Hypo-Osmotic-Like Stress Underlies General Cellular Defects of Aneuploidy

Aneuploidy, referring to unbalanced chromosome numbers, represents a class of genetic variation associated with cancer, birth defects and eukaryotic microbes(1–4). Whereas it is known that each aneuploid chromosome stoichiometry can give rise to a distinct pattern of gene expression and phenotypic profile(4,5), it has remained a fundamental question as to whether there are common cellular defects associated with aneuploidy. In this study, we designed a unique strategy that allowed for the observation of common transcriptome changes of aneuploidy by averaging out karyotype-specific dosage effects using aneuploid yeast cell populations with random and diverse chromosome stoichiometry. This analysis uncovered a common aneuploidy gene-expression (CAGE) signature suggestive of hypo-osmotic stress. Consistently, aneuploid yeast exhibited increased plasma membrane (PM) stress leading to impaired endocytosis, and this defect was also observed in aneuploid human cells. Thermodynamic modeling showed that hypo-osmotic-like stress is a general outcome of proteome imbalance caused by aneuploidy and predicted a ploidy-cell size relationship observed in yeast and aneuploid cancer cells. A genome-wide screen further uncovered a general dependency of aneuploid cells on a pathway of ubiquitin-mediated endocytic recycling of nutrient transporters. Loss of this pathway coupled with the aneuploidy-inherent endocytic defect leads to marked alteration of intracellular nutrient homeostasis.