A deep cellular atlas of the human ventral substantia nigra in Parkinson’s identifies a genetic and molecular overlap with insulin resistance

Parkinson’s disease (PD) is a complex neurodegenerative disorder characterised by selective neuronal loss. We integrate deep full-length single-nuclei sequencing of the human substantia nigra with novel genome-wide association studies (GWAS) identifying genetic and cellular drivers of PD. Genetic risk converges on AGTR1+ dopaminergic neurons and perineuronal oligodendrocytes (pODCs), both reduced in PD, as well as oligodendrocyte precursor cells, enriched among disease-disrupted intercellular interactions. AGTR1+ neurons represent a metabolically stressed state, characterised by renin-angiotensin system (RAS) and MAPK activation, oxidative stress, and mitochondrial dysfunction, rather than a distinct subtype. AGTR1+ neurons and pODCs link PD risk to metabolic traits; in pODCs, this association reflects insulin resistance with downregulated PI3K–AKT signalling. GWAS of comorbid PD and type 2 diabetes (T2D) identifies loci in AGTR1 and TCF7L2, while AGTR1+ neurons specifically upregulate RAS and T2D drug targets. Familial PD genes associated to comorbid PD/T2D associate with non-Lewy body PD, stratifying disease mechanisms.