Integrating Substantia Nigra Single-Nucleus Transcriptomics with GWAS Prioritizes Microglia and Reveals State-Specific Regulon Dysregulation in Parkinson’s Disease

Background/Objectives: Parkinson’s disease (PD) is a complex neurodegenerative disorder, yet the cellular contexts through which genetic susceptibility is translated into pathology remain incompletely understood. Methods: We integrated three independent single-nucleus RNA sequencing cohorts of the human substantia nigra to construct a large-scale disease-relevant atlas comprising 324,990 nuclei, and combined it with PD genome-wide association study summary statistics using the single-cell Disease Relevance Score framework. Single-nucleus findings were further tested at the donor level with adjustment for dataset, sex and age. Results: Among major cell populations, microglia showed the strongest association with PD genetic susceptibility. Sub-clustering of the microglial lineage resolved eight states, including primed and stress-associated microglia and border-associated macrophages (BAMs). The BAM cluster showed the most robust PD-associated changes, including the largest number of donor-level differentially expressed genes and attenuated THRB regulon activity supported at the donor level. Increased CEBPA regulon activity in primed and stress-associated microglia was observed only at the single-nucleus level. Connectivity Map analysis and structure-based modeling, including molecular docking and molecular dynamics simulation, nominated SU-11652 as a candidate compound structurally compatible with the active-state THRB ligand-binding domain. Conclusions: These findings implicate the microglial lineage, including BAMs, in PD genetic susceptibility, identify THRB attenuation in BAMs as a robust candidate regulatory change, and provide testable hypotheses for future experimental validation.