Comparison of Alternative pre-mRNA Splicing and Gene Expression Patterns in Midbrain Lineage Cells Carrying Familial Parkinson’s Disease Mutations

Abstract

SummaryParkinson’s disease (PD) is a devastating neurodegenerative disorder, with both genetic and environmental causes. Human genetic studies have identified ∼20 inherited familial genes that cause monogenic forms of PD. We have investigated the effects of individual familial PD mutations by developing a medium-throughput platform using genome-editing to install individual PD mutations in human pluripotent stem cells (hPSCs) that we subsequently differentiated into midbrain lineage cells including dopaminergic (DA) neurons in cell culture. Both global gene expression and pre-mRNA splicing patterns in midbrain cultures carrying inherited, pathogenic PD mutations in the PRKN and SNCA genes were analyzed. This analysis revealed that PD mutations lead to many more pre-mRNA splicing changes than changes in overall gene RNA expression levels. Importantly, we have also shown that these splicing changes overlap with changes found in PD patient postmortem brain sample RNA-seq datasets. These pre-mRNA splicing changes are in genes related to cytoskeletal and neuronal process formation, as well as splicing factors and spliceosome components. We predict that these mutation-specific pre-mRNA isoforms can be used as biomarkers for PD that are linked to the familial PD mutant genotypes.