Functional profiling of the chaperone systems interactome in breast cancer using experimental and machine-learning...

Breast cancer heterogeneity stems from diverse molecular alterations, including proteostasis loss due to chaperone system dysfunction. However, the impact of impaired chaperone activity on proteomic changes and tumorigenesis remains unclear. Here, characterized the expression patterns of major chaperone families and mapped their client protein interactions to elucidate their role in shaping tumor biology. We identified 53 chaperones expressed in breast tissue, of which 26 were differentially expressed between tumor and non-tumor samples. Using validated protein interaction data and machine-learning predictions, coupled with molecular docking, we constructed protein-protein interaction (PPI) networks for each chaperone family and subsequently performed enrichment analyses to assess their involvement in cancer-related pathways. Each chaperone family's PPI network comprised a distinct set of client proteins and was enriched in different biological pathways and processes. The HSP70 system PPI network included LYN, NFKB1, and PARP1, and was related to DNA repair and immunomodulation through interleukin and cytokine signaling. Although a partial overlap of client proteins was observed between the HSP70 and HSP90 sets, HSP90 was also associated with particular client proteins, including TRAF2, PDGFRB, and NUDC, which were enriched in MAPK and PI3K/AKT/mTOR signaling pathways, as well as epithelial-to-mesenchymal transition and cell cycle control. Our results also indicate an association between CCT/TRiC chaperonins and the regulation of tubulin/actin, supporting their involvement in cytoskeleton dynamics, the mitotic spindle, chromosome segregation, and autophagy/aggrephagy. Overall, our findings expand the repertoire of chaperone client proteins and provide insights into how chaperone dysregulation influence breast cancer biology, highlighting their potential as therapeutic targets.