Characterization of proteostasis loss in neurodegeneration using a proteomics approach

Chaperones such as HSP70s are the key proteins in the maintenance of protein homeostasis. They maintain protein balance from translation of nascent protein to degradation of misfolded proteins and aggregates. Therefore, chaperone–client interactions provide insights into protein homeostasis within cells. Here I show that chaperone-client interactions can be deciphered using ubiquitin-activated interaction traps (UBAITs). Using LC/MS label-free proteomics together with HSP/HSC70 UBAITs, I have identified both chaperone clients and their co-chaperones with higher confidence compared to traditional IP-LC/MS. The results demonstrated that HSP70/HSC70, despite their similarity, have non-overlapping sets of clients. Unstable subunits of a large protein complex are often recognized by either HSP70 or HSC70 but not both. Most importantly, HSP70/HSC70 UBAITs were sensitive enough to monitor change in chaperone-client interaction landscape caused by the presence of neurotoxic protein SOD1(A4V), demonstrating their application in the future studies of neurodegenerative disorders. Neurodegenerative disorders are a collection of diseases that are characterized by progressive death of neurons where, for most cases, the causes are still unknown. However, loss of protein homeostasis and an increase in protein aggregation are common hallmarks for neurodegenerative disorders. Ataxia-telangiectasia (A-T) is a rare neurodegenerative disorder that is caused by a mutation in the ATM gene. A-T patients suffer from a loss of cerebellum-specific neurons, causing early-onset ataxia. The A-T neurodegenerative disease, which was previously thought to be unrelated to other age-related neurodegenerative disorders, also has a similar protein homeostasis loss. Similar to other forms of neurodegenerative disorders, the cerebellum of A-T patients also shows widespread protein aggregation in cerebellum tissues. The loss of protein homeostasis in A-T is driven by an increase in poly-(ADP- ribosylation), caused by an increase in transcription-dependent single-strand DNA damage (SSBs) via an increase in formation of R-loops in the absence of ATM. Additionally, the protein homeostasis loss was limited to the cerebellum, further demonstrating that protein homeostasis loss correlates with neurodegeneration. These findings provide new methods that could be used to further our understanding of a relationship between protein homeostasis loss and neurodegeneration while providing important insights into how protein aggregation occurs in A-T neurodegenerative disorders.