Aggregate Deep Visual Proteomics reveals selective organization of α-synuclein inclusions

Parkinson's disease is characterized by the presence of α-synuclein inclusions, whose nature remains unclear. Are they protective, toxic, or simply a result of failed degradation? To resolve this, researchers developed a technique called Aggregate Deep Visual Proteomics. This method employs ultrasensitive mass spectrometry to profile laser-microdissected inclusions compared to the rest of the cell or a matched host tissue.

When tested on HEK293 cells, induced pluripotent stem cell-derived dopaminergic neurons, and post-mortem patient brain samples, the technique revealed that each inclusion selectively concentrates a unique subset of its cell's proteome. This concentration was independent of the abundance of proteins and was primarily observed in the neuronal membrane, particularly in presynaptic neurons. Intriguingly, the inclusions contained entire assemblies, with subunits moving together in 421 out of 438 complexes.

The study also found that the V-ATPase, a crucial ion transport protein, was enriched in all three systems. Degradation cargo was observed to remain with the receptors responsible for routing it, suggesting that sequestration and failed degradation may work together to form these inclusions.

Interestingly, neuritic and somatic inclusions differed in their composition. Neuritic inclusions were rich in UBQLN2, while somatic inclusions were enriched in intermediate filaments. In the cell line, phosphorylated α-synuclein was found to be tenfold higher in the inclusion than in the rest of the cell, with about one-third of this increase present even before the inclusion was visible.

By comparing the composition of an inclusion to its host cell, Aggregate Deep Visual Proteomics provides a readout of how the inclusion formed. This technique not only identifies candidate markers but also offers potential therapeutic targets for Parkinson's disease research.