Simple cell geometry metrics reveal cancer cell diversity and plasticity and guide combination therapy

Abstract Intra-tumour heterogeneity (ITH) and cellular plasticity contribute to therapy resistance. Single-cell transcriptomics is the gold standard for assessing ITH, but this approach remains costly and slow. Here, we show that distinct melanoma transcriptomic states exhibit unique cellular morphologies, and introduce ORIGAMI, a scalable flow cytometry assay leveraging cell surface area (S) and volume (V) measurements to resolve melanoma cell state diversity and to track therapy-induced transitions. MAPK- and CDK4/6-targeted therapies induce predictable shifts in cell geometry: drug-tolerant persister cancer cells increase cell surface area along a de-differentiation trajectory and/or increase volume while acquiring senescent-like features. Using ORIGAMI-guided screening, we identified brefeldin A (BFA) and other ER-Golgi modulators as agents that reduce surface area, promote differentiation, and sensitize melanoma cells to targeted therapies. Therapy-induced high-volume cells exhibit lysosomal scaling and increased sensitivity to nigericin, a natural polyether related to the lysosomal iron sequestering compounds and ferroptosis inducers salinomycin and narasin. Nigericin and BFA combined with MEK- and CDK4/6-inhibitors are highly potent in vitro across cell states and genotypes, and significantly extend survival in NRAS-mutant melanoma patient-derived xenografts without overt toxicity. Moreover, this combination induces hallmarks of immunogenic cell death and enhances anti–PD-1 efficacy in immunotherapy-refractory preclinical models. Beyond melanoma, the combination shows broad anti-tumour activity across a large panel of cancer lines derived from varied tissues. These findings establish a generalizable, geometry-based framework to monitor ITH, anticipate plasticity, and inform genotype-agnostic combination strategies that negate non-genetic adaptive resistance while potentiating immunotherapy.