Parkinson’s disease genetic risk converges on Lewy body pathology-associated microglial states

Parkinson’s disease (PD) and related α-synucleinopathies are defined by the spread of Lewy body (LB) pathology across vulnerable brain regions, yet how substantia nigra (SN) myeloid cells respond remains unresolved. Using SOX10-based oligodendrocyte depletion and CD11b-based myeloid enrichment, we profiled 169,799 brain myeloid cells and nuclei from 96 donors spanning the LB continuum, including 86,427 from the SN, and integrated them with AMP PD for a total of 298,592 profiles. Across eight conserved states, α-synucleinopathy is associated with a bidirectional signature: upregulated glycolytic and proteostatic-stress programs alongside downregulated lysosomal and mitochondrial pathways. Microglia shift from P2RY12-high sensome cells toward an HSP90AA1-high proteostatic stress state, a transition that intensifies at late Braak LB stages. Immunohistochemistry confirmed that HSP60 ⁺ proteostatic microglia state proportions increase with SN neuron loss. A rare NUCKS1-high state (∼1% of myeloid cells), more abundant in late-stage disease, carried the strongest PD polygenic-risk loading. The PD-protective rs3732765-A allele, a microglial cis-eQTL that lowers P2RY12 expression, was nominally associated with a higher proportion of P2RY12-high microglia and higher lysosomal program activity. These findings frame microglial involvement as structured and genetically tractable, nominating the P2RY12 genetic axis and NUCKS1-high microglia for mechanistic studies.