Cross Study Regulator Activity Analysis Reveals Convergent Programs in alpha Synuclein PFF Models of Parkinson Disease

Alpha-synuclein preformed fibril (PFF) models reproduce features of Parkinson disease (PD), but differences in brain region, cell composition, and experimental design complicate comparisons across studies. We reconstructed study-specific regulatory networks using ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) and inferred transcription factor (TF) and transcription cofactor activity using VIPER (Virtual Inference of Protein-activity by Enriched Regulon analysis). Five transcriptomic comparisons from four mouse PFF datasets were analyzed, with human PD single-nucleus RNA-sequencing data used to assess cross-species agreement. In the dopamine-neuron-enriched dataset GSE252967, PFF exposure was associated with increased activity of stress- and inflammation-related TFs, including JUND and RELA, and decreased activity of dopaminergic-identity regulators, including NR4A2, LMX1B, FOXA1, FOXA2, PITX3, and EN1. Several regulators were connected to Th in the inferred network. The substantia nigra bulk dataset GSE296779 showed reduced activity of ATF4- and XBP1-associated protein homeostasis and unfolded protein response programs, supported by regulon-weighted gene-set enrichment. Supporting mouse comparisons showed limited overlap in individual TFs but identified changes in inflammatory, glial, and stress-related programs. Agreement between inferred activity and transcript-level changes ranged from 64% to 100% in these comparisons. Human PD data showed cell-type-dependent agreement with mouse findings. EN1 and PITX3 were shared between the mouse and human networks upstream of Th/TH and showed reduced inferred activity in all seven human cell types, alongside nonsignificant decreases in the mouse dataset. These analyses identified changes in dopaminergic-identity, protein homeostasis, and inflammatory transcriptional programs across mouse PFF models, with partial support in human PD.