Uncovering proteomic alterations in Parkinson's disease using patient-specific iPSC-derived brain cells

Parkinson's disease (PD) is primarily associated with motor impairment due to the loss of dopaminergic neurons located in the substantia nigra pars compacta of the brain. Despite intense research, its initiation, pathogenicity, and development remains uncertain. PD can be divided into familial or idiopathic forms. Monogenic forms of PD account for ~ 30% of known familial cases but less than 10% of all cases. This means that we currently do not understand the origin of more than 90% of PD cases. In addition to specific hallmarks such as neuronal cell type-specific loss and the formation of protein inclusions, PD has intrinsic heterogeneity and many atypical cases.

Patient brain cell types are not accessible during the disease. However, these can be generated from induced pluripotent stem cells (iPSCs) to identify dysfunctions in cellular pathways. Preclinical findings have suggested that iPSC-based patient stratification may be key to patient management and therapeutic interventions, similar to what is currently used in certain cancers, where omics data are expected to play a major role. Moreover, iPSC-derived brain cell types generated from patients with idiopathic disease have been shown to have the intrinsic capability to exhibit disease phenotypes that resemble those present in brain cells of well-defined genetic cases.

Our goal is to identify early disease mechanisms leading to neuronal injury in PD by uncovering the relationship between the genetic makeup of a patient and its brain cells' dysfunctional networks. To this end, we performed MS-based proteomic and phosphoproteomic analyses of brain cells (dopaminergic neurons and astrocytes) and midbrain spheroids generated from patient iPSCs (n=50) available from the Parkinson's Progression Markers Initiative (PPMI) cohort. Proteomic analysis resulted in the quantification of more than 7500 proteins and 9000 phosphopeptides per sample in FACS sorted cells, and higher numbers were obtained from spheroid samples. Based on their proteomic and phosphoproteomic profiles, different brain cell types and patient groups with distinct genetic makeup can be clearly distinguished from each other. Dysregulation of certain processes was observed in all PD groups compared to controls (e.g., mitochondrial translation, integrin 3 pathway), but patient group-specific changes were also identified. In addition, we also found significant differences between the disease groups in terms of kinase activity.

The use of patient iPSC-derived brain cells may help to identify initial cellular dysfunctions and their development before neuronal damage prevails and leads to the appearance of the symptoms. Our results provide insight into the pathogenic processes of PD, which may contribute to better patient stratification and the development of personalized treatment strategies.

Funding: The Michael J. Fox Foundation for Parkinson's Research (MJFF-021548)