biostudies-literatureOren YHoward Hughes Medical InstituteNIAID NIH HHSNCI NIH HHS576-582https://www.ebi.ac.uk/biostudies/studies/S-EPMC9209846biostudies-literatureUnknown596(7873)Non-genetic mechanisms have recently emerged as important drivers of cancer therapy failure¹, where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment². Although most cancer persisters remain arrested in the presence of the drug, a rare subset can re-enter the cell cycle under constitutive drug treatment. Little is known about the non-genetic mechanisms that enable cancer persisters to maintain proliferative capacity in the presence of drugs. To study this rare, transiently resistant, proliferative persister population, we developed Watermelon, a high-complexity expressed barcode lentiviral library for simultaneous tracing of each cell's clonal origin and proliferative and transcriptional states. Here we show that cycling and non-cycling persisters arise from different cell lineages with distinct transcriptional and metabolic programs. Upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation are associated with persister proliferative capacity across multiple cancer types. Impeding oxidative stress or metabolic reprogramming alters the fraction of cycling persisters. In human tumours, programs associated with cycling persisters are induced in minimal residual disease in response to multiple targeted therapies. The Watermelon system enabled the identification of rare persister lineages that are preferentially poised to proliferate under drug pressure, thus exposing new vulnerabilities that can be targeted to delay or even prevent disease recurrence.NatureCycling cancer persister cells arise from lineages with distinct programs.PMC9209846R01 CA121210P30 CA016042R01 CA148761F32 AI138458K08 CA197389P50 CA196530R01 CA120247P30 CA016359Oren YThakore PIAmir-Zilberstein LPoliti KLahav GBrugge JSCuoco MSHurvitz SATabaka MColgan WHu BHutter JCDeik AZaganjor EClish CHata ANPierce KACabanos HFRegev ATsabar MFulco CPSlamon DJCuevas BMfalseCycling cancer persister cells arise from lineages with distinct programs.Non-genetic mechanisms have recently emerged as important drivers of cancer therapy failure¹, where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment². Although most cancer persisters remain arrested in the presence of the drug, a rare subset can re-enter the cell cycle under constitutive drug treatment. Little is known about the non-genetic mechanisms that enable cancer persisters to maintain proliferative capacity in the presence of drugs. To study this rare, transiently resistant, proliferative persister population, we developed Watermelon, a high-complexity expressed barcode lentiviral library for simultaneous tracing of each cell's clonal origin and proliferative and transcriptional states. Here we show that cycling and non-cycling persisters arise from different cell lineages with distinct transcriptional and metabolic programs. Upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation are associated with persister proliferative capacity across multiple cancer types. Impeding oxidative stress or metabolic reprogramming alters the fraction of cycling persisters. In human tumours, programs associated with cycling persisters are induced in minimal residual disease in response to multiple targeted therapies. The Watermelon system enabled the identification of rare persister lineages that are preferentially poised to proliferate under drug pressure, thus exposing new vulnerabilities that can be targeted to delay or even prevent disease recurrence.2021-01-01T00:00:00Z2021 Aug2026-05-09T19:20:57.071Z2025-04-25T18:10:35.501ZS-EPMC92098463438121010.1038/s41586-021-03796-6