CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy

Proceedings of the National Academy of Sciences of the United States of America
Leyuan MaDaniel N A Bolon

Abstract

Developing tools to accurately predict the clinical prevalence of drug-resistant mutations is a key step toward generating more effective therapeutics. Here we describe a high-throughput CRISPR-Cas9-based saturated mutagenesis approach to generate comprehensive libraries of point mutations at a defined genomic location and systematically study their effect on cell growth. As proof of concept, we mutagenized a selected region within the leukemic oncogene BCR-ABL1 Using bulk competitions with a deep-sequencing readout, we analyzed hundreds of mutations under multiple drug conditions and found that the effects of mutations on growth in the presence or absence of drug were critical for predicting clinically relevant resistant mutations, many of which were cancer adaptive in the absence of drug pressure. Using this approach, we identified all clinically isolated BCR-ABL1 mutations and achieved a prediction score that correlated highly with their clinical prevalence. The strategy described here can be broadly applied to a variety of oncogenes to predict patient mutations and evaluate resistance susceptibility in the development of new therapeutics.

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Citations

Aug 4, 2018·Human Genetics·Jochen Weile, Frederick P Roth
Jun 19, 2019·Nature Biotechnology·Anna J SimonAndrew D Ellington
Jan 12, 2020·Nature Structural & Molecular Biology·N S PerskyC M Johannessen
Jan 2, 2019·Nature Structural & Molecular Biology·Neel H Shah, John Kuriyan
Jul 23, 2020·Nature Chemical Biology·Rudolf Pisa, Tarun M Kapoor
Jun 7, 2018·Proceedings of the National Academy of Sciences of the United States of America·Ákos NyergesCsaba Pál
Mar 6, 2018·Current Opinion in Structural Biology·Kritika Gupta, Raghavan Varadarajan
Jul 22, 2020·Chemical Reviews·Richard A WardPaul D Smith
Apr 7, 2021·The Plant Cell·Christophe GaillochetThomas B Jacobs
Nov 21, 2021·Nature Chemical Biology·Allyson M Freedy, Brian B Liau
Jan 21, 2018·Current Opinion in Structural Biology·Aneth S CanaleDaniel Na Bolon

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