Integrated bulk, single-cell, and spatial transcriptomic analyses prioritize NOTCH1 as a candidate gene associated with neurovascular and immune-related alterations in Parkinson's disease.

Introduction: 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. Methods: 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. Results: 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. Discussion: 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.