Aneuploidy as a metabolic liability: Exploiting novel therapeutic targets in squamous cell carcinomas

Squamous cell carcinomas (SCCs) across epithelial tissues of the lung, head and neck, and esophagus lack canonical oncogenic mutations and urgently require therapeutic strategies. Aneuploidy-chromosomal gains or losses, is detrimental in normal cells yet occurs in >90% of solid tumors in tissue-specific patterns. SCCs exhibit near-universal chromosome 3q gain, which associates with progression, metastasis, and therapy resistance; however, the mechanisms linking aneuploidies to tumorigenesis remain unclear. To investigate aneuploidy-driven dependencies, we engineered isogenic human lung epithelial cells modeling chromosome 3 disomy and 3q gain and performed genome-wide CRISPRi and drug-repurposing screens. Both screens converged on a lipid metabolism dependency specific to 3q gain, with heightened sensitivity to disruption of the sterol regulatory element-binding protein (SREBP) pathway. SREBF1 emerged as the top genetic hit, while statins (HMGCR inhibitors), were the strongest chemical hits and preferentially induced apoptosis in 3q gain cells. Rescue with mevalonate confirmed on-target effects and additional cholesterol-lowering drugs also induced increased cytotoxicity. Transcriptomic and lipidomic profiling revealed altered cholesterol and fatty acid biosynthesis programs and distinct lipid composition in 3q gain cells. Protein and immunofluorescence analyses further demonstrated impaired SREBP1 activation in 3q gain cells. To identify potential causal gene drivers, we performed a chromosome 3q-focused CRISPRi screen alongside SREBP/HMGCR inhibition. This screen revealed multiple gene candidates-including TFG , SEC62 , SERP1 , and RAB43 -whose knockdown rescued drug-induced loss of viability, implicating ER-to-Golgi transport and cellular stress pathways in altered SREBP1 activation. Ongoing studies are determining whether these mechanisms directly explain reduced pathway activation in 3q gain cells. To assess translational relevance, we validated these dependencies in isogenic organoids and SCC cell lines. In vivo xenograft studies demonstrated that 3q gain SCC tumors exhibit increased sensitivity to suppression of SREBF1 and HMGCR, leading to reduced tumor volume and weight. These findings support chromosome 3q gain as a biomarker of pathway inhibitor response. Together, our results define an aneuploidy-driven, targetable metabolic vulnerability in SCC. Chromosome 3q gain imposes a metabolic cost that creates actionable therapeutic dependencies, nominating lipid metabolism and mevalonate pathway regulators as precision therapy targets for aneuploid SCC.