Evolution of drug resistance in cancer cells involves generation of numerous mutations in non-coding genome that reduces the chances of DNA breaks

The selection of drug-resistant mammalian cell mutants requires multiple drug exposures. Since cells in starting population could be genetically identical, selection of pre-existent mutations is unlikely. Therefore, adaptation must involve the generation of drug-resistant mutations de-novo. Understanding how adaptive mutations are generated and protect cells is important for our knowledge of cancer biology and evolution. Here, we studied the adaptation of cancer cells to topoisomerase (Top1) inhibitor irinotecan, which triggers DNA breaks, resulting in cytotoxicity. The resistance mechanism was based on the gradual accumulation of recurrent mutations in non-coding DNA at sequence-specific Top1 cleavage sites. Repair of DSBs at these sites following initial irinotecan exposures created mutant sequences that were resistant to further Top1 cleavage. Therefore, by virtue of creating DNA breaks Top1 increases the rate of highly protective mutations specifically at such spots, thus explaining a puzzling need for dose escalation in resistance development.