Increased RNA and protein degradation is required for counteracting transcriptional burden and proteotoxic stress in human aneuploid cells. Homo sapiens

Aneuploidy, an abnormal chromosome composition, results in a stoichiometric imbalance of protein complexes that jeopardizes cellular fitness. Aneuploid cells thus need to compensate for the imbalanced DNA levels by regulating their RNA and protein levels, but the underlying molecular mechanisms remain unknown. Here, we addressed this question via molecular dissection of multiple diploid vs. aneuploid cell models. We found that aneuploid cells cope with transcriptional burden by increasing several RNA degradation pathways, and are consequently more sensitive to the genetic or chemical perturbation of RNA degradation. At the protein level, aneuploid cells mitigate proteotoxic stress by reducing protein translation and increasing protein degradation, rendering them more sensitive to proteasome inhibition. These findings were recapitulated across hundreds of human cancer cell lines and primary tumors, and aneuploidy levels were significantly associated with the response of multiple myeloma patients to proteasome inhibitors. Our results therefore reveal that aneuploid cells are preferentially dependent on several key nodes along the gene expression process, identifying clinically-actionable vulnerabilities of aneuploid cells.