Strains used in this study.

<div><p>Aneuploidy produces myriad consequences in health and disease, yet models of the deleterious effects of chromosome amplification are still widely debated. To distinguish the molecular determinants of aneuploidy stress, we measured the effects of duplicating individual genes in cells with different chromosome duplications, in wild-type cells (<i>SSD1</i>+) and cells sensitized to aneuploidy by deletion of RNA-binding protein Ssd1 (<i>ssd1Δ</i>). We identified gene duplications that are nearly neutral in wild-type euploid cells but significantly deleterious in euploids lacking <i>SSD1</i> or in <i>SSD1+</i> aneuploid cells with different chromosome duplications. Several of the most deleterious genes are linked to translation. In contrast, duplication of other genes benefits multiple <i>ssd1Δ</i> aneuploids over controls, and this group is enriched for translational effectors. Furthermore, both wild-type and especially <i>ssd1Δ</i> aneuploids with different chromosome amplifications show increased sensitivity to translational inhibitor nourseothricin. We used comparative modeling of aneuploid growth defects, based on the cumulative fitness costs measured for single-gene duplication. Our results present a model in which the deleterious effects of aneuploidy emerge from an interaction between the cumulative burden of many amplified genes on a chromosome and a subset of duplicated genes that become toxic in that context. These findings provide a perspective on the dual impact of individual genes and overall genomic burden, offering new avenues for understanding aneuploidy and its cellular consequences.</p></div>