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
  • 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. [email protected].
  • 9. Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. [email protected].
  • 10. Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. [email protected].
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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