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

Author

Listed:
  • 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)

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.

Suggested Citation

  • 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 & Wil, 2018. "Target identification of small molecules using large-scale CRISPR-Cas mutagenesis scanning of essential genes," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-017-02349-8
    DOI: 10.1038/s41467-017-02349-8
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    Cited by:

    1. Tanveer Singh Batth & Marie Locard-Paulet & Nadezhda T. Doncheva & Blanca Lopez Mendez & Lars Juhl Jensen & Jesper Velgaard Olsen, 2024. "Streamlined analysis of drug targets by proteome integral solubility alteration indicates organ-specific engagement," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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