Familial Parkinson's Disease Mutations Converge on Alternative Splicing Programs Linked to Lysosomal, Autophagic and Vesicle Trafficking Pathways

Abstract

Parkinson's disease (PD) arises from genetic and environmental factors. Human genetics has identified mutations in ~20 inherited familial genes linked to monogenic forms of PD. To investigate the how individual familial PD mutations might affect pre-mRNA splicing patterns, human pluripotent stem cells (hPSCs) carrying 12 distinct familial PD mutations were differentiated into midbrain lineage cells, including dopaminergic (mDA) neurons. Using available snRNA-seq data from human brain substantia nigra pars compacta (SNc), we curated a set of ~ 2,250 genes expressed in DA neurons, where >90% of these genes were expressed in our differentiated hPSC cultures. We used the iSCORE-PD collection of edited hPSCs carrying pathogenic PD mutations in the PRKN, SNCA, LRRK2, PINK1, DNAJC6, FBXO7, SYNJ1, DJ1, VPS13C, ATP13A2 and GBA1 genes and carried out deep Illumina RNA-seq from these differentiated cultures to carry out pre-mRNA splicing analyses. Altered splicing patterns in familial PD mutant cells were categorized into five distinct functional classes: autosomal-dominant drivers (SNCA, LRRK2), mitochondrial quality control (PRKN, PINK1, PARK7), endolysosomal/vesicular trafficking (ATP13A2, DNAJC6, FBXO7, SYNJ1), lysosomal dysfunction (GBA1), and lipid transport/cellular stress pathways (VPS13C). Interestingly, we found common pre-mRNA splicing changes for the curated set of SN dopaminergic neuronal genes in the mutant cells, including for SYNJ1, itself a familial PD risk gene linked to dopamine release. These PD mutation-specific pre-mRNA isoform changes may serve as both diagnostic biomarkers for familial PD-associated genotypes and be promising therapeutic targets.