Integrated bulk, single-cell, and spatial transcriptomic analyses prioritize NOTCH1 as a candidate gene associated...

Parkinson's disease (PD) is classically defined by dopaminergic neurodegeneration in the substantia nigra, yet how immune activation is linked to neurovascular dysfunction in the diseased brain remains incompletely understood.

Here, we integrated bulk substantia nigra microarray expression datasets with single-cell and spatial transcriptomic data to delineate disease-associated neurovascular and immune-related transcriptomic programs in PD.

Across three independent human microarray cohorts, differential expression and weighted gene co-expression network analyses identified PD-associated genes enriched for synaptic processes together with immune, adhesion, and vascular-related pathways. Network topology analysis and machine-learning feature selection prioritized a five-gene candidate panel, among which NOTCH1 showed the most consistent cross-dataset association and external directional support. Importantly, quantitative real-time PCR (qRT-PCR) validation in the substantia nigra of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD model mice further supported dysregulated Notch1 expression. Single-cell mapping placed NOTCH1 expression within neurovascular and glial cellular contexts, including pericytes and endothelial cells, while CellChat and NicheNet analyses nominated transcriptome-derived ligand-receptor relationships involving NOTCH-related, vascular, inflammatory, extracellular-matrix, and growth-factor-associated programs. Spatial transcriptomics from mouse 6-hydroxydopamine (6-OHDA) substantia nigra sections provided model-based anatomical context for spatial proximity between pericyte and microglial signatures, without establishing direct functional communication. In parallel, exploratory in silico perturbation and docking-based screening generated hypotheses regarding the NOTCH1-associated regulatory context and compounds with predicted docking affinity toward NOTCH1.

Collectively, these analyses prioritize NOTCH1 as a reproducible PD-associated candidate gene and suggest that NOTCH1-related signals may be embedded within broader neurovascular, glial, inflammatory, extracellular-matrix, and immune-associated transcriptomic alterations. These findings provide a computational prioritization framework for future experimental validation rather than evidence of a defined NOTCH-driven mechanism.