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Discovering biomarkers of chemotherapy resistance using in vitro evolution in haploid human cells

By Juan Carlos Jado, Michelle Dow, Krypton Carolino, Gregory J Fonseca, Trey Ideker, Hannah Carter, Elizabeth A. Winzeler

Posted 18 Mar 2020
bioRxiv DOI: 10.1101/2020.03.17.982181

Understanding general mechanisms of chemotherapy resistance can assist with the design of new drugs and guide cancer treatment decisions. Here we applied i n vitro evolution and whole genome analysis (IVIEWGA) to the human, near - haploid cell line (HAP - 1) to directly identify resistance alleles. Clones (28) resistant to five d ifferent anticancer drugs (doxorubicin, gemcitabine, etoposide, topotecan, and paclitaxel), we re evolved and compared to their isogenic parents via whole genome and whole exome sequencing (WES). High frequency alleles predicted to change protein sequence, or alleles which appeared in the same gene for multiple independent selections with the same compound were identified in only 21 genes: The set included clinically - relevant resistance genes or drug targets ( TOP1, TOP2A , DCK , WDR33, SLCO3A1) , as well as ne w genes ( SLC13A4 ). In addition , some lines carried structural variants that encompassed additional known resistance genes ( ABCB1, WWOX and RRM1) . Gene expression knockdown and knockout experiments (via shRNA and CRISPR - Cas 9 respectively) of 10 validation t argets showed a high degree of specificity and accuracy in our calls and demonstrates that the same drug resistance mechanisms found in diverse clinical samples can be evolved, identified and studied in an isogenic background in the laboratory. ### Competing Interest Statement The authors have declared no competing interest.

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