Simultaneous Profiling of Gene Expression Patterns from Pooled Cell Samples of Large Parkinson’s Disease Cohorts

Study Rationale: The PPMI study provides a repository of stem cells that can be converted into dopamine-producing neurons and microglia for modeling Parkinson’s disease (PD). Maintaining these cells in separate containers is expensive and cumbersome, so we propose to pool cell samples and use a method called single-cell RNA sequencing to get a snapshot of which genes are active in hundreds of cells from people with PD at the same time. This approach will allow us to determine how PD-derived cells are different from the cells of healthy individuals and to study how these cells respond to potential therapeutic drugs for PD.

Hypothesis: Sample pooling will permit tracking the gene expression profiles of cells from groups of people under different conditions at the same time, for example, in response to PD treatments.

Study Design: In this pilot study, we will use 24 stem cell lines from individuals who are healthy, have sporadic PD or mutations in PD-associated genes. We will pool these cells, convert them into PD-relevant cell types, and use single-cell RNA sequencing to obtain a set of gene expression profiles. Using a computational pipeline to identify the original source of each cell, we will compare the profiles from each PD group to those of healthy cells. Finally, we will repeat the experiment to compare the cells’ response to LRRK2 inhibitors or to compounds that modify the activity of GCase.

Impact on Diagnosis/Treatment of Parkinson’s disease: The ability to produce gene expression profiles from pooled samples could lead to advances in precision medicine for PD. This approach will allow individuals to be grouped together for clinical trials to determine whether drugs work the same way for individuals with monogenic or sporadic forms of PD.

Next Steps for Development: If the proposed pilot project is successful, the next step would be to increase the scale of the sample pooling to include more PPMI cell lines. We would test more compounds to assess whether they improve the survival and healthy function of PD-derived cells