Single-cell RNA profiling of oligodendroglial lineage cells derived from iPSCs carrying Parkinson's disease-relevant LRRK2-G2019S mutation

Despite extensive research, the cell-type specific effects of the LRRK2 p.G2019S mutation in Parkinson’s disease (PD) remains unclear. Recent findings indicate oligodendrocytes (ODCs) and their progenitors are vulnerable in PD pathogenesis. Notably, oligodendrocyte precursor cells (OPCs) exhibit high endogenous expression of LRRK2. We differentiated iPSCs carrying the PD-relevant LRRK2 p.G2019S mutation into oligodendroglial lineages and performed single-cell RNA sequencing. Cell type composition analysis revealed an increase in OPCs, proliferating OPCs and ciliated ependymal cells in LRRK2 lines, all of which are characterized by LRRK2 expression. Differential expression analysis revealed transcriptomic changes in several pathways, including down-regulation of genes related to myelin assembly in ODCs, semaphorin-plexin pathway in OPCs, and cilium movement in proliferating OPCs. Cell-cell communication analysis identified significant alterations in several signaling pathways including a deactivation of PSAP signaling and an activation of MIF signaling in LRRK2 lines. Additionally, we observed an overall increase in SEMA6 signaling communication in LRRK2 cell lines; however, OPCs derived from these LRRK2 lines specifically lost SEMA6 signaling due to a down-regulation of SEMA6A and PLXNA2. A similar down-regulation trend of SEMA6A and PLXNA2 was observed in OPCs from post-mortem PD brain samples carrying LRRK2 mutations compared with controls. Pseudotemporal trajectory analysis revealed that SHH had significantly altered expression along the pseudotime, accompanied by higher expression levels in LRRK2 lines. We provide a single-cell transcriptomic atlas of iPSC-derived oligodendroglial lineage cells derived from LRRK2 p.G2019S PD and healthy control lines. This data submission is a reanalysis of snRNA-seq on the prefrontal cortex and anterior cingulate regions from post-mortem control and PD brain tissue pertaining to a previous publication which was re-analysed for this paper. Original data at: https://doi.org/10.5281/zenodo.7886802 Data and Code Availability• Data: Single-cell RNA-seq data are available at PPMI controlled‑access repository with Project ID 338 and can be downloaded after approval by the PPMI Data Access Committee. Apply for access here https://www.ppmi-info.org/access-data-specimens/download-data => Genetic data.• Code: All original code has been deposited at Github (https://github.com/nnkarma12/scRNAseq_iOligo) and is publicly available.