Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

Nat Med. 2015 May;21(5):440-8. doi: 10.1038/nm.3841. Epub 2015 Apr 13.


Resistance to cancer therapies presents a significant clinical challenge. Recent studies have revealed intratumoral heterogeneity as a source of therapeutic resistance. However, it is unclear whether resistance is driven predominantly by pre-existing or de novo alterations, in part because of the resolution limits of next-generation sequencing. To address this, we developed a high-complexity barcode library, ClonTracer, which enables the high-resolution tracking of more than 1 million cancer cells under drug treatment. In two clinically relevant models, ClonTracer studies showed that the majority of resistant clones were part of small, pre-existing subpopulations that selectively escaped under therapeutic challenge. Moreover, the ClonTracer approach enabled quantitative assessment of the ability of combination treatments to suppress resistant clones. These findings suggest that resistant clones are present before treatment, which would make up-front therapeutic combinations that target non-overlapping resistance a preferred approach. Thus, ClonTracer barcoding may be a valuable tool for optimizing therapeutic regimens with the goal of curative combination therapies for cancer.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Antineoplastic Combined Chemotherapy Protocols / therapeutic use
  • Carcinoma, Non-Small-Cell Lung / drug therapy
  • Carcinoma, Non-Small-Cell Lung / genetics
  • Cell Differentiation
  • Cell Line, Tumor
  • Crizotinib
  • DNA / chemistry
  • DNA Barcoding, Taxonomic / methods*
  • DNA, Complementary / metabolism
  • Epithelial-Mesenchymal Transition
  • Erlotinib Hydrochloride
  • Fusion Proteins, bcr-abl / genetics
  • Gene Dosage
  • Gene Library
  • Humans
  • Lung Neoplasms / drug therapy
  • Lung Neoplasms / genetics
  • Models, Theoretical
  • Neoplasms / drug therapy*
  • Neoplasms / genetics*
  • Oligonucleotides / genetics
  • Polymerase Chain Reaction
  • Proto-Oncogene Proteins c-abl / antagonists & inhibitors
  • Proto-Oncogene Proteins c-met / metabolism
  • Pyrazoles / administration & dosage
  • Pyridines / administration & dosage
  • Quinazolines / administration & dosage
  • Sequence Analysis, RNA


  • BCR-ABL1 fusion protein, human
  • DNA, Complementary
  • Oligonucleotides
  • Pyrazoles
  • Pyridines
  • Quinazolines
  • Crizotinib
  • DNA
  • Erlotinib Hydrochloride
  • Proto-Oncogene Proteins c-met
  • Fusion Proteins, bcr-abl
  • Proto-Oncogene Proteins c-abl