2. Academic Validation
  3. Quantitative and multiplexed chemical-genetic phenotyping in mammalian cells with QMAP-Seq

Quantitative and multiplexed chemical-genetic phenotyping in mammalian cells with QMAP-Seq

  • Nat Commun. 2020 Nov 12;11(1):5722. doi: 10.1038/s41467-020-19553-8.
Sonia Brockway 1 2 3 4,  Geng Wang 1 2 3,  Jasen M Jackson 1 2 3,  David R Amici 1 2 3 5,  Seesha R Takagishi 1 2 3,  Matthew R Clutter 3 6 7,  Elizabeth T Bartom 1 2,  Marc L Mendillo 8 9 10
Affiliations

Affiliations

  • 1 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
  • 2 Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
  • 3 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
  • 4 Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
  • 5 Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
  • 6 Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
  • 7 Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
  • 8 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. mendillo@northwestern.edu.
  • 9 Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. mendillo@northwestern.edu.
  • 10 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. mendillo@northwestern.edu.
PMID: 33184288 DOI: 10.1038/s41467-020-19553-8
Abstract

Chemical-genetic interaction profiling in model organisms has proven powerful in providing insights into compound mechanism of action and gene function. However, identifying chemical-genetic interactions in mammalian systems has been limited to low-throughput or computational methods. Here, we develop Quantitative and Multiplexed Analysis of Phenotype by Sequencing (QMAP-Seq), which leverages next-generation Sequencing for pooled high-throughput chemical-genetic profiling. We apply QMAP-Seq to investigate how cellular stress response factors affect therapeutic response in Cancer. Using minimal automation, we treat pools of 60 cell types-comprising 12 genetic perturbations in five cell lines-with 1440 compound-dose combinations, generating 86,400 chemical-genetic measurements. QMAP-Seq produces precise and accurate quantitative measures of acute drug response comparable to gold standard assays, but with increased throughput at lower cost. Moreover, QMAP-Seq reveals clinically actionable drug vulnerabilities and functional relationships involving these stress response factors, many of which are activated in Cancer. Thus, QMAP-Seq provides a broadly accessible and scalable strategy for chemical-genetic profiling in mammalian cells.

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