Aneuploidy is a hallmark feature of cancer. Relative to normal diploid tissue, aneuploid tumors are often net copy number increased, in a range from hyper-diploid to tetraploid. This results in widespread replication stress and proteotoxic stress that affects diverse cellular complexes. Utilizing multi-omics approaches in novel models of cancer-associated copy number alterations derived from diploid human mammary epithelial cells, we uncovered an aneuploidy stress response driven in part by Myc that transcriptionally upregulates biomass production capacity and stresses metabolic capacity. Basal and peak glycolytic and oxidative rates are increased in aneuploid cells compared to diploids, however free nucleotide pools and metabolic intermediates, particularly pyrimidines, are depleted. CRISPR screens revealed a universally increased dependence on de novo pyrimidine synthesis genes in aneuploid cells with diverse CNAs, suggesting a struggle to match pyrimidine synthesis capacity with need. The biosynthetic demand and inefficiency driven by aneuploidy may partially explain the switch to aerobic glycolysis in tumors and present vulnerabilities to be therapeutically exploited.
