Profiling and Defining Parkinson’s Disease

Parkinson’s disease (PD) is an incurable progressive neurodegenerative disorder that affects a growing proportion of the aging population, and its cause is largely unknown. We propose to gain insights into the molecular mechanisms of PD. Our objectives are: 1) Identify alterations in gene expression at a single cell level in PD samples by using powerful droplet microfluidics single-nuclei RNA-seq, single molecule FISH, in situ sequencing and bioinformatics analysis; and 2) Determine the function of genes with altered expression levels and their contribution to PD by using novel gene editing technologies and advanced midbrain differentiation protocols for pluripotent stem cells. Our project will systematically analyze and provide an unbiased understanding of the cell types and molecular mechanisms involved in PD. This will enable us to define molecular pathways, disease subtypes, markers and possible targets for future therapeutic intervention.

The team developed different spatial transcriptomics methods (osmFISH, EEL, HybISS, direct HybISS and pciSeq) and applied them to human post-mortem tissue. They also developed single nuclei transcriptomics (10X) and in situ reference datasets of the developing mouse, adult mouse, and human central nervous system. Additionally, they developed new protocols to make midbrain dopaminergic neurons from hPSCs, PD-iPSCs and isogenic controls, and methods to evaluate their quality by scRNA-seq compared to endogenous standards. They identified cell types in the adult substantia nigra by single nucleus RNA sequencing (10X), and cell types underlying genetic risk of idiopathic Parkinson’s disease, and examined the mechanism by which prosaposin and saposin C control the levels of a-synuclein.