Title

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

UMMS Affiliation

Department of Molecular, Cell and Cancer Biology; Department of Biochemistry and Molecular Pharmacology; Schiffer Lab

Publication Date

2017-10-31

Document Type

Article

Disciplines

Biochemistry | Genetics and Genomics | Medicinal Chemistry and Pharmaceutics | Medicinal-Pharmaceutical Chemistry | Molecular Biology

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.

Keywords

BCR-ABL, CRISPR-Cas9–based genome editing, drug resistance, saturated mutagenesis, tyrosine kinase inhibitors

DOI of Published Version

10.1073/pnas.1708268114

Source

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11751-11756. doi: 10.1073/pnas.1708268114. Epub 2017 Oct 16. Link to article on publisher's site

Journal/Book/Conference Title

Proceedings of the National Academy of Sciences of the United States of America

Related Resources

Link to Article in PubMed

PubMed ID

29078326

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