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bioRxiv · 10.1101/2025.03.26.645251

Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding

Whiting, F. J. H.·Mossner, M.·Gabbutt, C.·Kimberley, C.·Barnes, C. P.·Baker, A.-M.·Yara, E.·Sottoriva, A.·Nichols, R. A.·Graham, T. A.
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Abstract

Cancer treatment frequently fails due to the evolution of drug-resistant cell phenotypes driven by genetic or non-genetic changes. The origin, timing, and rate of spread of these adaptations are critical for understanding drug resistance mechanisms but remain challenging to observe directly. We present a mathematical framework to infer drug resistance dynamics from genetic lineage tracing and population size data without direct measurement of resistance phenotypes. Simulation experiments demonstrate that the framework accurately recovers ground-truth evolutionary dynamics. Experimental evolution to 5-Fu chemotherapy in colorectal cancer cell lines SW620 and HCT116 validates the framework. In SW620 cells, a stable pre-existing resistant subpopulation was inferred, whereas in HCT116 cells, resistance emerged through phenotypic switching into a slow-growing resistant state with stochastic progression to full resistance. Functional assays, including scRNA-seq and scDNA-seq, validate these distinct evolutionary routes. This framework facilitates rapid characterisation of resistance mechanisms across diverse experimental settings.

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Whiting, F. J. H., Mossner, M., Gabbutt, C., Kimberley, C., Barnes, C. P., Baker, A.-M., Yara, E., Sottoriva, A., Nichols, R. A., Graham, T. A.. 2025-03-28. Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding. https://doi.org/10.1101/2025.03.26.645251

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