Deciphering Regional Transcriptomic Alterations in a 6-OHDA Rat Model of Parkinson's Disease through Integrated Single Cell and Spatial Analyses

Parkinson's disease (PD) is characterized by progressive degeneration of dopaminergic neurons in the substantia nigra, yet the detailed spatial and temporal cellular responses to this loss remain unclear. We aimed to generate a high-resolution map of midbrain changes by integrating single-cell and spatial transcriptomics in a 6-hydroxydopamine rat model. Unbiased clustering of single-nucleus RNA-sequencing data revealed the compensatory expansion of specific Glutaminergic subtypes and the emergence of a previously uncharacterized population of Asic2 ⁺ dopaminergic neurons. Spatial transcriptomic mapping localized these cellular changes to anatomically distinct regions, including the substantia nigra, cortex, hippocampus, and thalamus. Cell–cell communication analysis revealed a widespread induction of cyclophilin A (CypA)-associated stress and inflammatory signaling, alongside a reduction in prosaposin (PSAP)-dependent neuroprotective interactions, particularly within Asic2 ⁺ neurons. These findings highlight a coordinated glial–neuronal response to dopaminergic injury, identify CypA and PSAP as potential contributors to PD pathogenesis, and suggest new targets for therapeutic intervention.