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ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53

Nature Chemical Biology volume 8, pages 646–654 (2012)Cite this article

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Abstract

The p53 tumor suppressor orchestrates alternative stress responses including cell cycle arrest and apoptosis, but the mechanisms defining cell fate upon p53 activation are poorly understood. Several small-molecule activators of p53 have been developed, including Nutlin-3, but their therapeutic potential is limited by the fact that they induce reversible cell cycle arrest in most cancer cell types. We report here the results of a genome-wide short hairpin RNA screen for genes that are lethal in combination with p53 activation by Nutlin-3, which showed that the ATM and MET kinases govern cell fate choice upon p53 activation. Genetic or pharmacological interference with ATM or MET activity converts the cellular response from cell cycle arrest into apoptosis in diverse cancer cell types without affecting expression of key p53 target genes. ATM and MET inhibitors also enable Nutlin-3 to kill tumor spheroids. These results identify new pathways controlling the cellular response to p53 activation and aid in the design of p53-based therapies.

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Figure 1: Genetic screen for identifying modulators of the cellular response to p53 activation by Nutlin-3.
Figure 2: Identification of synthetic lethal with nutlin-3 genes.
Figure 3: Pathway analysis points to ATM and MET as modulators of p53-dependent cell fate choice.
Figure 4: ATM protects cells from p53-dependent apoptosis upon Nutlin-3 treatment.
Figure 5: MET protects against p53-dependent apoptosis upon Nutlin-3 treatment.
Figure 6: ATM and MET do not affect the ability of p53 to transactivate key genes in the cell cycle arrest and apoptosis modules.
Figure 7: 53BP1 is not required for ATM synthetic lethality.

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Acknowledgements

This work was supported by US National Institutes of Health grant RO1 CA117907, a Lung SPORE Pilot Grant (P50 CA058187), a pilot grant from the Cancer League of Colorado and a Career Development Award from The Leukemia and Lymphoma Society to K.D.S. J.M.E. is a Howard Hughes Medical Institute Early Career Scientist. We thank members of the Espinosa lab for support and discussions and H. Kennedy and J. Kruk for inspiration.

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Authors and Affiliations

  1. Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado, USA

    Kelly D Sullivan, Nuria Padilla-Just, Ryan E Henry & Joaquín M Espinosa

  2. Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado, USA

    Kelly D Sullivan, Nuria Padilla-Just, Ryan E Henry & Joaquín M Espinosa

  3. Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA

    Christopher C Porter & James DeGregori

  4. Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA

    Jihye Kim, John J Tentler, S Gail Eckhardt & Aik Choon Tan

  5. Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA

    James DeGregori

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Contributions

K.D.S. conducted most experiments, interpreted all data and wrote the paper. N.P.-J. did cell culture, western blots and cell viability assays. R.E.H. carried out the microarray experiment. C.C.P. and J.D. shared unpublished protocols for synthetic lethal screens in human cells. J.K. and A.C.T. developed BiNGS and did most bioinformatics analyses. J.J.T. and S.G.E. conducted MCTS experiments and analyzed CI data. J.M.E. participated in project design, established the collaborations and co-wrote the paper.

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Correspondence to Joaquín M Espinosa.

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Supplementary information

Supplementary Text and Figures

Supplementary Results (PDF 5250 kb)

Supplementary Data Set 1

HCT116 screen data (XLSX 1642 kb)

Supplementary Data Set 2

Raw sequence counts from HCT116 screen (XLSX 2403 kb)

Supplementary Data Set 3

A549 screen data (XLSX 1204 kb)

Supplementary Data Set 4

Raw sequence counts from A549 screen (XLSX 3443 kb)

Supplementary Data Set 5

shRNA sequences used in this study (XLSX 58 kb)

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Sullivan, K., Padilla-Just, N., Henry, R. et al. ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53. Nat Chem Biol 8, 646–654 (2012). https://doi.org/10.1038/nchembio.965

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