkinson’s disease (PD) remain poorly defined. Incidental Lewy body disease (iLBD)—a prodromal state marked by brainstem-predominant Lewy pathology in the absence of clinical symptoms—offers a unique window into early pathogenesis. Here, we applied a multi-omic spatial profiling approach, integrating transcriptomics, proteomics, and α-synuclein seed amplification assays (SAA), to post-mortem midbrain tissue from neurologically unaffected individuals, iLBD cases, and patients with PD. We identified early and spatially distinct molecular alterations in the substantia nigra pars compacta (SNpc) of iLBD cases, including a marked upregulation of the microglial synaptic pruning factor C1QC. These changes emerged independently of overt Lewy pathology or detectable misfolded α-synuclein, as assessed by SAA or proximity ligation assay (PLA), and were preferentially enriched at GABAergic synapses—highlighting the early vulnerability of inhibitory circuits. Notably, these alterations were absent in Alzheimer’s disease cases with comorbid SNpc Lewy pathology, suggesting that α-synuclein aggregation alone is insufficient to trigger SNpc remodeling. Our findings implicate microglia-mediated synaptic dysfunction as an early, preclinical feature of PD and nominate this mechanism as a potential therapeutic target for halting disease progression before the onset of neurodegeneration. *Svenja-Lotta Rumpf & Felix Strübing contributed equally to this work.