Cycling cancer persister cells arise from lineages with distinct programs

Nature. 2021 Aug;596(7873):576-582. doi: 10.1038/s41586-021-03796-6. Epub 2021 Aug 11.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antioxidants / metabolism
  • Cell Cycle* / drug effects
  • Cell Line, Tumor
  • Cell Lineage* / drug effects
  • Cell Proliferation / drug effects
  • Cell Survival / drug effects
  • Clone Cells / drug effects
  • Clone Cells / metabolism
  • Clone Cells / pathology
  • DNA Barcoding, Taxonomic
  • Fatty Acids / metabolism
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Lentivirus / genetics
  • Neoplasm Recurrence, Local / drug therapy*
  • Neoplasm Recurrence, Local / genetics
  • Neoplasm Recurrence, Local / pathology*
  • Neoplasms / drug therapy*
  • Neoplasms / genetics
  • Neoplasms / metabolism
  • Neoplasms / pathology*
  • Oncogene Proteins / antagonists & inhibitors
  • Oxidation-Reduction
  • Oxidative Stress
  • Reactive Oxygen Species / metabolism
  • Transcription, Genetic / drug effects

Substances

  • Antioxidants
  • Fatty Acids
  • Oncogene Proteins
  • Reactive Oxygen Species