Target identification of small molecules using large-scale CRISPR-Cas mutagenesis scanning of essential genes

Jasper Edgar Neggers, Bert Kwanten, Tim Dierckx, Hiroki Noguchi, Arnout Voet, Lotte Bral, Kristien Minner, Bob Massant, Nicolas Kint, Michel Delforge, Thomas Vercruysse, Erkan Baloglu, William Senapedis, Maarten Jacquemyn and Dirk Daelemans ()
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Jasper Edgar Neggers: Rega Institute for Medical Research
Bert Kwanten: Rega Institute for Medical Research
Tim Dierckx: Rega Institute for Medical Research
Hiroki Noguchi: Biochemistry Molecular and Structural Biology Section
Arnout Voet: Biochemistry Molecular and Structural Biology Section
Lotte Bral: Rega Institute for Medical Research
Kristien Minner: Rega Institute for Medical Research
Bob Massant: Rega Institute for Medical Research
Nicolas Kint: University Hospital Leuven
Michel Delforge: University Hospital Leuven
Thomas Vercruysse: Rega Institute for Medical Research
Erkan Baloglu: Karyopharm Therapeutics Inc
William Senapedis: Karyopharm Therapeutics Inc
Maarten Jacquemyn: Rega Institute for Medical Research
Dirk Daelemans: Rega Institute for Medical Research

Nature Communications, 2018, vol. 9, issue 1, 1-14

Abstract: Abstract Unraveling the mechanism of action and molecular target of small molecules remains a major challenge in drug discovery. While many cancer drugs target genetic vulnerabilities, loss-of-function screens fail to identify essential genes in drug mechanism of action. Here, we report CRISPRres, a CRISPR-Cas-based genetic screening approach to rapidly derive and identify drug resistance mutations in essential genes. It exploits the local genetic variation created by CRISPR-Cas-induced non-homologous end-joining (NHEJ) repair to generate a wide variety of functional in-frame mutations. Using large sgRNA tiling libraries and known drug–target pairs, we validate it as a target identification approach. We apply CRISPRres to the anticancer agent KPT-9274 and identify nicotinamide phosphoribosyltransferase (NAMPT) as its main target. These results present a powerful and simple genetic approach to create many protein variants that, in combination with positive selection, can be applied to reveal the cellular target of small-molecule inhibitors.

Date: 2018
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DOI: 10.1038/s41467-017-02349-8

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