Targeting DNA topoisomerases or checkpoint kinases forces a shift in global protein homeostasis, triggering widespread protein aggregation

A loss of the checkpoint kinase ATM leads to impairments in the DNA damage response, and in humans causes cerebellar neurodegeneration, and a high risk to cancer. A loss of ATM is also associated with increased protein aggregation. The relevance and characteristics of this aggregation are still incompletely understood. Moreover, it is unclear to what extent other genotoxic conditions can trigger protein aggregation as well. Here, we show that targeting ATM, but also ATR or DNA topoisomerases result in a similar, widespread aggregation of a metastable, disease-associated subfraction of the proteome. Aggregation-prone model substrates, including expanded polyglutamine repeats, aggregate faster under these conditions. This increased aggregation results from an overload of chaperone systems, which lowers the cell-intrinsic threshold for proteins to aggregate. In line with this, we find that inhibition of the HSP70 chaperone system further exacerbates the increased protein aggregation. Moreover, we identify the molecular chaperone HSPB5 as a potent suppressor of it. Our findings reveal that various genotoxic conditions trigger protein aggregation, in a manner that is highly reminiscent of the widespread aggregation occurring in situations of proteotoxic stress and in proteinopathies. Bulk RNA-seq of RNA extracted from HEK293T and U2OS cells. HEK293T cells were treated with either DMSO of Camptothecin. U2OS cells were either wild type or knockout for ATM. 4 replicates per group.