Multi-omics integration combined with multi-source weighted analysis identifies a key microRNA combination that reverses α-synuclein aggregation and pathological phenotypes in Parkinson's disease

Background Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by pathological aggregation of α-synuclein and selective loss of dopaminergic neurons. The molecular mechanisms involving microRNA regulation of protein homeostasis remain incompletely understood. Methods We integrated single cell RNA-seq, miRNA-seq, bulk RNA-seq, weighted gene co-expression network analysis (WGCNA), and multi-source weighted data integration to screen key miRNAs and core gene modules. The candidate miRNA combination was validated in an MPP + -induced SH-SY5Y PD cell model by measuring TH, DAT, SNCA and LRRK2 using ELISA, and TUJ1 and MAP2 using immunofluorescence. Results Six miRNAs (miR-194-5p, miR-95-3p, miR-1303, miR-889-3p, miR-6506-5p, miR-1287-5p) were identified. Their combined transfection restored cell viability to ~98%, reversed PD-like morphology, reduced SNCA by ~46% and LRRK2 by ~51%, restored TH (~4.4-fold) and DAT (~3.6-fold), and induced neuronal fate transition. Conclusions This six-miRNA combination modulates multiple PD-related proteins, reverses PD-like cellular phenotypes in vitro, and induces neuronal-like marker expression, providing a preliminary basis for developing potential protein-targeted therapeutic strategies for PD.