Abstract
High-complexity DNA barcoding suggests that rare resistant clones are present prior to therapy.
Major finding: High-complexity DNA barcoding suggests that rare resistant clones are present prior to therapy.
Approach: The ClonTracer barcode library tracks the response of over 1 million individual cancer cells to drug treatment.
Impact: Up-front drug combinations that target nonoverlapping resistance mechanisms may be most effective.
Acquired de novo mutations are assumed to underlie resistance to targeted therapies, but it remains possible that rare preexisting clones harboring resistance-conferring mutations drive relapse. To overcome limitations in sensitivity of next-generation sequencing and address the question of whether drug resistance arises from de novo mutations or rare preexisting cell populations, Bhang and colleagues developed ClonTracer, a high-complexity DNA barcode library that allows monitoring of over 1 million individual cancer cells in response to drug treatment. The acquisition of de novo resistance mutations would cause distinct barcoded cell populations to emerge in replicate experiments, whereas the same barcodes would be enriched if preexisting clones drove drug resistance. In one application of this approach, an EGFR-mutant, erlotinib-sensitive non–small cell lung cancer cell line was transduced with the ClonTracer barcode library and treated with erlotinib. Of the barcodes enriched following erlotinib treatment, 90% were detected in at least two replicates and 40% were represented in all replicates, strongly suggesting that most erlotinib-resistant clones existed prior to treatment. In another example, a BCR–ABL1-expressing chronic myelogenous leukemia cell line was transduced with the ClonTracer library and exposed to catalytic ABL1 inhibitors (imatinib or nilotinib) or an allosteric ABL1 inhibitor (GNF-2). Again, replicates had highly similar barcode enrichment patterns, indicating that preexisting clones led to drug resistance, but the patterns seen for imatinib and nilotinib were very different from the patterns seen for GNF-2. Taken together, these results provide evidence that preexisting resistant cells may play a greater role in clinical relapse than previously appreciated and raise the possibility that up-front use of treatments with nonoverlapping resistance mechanisms could suppress the expansion of preexisting refractory clones. Further application of this approach in vivo could provide insight into tumor evolution and the role of the tumor microenvironment in driving drug resistance.
Note: Research Watch is written by Cancer Discovery Science Writers. Readers are encouraged to consult the original articles for full details. For more Research Watch, visit Cancer Discovery online at http://CDnews.aacrjournals.org.
RSS Feeds